ABIDE_fs-6.0.0/0050607/scripts/recon-all.log

Sun Oct  8 01:38:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050607 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050607/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050607
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-388 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:     264648720  253345352   11303368    1732324          0  247515784
-/+ buffers/cache:    5829568  258819152
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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $  User: ntraut  Machine: tars-388  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: 2017/10/07-23:38:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: ntraut  Machine: tars-388  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-6.0.0/0050607

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050607/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050607/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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/Yale/0050607/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-6.0.0/0050607/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sun Oct  8 01:38:41 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/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 float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sun Oct  8 01:38:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/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-388 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
Sun Oct  8 01:38:53 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.8839
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8839/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.8839/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.8839/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sun Oct  8 01:38:56 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.8839/nu0.mnc ./tmp.mri_nu_correct.mni.8839/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8839/0/ -iterations 1000 -distance 50
[ntraut@tars-388:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/] [2017-10-08 01:38:56] 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.8839/0/ ./tmp.mri_nu_correct.mni.8839/nu0.mnc ./tmp.mri_nu_correct.mni.8839/nu1.imp

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Number of iterations: 121 
CV of field change: 0.000995277
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.8839/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.8839/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.8839/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...
 
 
Sun Oct  8 01:41:10 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 Sun Oct 8 01:41:10 CEST 2017
Ended   at Sun Oct  8 01:42:00 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sun Oct  8 01:42:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7541, 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-6.0.0/0050607/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/transforms/talairach_avi.log 

TalAviQA: 0.97357
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Sun Oct  8 01:42:02 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-6.0.0/0050607/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-388 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
Sun Oct  8 01:42:02 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.10631
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10631/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10631/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.10631/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sun Oct  8 01:42:04 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10631/nu0.mnc ./tmp.mri_nu_correct.mni.10631/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10631/0/
[ntraut@tars-388:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/] [2017-10-08 01:42:04] 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.10631/0/ ./tmp.mri_nu_correct.mni.10631/nu0.mnc ./tmp.mri_nu_correct.mni.10631/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00149767
 
 
--------------------------------------------------------
Iteration 2 Sun Oct  8 01:43:02 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.10631/nu1.mnc ./tmp.mri_nu_correct.mni.10631/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.10631/1/
[ntraut@tars-388:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/] [2017-10-08 01:43:02] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10631/1/ ./tmp.mri_nu_correct.mni.10631/nu1.mnc ./tmp.mri_nu_correct.mni.10631/nu2.imp

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Number of iterations: 50 
CV of field change: 0.0011218
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.10631/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10631/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-6.0.0/0050607/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.10631/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.10631/ones.mgz 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.10631/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.10631/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.10631/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10631/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10631/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.10631/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.10631/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10631/input.mean.dat 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.10631/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.10631/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.10631/ones.mgz --i ./tmp.mri_nu_correct.mni.10631/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10631/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10631/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.10631/ones.mgz --i ./tmp.mri_nu_correct.mni.10631/nu2.mnc --sum ./tmp.mri_nu_correct.mni.10631/sum.junk --avgwf ./tmp.mri_nu_correct.mni.10631/output.mean.dat 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.10631/ones.mgz
Loading ./tmp.mri_nu_correct.mni.10631/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.10631/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.10631/nu2.mnc ./tmp.mri_nu_correct.mni.10631/nu2.mnc mul 1.05058586174571687347
Saving result to './tmp.mri_nu_correct.mni.10631/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.10631/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.10631/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.10631/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 9 seconds.
mapping ( 3, 75) to ( 3, 110)
 
 
Sun Oct  8 01:44:44 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sun Oct  8 01:44:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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
 1.05064  -0.00265  -0.01513  -42.03224;
-0.01751   0.99116   0.20879   29.07814;
 0.04788  -0.19208   1.06948  -34.28450;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 15
Starting OpenSpline(): npoints = 15
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 65 (65), valley at 19 (19)
csf peak at 33, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 64 (64), valley at 19 (19)
csf peak at 33, setting threshold to 53
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 37 seconds.
#--------------------------------------------
#@# Skull Stripping Sun Oct  8 01:47:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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=14.0
skull bounding box = (46, 43, 22) --> (205, 206, 231)
using (99, 97, 127) as brain centroid...
mean wm in atlas = 108, using box (79,77,101) --> (118, 117,152) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 101 +- 6.0
after smoothing, mri peak at 101, scaling input intensities by 1.069
scaling channel 0 by 1.06931
initial log_p = -4.460
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.440416 @ (-9.091, -9.091, -27.273)
max log p =    -4.288789 @ (4.545, 4.545, 4.545)
max log p =    -4.242712 @ (6.818, 2.273, 6.818)
max log p =    -4.218950 @ (1.136, -3.409, -3.409)
max log p =    -4.214293 @ (-2.841, 2.841, 2.841)
max log p =    -4.213903 @ (-0.852, -0.284, 0.284)
Found translation: (-0.3, -3.1, -16.2): log p = -4.214
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.062, old_max_log_p =-4.214 (thresh=-4.2)
 1.00000   0.00000   0.00000  -0.28409;
 0.00000   1.13509   0.16902  -44.23889;
 0.00000  -0.11161   0.99651   0.46764;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.062, old_max_log_p =-4.062 (thresh=-4.1)
 1.00000   0.00000   0.00000  -0.28409;
 0.00000   1.13509   0.16902  -44.23889;
 0.00000  -0.11161   0.99651   0.46764;
 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=-3.981, old_max_log_p =-4.062 (thresh=-4.1)
 1.03639   0.04320  -0.02552  -7.75272;
-0.03329   1.15025   0.20728  -45.33730;
 0.03395  -0.14723   0.99021   0.44388;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.981, old_max_log_p =-3.981 (thresh=-4.0)
 1.03639   0.04320  -0.02552  -7.75272;
-0.03329   1.15025   0.20728  -45.33730;
 0.03395  -0.14723   0.99021   0.44388;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.966, old_max_log_p =-3.981 (thresh=-4.0)
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.966, old_max_log_p =-3.966 (thresh=-4.0)
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 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
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.966 (old=-4.460)
transform before final EM align:
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 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
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.4  tol 0.000000
final transform:
 1.03369   0.02663  -0.04474  -2.09696;
-0.01721   1.15308   0.19036  -45.57959;
 0.05035  -0.12767   0.99291  -3.35817;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1437.031538
mri_em_register stimesec    2.118677
mri_em_register ru_maxrss   609824
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157588
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    60641
mri_em_register ru_nivcsw   3039
registration took 13 minutes and 35 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=125 y=120 z=126 r=73
      first estimation of the main basin volume: 1632573 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=107, y=100, z=92, Imax=255
      CSF=18, 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=9597913300 voxels, voxel volume =1.000 
                     = 9597913300 mmm3 = 9597913.088 cm3
done.
PostAnalyze...Basin Prior
 12 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=119, r=9850 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=9, CSF_MAX=45 , nb = 43623
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1037272234
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=35 , nb = -1033878289
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=47 , nb = 1109457661
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=9, CSF_MAX=44 , nb = 1079790604
    OTHER      CSF_MIN=0, CSF_intensity=23, CSF_MAX=53 , nb = 1067067496
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    45,      38,        33,   63
  after  analyzing :    30,      38,        38,   44
   RIGHT_CER   
  before analyzing :    24,      28,        36,   68
  after  analyzing :    24,      33,        36,   41
   LEFT_CER    
  before analyzing :    35,      38,        41,   68
  after  analyzing :    35,      40,        41,   47
  RIGHT_BRAIN  
  before analyzing :    47,      40,        35,   64
  after  analyzing :    32,      40,        40,   46
  LEFT_BRAIN   
  before analyzing :    44,      36,        30,   63
  after  analyzing :    29,      36,        36,   42
     OTHER     
  before analyzing :    53,      53,        54,   93
  after  analyzing :    41,      53,        54,   63
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...66 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.010
curvature mean = 72.406, std = 7.722

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 1.80, sigma = 2.85
      after  rotation: sse = 1.80, sigma = 2.85
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  1.80, its var is  2.11   
      before Erosion-Dilatation  0.00% 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 = 1856221 voxels, voxel volume = 1.000 mm3
           = 1856221 mmm3 = 1856.221 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    30.263399
mri_watershed stimesec    0.482926
mri_watershed ru_maxrss   823476
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   213199
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2840
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    2038
mri_watershed ru_nivcsw   1215
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sun Oct  8 02:01:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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=27.0
skull bounding box = (59, 57, 40) --> (192, 187, 210)
using (103, 100, 125) as brain centroid...
mean wm in atlas = 107, using box (87,84,104) --> (119, 115,145) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 100 +- 5.6
after smoothing, mri peak at 100, scaling input intensities by 1.070
scaling channel 0 by 1.07
initial log_p = -4.175
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.205711 @ (-9.091, -9.091, -9.091)
max log p =    -3.939516 @ (4.545, 4.545, -4.545)
max log p =    -3.886838 @ (6.818, 2.273, -2.273)
max log p =    -3.832303 @ (-1.136, 1.136, -1.136)
max log p =    -3.832303 @ (0.000, 0.000, 0.000)
max log p =    -3.828212 @ (-1.420, -3.125, 1.989)
Found translation: (-0.3, -4.3, -15.1): log p = -3.828
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.741, old_max_log_p =-3.828 (thresh=-3.8)
 1.00000   0.00000   0.00000  -0.28409;
 0.00000   1.06580   0.14032  -29.29965;
 0.00000  -0.12074   0.91709   9.85155;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.741, old_max_log_p =-3.741 (thresh=-3.7)
 1.00000   0.00000   0.00000  -0.28409;
 0.00000   1.06580   0.14032  -29.29965;
 0.00000  -0.12074   0.91709   9.85155;
 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=-3.647, old_max_log_p =-3.741 (thresh=-3.7)
 1.01750   0.00295  -0.03071   2.70011;
 0.00218   1.00205   0.16293  -22.62216;
 0.03327  -0.15570   0.92831   10.34785;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.647, old_max_log_p =-3.647 (thresh=-3.6)
 1.01750   0.00295  -0.03071   2.70011;
 0.00218   1.00205   0.16293  -22.62216;
 0.03327  -0.15570   0.92831   10.34785;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.636, old_max_log_p =-3.647 (thresh=-3.6)
 1.02108   0.00296  -0.03081   1.79495;
 0.00191   1.00446   0.15553  -21.53748;
 0.03325  -0.14731   0.92852   9.76885;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.623, old_max_log_p =-3.636 (thresh=-3.6)
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.623, old_max_log_p =-3.623 (thresh=-3.6)
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 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
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.623 (old=-4.175)
transform before final EM align:
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 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
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.0  tol 0.000000
final transform:
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1732.776577
mri_em_register stimesec    3.417480
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   159500
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    200862
mri_em_register ru_nivcsw   7359
registration took 18 minutes and 31 seconds.
#--------------------------------------
#@# CA Normalize Sun Oct  8 02:20:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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=27.0
skull bounding box = (59, 57, 40) --> (192, 187, 210)
using (103, 100, 125) as brain centroid...
mean wm in atlas = 107, using box (87,84,104) --> (119, 115,145) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 100 +- 5.6
after smoothing, mri peak at 100, scaling input intensities by 1.070
scaling channel 0 by 1.07
using 246344 sample points...
INFO: compute sample coordinates transform
 1.02019   0.01665  -0.01285  -2.81573;
-0.01421   0.99826   0.17034  -20.50318;
 0.01645  -0.16317   0.92298   15.39974;
 0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 56, 34) --> (191, 170, 212)
Left_Cerebral_White_Matter: limiting intensities to 102.0 --> 132.0
2 of 4902 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 57, 34) --> (128, 170, 212)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 4523 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 146, 63) --> (174, 189, 121)
Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0
0 of 64 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (81, 146, 61) --> (125, 186, 123)
Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0
0 of 119 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (109, 133, 102) --> (143, 203, 134)
Brain_Stem: limiting intensities to 89.0 --> 132.0
0 of 154 (0.0%) samples deleted
using 9762 total control points for intensity normalization...
bias field = 0.922 +- 0.053
16 of 9760 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 56, 34) --> (191, 170, 212)
Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
7 of 5852 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 57, 34) --> (128, 170, 212)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 5993 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 146, 63) --> (174, 189, 121)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
23 of 148 (15.5%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (81, 146, 61) --> (125, 186, 123)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
47 of 254 (18.5%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (109, 133, 102) --> (143, 203, 134)
Brain_Stem: limiting intensities to 88.0 --> 132.0
302 of 342 (88.3%) samples deleted
using 12589 total control points for intensity normalization...
bias field = 1.034 +- 0.053
1 of 12147 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 56, 34) --> (191, 170, 212)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
3 of 6155 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (63, 57, 34) --> (128, 170, 212)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 6225 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (126, 146, 63) --> (174, 189, 121)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
96 of 178 (53.9%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (81, 146, 61) --> (125, 186, 123)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
210 of 276 (76.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (109, 133, 102) --> (143, 203, 134)
Brain_Stem: limiting intensities to 88.0 --> 132.0
356 of 381 (93.4%) samples deleted
using 13215 total control points for intensity normalization...
bias field = 1.033 +- 0.050
10 of 12433 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 41 seconds.
#--------------------------------------
#@# CA Reg Sun Oct  8 02:21:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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) = 0.97 (predicted orig area = 8.3)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.854, neg=0, invalid=762
0001: dt=221.952000, rms=0.713 (16.558%), neg=0, invalid=762
0002: dt=285.697504, rms=0.687 (3.545%), neg=0, invalid=762
0003: dt=176.444444, rms=0.678 (1.340%), neg=0, invalid=762
0004: dt=295.936000, rms=0.673 (0.817%), neg=0, invalid=762
0005: dt=129.472000, rms=0.669 (0.595%), neg=0, invalid=762
0006: dt=517.888000, rms=0.664 (0.637%), neg=0, invalid=762
0007: dt=110.976000, rms=0.662 (0.397%), neg=0, invalid=762
0008: dt=1183.744000, rms=0.658 (0.637%), neg=0, invalid=762
0009: dt=110.976000, rms=0.656 (0.301%), neg=0, invalid=762
0010: dt=887.808000, rms=0.653 (0.327%), neg=0, invalid=762
0011: dt=110.976000, rms=0.652 (0.164%), neg=0, invalid=762
0012: dt=110.976000, rms=0.652 (0.049%), neg=0, invalid=762
0013: dt=110.976000, rms=0.652 (0.083%), neg=0, invalid=762
0014: dt=110.976000, rms=0.651 (0.111%), neg=0, invalid=762
0015: dt=110.976000, rms=0.650 (0.141%), neg=0, invalid=762
0016: dt=110.976000, rms=0.649 (0.151%), neg=0, invalid=762
0017: dt=110.976000, rms=0.648 (0.158%), neg=0, invalid=762
0018: dt=110.976000, rms=0.647 (0.141%), neg=0, invalid=762
0019: dt=110.976000, rms=0.646 (0.143%), neg=0, invalid=762
0020: dt=110.976000, rms=0.645 (0.145%), neg=0, invalid=762
0021: dt=110.976000, rms=0.644 (0.166%), neg=0, invalid=762
0022: dt=110.976000, rms=0.643 (0.202%), neg=0, invalid=762
0023: dt=110.976000, rms=0.641 (0.218%), neg=0, invalid=762
0024: dt=110.976000, rms=0.640 (0.202%), neg=0, invalid=762
0025: dt=110.976000, rms=0.639 (0.180%), neg=0, invalid=762
0026: dt=110.976000, rms=0.638 (0.159%), neg=0, invalid=762
0027: dt=110.976000, rms=0.637 (0.137%), neg=0, invalid=762
0028: dt=110.976000, rms=0.636 (0.132%), neg=0, invalid=762
0029: dt=110.976000, rms=0.635 (0.122%), neg=0, invalid=762
0030: dt=110.976000, rms=0.635 (0.099%), neg=0, invalid=762
0031: dt=443.904000, rms=0.635 (0.020%), neg=0, invalid=762
0032: dt=443.904000, rms=0.634 (0.058%), neg=0, invalid=762
0033: dt=443.904000, rms=0.634 (-0.392%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.635, neg=0, invalid=762
0034: dt=129.472000, rms=0.634 (0.134%), neg=0, invalid=762
0035: dt=517.888000, rms=0.633 (0.090%), neg=0, invalid=762
0036: dt=517.888000, rms=0.633 (-0.014%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.639, neg=0, invalid=762
0037: dt=155.526882, rms=0.632 (1.052%), neg=0, invalid=762
0038: dt=141.662921, rms=0.626 (1.083%), neg=0, invalid=762
0039: dt=80.207792, rms=0.622 (0.635%), neg=0, invalid=762
0040: dt=145.152000, rms=0.618 (0.561%), neg=0, invalid=762
0041: dt=111.354260, rms=0.616 (0.430%), neg=0, invalid=762
0042: dt=90.461538, rms=0.614 (0.294%), neg=0, invalid=762
0043: dt=145.152000, rms=0.611 (0.389%), neg=0, invalid=762
0044: dt=67.614618, rms=0.610 (0.239%), neg=0, invalid=762
0045: dt=67.614618, rms=0.609 (0.211%), neg=0, invalid=762
0046: dt=67.614618, rms=0.607 (0.276%), neg=0, invalid=762
0047: dt=67.614618, rms=0.605 (0.383%), neg=0, invalid=762
0048: dt=67.614618, rms=0.602 (0.409%), neg=0, invalid=762
0049: dt=67.614618, rms=0.599 (0.464%), neg=0, invalid=762
0050: dt=67.614618, rms=0.596 (0.488%), neg=0, invalid=762
0051: dt=67.614618, rms=0.594 (0.436%), neg=0, invalid=762
0052: dt=67.614618, rms=0.591 (0.385%), neg=0, invalid=762
0053: dt=67.614618, rms=0.590 (0.306%), neg=0, invalid=762
0054: dt=67.614618, rms=0.588 (0.269%), neg=0, invalid=762
0055: dt=67.614618, rms=0.587 (0.255%), neg=0, invalid=762
0056: dt=67.614618, rms=0.585 (0.216%), neg=0, invalid=762
0057: dt=67.614618, rms=0.584 (0.182%), neg=0, invalid=762
0058: dt=67.614618, rms=0.583 (0.157%), neg=0, invalid=762
0059: dt=67.614618, rms=0.583 (0.136%), neg=0, invalid=762
0060: dt=67.614618, rms=0.582 (0.123%), neg=0, invalid=762
0061: dt=67.614618, rms=0.581 (0.133%), neg=0, invalid=762
0062: dt=67.614618, rms=0.580 (0.111%), neg=0, invalid=762
0063: dt=67.614618, rms=0.580 (0.107%), neg=0, invalid=762
0064: dt=36.288000, rms=0.580 (0.002%), neg=0, invalid=762
0065: dt=36.288000, rms=0.580 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.580, neg=0, invalid=762
0066: dt=82.944000, rms=0.579 (0.226%), neg=0, invalid=762
0067: dt=145.152000, rms=0.578 (0.157%), neg=0, invalid=762
0068: dt=145.152000, rms=0.578 (-0.189%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.606, neg=0, invalid=762
0069: dt=8.000000, rms=0.605 (0.197%), neg=0, invalid=762
0070: dt=2.400000, rms=0.605 (0.002%), neg=0, invalid=762
0071: dt=2.400000, rms=0.605 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.605, neg=0, invalid=762
0072: dt=1.600000, rms=0.605 (0.091%), neg=0, invalid=762
0073: dt=0.175000, rms=0.605 (-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=0.675, neg=0, invalid=762
0074: dt=6.163701, rms=0.654 (3.078%), neg=0, invalid=762
0075: dt=3.456000, rms=0.653 (0.128%), neg=0, invalid=762
0076: dt=3.456000, rms=0.653 (-0.025%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.653, neg=0, invalid=762
0077: dt=0.000000, rms=0.653 (0.069%), neg=0, invalid=762
0078: dt=0.000000, rms=0.653 (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=0.720, neg=0, invalid=762
0079: dt=1.024000, rms=0.717 (0.369%), neg=0, invalid=762
0080: dt=2.063636, rms=0.712 (0.635%), neg=0, invalid=762
0081: dt=1.280000, rms=0.712 (0.102%), neg=0, invalid=762
0082: dt=1.280000, rms=0.710 (0.263%), neg=0, invalid=762
0083: dt=1.280000, rms=0.709 (0.101%), neg=0, invalid=762
0084: dt=1.280000, rms=0.709 (-0.212%), neg=0, invalid=762
0085: dt=0.000000, rms=0.709 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.709, neg=0, invalid=762
0086: dt=0.448000, rms=0.709 (0.084%), neg=0, invalid=762
0087: dt=0.448000, rms=0.709 (0.013%), neg=0, invalid=762
0088: dt=0.448000, rms=0.709 (0.009%), neg=0, invalid=762
0089: dt=0.448000, rms=0.709 (0.005%), neg=0, invalid=762
0090: dt=0.448000, rms=0.709 (-0.004%), 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=0.656, neg=0, invalid=762
0091: dt=0.728947, rms=0.642 (2.134%), neg=0, invalid=762
0092: dt=0.064000, rms=0.642 (0.090%), neg=0, invalid=762
0093: dt=0.064000, rms=0.642 (-0.043%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.642, neg=0, invalid=762
0094: dt=0.028000, rms=0.642 (0.081%), neg=0, invalid=762
0095: dt=0.003000, rms=0.642 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.04405 (19)
Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (1359 voxels, overlap=0.487)
Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (1359 voxels, peak = 24), gca=24.5
gca peak = 0.15565 (16)
mri peak = 0.09510 (13)
Right_Lateral_Ventricle (43): linear fit = 0.82 x + 0.0 (2008 voxels, overlap=0.716)
Right_Lateral_Ventricle (43): linear fit = 0.82 x + 0.0 (2008 voxels, peak = 13), gca=13.2
gca peak = 0.26829 (96)
mri peak = 0.10146 (88)
Right_Pallidum (52): linear fit = 0.93 x + 0.0 (1379 voxels, overlap=0.491)
Right_Pallidum (52): linear fit = 0.93 x + 0.0 (1379 voxels, peak = 89), gca=88.8
gca peak = 0.20183 (93)
mri peak = 0.07679 (95)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (1218 voxels, overlap=0.843)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (1218 voxels, peak = 91), gca=90.7
gca peak = 0.21683 (55)
mri peak = 0.09803 (64)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1458 voxels, overlap=0.506)
Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1458 voxels, peak = 60), gca=60.2
gca peak = 0.30730 (58)
mri peak = 0.09005 (66)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1498 voxels, overlap=0.973)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1498 voxels, peak = 65), gca=64.7
gca peak = 0.11430 (101)
mri peak = 0.09682 (101)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (89512 voxels, overlap=0.858)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (89512 voxels, peak = 104), gca=103.5
gca peak = 0.12076 (102)
mri peak = 0.07726 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (93575 voxels, overlap=0.510)
Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (93575 voxels, peak = 108), gca=107.6
gca peak = 0.14995 (59)
mri peak = 0.03173 (62)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (50831 voxels, overlap=0.804)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (50831 voxels, peak = 60), gca=60.5
gca peak = 0.15082 (58)
mri peak = 0.03343 (56)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (46665 voxels, overlap=0.990)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (46665 voxels, peak = 59), gca=59.4
gca peak = 0.14161 (67)
mri peak = 0.09250 (65)
Right_Caudate (50): linear fit = 0.95 x + 0.0 (1354 voxels, overlap=0.987)
Right_Caudate (50): linear fit = 0.95 x + 0.0 (1354 voxels, peak = 64), gca=64.0
gca peak = 0.15243 (71)
mri peak = 0.08405 (75)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (1270 voxels, overlap=0.987)
Left_Caudate (11): linear fit = 1.03 x + 0.0 (1270 voxels, peak = 73), gca=73.5
gca peak = 0.13336 (57)
mri peak = 0.04140 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (32415 voxels, overlap=0.808)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (32415 voxels, peak = 60), gca=59.6
gca peak = 0.13252 (56)
mri peak = 0.04125 (59)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (41046 voxels, overlap=0.886)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (41046 voxels, peak = 60), gca=59.6
gca peak = 0.18181 (84)
mri peak = 0.05924 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (13414 voxels, overlap=0.633)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (13414 voxels, peak = 89), gca=88.6
gca peak = 0.20573 (83)
mri peak = 0.07324 (86)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (11432 voxels, overlap=0.580)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (11432 voxels, peak = 86), gca=85.9
gca peak = 0.21969 (57)
mri peak = 0.09405 (62)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (635 voxels, overlap=1.001)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (635 voxels, peak = 60), gca=59.6
gca peak = 0.39313 (56)
mri peak = 0.10120 (62)
Right_Amygdala (54): linear fit = 1.10 x + 0.0 (751 voxels, overlap=0.796)
Right_Amygdala (54): linear fit = 1.10 x + 0.0 (751 voxels, peak = 61), gca=61.3
gca peak = 0.14181 (85)
mri peak = 0.06426 (82)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (7211 voxels, overlap=0.925)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (7211 voxels, peak = 81), gca=81.2
gca peak = 0.11978 (83)
mri peak = 0.11681 (80)
Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (5926 voxels, overlap=0.870)
Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (5926 voxels, peak = 79), gca=79.3
gca peak = 0.13399 (79)
mri peak = 0.07467 (81)
Left_Putamen (12): linear fit = 1.09 x + 0.0 (3376 voxels, overlap=0.680)
Left_Putamen (12): linear fit = 1.09 x + 0.0 (3376 voxels, peak = 86), gca=85.7
gca peak = 0.14159 (79)
mri peak = 0.07827 (80)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (3544 voxels, overlap=0.997)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (3544 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.13611 (80)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (16130 voxels, overlap=0.401)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (16130 voxels, peak = 84), gca=84.4
gca peak = 0.13281 (86)
mri peak = 0.09375 (89)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (2286 voxels, overlap=0.724)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (2286 voxels, peak = 88), gca=88.2
gca peak = 0.12801 (89)
mri peak = 0.07746 (88)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (2230 voxels, overlap=0.800)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (2230 voxels, peak = 91), gca=91.2
gca peak = 0.20494 (23)
mri peak = 0.05324 (42)
Third_Ventricle (14): linear fit = 1.76 x + 0.0 (124 voxels, overlap=0.649)
Third_Ventricle (14): linear fit = 1.76 x + 0.0 (124 voxels, peak = 41), gca=40.6
gca peak = 0.15061 (21)
mri peak = 0.08986 (14)
Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (528 voxels, overlap=0.465)
Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (528 voxels, peak = 15), gca=14.8
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.07 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.92 x + 0.0
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.654, neg=0, invalid=762
0096: dt=166.448669, rms=0.640 (2.251%), neg=0, invalid=762
0097: dt=295.936000, rms=0.635 (0.692%), neg=0, invalid=762
0098: dt=129.472000, rms=0.633 (0.379%), neg=0, invalid=762
0099: dt=295.936000, rms=0.631 (0.266%), neg=0, invalid=762
0100: dt=110.976000, rms=0.630 (0.181%), neg=0, invalid=762
0101: dt=369.920000, rms=0.629 (0.176%), neg=0, invalid=762
0102: dt=110.976000, rms=0.628 (0.136%), neg=0, invalid=762
0103: dt=295.936000, rms=0.627 (0.115%), neg=0, invalid=762
0104: dt=110.976000, rms=0.627 (0.081%), neg=0, invalid=762
0105: dt=443.904000, rms=0.626 (0.119%), neg=0, invalid=762
0106: dt=92.480000, rms=0.625 (0.092%), neg=0, invalid=762
0107: dt=1183.744000, rms=0.624 (0.227%), neg=0, invalid=762
0108: dt=92.480000, rms=0.623 (0.116%), neg=0, invalid=762
0109: dt=517.888000, rms=0.623 (0.087%), neg=0, invalid=762
0110: dt=110.976000, rms=0.623 (0.036%), neg=0, invalid=762
0111: dt=110.976000, rms=0.622 (0.022%), neg=0, invalid=762
0112: dt=110.976000, rms=0.622 (0.035%), neg=0, invalid=762
0113: dt=110.976000, rms=0.622 (0.046%), neg=0, invalid=762
0114: dt=110.976000, rms=0.622 (0.055%), neg=0, invalid=762
0115: dt=110.976000, rms=0.621 (0.064%), neg=0, invalid=762
0116: dt=110.976000, rms=0.621 (0.069%), neg=0, invalid=762
0117: dt=110.976000, rms=0.620 (0.069%), neg=0, invalid=762
0118: dt=110.976000, rms=0.620 (0.065%), neg=0, invalid=762
0119: dt=110.976000, rms=0.620 (0.061%), neg=0, invalid=762
0120: dt=110.976000, rms=0.619 (0.059%), neg=0, invalid=762
0121: dt=110.976000, rms=0.619 (0.057%), neg=0, invalid=762
0122: dt=110.976000, rms=0.618 (0.054%), neg=0, invalid=762
0123: dt=110.976000, rms=0.618 (0.051%), neg=0, invalid=762
0124: dt=110.976000, rms=0.618 (0.046%), neg=0, invalid=762
0125: dt=110.976000, rms=0.618 (0.048%), neg=0, invalid=762
0126: dt=110.976000, rms=0.617 (0.051%), neg=0, invalid=762
0127: dt=110.976000, rms=0.617 (0.050%), neg=0, invalid=762
0128: dt=110.976000, rms=0.617 (0.044%), neg=0, invalid=762
0129: dt=110.976000, rms=0.616 (0.042%), neg=0, invalid=762
0130: dt=110.976000, rms=0.616 (0.040%), neg=0, invalid=762
0131: dt=110.976000, rms=0.616 (0.040%), neg=0, invalid=762
0132: dt=110.976000, rms=0.616 (0.044%), neg=0, invalid=762
0133: dt=110.976000, rms=0.615 (0.038%), neg=0, invalid=762
0134: dt=110.976000, rms=0.615 (0.040%), neg=0, invalid=762
0135: dt=110.976000, rms=0.615 (0.040%), neg=0, invalid=762
0136: dt=110.976000, rms=0.615 (0.044%), neg=0, invalid=762
0137: dt=110.976000, rms=0.614 (0.042%), neg=0, invalid=762
0138: dt=110.976000, rms=0.614 (0.037%), neg=0, invalid=762
0139: dt=110.976000, rms=0.614 (0.040%), neg=0, invalid=762
0140: dt=110.976000, rms=0.614 (0.040%), neg=0, invalid=762
0141: dt=110.976000, rms=0.613 (0.040%), neg=0, invalid=762
0142: dt=110.976000, rms=0.613 (0.038%), neg=0, invalid=762
0143: dt=110.976000, rms=0.613 (0.036%), neg=0, invalid=762
0144: dt=110.976000, rms=0.613 (0.035%), neg=0, invalid=762
0145: dt=110.976000, rms=0.613 (0.035%), neg=0, invalid=762
0146: dt=110.976000, rms=0.612 (0.035%), neg=0, invalid=762
0147: dt=110.976000, rms=0.612 (0.035%), neg=0, invalid=762
0148: dt=110.976000, rms=0.612 (0.034%), neg=0, invalid=762
0149: dt=110.976000, rms=0.612 (0.033%), neg=0, invalid=762
0150: dt=110.976000, rms=0.612 (0.030%), neg=0, invalid=762
0151: dt=110.976000, rms=0.611 (0.029%), neg=0, invalid=762
0152: dt=110.976000, rms=0.611 (0.028%), neg=0, invalid=762
0153: dt=110.976000, rms=0.611 (0.027%), neg=0, invalid=762
0154: dt=110.976000, rms=0.611 (0.027%), neg=0, invalid=762
0155: dt=110.976000, rms=0.611 (0.028%), neg=0, invalid=762
0156: dt=110.976000, rms=0.610 (0.028%), neg=0, invalid=762
0157: dt=110.976000, rms=0.610 (0.027%), neg=0, invalid=762
0158: dt=110.976000, rms=0.610 (0.030%), neg=0, invalid=762
0159: dt=110.976000, rms=0.610 (0.027%), neg=0, invalid=762
0160: dt=110.976000, rms=0.610 (0.028%), neg=0, invalid=762
0161: dt=110.976000, rms=0.610 (0.027%), neg=0, invalid=762
0162: dt=110.976000, rms=0.609 (0.029%), neg=0, invalid=762
0163: dt=110.976000, rms=0.609 (0.026%), neg=0, invalid=762
0164: dt=110.976000, rms=0.609 (0.024%), neg=0, invalid=762
0165: dt=110.976000, rms=0.609 (0.024%), neg=0, invalid=762
0166: dt=110.976000, rms=0.609 (0.024%), neg=0, invalid=762
0167: dt=110.976000, rms=0.609 (0.024%), neg=0, invalid=762
0168: dt=110.976000, rms=0.609 (0.023%), neg=0, invalid=762
0169: dt=2071.552000, rms=0.608 (0.019%), neg=0, invalid=762
0170: dt=2071.552000, rms=0.608 (-2.926%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.609, neg=0, invalid=762
0171: dt=129.472000, rms=0.608 (0.175%), neg=0, invalid=762
0172: dt=517.888000, rms=0.607 (0.109%), neg=0, invalid=762
0173: dt=129.472000, rms=0.607 (0.029%), neg=0, invalid=762
0174: dt=129.472000, rms=0.607 (0.013%), neg=0, invalid=762
0175: dt=129.472000, rms=0.607 (0.024%), neg=0, invalid=762
0176: dt=129.472000, rms=0.607 (0.032%), neg=0, invalid=762
0177: dt=129.472000, rms=0.606 (0.035%), neg=0, invalid=762
0178: dt=129.472000, rms=0.606 (0.038%), neg=0, invalid=762
0179: dt=129.472000, rms=0.606 (0.035%), neg=0, invalid=762
0180: dt=129.472000, rms=0.606 (0.025%), neg=0, invalid=762
0181: dt=129.472000, rms=0.606 (0.027%), neg=0, invalid=762
0182: dt=129.472000, rms=0.606 (0.025%), neg=0, invalid=762
0183: dt=129.472000, rms=0.605 (0.027%), neg=0, invalid=762
0184: dt=129.472000, rms=0.605 (0.023%), neg=0, invalid=762
0185: dt=129.472000, rms=0.605 (0.021%), neg=0, invalid=762
0186: dt=221.952000, rms=0.605 (0.006%), neg=0, invalid=762
0187: dt=221.952000, rms=0.605 (0.006%), neg=0, invalid=762
0188: dt=221.952000, rms=0.605 (0.007%), neg=0, invalid=762
0189: dt=221.952000, rms=0.605 (0.007%), neg=0, invalid=762
0190: dt=221.952000, rms=0.605 (0.020%), neg=0, invalid=762
0191: dt=221.952000, rms=0.605 (0.017%), neg=0, invalid=762
0192: dt=221.952000, rms=0.605 (0.020%), neg=0, invalid=762
0193: dt=221.952000, rms=0.605 (0.019%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.606, neg=0, invalid=762
0194: dt=124.416000, rms=0.603 (0.528%), neg=0, invalid=762
0195: dt=145.152000, rms=0.598 (0.722%), neg=0, invalid=762
0196: dt=62.871537, rms=0.596 (0.395%), neg=0, invalid=762
0197: dt=497.664000, rms=0.589 (1.200%), neg=0, invalid=762
0198: dt=60.540541, rms=0.585 (0.628%), neg=0, invalid=762
0199: dt=145.152000, rms=0.583 (0.370%), neg=0, invalid=762
0200: dt=67.329480, rms=0.582 (0.145%), neg=0, invalid=762
0201: dt=145.152000, rms=0.581 (0.250%), neg=0, invalid=762
0202: dt=64.000000, rms=0.580 (0.164%), neg=0, invalid=762
0203: dt=145.152000, rms=0.579 (0.224%), neg=0, invalid=762
0204: dt=67.329480, rms=0.578 (0.140%), neg=0, invalid=762
0205: dt=124.416000, rms=0.577 (0.146%), neg=0, invalid=762
0206: dt=66.876404, rms=0.576 (0.144%), neg=0, invalid=762
0207: dt=145.152000, rms=0.575 (0.133%), neg=0, invalid=762
0208: dt=36.288000, rms=0.575 (0.121%), neg=0, invalid=762
0209: dt=414.720000, rms=0.573 (0.267%), neg=0, invalid=762
0210: dt=36.288000, rms=0.572 (0.232%), neg=0, invalid=762
0211: dt=62.208000, rms=0.571 (0.091%), neg=0, invalid=762
0212: dt=145.152000, rms=0.571 (0.126%), neg=0, invalid=762
0213: dt=36.288000, rms=0.570 (0.070%), neg=0, invalid=762
0214: dt=414.720000, rms=0.569 (0.151%), neg=0, invalid=762
0215: dt=36.288000, rms=0.568 (0.208%), neg=0, invalid=762
0216: dt=124.416000, rms=0.567 (0.121%), neg=0, invalid=762
0217: dt=36.288000, rms=0.567 (0.054%), neg=0, invalid=762
0218: dt=580.608000, rms=0.565 (0.294%), neg=0, invalid=762
0219: dt=36.288000, rms=0.565 (0.142%), neg=0, invalid=762
0220: dt=145.152000, rms=0.564 (0.106%), neg=0, invalid=762
0221: dt=36.288000, rms=0.564 (0.048%), neg=0, invalid=762
0222: dt=36.288000, rms=0.564 (0.027%), neg=0, invalid=762
0223: dt=36.288000, rms=0.563 (0.035%), neg=0, invalid=762
0224: dt=36.288000, rms=0.563 (0.053%), neg=0, invalid=762
0225: dt=36.288000, rms=0.563 (0.074%), neg=0, invalid=762
0226: dt=36.288000, rms=0.562 (0.094%), neg=0, invalid=762
0227: dt=36.288000, rms=0.562 (0.107%), neg=0, invalid=762
0228: dt=36.288000, rms=0.561 (0.111%), neg=0, invalid=762
0229: dt=36.288000, rms=0.560 (0.116%), neg=0, invalid=762
0230: dt=36.288000, rms=0.560 (0.115%), neg=0, invalid=762
0231: dt=36.288000, rms=0.559 (0.118%), neg=0, invalid=762
0232: dt=36.288000, rms=0.558 (0.124%), neg=0, invalid=762
0233: dt=36.288000, rms=0.558 (0.126%), neg=0, invalid=762
0234: dt=36.288000, rms=0.557 (0.128%), neg=0, invalid=762
0235: dt=36.288000, rms=0.556 (0.125%), neg=0, invalid=762
0236: dt=36.288000, rms=0.556 (0.117%), neg=0, invalid=762
0237: dt=36.288000, rms=0.555 (0.118%), neg=0, invalid=762
0238: dt=18.144000, rms=0.555 (0.009%), neg=0, invalid=762
0239: dt=9.072000, rms=0.555 (0.004%), neg=0, invalid=762
0240: dt=2.268000, rms=0.555 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.555, neg=0, invalid=762
0241: dt=124.416000, rms=0.553 (0.411%), neg=0, invalid=762
0242: dt=74.105263, rms=0.552 (0.136%), neg=0, invalid=762
0243: dt=82.944000, rms=0.552 (0.073%), neg=0, invalid=762
0244: dt=103.680000, rms=0.552 (0.074%), neg=0, invalid=762
0245: dt=36.288000, rms=0.551 (0.054%), neg=0, invalid=762
0246: dt=497.664000, rms=0.550 (0.179%), neg=0, invalid=762
0247: dt=36.288000, rms=0.550 (0.122%), neg=0, invalid=762
0248: dt=145.152000, rms=0.549 (0.066%), neg=0, invalid=762
0249: dt=36.288000, rms=0.549 (0.018%), neg=0, invalid=762
0250: dt=36.288000, rms=0.549 (0.014%), neg=0, invalid=762
0251: dt=36.288000, rms=0.549 (0.026%), neg=0, invalid=762
0252: dt=36.288000, rms=0.549 (0.041%), neg=0, invalid=762
0253: dt=36.288000, rms=0.548 (0.049%), neg=0, invalid=762
0254: dt=36.288000, rms=0.548 (0.054%), neg=0, invalid=762
0255: dt=36.288000, rms=0.548 (0.056%), neg=0, invalid=762
0256: dt=36.288000, rms=0.547 (0.063%), neg=0, invalid=762
0257: dt=36.288000, rms=0.547 (0.069%), neg=0, invalid=762
0258: dt=36.288000, rms=0.547 (0.069%), neg=0, invalid=762
0259: dt=36.288000, rms=0.546 (0.070%), neg=0, invalid=762
0260: dt=36.288000, rms=0.546 (0.070%), neg=0, invalid=762
0261: dt=36.288000, rms=0.546 (0.068%), neg=0, invalid=762
0262: dt=36.288000, rms=0.545 (0.070%), neg=0, invalid=762
0263: dt=36.288000, rms=0.545 (0.065%), neg=0, invalid=762
0264: dt=36.288000, rms=0.544 (0.067%), neg=0, invalid=762
0265: dt=36.288000, rms=0.544 (0.068%), neg=0, invalid=762
0266: dt=36.288000, rms=0.544 (0.067%), neg=0, invalid=762
0267: dt=36.288000, rms=0.543 (0.067%), neg=0, invalid=762
0268: dt=36.288000, rms=0.543 (0.064%), neg=0, invalid=762
0269: dt=36.288000, rms=0.543 (0.062%), neg=0, invalid=762
0270: dt=36.288000, rms=0.542 (0.061%), neg=0, invalid=762
0271: dt=36.288000, rms=0.542 (0.061%), neg=0, invalid=762
0272: dt=36.288000, rms=0.542 (0.059%), neg=0, invalid=762
0273: dt=36.288000, rms=0.541 (0.057%), neg=0, invalid=762
0274: dt=36.288000, rms=0.541 (0.057%), neg=0, invalid=762
0275: dt=36.288000, rms=0.541 (0.054%), neg=0, invalid=762
0276: dt=36.288000, rms=0.541 (0.055%), neg=0, invalid=762
0277: dt=36.288000, rms=0.540 (0.050%), neg=0, invalid=762
0278: dt=36.288000, rms=0.540 (0.052%), neg=0, invalid=762
0279: dt=36.288000, rms=0.540 (0.049%), neg=0, invalid=762
0280: dt=36.288000, rms=0.539 (0.049%), neg=0, invalid=762
0281: dt=36.288000, rms=0.539 (0.051%), neg=0, invalid=762
0282: dt=36.288000, rms=0.539 (0.048%), neg=0, invalid=762
0283: dt=36.288000, rms=0.539 (0.042%), neg=0, invalid=762
0284: dt=36.288000, rms=0.538 (0.044%), neg=0, invalid=762
0285: dt=36.288000, rms=0.538 (0.042%), neg=0, invalid=762
0286: dt=36.288000, rms=0.538 (0.044%), neg=0, invalid=762
0287: dt=36.288000, rms=0.538 (0.042%), neg=0, invalid=762
0288: dt=36.288000, rms=0.538 (0.039%), neg=0, invalid=762
0289: dt=36.288000, rms=0.537 (0.038%), neg=0, invalid=762
0290: dt=36.288000, rms=0.537 (0.037%), neg=0, invalid=762
0291: dt=36.288000, rms=0.537 (0.038%), neg=0, invalid=762
0292: dt=36.288000, rms=0.537 (0.035%), neg=0, invalid=762
0293: dt=36.288000, rms=0.537 (0.036%), neg=0, invalid=762
0294: dt=36.288000, rms=0.536 (0.032%), neg=0, invalid=762
0295: dt=36.288000, rms=0.536 (0.033%), neg=0, invalid=762
0296: dt=36.288000, rms=0.536 (0.033%), neg=0, invalid=762
0297: dt=36.288000, rms=0.536 (0.030%), neg=0, invalid=762
0298: dt=36.288000, rms=0.536 (0.028%), neg=0, invalid=762
0299: dt=36.288000, rms=0.536 (0.028%), neg=0, invalid=762
0300: dt=36.288000, rms=0.535 (0.028%), neg=0, invalid=762
0301: dt=36.288000, rms=0.535 (0.034%), neg=0, invalid=762
0302: dt=36.288000, rms=0.535 (0.030%), neg=0, invalid=762
0303: dt=36.288000, rms=0.535 (0.027%), neg=0, invalid=762
0304: dt=36.288000, rms=0.535 (0.027%), neg=0, invalid=762
0305: dt=36.288000, rms=0.535 (0.026%), neg=0, invalid=762
0306: dt=36.288000, rms=0.535 (0.022%), neg=0, invalid=762
0307: dt=36.288000, rms=0.534 (0.025%), neg=0, invalid=762
0308: dt=36.288000, rms=0.534 (0.024%), neg=0, invalid=762
0309: dt=331.776000, rms=0.534 (0.018%), neg=0, invalid=762
0310: dt=331.776000, rms=0.534 (-0.585%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.543, neg=0, invalid=762
0311: dt=38.400000, rms=0.540 (0.518%), neg=0, invalid=762
0312: dt=69.500000, rms=0.537 (0.723%), neg=0, invalid=762
0313: dt=23.668639, rms=0.534 (0.459%), neg=0, invalid=762
0314: dt=179.200000, rms=0.528 (1.225%), neg=0, invalid=762
0315: dt=23.682119, rms=0.525 (0.559%), neg=0, invalid=762
0316: dt=44.800000, rms=0.523 (0.286%), neg=0, invalid=762
0317: dt=44.800000, rms=0.522 (0.200%), neg=0, invalid=762
0318: dt=32.000000, rms=0.521 (0.163%), neg=0, invalid=762
0319: dt=38.400000, rms=0.520 (0.172%), neg=0, invalid=762
0320: dt=25.600000, rms=0.520 (0.114%), neg=0, invalid=762
0321: dt=44.800000, rms=0.519 (0.194%), neg=0, invalid=762
0322: dt=25.600000, rms=0.518 (0.072%), neg=0, invalid=762
0323: dt=76.800000, rms=0.517 (0.215%), neg=0, invalid=762
0324: dt=19.200000, rms=0.517 (0.109%), neg=0, invalid=762
0325: dt=512.000000, rms=0.512 (0.881%), neg=0, invalid=762
0326: dt=32.000000, rms=0.510 (0.344%), neg=0, invalid=762
0327: dt=25.600000, rms=0.510 (0.110%), neg=0, invalid=762
0328: dt=44.800000, rms=0.509 (0.094%), neg=0, invalid=762
0329: dt=19.200000, rms=0.509 (0.024%), neg=0, invalid=762
0330: dt=19.200000, rms=0.509 (0.037%), neg=0, invalid=762
0331: dt=19.200000, rms=0.509 (0.039%), neg=0, invalid=762
0332: dt=19.200000, rms=0.509 (0.049%), neg=0, invalid=762
0333: dt=19.200000, rms=0.508 (0.054%), neg=0, invalid=762
0334: dt=19.200000, rms=0.508 (0.079%), neg=0, invalid=762
0335: dt=19.200000, rms=0.507 (0.089%), neg=0, invalid=762
0336: dt=19.200000, rms=0.507 (0.089%), neg=0, invalid=762
0337: dt=19.200000, rms=0.507 (0.090%), neg=0, invalid=762
0338: dt=19.200000, rms=0.506 (0.095%), neg=0, invalid=762
0339: dt=19.200000, rms=0.505 (0.108%), neg=0, invalid=762
0340: dt=19.200000, rms=0.505 (0.023%), neg=0, invalid=762
0341: dt=19.200000, rms=0.505 (0.032%), neg=0, invalid=762
0342: dt=19.200000, rms=0.505 (0.009%), neg=0, invalid=762
0343: dt=19.200000, rms=0.505 (0.016%), neg=0, invalid=762
0344: dt=4.800000, rms=0.505 (0.007%), neg=0, invalid=762
0345: dt=0.150000, rms=0.505 (-0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.506, neg=0, invalid=762
0346: dt=44.800000, rms=0.503 (0.430%), neg=0, invalid=762
0347: dt=32.000000, rms=0.503 (0.137%), neg=0, invalid=762
0348: dt=25.600000, rms=0.503 (0.047%), neg=0, invalid=762
0349: dt=25.600000, rms=0.502 (0.043%), neg=0, invalid=762
0350: dt=25.600000, rms=0.502 (0.057%), neg=0, invalid=762
0351: dt=25.600000, rms=0.502 (0.055%), neg=0, invalid=762
0352: dt=25.600000, rms=0.502 (0.048%), neg=0, invalid=762
0353: dt=25.600000, rms=0.501 (0.039%), neg=0, invalid=762
0354: dt=25.600000, rms=0.501 (0.039%), neg=0, invalid=762
0355: dt=25.600000, rms=0.501 (0.054%), neg=0, invalid=762
0356: dt=25.600000, rms=0.501 (0.061%), neg=0, invalid=762
0357: dt=25.600000, rms=0.500 (0.069%), neg=0, invalid=762
0358: dt=25.600000, rms=0.500 (0.095%), neg=0, invalid=762
0359: dt=25.600000, rms=0.499 (0.108%), neg=0, invalid=762
0360: dt=25.600000, rms=0.499 (0.099%), neg=0, invalid=762
0361: dt=25.600000, rms=0.498 (0.074%), neg=0, invalid=762
0362: dt=25.600000, rms=0.498 (0.108%), neg=0, invalid=762
0363: dt=25.600000, rms=0.497 (0.108%), neg=0, invalid=762
0364: dt=25.600000, rms=0.497 (0.003%), neg=0, invalid=762
0365: dt=25.600000, rms=0.497 (0.040%), neg=0, invalid=762
0366: dt=25.600000, rms=0.497 (0.048%), neg=0, invalid=762
0367: dt=25.600000, rms=0.497 (0.030%), neg=0, invalid=762
0368: dt=25.600000, rms=0.497 (0.009%), neg=0, invalid=762
0369: dt=25.600000, rms=0.496 (0.050%), neg=0, invalid=762
0370: dt=25.600000, rms=0.496 (0.058%), neg=0, invalid=762
0371: dt=25.600000, rms=0.496 (0.043%), neg=0, invalid=762
0372: dt=25.600000, rms=0.496 (0.028%), neg=0, invalid=762
0373: dt=25.600000, rms=0.495 (0.066%), neg=0, invalid=762
0374: dt=25.600000, rms=0.495 (0.026%), neg=0, invalid=762
0375: dt=25.600000, rms=0.495 (0.014%), neg=0, invalid=762
0376: dt=6.400000, rms=0.495 (-0.000%), neg=0, invalid=762
0377: dt=2.800000, rms=0.495 (0.000%), neg=0, invalid=762
0378: dt=2.800000, rms=0.495 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.518, neg=0, invalid=762
0379: dt=0.000000, rms=0.517 (0.104%), neg=0, invalid=762
0380: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=762
0381: dt=0.150000, rms=0.517 (-0.014%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.518, neg=0, invalid=762
0382: dt=0.000000, rms=0.517 (0.104%), neg=0, invalid=762
0383: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=762
0384: dt=0.150000, rms=0.517 (-0.014%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.562, neg=0, invalid=762
0385: dt=1.792000, rms=0.557 (0.885%), neg=0, invalid=762
0386: dt=0.256000, rms=0.557 (0.011%), neg=0, invalid=762
0387: dt=0.256000, rms=0.557 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.557, neg=0, invalid=762
0388: dt=0.768000, rms=0.556 (0.167%), neg=0, invalid=762
0389: dt=0.192000, rms=0.556 (0.004%), neg=0, invalid=762
0390: dt=0.192000, rms=0.556 (-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=0.510, neg=0, invalid=762
0391: dt=0.448000, rms=0.499 (2.262%), neg=0, invalid=762
0392: dt=0.448000, rms=0.496 (0.568%), neg=0, invalid=762
0393: dt=0.448000, rms=0.494 (0.328%), neg=0, invalid=762
0394: dt=0.448000, rms=0.493 (0.208%), neg=0, invalid=762
0395: dt=0.500000, rms=0.493 (0.167%), neg=0, invalid=762
0396: dt=0.448000, rms=0.492 (0.110%), neg=0, invalid=762
0397: dt=0.448000, rms=0.492 (0.087%), neg=0, invalid=762
0398: dt=0.448000, rms=0.491 (0.072%), neg=0, invalid=762
0399: dt=0.448000, rms=0.491 (0.057%), neg=0, invalid=762
0400: dt=0.448000, rms=0.491 (0.050%), neg=0, invalid=762
0401: dt=0.448000, rms=0.491 (0.040%), neg=0, invalid=762
0402: dt=0.448000, rms=0.490 (0.038%), neg=0, invalid=762
0403: dt=0.448000, rms=0.490 (0.058%), neg=0, invalid=762
0404: dt=0.448000, rms=0.490 (0.080%), neg=0, invalid=762
0405: dt=0.448000, rms=0.489 (0.080%), neg=0, invalid=762
0406: dt=0.448000, rms=0.489 (0.069%), neg=0, invalid=762
0407: dt=0.448000, rms=0.489 (0.056%), neg=0, invalid=762
0408: dt=0.448000, rms=0.489 (0.040%), neg=0, invalid=762
0409: dt=0.448000, rms=0.488 (0.021%), neg=0, invalid=762
0410: dt=0.448000, rms=0.488 (0.004%), neg=0, invalid=762
0411: dt=0.048000, rms=0.488 (0.003%), neg=0, invalid=762
0412: dt=0.048000, rms=0.488 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.489, neg=0, invalid=762
0413: dt=0.448000, rms=0.485 (0.757%), neg=0, invalid=762
0414: dt=0.448000, rms=0.485 (0.065%), neg=0, invalid=762
0415: dt=0.448000, rms=0.485 (0.014%), neg=0, invalid=762
0416: dt=0.448000, rms=0.485 (-0.006%), 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=0.483, neg=0, invalid=762
0417: dt=0.000000, rms=0.482 (0.140%), neg=0, invalid=762
0418: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0419: dt=129.472000, rms=0.482 (0.174%), neg=0, invalid=762
0420: dt=369.920000, rms=0.482 (0.040%), neg=0, invalid=762
0421: dt=369.920000, rms=0.482 (-0.643%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0422: dt=31.104000, rms=0.482 (0.200%), neg=0, invalid=762
0423: dt=36.288000, rms=0.482 (0.019%), neg=0, invalid=762
0424: dt=36.288000, rms=0.481 (0.020%), neg=0, invalid=762
0425: dt=36.288000, rms=0.481 (0.011%), neg=0, invalid=762
0426: dt=36.288000, rms=0.481 (-0.016%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.482, neg=0, invalid=762
0427: dt=97.777778, rms=0.480 (0.485%), neg=0, invalid=762
0428: dt=36.288000, rms=0.479 (0.134%), neg=0, invalid=762
0429: dt=36.288000, rms=0.479 (0.045%), neg=0, invalid=762
0430: dt=36.288000, rms=0.479 (0.080%), neg=0, invalid=762
0431: dt=36.288000, rms=0.478 (0.099%), neg=0, invalid=762
0432: dt=36.288000, rms=0.478 (0.110%), neg=0, invalid=762
0433: dt=36.288000, rms=0.477 (0.107%), neg=0, invalid=762
0434: dt=36.288000, rms=0.477 (0.098%), neg=0, invalid=762
0435: dt=145.152000, rms=0.476 (0.047%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.477, neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0436: dt=44.800000, rms=0.474 (0.784%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0437: dt=66.642202, rms=0.470 (0.666%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0438: dt=21.204819, rms=0.469 (0.285%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 10 iterations, nbhd size=1, neg = 0
0439: dt=44.800000, rms=0.468 (0.192%), neg=0, invalid=762
0440: dt=44.800000, rms=0.467 (0.193%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0441: dt=44.800000, rms=0.466 (0.374%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0442: dt=44.800000, rms=0.465 (0.073%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 9 iterations, nbhd size=1, neg = 0
0443: dt=44.800000, rms=0.463 (0.472%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 3 iterations, nbhd size=0, neg = 0
0444: dt=44.800000, rms=0.462 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 10 iterations, nbhd size=1, neg = 0
0445: dt=44.800000, rms=0.461 (0.324%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 2 iterations, nbhd size=0, neg = 0
0446: dt=44.800000, rms=0.461 (-0.089%), neg=0, invalid=762
0447: dt=25.600000, rms=0.460 (0.110%), neg=0, invalid=762
0448: dt=44.800000, rms=0.460 (0.099%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0449: dt=44.800000, rms=0.457 (0.650%), neg=0, invalid=762
0450: dt=30.967742, rms=0.456 (0.280%), neg=0, invalid=762
0451: dt=11.200000, rms=0.456 (0.078%), neg=0, invalid=762
0452: dt=11.200000, rms=0.456 (0.059%), neg=0, invalid=762
0453: dt=11.200000, rms=0.455 (0.072%), neg=0, invalid=762
0454: dt=11.200000, rms=0.455 (0.087%), neg=0, invalid=762
0455: dt=11.200000, rms=0.454 (0.091%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0456: dt=11.200000, rms=0.454 (0.080%), neg=0, invalid=762
0457: dt=11.200000, rms=0.454 (0.066%), neg=0, invalid=762
0458: dt=44.800000, rms=0.454 (0.027%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.461, neg=0, invalid=762
0459: dt=3.456000, rms=0.460 (0.213%), neg=0, invalid=762
0460: dt=2.000000, rms=0.460 (0.004%), neg=0, invalid=762
0461: dt=2.000000, rms=0.460 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.461, neg=0, invalid=762
0462: dt=7.000000, rms=0.460 (0.264%), neg=0, invalid=762
0463: dt=8.303797, rms=0.460 (0.062%), neg=0, invalid=762
0464: dt=8.303797, rms=0.459 (0.079%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0465: dt=8.303797, rms=0.459 (0.068%), neg=0, invalid=762
0466: dt=8.303797, rms=0.459 (0.062%), neg=0, invalid=762
iter 0, gcam->neg = 13
after 12 iterations, nbhd size=1, neg = 0
0467: dt=84.164384, rms=0.453 (1.296%), neg=0, invalid=762
0468: dt=5.818182, rms=0.453 (0.008%), neg=0, invalid=762
0469: dt=5.818182, rms=0.453 (0.002%), neg=0, invalid=762
0470: dt=5.818182, rms=0.453 (-0.162%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0471: dt=0.000000, rms=0.459 (0.160%), neg=0, invalid=762
0472: dt=0.000000, rms=0.459 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.460, neg=0, invalid=762
0473: dt=0.000000, rms=0.459 (0.160%), neg=0, invalid=762
0474: dt=0.000000, rms=0.459 (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=0.449, neg=0, invalid=762
iter 0, gcam->neg = 531
after 12 iterations, nbhd size=1, neg = 0
0475: dt=1.845651, rms=0.429 (4.421%), neg=0, invalid=762
0476: dt=0.012000, rms=0.429 (0.026%), neg=0, invalid=762
0477: dt=0.012000, 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
0478: dt=0.080000, rms=0.429 (0.224%), neg=0, invalid=762
0479: dt=0.000078, rms=0.429 (0.002%), neg=0, invalid=762
0480: dt=0.000078, rms=0.429 (0.000%), neg=0, invalid=762
0481: dt=0.000078, rms=0.429 (-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=0.418, neg=0, invalid=762
0482: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0483: dt=18.496000, rms=0.418 (0.001%), neg=0, invalid=762
0484: dt=0.361250, rms=0.418 (0.000%), neg=0, invalid=762
0485: dt=0.361250, rms=0.418 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0486: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0487: dt=36.288000, rms=0.418 (0.031%), neg=0, invalid=762
0488: dt=103.680000, rms=0.418 (0.031%), neg=0, invalid=762
0489: dt=103.680000, rms=0.418 (0.049%), neg=0, invalid=762
0490: dt=103.680000, rms=0.418 (0.035%), neg=0, invalid=762
0491: dt=103.680000, rms=0.418 (0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0492: dt=11.200000, rms=0.418 (0.089%), neg=0, invalid=762
0493: dt=11.200000, rms=0.418 (0.035%), neg=0, invalid=762
0494: dt=11.200000, rms=0.418 (0.016%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0495: dt=11.200000, rms=0.418 (-0.019%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0496: dt=44.800000, rms=0.416 (0.464%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0497: dt=38.400000, rms=0.415 (0.232%), neg=0, invalid=762
0498: dt=38.400000, rms=0.414 (0.102%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
0499: dt=38.400000, rms=0.413 (0.245%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 11 iterations, nbhd size=1, neg = 0
0500: dt=38.400000, rms=0.412 (0.243%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 3 iterations, nbhd size=0, neg = 0
0501: dt=38.400000, rms=0.411 (0.227%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 11 iterations, nbhd size=1, neg = 0
0502: dt=38.400000, rms=0.411 (0.130%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 9 iterations, nbhd size=1, neg = 0
0503: dt=38.400000, rms=0.410 (0.150%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 8 iterations, nbhd size=1, neg = 0
0504: dt=38.400000, rms=0.410 (0.142%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
0505: dt=38.400000, rms=0.409 (0.102%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0506: dt=38.400000, rms=0.409 (0.067%), neg=0, invalid=762
0507: dt=25.600000, rms=0.409 (0.054%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0508: dt=25.600000, rms=0.409 (0.008%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0509: dt=25.600000, rms=0.409 (0.007%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0510: dt=25.600000, rms=0.409 (0.017%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0511: dt=25.600000, rms=0.409 (0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
0512: dt=1.008000, rms=0.413 (0.004%), neg=0, invalid=762
0513: dt=0.252000, rms=0.413 (0.000%), neg=0, invalid=762
0514: dt=0.252000, rms=0.413 (0.000%), neg=0, invalid=762
0515: dt=0.252000, rms=0.413 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.413, neg=0, invalid=762
0516: dt=6.000000, rms=0.413 (0.042%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
0517: dt=7.000000, rms=0.412 (0.021%), neg=0, invalid=762
0518: dt=7.000000, rms=0.412 (0.021%), neg=0, invalid=762
0519: dt=7.000000, rms=0.412 (0.003%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0520: dt=7.000000, rms=0.412 (-0.018%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0521: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0522: dt=0.000000, rms=0.418 (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=0.409, neg=0, invalid=762
iter 0, gcam->neg = 451
after 12 iterations, nbhd size=1, neg = 0
0523: dt=1.280000, rms=0.400 (2.077%), neg=0, invalid=762
0524: dt=0.000023, rms=0.400 (0.000%), neg=0, invalid=762
0525: dt=0.000023, rms=0.400 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.400, neg=0, invalid=762
0526: dt=0.096000, rms=0.400 (0.038%), neg=0, invalid=762
0527: dt=0.028000, rms=0.400 (0.005%), neg=0, invalid=762
0528: dt=0.028000, rms=0.400 (0.002%), neg=0, invalid=762
0529: dt=0.028000, rms=0.400 (-0.004%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 59 minutes and 1 seconds.
mri_ca_register utimesec    11752.725314
mri_ca_register stimesec    10.353426
mri_ca_register ru_maxrss   1340416
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4665874
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  62984
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    6911
mri_ca_register ru_nivcsw   37058
FSRUNTIME@ mri_ca_register  2.9835 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sun Oct  8 05:20:43 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-388
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-6.0.0/0050607/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 8.26
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 = 0.06391 (17)
Left_Lateral_Ventricle (4): linear fit = 0.92 x + 0.0 (430 voxels, overlap=0.814)
Left_Lateral_Ventricle (4): linear fit = 0.92 x + 0.0 (430 voxels, peak = 18), gca=18.3
gca peak = 0.17677 (13)
mri peak = 0.10087 (13)
Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (419 voxels, overlap=0.784)
Right_Lateral_Ventricle (43): linear fit = 0.92 x + 0.0 (419 voxels, peak = 12), gca=11.9
gca peak = 0.28129 (95)
mri peak = 0.14373 (89)
Right_Pallidum (52): linear fit = 0.94 x + 0.0 (821 voxels, overlap=0.757)
Right_Pallidum (52): linear fit = 0.94 x + 0.0 (821 voxels, peak = 89), gca=88.8
gca peak = 0.16930 (96)
mri peak = 0.11675 (95)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (855 voxels, overlap=1.011)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (855 voxels, peak = 94), gca=93.6
gca peak = 0.24553 (55)
mri peak = 0.09624 (66)
Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (1287 voxels, overlap=0.476)
Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (1287 voxels, peak = 59), gca=59.1
gca peak = 0.30264 (59)
mri peak = 0.08285 (65)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1284 voxels, overlap=1.015)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1284 voxels, peak = 66), gca=65.8
gca peak = 0.07580 (103)
mri peak = 0.10280 (101)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (55865 voxels, overlap=0.774)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (55865 voxels, peak = 102), gca=102.5
gca peak = 0.07714 (104)
mri peak = 0.08387 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (58882 voxels, overlap=0.519)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (58882 voxels, peak = 109), gca=108.7
gca peak = 0.09712 (58)
mri peak = 0.03868 (61)
Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (53689 voxels, overlap=0.893)
Left_Cerebral_Cortex (3): linear fit = 1.04 x + 0.0 (53689 voxels, peak = 61), gca=60.6
gca peak = 0.11620 (58)
mri peak = 0.03748 (60)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (51837 voxels, overlap=0.971)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (51837 voxels, peak = 59), gca=59.4
gca peak = 0.30970 (66)
mri peak = 0.13044 (72)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (1101 voxels, overlap=1.003)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (1101 voxels, peak = 70), gca=70.3
gca peak = 0.15280 (69)
mri peak = 0.10677 (75)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1082 voxels, overlap=1.002)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1082 voxels, peak = 69), gca=69.0
gca peak = 0.13902 (56)
mri peak = 0.05695 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (30114 voxels, overlap=0.864)
Left_Cerebellum_Cortex (8): linear fit = 1.07 x + 0.0 (30114 voxels, peak = 60), gca=59.6
gca peak = 0.14777 (55)
mri peak = 0.06595 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.09 x + 0.0 (32355 voxels, overlap=0.940)
Right_Cerebellum_Cortex (47): linear fit = 1.09 x + 0.0 (32355 voxels, peak = 60), gca=59.7
gca peak = 0.16765 (84)
mri peak = 0.10553 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6855 voxels, overlap=0.810)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6855 voxels, peak = 89), gca=88.6
gca peak = 0.18739 (84)
mri peak = 0.13372 (86)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6066 voxels, overlap=0.801)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6066 voxels, peak = 86), gca=86.1
gca peak = 0.29869 (57)
mri peak = 0.09125 (62)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (800 voxels, overlap=0.811)
Left_Amygdala (18): linear fit = 1.10 x + 0.0 (800 voxels, peak = 62), gca=62.4
gca peak = 0.33601 (57)
mri peak = 0.10436 (61)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (755 voxels, overlap=1.005)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (755 voxels, peak = 60), gca=59.6
gca peak = 0.11131 (90)
mri peak = 0.08964 (82)
Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (4700 voxels, overlap=0.915)
Left_Thalamus_Proper (10): linear fit = 0.96 x + 0.0 (4700 voxels, peak = 87), gca=86.8
gca peak = 0.11793 (83)
mri peak = 0.11747 (80)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5202 voxels, overlap=0.960)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (5202 voxels, peak = 82), gca=81.8
gca peak = 0.08324 (81)
mri peak = 0.08166 (80)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (2731 voxels, overlap=0.678)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (2731 voxels, peak = 86), gca=86.3
gca peak = 0.10360 (77)
mri peak = 0.08555 (80)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2991 voxels, overlap=0.938)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2991 voxels, peak = 77), gca=77.0
gca peak = 0.08424 (78)
mri peak = 0.13133 (82)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (14092 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (14092 voxels, peak = 81), gca=80.7
gca peak = 0.12631 (89)
mri peak = 0.09538 (89)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (2014 voxels, overlap=0.823)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (2014 voxels, peak = 90), gca=90.3
gca peak = 0.14500 (87)
mri peak = 0.08164 (90)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (2111 voxels, overlap=0.900)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (2111 voxels, peak = 89), gca=89.2
gca peak = 0.14975 (24)
mri peak = 0.09817 (48)
Third_Ventricle (14): linear fit = 1.75 x + 0.0 (67 voxels, overlap=0.580)
Third_Ventricle (14): linear fit = 1.75 x + 0.0 (67 voxels, peak = 42), gca=42.1
gca peak = 0.19357 (14)
mri peak = 0.13759 (14)
Fourth_Ventricle (15): linear fit = 0.83 x + 0.0 (149 voxels, overlap=0.708)
Fourth_Ventricle (15): linear fit = 0.83 x + 0.0 (149 voxels, peak = 12), gca=11.7
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 1.07 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.89 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15970 (17)
mri peak = 0.06391 (17)
Left_Lateral_Ventricle (4): linear fit = 1.09 x + 0.0 (430 voxels, overlap=0.849)
Left_Lateral_Ventricle (4): linear fit = 1.09 x + 0.0 (430 voxels, peak = 18), gca=18.4
gca peak = 0.18581 (12)
mri peak = 0.10087 (13)
Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (419 voxels, overlap=0.705)
Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (419 voxels, peak = 14), gca=13.5
gca peak = 0.26033 (88)
mri peak = 0.14373 (89)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (821 voxels, overlap=1.006)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (821 voxels, peak = 88), gca=88.0
gca peak = 0.18684 (94)
mri peak = 0.11675 (95)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (855 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (855 voxels, peak = 94), gca=93.5
gca peak = 0.28160 (60)
mri peak = 0.09624 (66)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1287 voxels, overlap=1.002)
Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1287 voxels, peak = 62), gca=61.5
gca peak = 0.29136 (63)
mri peak = 0.08285 (65)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1284 voxels, overlap=1.012)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1284 voxels, peak = 62), gca=62.1
gca peak = 0.07845 (102)
mri peak = 0.10280 (101)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (55865 voxels, overlap=0.760)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (55865 voxels, peak = 101), gca=101.5
gca peak = 0.07807 (109)
mri peak = 0.08387 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (58882 voxels, overlap=0.717)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (58882 voxels, peak = 109), gca=109.0
gca peak = 0.09227 (61)
mri peak = 0.03868 (61)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (53689 voxels, overlap=0.961)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (53689 voxels, peak = 63), gca=62.5
gca peak = 0.11330 (59)
mri peak = 0.03748 (60)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (51837 voxels, overlap=0.981)
Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (51837 voxels, peak = 60), gca=60.5
gca peak = 0.26062 (71)
mri peak = 0.13044 (72)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (1101 voxels, overlap=1.007)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (1101 voxels, peak = 70), gca=69.9
gca peak = 0.16042 (69)
mri peak = 0.10677 (75)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1082 voxels, overlap=1.002)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1082 voxels, peak = 69), gca=69.0
gca peak = 0.13228 (60)
mri peak = 0.05695 (60)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (30114 voxels, overlap=0.980)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (30114 voxels, peak = 62), gca=61.5
gca peak = 0.13381 (59)
mri peak = 0.06595 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (32355 voxels, overlap=0.996)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (32355 voxels, peak = 60), gca=60.5
gca peak = 0.16035 (89)
mri peak = 0.10553 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6855 voxels, overlap=0.960)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6855 voxels, peak = 89), gca=89.0
gca peak = 0.16001 (86)
mri peak = 0.13372 (86)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6066 voxels, overlap=0.906)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6066 voxels, peak = 86), gca=86.0
gca peak = 0.27441 (62)
mri peak = 0.09125 (62)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (800 voxels, overlap=1.016)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (800 voxels, peak = 62), gca=62.0
gca peak = 0.31520 (60)
mri peak = 0.10436 (61)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (755 voxels, overlap=1.028)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (755 voxels, peak = 62), gca=61.5
gca peak = 0.10682 (85)
mri peak = 0.08964 (82)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4700 voxels, overlap=0.973)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4700 voxels, peak = 85), gca=84.6
gca peak = 0.10448 (82)
mri peak = 0.11747 (80)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5202 voxels, overlap=0.942)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5202 voxels, peak = 82), gca=82.0
gca peak = 0.08593 (80)
mri peak = 0.08166 (80)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2731 voxels, overlap=0.874)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2731 voxels, peak = 79), gca=78.8
gca peak = 0.09691 (77)
mri peak = 0.08555 (80)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2991 voxels, overlap=0.938)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2991 voxels, peak = 77), gca=77.0
gca peak = 0.08720 (81)
mri peak = 0.13133 (82)
Brain_Stem: unreasonable value (79.8/82.0), not in range [80, 110] - rejecting
gca peak = 0.13540 (89)
mri peak = 0.09538 (89)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (2014 voxels, overlap=0.840)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (2014 voxels, peak = 88), gca=87.7
gca peak = 0.13891 (88)
mri peak = 0.08164 (90)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (2111 voxels, overlap=0.895)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (2111 voxels, peak = 87), gca=86.7
gca peak = 0.19089 (23)
mri peak = 0.09817 (48)
Third_Ventricle (14): linear fit = 2.05 x + 0.0 (67 voxels, overlap=0.511)
Third_Ventricle (14): linear fit = 2.05 x + 0.0 (67 voxels, peak = 47), gca=47.0
gca peak = 0.24326 (13)
mri peak = 0.13759 (14)
Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (149 voxels, overlap=0.796)
Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (149 voxels, peak = 13), gca=12.7
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16626 (36)
gca peak Left_Thalamus = 0.64095 (100)
gca peak Third_Ventricle = 0.19089 (23)
gca peak Brain_Stem = 0.08720 (81)
gca peak CSF = 0.26232 (32)
gca peak Left_Accumbens_area = 0.67956 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24205 (25)
gca peak Right_Accumbens_area = 0.29895 (69)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.89470 (28)
gca peak WM_hypointensities = 0.07705 (77)
gca peak non_WM_hypointensities = 0.08683 (44)
gca peak Optic_Chiasm = 0.70922 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.06 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
61908 voxels changed in iteration 0 of unlikely voxel relabeling
227 voxels changed in iteration 1 of unlikely voxel relabeling
12 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
41689 gm and wm labels changed (%31 to gray, %69 to white out of all changed labels)
1281 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 70949 changed. image ll: -2.133, PF=0.500
pass 2: 20942 changed. image ll: -2.132, PF=0.500
pass 3: 7398 changed.
pass 4: 2965 changed.
44112 voxels changed in iteration 0 of unlikely voxel relabeling
342 voxels changed in iteration 1 of unlikely voxel relabeling
16 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
7173 voxels changed in iteration 0 of unlikely voxel relabeling
135 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6322 voxels changed in iteration 0 of unlikely voxel relabeling
59 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5989 voxels changed in iteration 0 of unlikely voxel relabeling
32 voxels changed in iteration 1 of unlikely voxel relabeling
6 voxels changed in iteration 2 of unlikely voxel relabeling
5 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 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    3716.909943
mri_ca_label stimesec    1.358793
mri_ca_label ru_maxrss   2105896
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   654658
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  62976
mri_ca_label ru_oublock  488
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    288
mri_ca_label ru_nivcsw   7132
auto-labeling took 61 minutes and 13 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/transforms/cc_up.lta 0050607 

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-6.0.0/0050607/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/norm.mgz
26090 voxels in left wm, 47910 in right wm, xrange [123, 130]
searching rotation angles z=[-6  8], y=[-7  7]

searching scale 1 Z rot -6.4  
searching scale 1 Z rot -6.1  
searching scale 1 Z rot -5.9  
searching scale 1 Z rot -5.6  
searching scale 1 Z rot -5.4  
searching scale 1 Z rot -5.1  
searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.4  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.9  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.4  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.9  global minimum found at slice 127.0, rotations (0.08, 1.13)
final transformation (x=127.0, yr=0.082, zr=1.128):
 0.99981  -0.01968   0.00144   2.96368;
 0.01968   0.99981   0.00003   18.51827;
-0.00144   0.00000   1.00000   12.18258;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 107 116
eigenvectors:
 0.00006  -0.00022   1.00000;
-0.09470  -0.99551  -0.00022;
 0.99551  -0.09470  -0.00008;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.8 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 06:22:42 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 06:22:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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...
1021 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 68 (68), valley at 27 (27)
csf peak at 35, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 69 (69), valley at 28 (28)
csf peak at 35, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 18 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 06:26:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1824248 voxels in mask (pct= 10.87)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 06:26:05 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): 102.8 +- 5.9 [79.0 --> 125.0]
GM (73.0) : 71.9 +- 9.0 [30.0 --> 95.0]
setting bottom of white matter range to 80.9
setting top of gray matter range to 89.9
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...
3551 sparsely connected voxels removed...
thickening thin strands....
20 segments, 3592 filled
2460 bright non-wm voxels segmented.
1766 diagonally connected voxels added...
white matter segmentation took 1.7 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

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

preserving editing changes in input volume...
auto filling took 0.64 minutes
reading wm segmentation from wm.seg.mgz...
533 voxels added to wm to prevent paths from MTL structures to cortex
2378 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 29844 voxels turned on, 48655 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+):   8 found -   8 modified     |    TOTAL:   8
pass   2 (xy+):   0 found -   8 modified     |    TOTAL:   8
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:  11
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:  11
pass   1 (yz+):  19 found -  19 modified     |    TOTAL:  30
pass   2 (yz+):   0 found -  19 modified     |    TOTAL:  30
pass   1 (yz-):  20 found -  20 modified     |    TOTAL:  50
pass   2 (yz-):   0 found -  20 modified     |    TOTAL:  50
pass   1 (xz+):  11 found -  11 modified     |    TOTAL:  61
pass   2 (xz+):   0 found -  11 modified     |    TOTAL:  61
pass   1 (xz-):  13 found -  13 modified     |    TOTAL:  74
pass   2 (xz-):   0 found -  13 modified     |    TOTAL:  74
Iteration Number : 1
pass   1 (+++):  22 found -  22 modified     |    TOTAL:  22
pass   2 (+++):   0 found -  22 modified     |    TOTAL:  22
pass   1 (+++):  13 found -  13 modified     |    TOTAL:  35
pass   2 (+++):   0 found -  13 modified     |    TOTAL:  35
pass   1 (+++):  14 found -  14 modified     |    TOTAL:  49
pass   2 (+++):   0 found -  14 modified     |    TOTAL:  49
pass   1 (+++):   8 found -   8 modified     |    TOTAL:  57
pass   2 (+++):   0 found -   8 modified     |    TOTAL:  57
Iteration Number : 1
pass   1 (++):  36 found -  36 modified     |    TOTAL:  36
pass   2 (++):   0 found -  36 modified     |    TOTAL:  36
pass   1 (+-):  24 found -  24 modified     |    TOTAL:  60
pass   2 (+-):   0 found -  24 modified     |    TOTAL:  60
pass   1 (--):  43 found -  43 modified     |    TOTAL: 103
pass   2 (--):   0 found -  43 modified     |    TOTAL: 103
pass   1 (-+):  47 found -  47 modified     |    TOTAL: 150
pass   2 (-+):   0 found -  47 modified     |    TOTAL: 150
Iteration Number : 2
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-):   3 found -   3 modified     |    TOTAL:   8
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   8
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   8
pass   1 (xz-):   6 found -   6 modified     |    TOTAL:  14
pass   2 (xz-):   0 found -   6 modified     |    TOTAL:  14
Iteration Number : 2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (--):   1 found -   1 modified     |    TOTAL:   4
pass   2 (--):   0 found -   1 modified     |    TOTAL:   4
pass   1 (-+):   3 found -   3 modified     |    TOTAL:   7
pass   2 (-+):   0 found -   3 modified     |    TOTAL:   7
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   2 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 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 310 (out of 651611: 0.047574)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 06:28:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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
 1.02019   0.01665  -0.01285  -2.81572;
-0.01421   0.99826   0.17034  -20.50317;
 0.01645  -0.16317   0.92298   15.39975;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.02019   0.01665  -0.01285  -2.81572;
-0.01421   0.99826   0.17034  -20.50317;
 0.01645  -0.16317   0.92298   15.39975;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1011 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75)
no need to search
using seed (127, 121, 148), TAL = (1.0, 20.0, 7.0)
talairach voxel to voxel transform
 0.97976  -0.01370   0.01617   2.22881;
 0.01643   0.97218  -0.17919   22.73856;
-0.01455   0.17212   1.05148  -12.70462;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (127,  121,  148) --> (1.0, 20.0, 7.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (1.00, 20.00, 7.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, 20.00, 7.00) SRC: (109.76, 115.64, 162.15)
search lh wm seed point around talairach space (-17.00, 20.00, 7.00), SRC: (145.03, 116.24, 161.63)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sun Oct  8 06:29:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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


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

Total Number of Modified Voxels = 7 (out of 310138: 0.002257)
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: 22 vertices, 30 faces
slice 50: 4483 vertices, 4687 faces
slice 60: 12436 vertices, 12779 faces
slice 70: 23039 vertices, 23443 faces
slice 80: 34400 vertices, 34801 faces
slice 90: 45867 vertices, 46233 faces
slice 100: 56832 vertices, 57237 faces
slice 110: 69107 vertices, 69509 faces
slice 120: 80522 vertices, 80973 faces
slice 130: 91580 vertices, 91999 faces
slice 140: 102611 vertices, 103026 faces
slice 150: 112918 vertices, 113298 faces
slice 160: 121317 vertices, 121661 faces
slice 170: 130167 vertices, 130542 faces
slice 180: 137249 vertices, 137562 faces
slice 190: 144068 vertices, 144375 faces
slice 200: 149043 vertices, 149236 faces
slice 210: 151212 vertices, 151299 faces
slice 220: 151248 vertices, 151318 faces
slice 230: 151248 vertices, 151318 faces
slice 240: 151248 vertices, 151318 faces
slice 250: 151248 vertices, 151318 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...
   151248 voxel in cpt #1: X=-70 [v=151248,e=453954,f=302636] located at (-26.322556, -10.996655, 11.280664)
For the whole surface: X=-70 [v=151248,e=453954,f=302636]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 06:29:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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


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

Total Number of Modified Voxels = 5 (out of 318423: 0.001570)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 1785 vertices, 1939 faces
slice 60: 7946 vertices, 8202 faces
slice 70: 17658 vertices, 18038 faces
slice 80: 30144 vertices, 30608 faces
slice 90: 42913 vertices, 43355 faces
slice 100: 55378 vertices, 55780 faces
slice 110: 67791 vertices, 68247 faces
slice 120: 80535 vertices, 80996 faces
slice 130: 92917 vertices, 93365 faces
slice 140: 105061 vertices, 105545 faces
slice 150: 116539 vertices, 116955 faces
slice 160: 126446 vertices, 126816 faces
slice 170: 135560 vertices, 135908 faces
slice 180: 143601 vertices, 143900 faces
slice 190: 150704 vertices, 150986 faces
slice 200: 156148 vertices, 156363 faces
slice 210: 158793 vertices, 158878 faces
slice 220: 158838 vertices, 158902 faces
slice 230: 158838 vertices, 158902 faces
slice 240: 158838 vertices, 158902 faces
slice 250: 158838 vertices, 158902 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...
   158838 voxel in cpt #1: X=-64 [v=158838,e=476706,f=317804] located at (29.052790, -7.805059, 9.670891)
For the whole surface: X=-64 [v=158838,e=476706,f=317804]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 06:29:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 06:29:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

Waiting for PID 29205 of (29205 29208) to complete...
Waiting for PID 29208 of (29205 29208) 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 (29205 29208) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 06:29:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 06:29:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

Waiting for PID 29255 of (29255 29258) to complete...
Waiting for PID 29258 of (29255 29258) to complete...

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

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 49.7 mm, total surface area = 80577 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.155 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.060 (target=0.015)   
step 030: RMS=0.053 (target=0.015)   
step 035: RMS=0.050 (target=0.015)   
step 040: RMS=0.047 (target=0.015)   
step 045: RMS=0.045 (target=0.015)   
step 050: RMS=0.043 (target=0.015)   
step 055: RMS=0.044 (target=0.015)   
step 060: RMS=0.044 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    46.589917
mris_inflate stimesec    0.134979
mris_inflate ru_maxrss   220632
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31592
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10640
mris_inflate ru_oublock  10664
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    7519
mris_inflate ru_nivcsw   4763

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 48.8 mm, total surface area = 84452 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.154 (target=0.015)   
step 005: RMS=0.118 (target=0.015)   
step 010: RMS=0.089 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.065 (target=0.015)   
step 025: RMS=0.057 (target=0.015)   
step 030: RMS=0.052 (target=0.015)   
step 035: RMS=0.047 (target=0.015)   
step 040: RMS=0.044 (target=0.015)   
step 045: RMS=0.042 (target=0.015)   
step 050: RMS=0.041 (target=0.015)   
step 055: RMS=0.040 (target=0.015)   
step 060: RMS=0.040 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    60.372821
mris_inflate stimesec    0.144977
mris_inflate ru_maxrss   231496
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33288
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11176
mris_inflate ru_oublock  11192
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    4840
mris_inflate ru_nivcsw   6414
PIDs (29255 29258) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 06:30:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 06:30:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

Waiting for PID 29357 of (29357 29361) to complete...
Waiting for PID 29361 of (29357 29361) 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 0.92 +- 0.57 (0.00-->6.25) (max @ vno 54263 --> 55375)
face area 0.02 +- 0.03 (-0.15-->0.51)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.296...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.582, avgs=0
005/300: dt: 0.9000, rms radial error=176.321, avgs=0
010/300: dt: 0.9000, rms radial error=175.763, avgs=0
015/300: dt: 0.9000, rms radial error=175.030, avgs=0
020/300: dt: 0.9000, rms radial error=174.195, avgs=0
025/300: dt: 0.9000, rms radial error=173.303, avgs=0
030/300: dt: 0.9000, rms radial error=172.378, avgs=0
035/300: dt: 0.9000, rms radial error=171.435, avgs=0
040/300: dt: 0.9000, rms radial error=170.485, avgs=0
045/300: dt: 0.9000, rms radial error=169.532, avgs=0
050/300: dt: 0.9000, rms radial error=168.580, avgs=0
055/300: dt: 0.9000, rms radial error=167.630, avgs=0
060/300: dt: 0.9000, rms radial error=166.684, avgs=0
065/300: dt: 0.9000, rms radial error=165.742, avgs=0
070/300: dt: 0.9000, rms radial error=164.804, avgs=0
075/300: dt: 0.9000, rms radial error=163.872, avgs=0
080/300: dt: 0.9000, rms radial error=162.944, avgs=0
085/300: dt: 0.9000, rms radial error=162.021, avgs=0
090/300: dt: 0.9000, rms radial error=161.103, avgs=0
095/300: dt: 0.9000, rms radial error=160.190, avgs=0
100/300: dt: 0.9000, rms radial error=159.282, avgs=0
105/300: dt: 0.9000, rms radial error=158.379, avgs=0
110/300: dt: 0.9000, rms radial error=157.481, avgs=0
115/300: dt: 0.9000, rms radial error=156.588, avgs=0
120/300: dt: 0.9000, rms radial error=155.701, avgs=0
125/300: dt: 0.9000, rms radial error=154.824, avgs=0
130/300: dt: 0.9000, rms radial error=153.953, avgs=0
135/300: dt: 0.9000, rms radial error=153.086, avgs=0
140/300: dt: 0.9000, rms radial error=152.224, avgs=0
145/300: dt: 0.9000, rms radial error=151.367, avgs=0
150/300: dt: 0.9000, rms radial error=150.515, avgs=0
155/300: dt: 0.9000, rms radial error=149.667, avgs=0
160/300: dt: 0.9000, rms radial error=148.824, avgs=0
165/300: dt: 0.9000, rms radial error=147.986, avgs=0
170/300: dt: 0.9000, rms radial error=147.152, avgs=0
175/300: dt: 0.9000, rms radial error=146.323, avgs=0
180/300: dt: 0.9000, rms radial error=145.498, avgs=0
185/300: dt: 0.9000, rms radial error=144.679, avgs=0
190/300: dt: 0.9000, rms radial error=143.863, avgs=0
195/300: dt: 0.9000, rms radial error=143.052, avgs=0
200/300: dt: 0.9000, rms radial error=142.246, avgs=0
205/300: dt: 0.9000, rms radial error=141.444, avgs=0
210/300: dt: 0.9000, rms radial error=140.647, avgs=0
215/300: dt: 0.9000, rms radial error=139.854, avgs=0
220/300: dt: 0.9000, rms radial error=139.065, avgs=0
225/300: dt: 0.9000, rms radial error=138.281, avgs=0
230/300: dt: 0.9000, rms radial error=137.502, avgs=0
235/300: dt: 0.9000, rms radial error=136.726, avgs=0
240/300: dt: 0.9000, rms radial error=135.955, avgs=0
245/300: dt: 0.9000, rms radial error=135.188, avgs=0
250/300: dt: 0.9000, rms radial error=134.426, avgs=0
255/300: dt: 0.9000, rms radial error=133.667, avgs=0
260/300: dt: 0.9000, rms radial error=132.913, avgs=0
265/300: dt: 0.9000, rms radial error=132.164, avgs=0
270/300: dt: 0.9000, rms radial error=131.418, avgs=0
275/300: dt: 0.9000, rms radial error=130.677, avgs=0
280/300: dt: 0.9000, rms radial error=129.940, avgs=0
285/300: dt: 0.9000, rms radial error=129.206, avgs=0
290/300: dt: 0.9000, rms radial error=128.477, avgs=0
295/300: dt: 0.9000, rms radial error=127.753, avgs=0
300/300: dt: 0.9000, rms radial error=127.032, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17977.61
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 = 3146.32
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
epoch 3 (K=160.0), pass 1, starting sse = 359.85
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00299
epoch 4 (K=640.0), pass 1, starting sse = 30.19
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00393
final distance error %29.01
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    334.919084
mris_sphere stimesec    0.232964
mris_sphere ru_maxrss   220836
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   31642
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  10648
mris_sphere ru_oublock  10688
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    10544
mris_sphere ru_nivcsw   25301
FSRUNTIME@ mris_sphere  0.0933 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 +- 0.54 (0.00-->7.09) (max @ vno 59780 --> 61051)
face area 0.02 +- 0.03 (-0.08-->0.88)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.299...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.174, avgs=0
005/300: dt: 0.9000, rms radial error=175.913, avgs=0
010/300: dt: 0.9000, rms radial error=175.354, avgs=0
015/300: dt: 0.9000, rms radial error=174.618, avgs=0
020/300: dt: 0.9000, rms radial error=173.781, avgs=0
025/300: dt: 0.9000, rms radial error=172.885, avgs=0
030/300: dt: 0.9000, rms radial error=171.958, avgs=0
035/300: dt: 0.9000, rms radial error=171.015, avgs=0
040/300: dt: 0.9000, rms radial error=170.064, avgs=0
045/300: dt: 0.9000, rms radial error=169.110, avgs=0
050/300: dt: 0.9000, rms radial error=168.162, avgs=0
055/300: dt: 0.9000, rms radial error=167.218, avgs=0
060/300: dt: 0.9000, rms radial error=166.277, avgs=0
065/300: dt: 0.9000, rms radial error=165.342, avgs=0
070/300: dt: 0.9000, rms radial error=164.411, avgs=0
075/300: dt: 0.9000, rms radial error=163.485, avgs=0
080/300: dt: 0.9000, rms radial error=162.564, avgs=0
085/300: dt: 0.9000, rms radial error=161.649, avgs=0
090/300: dt: 0.9000, rms radial error=160.738, avgs=0
095/300: dt: 0.9000, rms radial error=159.832, avgs=0
100/300: dt: 0.9000, rms radial error=158.932, avgs=0
105/300: dt: 0.9000, rms radial error=158.037, avgs=0
110/300: dt: 0.9000, rms radial error=157.147, avgs=0
115/300: dt: 0.9000, rms radial error=156.262, avgs=0
120/300: dt: 0.9000, rms radial error=155.382, avgs=0
125/300: dt: 0.9000, rms radial error=154.506, avgs=0
130/300: dt: 0.9000, rms radial error=153.638, avgs=0
135/300: dt: 0.9000, rms radial error=152.774, avgs=0
140/300: dt: 0.9000, rms radial error=151.915, avgs=0
145/300: dt: 0.9000, rms radial error=151.061, avgs=0
150/300: dt: 0.9000, rms radial error=150.212, avgs=0
155/300: dt: 0.9000, rms radial error=149.367, avgs=0
160/300: dt: 0.9000, rms radial error=148.527, avgs=0
165/300: dt: 0.9000, rms radial error=147.692, avgs=0
170/300: dt: 0.9000, rms radial error=146.861, avgs=0
175/300: dt: 0.9000, rms radial error=146.034, avgs=0
180/300: dt: 0.9000, rms radial error=145.213, avgs=0
185/300: dt: 0.9000, rms radial error=144.395, avgs=0
190/300: dt: 0.9000, rms radial error=143.583, avgs=0
195/300: dt: 0.9000, rms radial error=142.775, avgs=0
200/300: dt: 0.9000, rms radial error=141.972, avgs=0
205/300: dt: 0.9000, rms radial error=141.173, avgs=0
210/300: dt: 0.9000, rms radial error=140.378, avgs=0
215/300: dt: 0.9000, rms radial error=139.588, avgs=0
220/300: dt: 0.9000, rms radial error=138.803, avgs=0
225/300: dt: 0.9000, rms radial error=138.021, avgs=0
230/300: dt: 0.9000, rms radial error=137.244, avgs=0
235/300: dt: 0.9000, rms radial error=136.471, avgs=0
240/300: dt: 0.9000, rms radial error=135.703, avgs=0
245/300: dt: 0.9000, rms radial error=134.939, avgs=0
250/300: dt: 0.9000, rms radial error=134.179, avgs=0
255/300: dt: 0.9000, rms radial error=133.423, avgs=0
260/300: dt: 0.9000, rms radial error=132.672, avgs=0
265/300: dt: 0.9000, rms radial error=131.925, avgs=0
270/300: dt: 0.9000, rms radial error=131.181, avgs=0
275/300: dt: 0.9000, rms radial error=130.442, avgs=0
280/300: dt: 0.9000, rms radial error=129.707, avgs=0
285/300: dt: 0.9000, rms radial error=128.976, avgs=0
290/300: dt: 0.9000, rms radial error=128.250, avgs=0
295/300: dt: 0.9000, rms radial error=127.527, avgs=0
300/300: dt: 0.9000, rms radial error=126.808, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18804.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
epoch 2 (K=40.0), pass 1, starting sse = 3219.13
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
epoch 3 (K=160.0), pass 1, starting sse = 344.70
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00631
epoch 4 (K=640.0), pass 1, starting sse = 23.95
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/11 = 0.00460
final distance error %26.71
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    357.021724
mris_sphere stimesec    0.219966
mris_sphere ru_maxrss   231700
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33334
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11216
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    11056
mris_sphere ru_nivcsw   26479
FSRUNTIME@ mris_sphere  0.0994 hours 1 threads
PIDs (29357 29361) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 06:36:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 06:36:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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


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

#@# Fix Topology lh Sun Oct  8 06:36:34 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050607 lh 

#@# Fix Topology rh Sun Oct  8 06:36:34 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050607 rh 

Waiting for PID 29665 of (29665 29668) to complete...
Waiting for PID 29668 of (29665 29668) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050607 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=-70 (nv=151248, nf=302636, ne=453954, g=36)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
7270 ambiguous faces found in tessellation
segmenting defects...
52 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 21 into 19
      -merging segment 29 into 25
      -merging segment 30 into 27
      -merging segment 48 into 46
48 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.0759  (-4.5380)
      -vertex     loglikelihood: -5.9195  (-2.9597)
      -normal dot loglikelihood: -3.6307  (-3.6307)
      -quad curv  loglikelihood: -6.1245  (-3.0622)
      Total Loglikelihood : -24.7506

CORRECTING DEFECT 0 (vertices=124, convex hull=99, v0=2635)
After retessellation of defect 0 (v0=2635), euler #=-49 (146887,438968,292032) : difference with theory (-45) = 4 

CORRECTING DEFECT 1 (vertices=81, convex hull=89, v0=3838)
After retessellation of defect 1 (v0=3838), euler #=-48 (146911,439077,292118) : difference with theory (-44) = 4 

CORRECTING DEFECT 2 (vertices=55, convex hull=90, v0=6212)
After retessellation of defect 2 (v0=6212), euler #=-47 (146926,439155,292182) : difference with theory (-43) = 4 

CORRECTING DEFECT 3 (vertices=16, convex hull=29, v0=8271)
After retessellation of defect 3 (v0=8271), euler #=-46 (146927,439168,292195) : difference with theory (-42) = 4 

CORRECTING DEFECT 4 (vertices=26, convex hull=63, v0=9708)
After retessellation of defect 4 (v0=9708), euler #=-45 (146938,439225,292242) : difference with theory (-41) = 4 

CORRECTING DEFECT 5 (vertices=77, convex hull=66, v0=12626)
After retessellation of defect 5 (v0=12626), euler #=-44 (146958,439312,292310) : difference with theory (-40) = 4 

CORRECTING DEFECT 6 (vertices=53, convex hull=51, v0=13271)
After retessellation of defect 6 (v0=13271), euler #=-43 (146966,439357,292348) : difference with theory (-39) = 4 

CORRECTING DEFECT 7 (vertices=122, convex hull=106, v0=19308)
After retessellation of defect 7 (v0=19308), euler #=-42 (147000,439512,292470) : difference with theory (-38) = 4 

CORRECTING DEFECT 8 (vertices=103, convex hull=100, v0=23684)
After retessellation of defect 8 (v0=23684), euler #=-41 (147018,439610,292551) : difference with theory (-37) = 4 

CORRECTING DEFECT 9 (vertices=163, convex hull=105, v0=25875)
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
normal vector of length zero at vertex 29773 with 4 faces
After retessellation of defect 9 (v0=25875), euler #=-40 (147042,439732,292650) : difference with theory (-36) = 4 

CORRECTING DEFECT 10 (vertices=80, convex hull=76, v0=26104)
After retessellation of defect 10 (v0=26104), euler #=-39 (147063,439823,292721) : difference with theory (-35) = 4 

CORRECTING DEFECT 11 (vertices=32, convex hull=80, v0=26595)
After retessellation of defect 11 (v0=26595), euler #=-38 (147076,439897,292783) : difference with theory (-34) = 4 

CORRECTING DEFECT 12 (vertices=28, convex hull=54, v0=28008)
After retessellation of defect 12 (v0=28008), euler #=-37 (147087,439952,292828) : difference with theory (-33) = 4 

CORRECTING DEFECT 13 (vertices=175, convex hull=146, v0=31294)
After retessellation of defect 13 (v0=31294), euler #=-36 (147169,440267,293062) : difference with theory (-32) = 4 

CORRECTING DEFECT 14 (vertices=116, convex hull=99, v0=35224)
After retessellation of defect 14 (v0=35224), euler #=-35 (147200,440404,293169) : difference with theory (-31) = 4 

CORRECTING DEFECT 15 (vertices=61, convex hull=86, v0=37935)
After retessellation of defect 15 (v0=37935), euler #=-34 (147228,440521,293259) : difference with theory (-30) = 4 

CORRECTING DEFECT 16 (vertices=189, convex hull=90, v0=45755)
After retessellation of defect 16 (v0=45755), euler #=-33 (147255,440646,293358) : difference with theory (-29) = 4 

CORRECTING DEFECT 17 (vertices=31, convex hull=58, v0=55411)
After retessellation of defect 17 (v0=55411), euler #=-32 (147272,440722,293418) : difference with theory (-28) = 4 

CORRECTING DEFECT 18 (vertices=22, convex hull=61, v0=55535)
After retessellation of defect 18 (v0=55535), euler #=-31 (147284,440782,293467) : difference with theory (-27) = 4 

CORRECTING DEFECT 19 (vertices=20, convex hull=42, v0=60397)
After retessellation of defect 19 (v0=60397), euler #=-29 (147290,440816,293497) : difference with theory (-26) = 3 

CORRECTING DEFECT 20 (vertices=104, convex hull=104, v0=60623)
After retessellation of defect 20 (v0=60623), euler #=-28 (147334,440996,293634) : difference with theory (-25) = 3 

CORRECTING DEFECT 21 (vertices=10, convex hull=20, v0=68655)
After retessellation of defect 21 (v0=68655), euler #=-27 (147336,441009,293646) : difference with theory (-24) = 3 

CORRECTING DEFECT 22 (vertices=28, convex hull=60, v0=68707)
After retessellation of defect 22 (v0=68707), euler #=-26 (147352,441078,293700) : difference with theory (-23) = 3 

CORRECTING DEFECT 23 (vertices=70, convex hull=134, v0=74123)
After retessellation of defect 23 (v0=74123), euler #=-25 (147400,441282,293857) : difference with theory (-22) = 3 

CORRECTING DEFECT 24 (vertices=455, convex hull=368, v0=76933)
After retessellation of defect 24 (v0=76933), euler #=-23 (147609,442094,294462) : difference with theory (-21) = 2 

CORRECTING DEFECT 25 (vertices=85, convex hull=107, v0=77637)
After retessellation of defect 25 (v0=77637), euler #=-22 (147648,442256,294586) : difference with theory (-20) = 2 

CORRECTING DEFECT 26 (vertices=93, convex hull=83, v0=78126)
After retessellation of defect 26 (v0=78126), euler #=-20 (147673,442368,294675) : difference with theory (-19) = 1 

CORRECTING DEFECT 27 (vertices=189, convex hull=226, v0=78713)
After retessellation of defect 27 (v0=78713), euler #=-19 (147793,442836,295024) : difference with theory (-18) = 1 

CORRECTING DEFECT 28 (vertices=57, convex hull=41, v0=89052)
After retessellation of defect 28 (v0=89052), euler #=-18 (147805,442885,295062) : difference with theory (-17) = 1 

CORRECTING DEFECT 29 (vertices=45, convex hull=81, v0=90558)
After retessellation of defect 29 (v0=90558), euler #=-17 (147836,443015,295162) : difference with theory (-16) = 1 

CORRECTING DEFECT 30 (vertices=119, convex hull=26, v0=93653)
After retessellation of defect 30 (v0=93653), euler #=-16 (147844,443048,295188) : difference with theory (-15) = 1 

CORRECTING DEFECT 31 (vertices=116, convex hull=34, v0=94712)
After retessellation of defect 31 (v0=94712), euler #=-15 (147851,443081,295215) : difference with theory (-14) = 1 

CORRECTING DEFECT 32 (vertices=98, convex hull=108, v0=97829)
After retessellation of defect 32 (v0=97829), euler #=-14 (147895,443261,295352) : difference with theory (-13) = 1 

CORRECTING DEFECT 33 (vertices=120, convex hull=71, v0=99331)
After retessellation of defect 33 (v0=99331), euler #=-13 (147921,443372,295438) : difference with theory (-12) = 1 

CORRECTING DEFECT 34 (vertices=172, convex hull=62, v0=100233)
After retessellation of defect 34 (v0=100233), euler #=-12 (147939,443453,295502) : difference with theory (-11) = 1 

CORRECTING DEFECT 35 (vertices=29, convex hull=75, v0=101250)
After retessellation of defect 35 (v0=101250), euler #=-11 (147954,443528,295563) : difference with theory (-10) = 1 

CORRECTING DEFECT 36 (vertices=30, convex hull=41, v0=105581)
After retessellation of defect 36 (v0=105581), euler #=-10 (147964,443571,295597) : difference with theory (-9) = 1 

CORRECTING DEFECT 37 (vertices=144, convex hull=43, v0=106394)
After retessellation of defect 37 (v0=106394), euler #=-9 (147979,443635,295647) : difference with theory (-8) = 1 

CORRECTING DEFECT 38 (vertices=10, convex hull=38, v0=106536)
After retessellation of defect 38 (v0=106536), euler #=-8 (147983,443660,295669) : difference with theory (-7) = 1 

CORRECTING DEFECT 39 (vertices=10, convex hull=19, v0=109728)
After retessellation of defect 39 (v0=109728), euler #=-7 (147983,443667,295677) : difference with theory (-6) = 1 

CORRECTING DEFECT 40 (vertices=88, convex hull=88, v0=112856)
After retessellation of defect 40 (v0=112856), euler #=-6 (148022,443818,295790) : difference with theory (-5) = 1 

CORRECTING DEFECT 41 (vertices=152, convex hull=120, v0=115388)
After retessellation of defect 41 (v0=115388), euler #=-5 (148067,444010,295938) : difference with theory (-4) = 1 

CORRECTING DEFECT 42 (vertices=11, convex hull=30, v0=115559)
After retessellation of defect 42 (v0=115559), euler #=-4 (148069,444026,295953) : difference with theory (-3) = 1 

CORRECTING DEFECT 43 (vertices=217, convex hull=188, v0=117709)
After retessellation of defect 43 (v0=117709), euler #=-2 (148094,444201,296105) : difference with theory (-2) = 0 

CORRECTING DEFECT 44 (vertices=108, convex hull=45, v0=121893)
After retessellation of defect 44 (v0=121893), euler #=-1 (148103,444246,296142) : difference with theory (-1) = 0 

CORRECTING DEFECT 45 (vertices=11, convex hull=28, v0=132536)
After retessellation of defect 45 (v0=132536), euler #=0 (148104,444260,296156) : difference with theory (0) = 0 

CORRECTING DEFECT 46 (vertices=238, convex hull=76, v0=140705)
After retessellation of defect 46 (v0=140705), euler #=1 (148124,444356,296233) : difference with theory (1) = 0 

CORRECTING DEFECT 47 (vertices=7, convex hull=31, v0=150936)
After retessellation of defect 47 (v0=150936), euler #=2 (148125,444369,296246) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.24 (0.03-->10.60) (max @ vno 117327 --> 125014)
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 (0.03-->10.60) (max @ vno 117327 --> 125014)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
135 mutations (34.0%), 262 crossovers (66.0%), 114 vertices were eliminated
building final representation...
3123 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=148125, nf=296246, ne=444369, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 27.8 minutes
0 defective edges
removing intersecting faces
000: 297 intersecting
001: 27 intersecting
002: 6 intersecting
expanding nbhd size to 2
003: 10 intersecting
mris_fix_topology utimesec    1666.154705
mris_fix_topology stimesec    0.216967
mris_fix_topology ru_maxrss   469868
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   55246
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  10648
mris_fix_topology ru_oublock  14272
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    624
mris_fix_topology ru_nivcsw   3357
FSRUNTIME@ mris_fix_topology lh  0.4637 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050607 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=-64 (nv=158838, nf=317804, ne=476706, g=33)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
5686 ambiguous faces found in tessellation
segmenting defects...
44 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 6 into 5
      -merging segment 16 into 22
42 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.0621  (-4.5310)
      -vertex     loglikelihood: -5.8588  (-2.9294)
      -normal dot loglikelihood: -3.5094  (-3.5094)
      -quad curv  loglikelihood: -6.4863  (-3.2431)
      Total Loglikelihood : -24.9165

CORRECTING DEFECT 0 (vertices=48, convex hull=81, v0=32)
After retessellation of defect 0 (v0=32), euler #=-41 (155359,464627,309227) : difference with theory (-39) = 2 

CORRECTING DEFECT 1 (vertices=81, convex hull=93, v0=221)
After retessellation of defect 1 (v0=221), euler #=-40 (155406,464813,309367) : difference with theory (-38) = 2 

CORRECTING DEFECT 2 (vertices=30, convex hull=50, v0=2639)
After retessellation of defect 2 (v0=2639), euler #=-39 (155409,464840,309392) : difference with theory (-37) = 2 

CORRECTING DEFECT 3 (vertices=90, convex hull=76, v0=9560)
After retessellation of defect 3 (v0=9560), euler #=-38 (155447,464988,309503) : difference with theory (-36) = 2 

CORRECTING DEFECT 4 (vertices=40, convex hull=93, v0=9657)
After retessellation of defect 4 (v0=9657), euler #=-37 (155467,465086,309582) : difference with theory (-35) = 2 

CORRECTING DEFECT 5 (vertices=59, convex hull=107, v0=15803)
After retessellation of defect 5 (v0=15803), euler #=-35 (155496,465226,309695) : difference with theory (-34) = 1 

CORRECTING DEFECT 6 (vertices=54, convex hull=106, v0=33863)
After retessellation of defect 6 (v0=33863), euler #=-34 (155533,465381,309814) : difference with theory (-33) = 1 

CORRECTING DEFECT 7 (vertices=61, convex hull=91, v0=37372)
After retessellation of defect 7 (v0=37372), euler #=-33 (155551,465477,309893) : difference with theory (-32) = 1 

CORRECTING DEFECT 8 (vertices=25, convex hull=76, v0=47132)
After retessellation of defect 8 (v0=47132), euler #=-32 (155565,465547,309950) : difference with theory (-31) = 1 

CORRECTING DEFECT 9 (vertices=54, convex hull=91, v0=53694)
After retessellation of defect 9 (v0=53694), euler #=-31 (155593,465670,310046) : difference with theory (-30) = 1 

CORRECTING DEFECT 10 (vertices=34, convex hull=51, v0=64581)
After retessellation of defect 10 (v0=64581), euler #=-30 (155605,465726,310091) : difference with theory (-29) = 1 

CORRECTING DEFECT 11 (vertices=65, convex hull=99, v0=65035)
After retessellation of defect 11 (v0=65035), euler #=-29 (155634,465859,310196) : difference with theory (-28) = 1 

CORRECTING DEFECT 12 (vertices=18, convex hull=37, v0=66474)
After retessellation of defect 12 (v0=66474), euler #=-28 (155635,465876,310213) : difference with theory (-27) = 1 

CORRECTING DEFECT 13 (vertices=9, convex hull=23, v0=67209)
After retessellation of defect 13 (v0=67209), euler #=-27 (155637,465890,310226) : difference with theory (-26) = 1 

CORRECTING DEFECT 14 (vertices=60, convex hull=36, v0=71603)
After retessellation of defect 14 (v0=71603), euler #=-26 (155647,465930,310257) : difference with theory (-25) = 1 

CORRECTING DEFECT 15 (vertices=49, convex hull=53, v0=90462)
After retessellation of defect 15 (v0=90462), euler #=-25 (155660,465987,310302) : difference with theory (-24) = 1 

CORRECTING DEFECT 16 (vertices=161, convex hull=186, v0=91112)
After retessellation of defect 16 (v0=91112), euler #=-24 (155740,466314,310550) : difference with theory (-23) = 1 

CORRECTING DEFECT 17 (vertices=68, convex hull=48, v0=96034)
After retessellation of defect 17 (v0=96034), euler #=-23 (155755,466377,310599) : difference with theory (-22) = 1 

CORRECTING DEFECT 18 (vertices=6, convex hull=28, v0=96263)
After retessellation of defect 18 (v0=96263), euler #=-22 (155757,466390,310611) : difference with theory (-21) = 1 

CORRECTING DEFECT 19 (vertices=73, convex hull=91, v0=98703)
After retessellation of defect 19 (v0=98703), euler #=-21 (155790,466530,310719) : difference with theory (-20) = 1 

CORRECTING DEFECT 20 (vertices=684, convex hull=481, v0=102143)
L defect detected...
After retessellation of defect 20 (v0=102143), euler #=-19 (156057,467567,311491) : difference with theory (-19) = 0 

CORRECTING DEFECT 21 (vertices=358, convex hull=98, v0=104481)
After retessellation of defect 21 (v0=104481), euler #=-18 (156090,467715,311607) : difference with theory (-18) = 0 

CORRECTING DEFECT 22 (vertices=14, convex hull=20, v0=105875)
After retessellation of defect 22 (v0=105875), euler #=-17 (156093,467729,311619) : difference with theory (-17) = 0 

CORRECTING DEFECT 23 (vertices=183, convex hull=137, v0=106001)
After retessellation of defect 23 (v0=106001), euler #=-16 (156106,467830,311708) : difference with theory (-16) = 0 

CORRECTING DEFECT 24 (vertices=23, convex hull=48, v0=108357)
After retessellation of defect 24 (v0=108357), euler #=-15 (156118,467883,311750) : difference with theory (-15) = 0 

CORRECTING DEFECT 25 (vertices=63, convex hull=75, v0=109896)
After retessellation of defect 25 (v0=109896), euler #=-14 (156136,467968,311818) : difference with theory (-14) = 0 

CORRECTING DEFECT 26 (vertices=46, convex hull=68, v0=114190)
After retessellation of defect 26 (v0=114190), euler #=-13 (156140,468008,311855) : difference with theory (-13) = 0 

CORRECTING DEFECT 27 (vertices=87, convex hull=61, v0=115464)
After retessellation of defect 27 (v0=115464), euler #=-12 (156152,468068,311904) : difference with theory (-12) = 0 

CORRECTING DEFECT 28 (vertices=10, convex hull=23, v0=117627)
After retessellation of defect 28 (v0=117627), euler #=-11 (156152,468074,311911) : difference with theory (-11) = 0 

CORRECTING DEFECT 29 (vertices=133, convex hull=64, v0=121779)
After retessellation of defect 29 (v0=121779), euler #=-10 (156168,468151,311973) : difference with theory (-10) = 0 

CORRECTING DEFECT 30 (vertices=29, convex hull=30, v0=125167)
After retessellation of defect 30 (v0=125167), euler #=-9 (156172,468173,311992) : difference with theory (-9) = 0 

CORRECTING DEFECT 31 (vertices=135, convex hull=144, v0=126210)
After retessellation of defect 31 (v0=126210), euler #=-8 (156253,468481,312220) : difference with theory (-8) = 0 

CORRECTING DEFECT 32 (vertices=60, convex hull=44, v0=129964)
After retessellation of defect 32 (v0=129964), euler #=-7 (156254,468504,312243) : difference with theory (-7) = 0 

CORRECTING DEFECT 33 (vertices=26, convex hull=54, v0=130940)
After retessellation of defect 33 (v0=130940), euler #=-6 (156264,468554,312284) : difference with theory (-6) = 0 

CORRECTING DEFECT 34 (vertices=355, convex hull=150, v0=132737)
After retessellation of defect 34 (v0=132737), euler #=-5 (156347,468879,312527) : difference with theory (-5) = 0 

CORRECTING DEFECT 35 (vertices=45, convex hull=58, v0=132877)
After retessellation of defect 35 (v0=132877), euler #=-4 (156358,468935,312573) : difference with theory (-4) = 0 

CORRECTING DEFECT 36 (vertices=6, convex hull=26, v0=133765)
After retessellation of defect 36 (v0=133765), euler #=-3 (156359,468944,312582) : difference with theory (-3) = 0 

CORRECTING DEFECT 37 (vertices=18, convex hull=58, v0=136437)
After retessellation of defect 37 (v0=136437), euler #=-2 (156368,468991,312621) : difference with theory (-2) = 0 

CORRECTING DEFECT 38 (vertices=28, convex hull=69, v0=155562)
After retessellation of defect 38 (v0=155562), euler #=-1 (156383,469063,312679) : difference with theory (-1) = 0 

CORRECTING DEFECT 39 (vertices=22, convex hull=63, v0=155681)
After retessellation of defect 39 (v0=155681), euler #=0 (156394,469119,312725) : difference with theory (0) = 0 

CORRECTING DEFECT 40 (vertices=27, convex hull=60, v0=157281)
After retessellation of defect 40 (v0=157281), euler #=1 (156403,469170,312768) : difference with theory (1) = 0 

CORRECTING DEFECT 41 (vertices=63, convex hull=68, v0=157288)
After retessellation of defect 41 (v0=157288), euler #=2 (156423,469263,312842) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.23 (0.05-->9.03) (max @ vno 129814 --> 158277)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.23 (0.05-->9.03) (max @ vno 129814 --> 158277)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
152 mutations (35.0%), 282 crossovers (65.0%), 140 vertices were eliminated
building final representation...
2415 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=156423, nf=312842, ne=469263, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 34.4 minutes
0 defective edges
removing intersecting faces
000: 227 intersecting
001: 19 intersecting
mris_fix_topology utimesec    2059.762868
mris_fix_topology stimesec    0.258960
mris_fix_topology ru_maxrss   504680
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   55905
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  33528
mris_fix_topology ru_oublock  15024
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    752
mris_fix_topology ru_nivcsw   6032
FSRUNTIME@ mris_fix_topology rh  0.5731 hours 1 threads
PIDs (29665 29668) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 148125 - 444369 + 296246 = 2 --> 0 holes
      F =2V-4:          296246 = 296250-4 (0)
      2E=3F:            888738 = 888738 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 156423 - 469263 + 312842 = 2 --> 0 holes
      F =2V-4:          312842 = 312846-4 (0)
      2E=3F:            938526 = 938526 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 31 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 37 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 07:11:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050607 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 07:11:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050607 rh 

Waiting for PID 31226 of (31226 31229) to complete...
Waiting for PID 31229 of (31226 31229) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050607 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-6.0.0/0050607/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
12985 bright wm thresholded.
2603 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.orig...
computing class statistics...
border white:    287934 voxels (1.72%)
border gray      326636 voxels (1.95%)
WM (96.0): 96.7 +- 7.6 [70.0 --> 110.0]
GM (74.0) : 73.6 +- 9.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 60.7 (was 70)
setting MAX_BORDER_WHITE to 107.6 (was 105)
setting MIN_BORDER_WHITE to 70.0 (was 85)
setting MAX_CSF to 51.3 (was 40)
setting MAX_GRAY to 92.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 60.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.0 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.83 +- 0.22 (0.03-->5.02) (max @ vno 117327 --> 125005)
face area 0.28 +- 0.12 (0.00-->4.15)
mean absolute distance = 0.66 +- 0.81
4121 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-6.1,    GM=70+-7.0
mean inside = 92.7, mean outside = 77.4
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=81.2, 93 (93) missing vertices, mean dist 0.3 [0.5 (%37.0)->0.8 (%63.0))]
%70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.25 (0.10-->4.92) (max @ vno 117327 --> 125015)
face area 0.28 +- 0.13 (0.00-->3.31)
mean absolute distance = 0.33 +- 0.62
3695 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2693288.2, rms=8.546
001: dt: 0.5000, sse=1616028.5, rms=5.983 (29.995%)
002: dt: 0.5000, sse=1150429.2, rms=4.416 (26.186%)
003: dt: 0.5000, sse=939431.2, rms=3.483 (21.133%)
004: dt: 0.5000, sse=843005.9, rms=2.963 (14.923%)
005: dt: 0.5000, sse=805897.6, rms=2.734 (7.741%)
006: dt: 0.5000, sse=790330.1, rms=2.627 (3.908%)
rms = 2.60, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=786338.9, rms=2.596 (1.156%)
008: dt: 0.2500, sse=673178.9, rms=1.509 (41.875%)
009: dt: 0.2500, sse=658406.7, rms=1.315 (12.862%)
rms = 1.27, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=656979.0, rms=1.270 (3.418%)
rms = 1.24, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=653172.1, rms=1.240 (2.389%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=83.0, 120 (55) missing vertices, mean dist -0.2 [0.4 (%65.2)->0.2 (%34.8))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.24 (0.09-->4.93) (max @ vno 117327 --> 125015)
face area 0.35 +- 0.16 (0.00-->4.23)
mean absolute distance = 0.30 +- 0.47
4599 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1084239.6, rms=3.361
012: dt: 0.5000, sse=886905.6, rms=2.102 (37.473%)
013: dt: 0.5000, sse=877891.1, rms=1.960 (6.727%)
rms = 1.94, time step reduction 1 of 3 to 0.250...
014: dt: 0.5000, sse=866792.4, rms=1.943 (0.887%)
015: dt: 0.2500, sse=802916.8, rms=1.221 (37.150%)
016: dt: 0.2500, sse=796225.0, rms=1.108 (9.252%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=794893.5, rms=1.091 (1.587%)
rms = 1.07, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=793783.3, rms=1.067 (2.154%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=84.7, 104 (42) missing vertices, mean dist -0.1 [0.3 (%63.7)->0.2 (%36.3))]
%81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.24 (0.10-->4.87) (max @ vno 117327 --> 125015)
face area 0.35 +- 0.16 (0.00-->4.23)
mean absolute distance = 0.27 +- 0.38
4232 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=944655.4, rms=2.644
019: dt: 0.5000, sse=839309.2, rms=1.800 (31.913%)
rms = 1.79, time step reduction 1 of 3 to 0.250...
020: dt: 0.5000, sse=835525.6, rms=1.791 (0.519%)
021: dt: 0.2500, sse=784873.4, rms=1.080 (39.686%)
022: dt: 0.2500, sse=774685.3, rms=1.000 (7.361%)
rms = 0.99, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=776751.9, rms=0.987 (1.311%)
rms = 0.97, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=772787.2, rms=0.969 (1.830%)
positioning took 0.7 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
mean border=85.4, 101 (41) missing vertices, mean dist -0.1 [0.3 (%55.3)->0.2 (%44.7))]
%85 local maxima, %11 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-6.0.0/0050607/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=796224.4, rms=1.511
025: dt: 0.5000, sse=770345.8, rms=1.138 (24.684%)
rms = 1.40, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=753052.5, rms=0.876 (23.053%)
027: dt: 0.2500, sse=749050.7, rms=0.793 (9.380%)
rms = 0.77, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=746617.3, rms=0.773 (2.536%)
rms = 0.77, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=746161.9, rms=0.770 (0.451%)
positioning took 0.7 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 7534 vertices
erasing segment 1 (vno[0] = 80774)
erasing segment 2 (vno[0] = 82974)
erasing segment 3 (vno[0] = 86727)
erasing segment 4 (vno[0] = 86815)
erasing segment 5 (vno[0] = 88827)
erasing segment 6 (vno[0] = 104256)
erasing segment 7 (vno[0] = 105219)
erasing segment 8 (vno[0] = 105221)
erasing segment 9 (vno[0] = 111747)
erasing segment 10 (vno[0] = 113128)
erasing segment 11 (vno[0] = 124744)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.area
vertex spacing 0.90 +- 0.24 (0.03-->4.84) (max @ vno 117327 --> 125015)
face area 0.34 +- 0.16 (0.00-->4.20)
refinement took 6.2 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050607 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-6.0.0/0050607/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
12985 bright wm thresholded.
2603 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.orig...
computing class statistics...
border white:    287934 voxels (1.72%)
border gray      326636 voxels (1.95%)
WM (96.0): 96.7 +- 7.6 [70.0 --> 110.0]
GM (74.0) : 73.6 +- 9.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 60.7 (was 70)
setting MAX_BORDER_WHITE to 106.6 (was 105)
setting MIN_BORDER_WHITE to 70.0 (was 85)
setting MAX_CSF to 51.3 (was 40)
setting MAX_GRAY to 91.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 60.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.0 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->5.34) (max @ vno 128920 --> 156264)
face area 0.28 +- 0.12 (0.00-->2.52)
mean absolute distance = 0.66 +- 0.81
4653 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=99+-6.1,    GM=70+-7.0
mean inside = 92.8, mean outside = 77.5
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
mean border=81.7, 30 (30) missing vertices, mean dist 0.3 [0.5 (%38.1)->0.7 (%61.9))]
%72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.08-->5.22) (max @ vno 128920 --> 156264)
face area 0.28 +- 0.13 (0.00-->3.27)
mean absolute distance = 0.33 +- 0.60
4335 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2741993.2, rms=8.348
001: dt: 0.5000, sse=1652806.1, rms=5.833 (30.126%)
002: dt: 0.5000, sse=1187493.2, rms=4.326 (25.837%)
003: dt: 0.5000, sse=983475.9, rms=3.461 (20.006%)
004: dt: 0.5000, sse=888778.8, rms=2.971 (14.132%)
005: dt: 0.5000, sse=852792.8, rms=2.762 (7.044%)
006: dt: 0.5000, sse=835801.9, rms=2.649 (4.097%)
rms = 2.62, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=832626.8, rms=2.622 (1.026%)
008: dt: 0.2500, sse=711466.1, rms=1.551 (40.859%)
009: dt: 0.2500, sse=695534.3, rms=1.355 (12.618%)
010: dt: 0.2500, sse=691727.6, rms=1.301 (3.995%)
rms = 1.27, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=688986.9, rms=1.270 (2.400%)
rms = 1.25, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=688388.5, rms=1.245 (1.898%)
positioning took 1.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=83.4, 36 (6) missing vertices, mean dist -0.2 [0.4 (%64.9)->0.2 (%35.1))]
%75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.24 (0.15-->5.08) (max @ vno 128920 --> 156264)
face area 0.35 +- 0.16 (0.00-->4.05)
mean absolute distance = 0.30 +- 0.48
4659 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1122652.4, rms=3.253
013: dt: 0.5000, sse=920502.4, rms=1.981 (39.096%)
014: dt: 0.5000, sse=905839.1, rms=1.889 (4.670%)
rms = 1.88, time step reduction 1 of 3 to 0.250...
015: dt: 0.5000, sse=901507.9, rms=1.876 (0.657%)
016: dt: 0.2500, sse=842964.6, rms=1.170 (37.634%)
017: dt: 0.2500, sse=835078.1, rms=1.065 (8.986%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=834414.0, rms=1.049 (1.491%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=832594.8, rms=1.028 (2.055%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=85.1, 27 (3) missing vertices, mean dist -0.1 [0.3 (%63.9)->0.2 (%36.1))]
%81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.24 (0.07-->5.19) (max @ vno 98260 --> 97217)
face area 0.35 +- 0.15 (0.00-->4.07)
mean absolute distance = 0.28 +- 0.40
4432 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=994108.3, rms=2.637
020: dt: 0.5000, sse=882916.2, rms=1.790 (32.119%)
rms = 1.78, time step reduction 1 of 3 to 0.250...
021: dt: 0.5000, sse=880254.4, rms=1.784 (0.354%)
022: dt: 0.2500, sse=819913.6, rms=1.059 (40.625%)
023: dt: 0.2500, sse=819185.8, rms=0.973 (8.092%)
rms = 0.96, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=813462.6, rms=0.962 (1.192%)
rms = 0.94, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=812405.6, rms=0.945 (1.776%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=85.9, 38 (2) missing vertices, mean dist -0.1 [0.3 (%55.7)->0.2 (%44.3))]
%85 local maxima, %11 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-6.0.0/0050607/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=837784.8, rms=1.516
026: dt: 0.5000, sse=809975.6, rms=1.133 (25.287%)
rms = 1.38, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=792411.2, rms=0.865 (23.639%)
028: dt: 0.2500, sse=788318.0, rms=0.776 (10.337%)
rms = 0.75, time step reduction 2 of 3 to 0.125...
029: dt: 0.2500, sse=784380.9, rms=0.752 (2.994%)
rms = 0.75, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=784106.6, rms=0.750 (0.324%)
positioning took 0.7 minutes
generating cortex label...
15 non-cortical segments detected
only using segment with 7679 vertices
erasing segment 1 (vno[0] = 76912)
erasing segment 2 (vno[0] = 98488)
erasing segment 3 (vno[0] = 100705)
erasing segment 4 (vno[0] = 101751)
erasing segment 5 (vno[0] = 108658)
erasing segment 6 (vno[0] = 108705)
erasing segment 7 (vno[0] = 110766)
erasing segment 8 (vno[0] = 110918)
erasing segment 9 (vno[0] = 111829)
erasing segment 10 (vno[0] = 111911)
erasing segment 11 (vno[0] = 113839)
erasing segment 12 (vno[0] = 114852)
erasing segment 13 (vno[0] = 115903)
erasing segment 14 (vno[0] = 118277)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.area
vertex spacing 0.90 +- 0.24 (0.04-->5.19) (max @ vno 97217 --> 98260)
face area 0.34 +- 0.15 (0.00-->4.04)
refinement took 6.2 minutes
PIDs (31226 31229) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 07:17:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 07:17:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

Waiting for PID 31574 of (31574 31577) to complete...
Waiting for PID 31577 of (31574 31577) 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 (31574 31577) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 07:17:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 07:17:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 31624 of (31624 31627) to complete...
Waiting for PID 31627 of (31624 31627) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 49.8 mm, total surface area = 91471 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.174 (target=0.015)   
step 005: RMS=0.124 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.052 (target=0.015)   
step 030: RMS=0.042 (target=0.015)   
step 035: RMS=0.036 (target=0.015)   
step 040: RMS=0.031 (target=0.015)   
step 045: RMS=0.028 (target=0.015)   
step 050: RMS=0.026 (target=0.015)   
step 055: RMS=0.024 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
inflation took 0.9 minutes
mris_inflate utimesec    46.767890
mris_inflate stimesec    0.134979
mris_inflate ru_maxrss   216332
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31663
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11600
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2332
mris_inflate ru_nivcsw   3725

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 48.9 mm, total surface area = 95889 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.174 (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=0.062 (target=0.015)   
step 025: RMS=0.052 (target=0.015)   
step 030: RMS=0.044 (target=0.015)   
step 035: RMS=0.037 (target=0.015)   
step 040: RMS=0.032 (target=0.015)   
step 045: RMS=0.028 (target=0.015)   
step 050: RMS=0.025 (target=0.015)   
step 055: RMS=0.023 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
inflation took 1.0 minutes
mris_inflate utimesec    61.293681
mris_inflate stimesec    0.139978
mris_inflate ru_maxrss   228120
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   33076
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11008
mris_inflate ru_oublock  12248
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1911
mris_inflate ru_nivcsw   4103
PIDs (31624 31627) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 07:18:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 07:18:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 31728 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31731 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31734 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31737 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31740 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31743 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31746 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31750 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31753 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31756 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31759 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...
Waiting for PID 31762 of (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 7.369*4pi (92.602) --> -6 handles
ICI = 172.7, FI = 1658.0, variation=26552.947
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
190 vertices thresholded to be in k1 ~ [-0.82 0.26], k2 ~ [-0.32 0.06]
total integrated curvature = 0.429*4pi (5.389) --> 1 handles
ICI = 1.5, FI = 8.5, variation=151.260
140 vertices thresholded to be in [-0.03 0.03]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
120 vertices thresholded to be in [-0.22 0.09]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.020
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 12.944*4pi (162.660) --> -12 handles
ICI = 191.4, FI = 1789.3, variation=28746.843
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
209 vertices thresholded to be in k1 ~ [-0.26 0.35], k2 ~ [-0.14 0.07]
total integrated curvature = 0.362*4pi (4.553) --> 1 handles
ICI = 1.5, FI = 9.4, variation=164.788
165 vertices thresholded to be in [-0.02 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
164 vertices thresholded to be in [-0.14 0.15]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.021
done.
PIDs (31728 31731 31734 31737 31740 31743 31746 31750 31753 31756 31759 31762) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 07:21:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050607 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      [ 0050607/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                      [ 251 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.315417
WARN:    S explicit min:                          0.000000	vertex = 1029

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 07:21:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050607 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      [ 0050607/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                      [ 317 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.128386
WARN:    S explicit min:                          0.000000	vertex = 425
#--------------------------------------------
#@# Sphere lh Sun Oct  8 07:21:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 07:21:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 31965 of (31965 31969) to complete...
Waiting for PID 31969 of (31965 31969) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0.277...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.52
pass 1: epoch 2 of 3 starting distance error %20.54
unfolding complete - removing small folds...
starting distance error %20.46
removing remaining folds...
final distance error %20.49
MRISunfold() return, current seed 1234
-01: dt=0.0000, 62 negative triangles
192: dt=0.9900, 62 negative triangles
193: dt=0.9900, 19 negative triangles
194: dt=0.9900, 18 negative triangles
195: dt=0.9900, 15 negative triangles
196: dt=0.9900, 6 negative triangles
197: dt=0.9900, 12 negative triangles
198: dt=0.9900, 5 negative triangles
199: dt=0.9900, 8 negative triangles
200: dt=0.9900, 4 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.05 hours
mris_sphere utimesec    3754.952160
mris_sphere stimesec    1.990697
mris_sphere ru_maxrss   304856
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   53932
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10448
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    130192
mris_sphere ru_nivcsw   319323
FSRUNTIME@ mris_sphere  1.0521 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0.279...
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

singular matrix in quadratic form
--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %19.80
pass 1: epoch 2 of 3 starting distance error %19.79
unfolding complete - removing small folds...
starting distance error %19.73
removing remaining folds...
final distance error %19.75
MRISunfold() return, current seed 1234
-01: dt=0.0000, 84 negative triangles
200: dt=0.9900, 84 negative triangles
201: dt=0.9900, 23 negative triangles
202: dt=0.9900, 14 negative triangles
203: dt=0.9900, 6 negative triangles
204: dt=0.9900, 7 negative triangles
205: dt=0.9900, 4 negative triangles
206: dt=0.9900, 7 negative triangles
207: dt=0.9900, 5 negative triangles
208: dt=0.9900, 7 negative triangles
209: dt=0.9900, 4 negative triangles
210: dt=0.9900, 6 negative triangles
211: dt=0.9900, 4 negative triangles
212: dt=0.9900, 3 negative triangles
213: dt=0.9900, 2 negative triangles
214: dt=0.9900, 4 negative triangles
215: dt=0.9900, 2 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.19 hours
mris_sphere utimesec    4573.891662
mris_sphere stimesec    2.174669
mris_sphere ru_maxrss   321988
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   56179
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11040
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    118132
mris_sphere ru_nivcsw   332801
FSRUNTIME@ mris_sphere  1.1894 hours 1 threads
PIDs (31965 31969) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 08:33:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 08:33:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 4182 of (4182 4188) to complete...
Waiting for PID 4188 of (4182 4188) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 = 5.616
curvature mean = 0.032, std = 0.817
curvature mean = 0.012, std = 0.855
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 361350.0, tmin=1.2874
  d=32.00 min @ (-8.00, -8.00, 0.00) sse = 270809.2, tmin=2.5884
  d=16.00 min @ (0.00, 0.00, 4.00) sse = 241351.7, tmin=3.8895
  d=4.00 min @ (-1.00, -1.00, 0.00) sse = 240227.7, tmin=6.5118
  d=2.00 min @ (0.50, 0.50, -0.50) sse = 239318.8, tmin=7.8322
  d=1.00 min @ (0.00, -0.25, 0.00) sse = 239187.8, tmin=9.1495
  d=0.50 min @ (0.12, 0.12, 0.12) sse = 239116.1, tmin=10.4766
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done  10.48 min
curvature mean = -0.006, std = 0.835
curvature mean = 0.005, std = 0.944
curvature mean = -0.010, std = 0.844
curvature mean = 0.002, std = 0.977
curvature mean = -0.011, std = 0.847
curvature mean = 0.001, std = 0.990
2 Reading smoothwm
curvature mean = -0.029, std = 0.260
curvature mean = 0.038, std = 0.246
curvature mean = 0.052, std = 0.390
curvature mean = 0.033, std = 0.303
curvature mean = 0.035, std = 0.588
curvature mean = 0.033, std = 0.329
curvature mean = 0.019, std = 0.734
curvature mean = 0.033, std = 0.340
curvature mean = 0.006, std = 0.839
MRISregister() return, current seed 0
-01: dt=0.0000, 102 negative triangles
115: dt=0.9900, 102 negative triangles
expanding nbhd size to 1
116: dt=0.9900, 109 negative triangles
117: dt=0.9900, 98 negative triangles
118: dt=0.9900, 94 negative triangles
119: dt=0.9900, 87 negative triangles
120: dt=0.9900, 86 negative triangles
121: dt=0.9900, 82 negative triangles
122: dt=0.9900, 80 negative triangles
123: dt=0.9900, 81 negative triangles
124: dt=0.9900, 77 negative triangles
125: dt=0.9900, 78 negative triangles
126: dt=0.9900, 72 negative triangles
127: dt=0.9900, 73 negative triangles
128: dt=0.9900, 70 negative triangles
129: dt=0.9900, 70 negative triangles
130: dt=0.9900, 67 negative triangles
131: dt=0.9900, 65 negative triangles
132: dt=0.9900, 60 negative triangles
133: dt=0.9900, 59 negative triangles
134: dt=0.9900, 58 negative triangles
135: dt=0.9900, 56 negative triangles
136: dt=0.9900, 53 negative triangles
137: dt=0.9900, 49 negative triangles
138: dt=0.9900, 45 negative triangles
139: dt=0.9900, 46 negative triangles
140: dt=0.9900, 45 negative triangles
141: dt=0.9900, 43 negative triangles
142: dt=0.9900, 43 negative triangles
143: dt=0.9900, 40 negative triangles
144: dt=0.9900, 37 negative triangles
145: dt=0.9900, 39 negative triangles
146: dt=0.9900, 39 negative triangles
147: dt=0.9900, 38 negative triangles
148: dt=0.9900, 38 negative triangles
149: dt=0.9900, 36 negative triangles
150: dt=0.9900, 36 negative triangles
151: dt=0.9900, 34 negative triangles
152: dt=0.9900, 31 negative triangles
153: dt=0.9900, 30 negative triangles
154: dt=0.9900, 27 negative triangles
155: dt=0.9900, 29 negative triangles
156: dt=0.9900, 33 negative triangles
157: dt=0.9900, 27 negative triangles
158: dt=0.9900, 26 negative triangles
159: dt=0.9900, 20 negative triangles
160: dt=0.9900, 20 negative triangles
161: dt=0.9900, 20 negative triangles
162: dt=0.9900, 20 negative triangles
163: dt=0.9900, 23 negative triangles
164: dt=0.9900, 24 negative triangles
165: dt=0.9900, 20 negative triangles
166: dt=0.9900, 17 negative triangles
167: dt=0.9900, 17 negative triangles
168: dt=0.9900, 18 negative triangles
169: dt=0.9900, 20 negative triangles
170: dt=0.9900, 16 negative triangles
171: dt=0.9900, 14 negative triangles
172: dt=0.9900, 14 negative triangles
173: dt=0.9900, 14 negative triangles
174: dt=0.9900, 14 negative triangles
175: dt=0.9900, 14 negative triangles
176: dt=0.9900, 15 negative triangles
177: dt=0.9900, 15 negative triangles
178: dt=0.9900, 13 negative triangles
179: dt=0.9900, 13 negative triangles
180: dt=0.9900, 12 negative triangles
181: dt=0.9900, 10 negative triangles
182: dt=0.9900, 10 negative triangles
183: dt=0.9900, 11 negative triangles
184: dt=0.9900, 10 negative triangles
185: dt=0.9900, 9 negative triangles
186: dt=0.9900, 7 negative triangles
187: dt=0.9900, 6 negative triangles
188: dt=0.9900, 6 negative triangles
189: dt=0.9900, 7 negative triangles
190: dt=0.9900, 6 negative triangles
191: dt=0.9900, 6 negative triangles
192: dt=0.9900, 5 negative triangles
193: dt=0.9900, 4 negative triangles
194: dt=0.9900, 3 negative triangles
195: dt=0.9900, 2 negative triangles
196: dt=0.9900, 2 negative triangles
197: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.41 hours
mris_register utimesec    5661.735285
mris_register stimesec    3.166518
mris_register ru_maxrss   269904
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   37954
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10520
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    271873
mris_register ru_nivcsw   177636
FSRUNTIME@ mris_register  1.4079 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 = 5.662
curvature mean = 0.021, std = 0.814
curvature mean = 0.015, std = 0.856
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 375765.7, tmin=1.1811
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 228648.6, tmin=2.3866
  d=8.00 min @ (0.00, 0.00, -2.00) sse = 221302.7, tmin=4.7976
  d=4.00 min @ (-1.00, 0.00, 0.00) sse = 219108.0, tmin=6.0228
  d=2.00 min @ (0.00, -0.50, 0.50) sse = 217590.3, tmin=7.2534
  d=1.00 min @ (-0.25, 0.00, 0.00) sse = 217564.5, tmin=8.4856
  d=0.50 min @ (0.12, 0.00, 0.00) sse = 217528.9, tmin=9.7177
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   9.72 min
curvature mean = -0.026, std = 0.820
curvature mean = 0.007, std = 0.944
curvature mean = -0.038, std = 0.825
curvature mean = 0.003, std = 0.977
curvature mean = -0.041, std = 0.825
curvature mean = 0.000, std = 0.991
2 Reading smoothwm
curvature mean = -0.029, std = 0.267
curvature mean = 0.028, std = 0.240
curvature mean = 0.056, std = 0.367
curvature mean = 0.025, std = 0.295
curvature mean = 0.037, std = 0.566
curvature mean = 0.025, std = 0.321
curvature mean = 0.020, std = 0.714
curvature mean = 0.024, std = 0.332
curvature mean = 0.008, std = 0.818
MRISregister() return, current seed 0
-01: dt=0.0000, 19 negative triangles
117: dt=0.9900, 19 negative triangles
expanding nbhd size to 1
118: dt=0.9900, 30 negative triangles
119: dt=0.9900, 13 negative triangles
120: dt=0.9900, 14 negative triangles
121: dt=0.9900, 10 negative triangles
122: dt=0.9900, 12 negative triangles
123: dt=0.9900, 7 negative triangles
124: dt=0.9900, 10 negative triangles
125: dt=0.9900, 6 negative triangles
126: dt=0.9900, 10 negative triangles
127: dt=0.9900, 3 negative triangles
128: dt=0.9900, 7 negative triangles
129: dt=0.9900, 5 negative triangles
130: dt=0.9900, 5 negative triangles
131: dt=0.9900, 3 negative triangles
132: dt=0.9900, 3 negative triangles
133: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.13 hours
mris_register utimesec    4045.906928
mris_register stimesec    3.714435
mris_register ru_maxrss   282960
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39122
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  11088
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    280342
mris_register ru_nivcsw   184934
FSRUNTIME@ mris_register  1.1273 hours 1 threads
PIDs (4182 4188) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 09:57:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 09:57:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

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

Waiting for PID 8074 of (8074 8077) to complete...
Waiting for PID 8077 of (8074 8077) 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 (8074 8077) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 09:57:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 09:57:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 8127 of (8127 8130) to complete...
Waiting for PID 8130 of (8127 8130) 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 (8127 8130) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 09:57:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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 09:57:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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 8178 of (8178 8181) to complete...
Waiting for PID 8181 of (8178 8181) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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...
1274 labels changed using aseg
relabeling using gibbs priors...
000:   3131 changed, 148125 examined...
001:    718 changed, 13330 examined...
002:    176 changed, 4012 examined...
003:     49 changed, 1039 examined...
004:     18 changed, 284 examined...
005:      6 changed, 112 examined...
006:      0 changed, 36 examined...
240 labels changed using aseg
000: 125 total segments, 81 labels (324 vertices) changed
001: 40 total segments, 1 labels (3 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 15 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2096 vertices marked for relabeling...
2096 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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...
1109 labels changed using aseg
relabeling using gibbs priors...
000:   3025 changed, 156423 examined...
001:    757 changed, 13003 examined...
002:    177 changed, 4208 examined...
003:     59 changed, 1094 examined...
004:     21 changed, 351 examined...
005:      8 changed, 130 examined...
006:      2 changed, 50 examined...
007:      0 changed, 15 examined...
162 labels changed using aseg
000: 109 total segments, 72 labels (264 vertices) changed
001: 40 total segments, 3 labels (5 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 2 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1803 vertices marked for relabeling...
1803 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 17 seconds.
PIDs (8178 8181) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 09:57:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050607 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 09:57:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050607 rh 

Waiting for PID 8232 of (8232 8235) to complete...
Waiting for PID 8235 of (8232 8235) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050607 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-6.0.0/0050607/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
12985 bright wm thresholded.
2603 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.orig...
computing class statistics...
border white:    287934 voxels (1.72%)
border gray      326636 voxels (1.95%)
WM (96.0): 96.7 +- 7.6 [70.0 --> 110.0]
GM (74.0) : 73.6 +- 9.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 60.7 (was 70)
setting MAX_BORDER_WHITE to 107.6 (was 105)
setting MIN_BORDER_WHITE to 70.0 (was 85)
setting MAX_CSF to 51.3 (was 40)
setting MAX_GRAY to 92.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 60.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.0 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=100+-6.1,    GM=70+-7.0
mean inside = 92.7, mean outside = 77.4
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.24 (0.03-->4.84) (max @ vno 117327 --> 125015)
face area 0.34 +- 0.16 (0.00-->4.15)
mean absolute distance = 0.53 +- 0.81
3934 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 15 points - only 0.00% unknown
deleting segment 2 with 12 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 78 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 6 with 15 points - only 0.00% unknown
deleting segment 7 with 37 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
mean border=81.0, 74 (73) missing vertices, mean dist 0.3 [0.6 (%18.9)->0.5 (%81.1))]
%67 local maxima, %28 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 0.93 +- 0.26 (0.09-->4.35) (max @ vno 117327 --> 125015)
face area 0.34 +- 0.16 (0.00-->3.88)
mean absolute distance = 0.34 +- 0.64
3877 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1855750.6, rms=6.323
001: dt: 0.5000, sse=1176307.2, rms=3.997 (36.789%)
002: dt: 0.5000, sse=963061.9, rms=2.936 (26.540%)
003: dt: 0.5000, sse=902811.2, rms=2.568 (12.537%)
004: dt: 0.5000, sse=875075.1, rms=2.354 (8.326%)
rms = 2.37, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=811524.0, rms=1.782 (24.309%)
006: dt: 0.2500, sse=789520.3, rms=1.465 (17.809%)
007: dt: 0.2500, sse=778410.1, rms=1.357 (7.366%)
008: dt: 0.2500, sse=776263.1, rms=1.301 (4.108%)
rms = 1.26, time step reduction 2 of 3 to 0.125...
009: dt: 0.2500, sse=772012.8, rms=1.262 (2.966%)
rms = 1.23, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=769173.4, rms=1.233 (2.289%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 9 points - only 0.00% unknown
deleting segment 1 with 12 points - only 0.00% unknown
deleting segment 2 with 38 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 7 points - only 0.00% unknown
deleting segment 5 with 16 points - only 18.75% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
mean border=82.9, 109 (43) missing vertices, mean dist -0.2 [0.4 (%65.0)->0.2 (%35.0))]
%74 local maxima, %22 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 0.92 +- 0.25 (0.08-->4.42) (max @ vno 117327 --> 125015)
face area 0.36 +- 0.17 (0.00-->4.28)
mean absolute distance = 0.30 +- 0.48
4043 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1090144.9, rms=3.325
011: dt: 0.5000, sse=897567.6, rms=2.077 (37.548%)
012: dt: 0.5000, sse=873424.9, rms=1.890 (9.005%)
rms = 1.87, time step reduction 1 of 3 to 0.250...
013: dt: 0.5000, sse=891057.9, rms=1.875 (0.783%)
014: dt: 0.2500, sse=815164.4, rms=1.161 (38.091%)
015: dt: 0.2500, sse=807132.3, rms=1.052 (9.379%)
rms = 1.04, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=805997.8, rms=1.036 (1.485%)
rms = 1.01, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=804190.2, rms=1.014 (2.104%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 11 points - only 0.00% unknown
deleting segment 1 with 12 points - only 0.00% unknown
deleting segment 2 with 46 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 9 points - only 0.00% unknown
deleting segment 5 with 16 points - only 18.75% unknown
deleting segment 6 with 6 points - only 0.00% unknown
mean border=84.6, 122 (40) missing vertices, mean dist -0.1 [0.3 (%64.0)->0.2 (%36.0))]
%81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.91 +- 0.25 (0.05-->4.29) (max @ vno 117327 --> 125014)
face area 0.35 +- 0.17 (0.00-->4.24)
mean absolute distance = 0.27 +- 0.38
4272 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=952171.9, rms=2.661
018: dt: 0.5000, sse=847329.1, rms=1.787 (32.841%)
rms = 1.76, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=842933.7, rms=1.757 (1.702%)
020: dt: 0.2500, sse=784401.6, rms=1.046 (40.465%)
021: dt: 0.2500, sse=778612.2, rms=0.966 (7.640%)
rms = 0.96, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=778015.8, rms=0.956 (1.010%)
rms = 0.94, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=776665.9, rms=0.937 (1.973%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 13 points - only 0.00% unknown
deleting segment 1 with 12 points - only 0.00% unknown
deleting segment 2 with 45 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 9 points - only 0.00% unknown
deleting segment 5 with 37 points - only 8.11% unknown
deleting segment 6 with 25 points - only 0.00% unknown
deleting segment 7 with 7 points - only 0.00% unknown
mean border=85.4, 109 (35) missing vertices, mean dist -0.1 [0.3 (%55.5)->0.2 (%44.5))]
%85 local maxima, %11 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-6.0.0/0050607/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=798911.8, rms=1.490
024: dt: 0.5000, sse=773388.9, rms=1.120 (24.795%)
rms = 1.37, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=757236.3, rms=0.854 (23.809%)
026: dt: 0.2500, sse=752677.2, rms=0.770 (9.736%)
rms = 0.75, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=750848.8, rms=0.750 (2.683%)
rms = 0.75, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=750548.9, rms=0.745 (0.594%)
positioning took 0.6 minutes
generating cortex label...
10 non-cortical segments detected
only using segment with 7525 vertices
erasing segment 1 (vno[0] = 80774)
erasing segment 2 (vno[0] = 86727)
erasing segment 3 (vno[0] = 104311)
erasing segment 4 (vno[0] = 105219)
erasing segment 5 (vno[0] = 105221)
erasing segment 6 (vno[0] = 106080)
erasing segment 7 (vno[0] = 111747)
erasing segment 8 (vno[0] = 113128)
erasing segment 9 (vno[0] = 124743)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.area
vertex spacing 0.90 +- 0.25 (0.03-->4.30) (max @ vno 117327 --> 125015)
face area 0.34 +- 0.16 (0.00-->4.20)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=59.0, 79 (79) missing vertices, mean dist 1.7 [4.8 (%0.0)->2.7 (%100.0))]
%13 local maxima, %48 large gradients and %35 min vals, 698 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=21608428.0, rms=27.132
001: dt: 0.0500, sse=19308428.0, rms=25.595 (5.666%)
002: dt: 0.0500, sse=17654844.0, rms=24.429 (4.553%)
003: dt: 0.0500, sse=16376988.0, rms=23.489 (3.849%)
004: dt: 0.0500, sse=15331863.0, rms=22.691 (3.397%)
005: dt: 0.0500, sse=14441900.0, rms=21.989 (3.096%)
006: dt: 0.0500, sse=13662265.0, rms=21.354 (2.885%)
007: dt: 0.0500, sse=12964610.0, rms=20.770 (2.736%)
008: dt: 0.0500, sse=12330593.0, rms=20.224 (2.627%)
009: dt: 0.0500, sse=11748360.0, rms=19.710 (2.544%)
010: dt: 0.0500, sse=11209034.0, rms=19.221 (2.481%)
positioning took 1.0 minutes
mean border=58.8, 84 (47) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.2 (%100.0))]
%14 local maxima, %48 large gradients and %34 min vals, 640 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=11845273.0, rms=19.795
011: dt: 0.0500, sse=11340139.0, rms=19.340 (2.301%)
012: dt: 0.0500, sse=10867222.0, rms=18.903 (2.257%)
013: dt: 0.0500, sse=10423523.0, rms=18.484 (2.216%)
014: dt: 0.0500, sse=10006254.0, rms=18.082 (2.180%)
015: dt: 0.0500, sse=9613245.0, rms=17.694 (2.146%)
016: dt: 0.0500, sse=9242886.0, rms=17.320 (2.112%)
017: dt: 0.0500, sse=8894265.0, rms=16.960 (2.075%)
018: dt: 0.0500, sse=8565810.0, rms=16.615 (2.039%)
019: dt: 0.0500, sse=8256429.0, rms=16.282 (2.001%)
020: dt: 0.0500, sse=7965019.0, rms=15.962 (1.963%)
positioning took 1.0 minutes
mean border=58.7, 112 (37) missing vertices, mean dist 1.2 [0.1 (%0.6)->1.8 (%99.4))]
%14 local maxima, %48 large gradients and %34 min vals, 636 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=8057473.0, rms=16.069
021: dt: 0.0500, sse=7776539.0, rms=15.756 (1.944%)
022: dt: 0.0500, sse=7512624.0, rms=15.457 (1.899%)
023: dt: 0.0500, sse=7263250.0, rms=15.169 (1.865%)
024: dt: 0.0500, sse=7028870.5, rms=14.893 (1.820%)
025: dt: 0.0500, sse=6808457.0, rms=14.628 (1.776%)
026: dt: 0.0500, sse=6600728.5, rms=14.374 (1.736%)
027: dt: 0.0500, sse=6404302.5, rms=14.130 (1.700%)
028: dt: 0.0500, sse=6217283.5, rms=13.893 (1.676%)
029: dt: 0.0500, sse=6038724.0, rms=13.663 (1.655%)
030: dt: 0.0500, sse=5868225.5, rms=13.440 (1.635%)
positioning took 1.0 minutes
mean border=58.6, 134 (29) missing vertices, mean dist 1.0 [0.1 (%10.2)->1.7 (%89.8))]
%14 local maxima, %49 large gradients and %33 min vals, 602 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=5933173.0, rms=13.523
031: dt: 0.5000, sse=4723974.0, rms=11.830 (12.518%)
032: dt: 0.5000, sse=3892207.8, rms=10.501 (11.236%)
033: dt: 0.5000, sse=3269754.2, rms=9.385 (10.624%)
034: dt: 0.5000, sse=2806030.2, rms=8.452 (9.943%)
035: dt: 0.5000, sse=2438733.5, rms=7.633 (9.688%)
036: dt: 0.5000, sse=2152467.2, rms=6.925 (9.278%)
037: dt: 0.5000, sse=1930309.9, rms=6.324 (8.680%)
038: dt: 0.5000, sse=1765879.1, rms=5.837 (7.699%)
039: dt: 0.5000, sse=1643600.2, rms=5.449 (6.640%)
040: dt: 0.5000, sse=1552295.2, rms=5.138 (5.714%)
041: dt: 0.5000, sse=1484835.9, rms=4.898 (4.671%)
042: dt: 0.5000, sse=1436941.9, rms=4.718 (3.681%)
043: dt: 0.5000, sse=1401328.4, rms=4.581 (2.902%)
044: dt: 0.5000, sse=1375203.6, rms=4.477 (2.261%)
045: dt: 0.5000, sse=1357569.0, rms=4.406 (1.594%)
046: dt: 0.5000, sse=1344258.2, rms=4.351 (1.253%)
rms = 4.31, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1333785.0, rms=4.308 (0.993%)
048: dt: 0.2500, sse=1279081.0, rms=4.030 (6.432%)
049: dt: 0.2500, sse=1265021.0, rms=3.966 (1.609%)
rms = 3.96, time step reduction 2 of 3 to 0.125...
050: dt: 0.2500, sse=1264796.1, rms=3.963 (0.070%)
rms = 3.93, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1258917.9, rms=3.933 (0.764%)
positioning took 2.7 minutes
mean border=57.9, 2256 (10) missing vertices, mean dist 0.2 [0.2 (%52.0)->0.7 (%48.0))]
%24 local maxima, %41 large gradients and %29 min vals, 362 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=1462421.0, rms=3.932
052: dt: 0.5000, sse=1377111.4, rms=3.531 (10.197%)
053: dt: 0.5000, sse=1345105.8, rms=3.393 (3.908%)
rms = 3.37, time step reduction 1 of 3 to 0.250...
054: dt: 0.5000, sse=1337896.0, rms=3.369 (0.712%)
055: dt: 0.2500, sse=1278703.1, rms=2.977 (11.620%)
056: dt: 0.2500, sse=1263878.8, rms=2.885 (3.092%)
rms = 2.87, time step reduction 2 of 3 to 0.125...
057: dt: 0.2500, sse=1260613.5, rms=2.866 (0.664%)
rms = 2.82, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1254654.1, rms=2.824 (1.478%)
positioning took 1.1 minutes
mean border=57.2, 2526 (10) missing vertices, mean dist 0.1 [0.2 (%51.0)->0.5 (%49.0))]
%35 local maxima, %31 large gradients and %28 min vals, 445 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=1304857.9, rms=3.066
rms = 3.05, time step reduction 1 of 3 to 0.250...
059: dt: 0.5000, sse=1300449.4, rms=3.048 (0.579%)
060: dt: 0.2500, sse=1266541.8, rms=2.842 (6.756%)
061: dt: 0.2500, sse=1256431.6, rms=2.785 (2.018%)
rms = 2.78, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1254726.5, rms=2.778 (0.246%)
063: dt: 0.1250, sse=1247509.5, rms=2.727 (1.824%)
rms = 2.72, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1245607.0, rms=2.717 (0.360%)
positioning took 1.0 minutes
mean border=56.6, 4820 (10) missing vertices, mean dist 0.1 [0.2 (%49.4)->0.4 (%50.6))]
%41 local maxima, %24 large gradients and %27 min vals, 443 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-6.0.0/0050607/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1273639.0, rms=2.834
rms = 2.85, time step reduction 1 of 3 to 0.250...
065: dt: 0.2500, sse=1260426.0, rms=2.745 (3.133%)
066: dt: 0.2500, sse=1247674.5, rms=2.668 (2.784%)
rms = 2.63, time step reduction 2 of 3 to 0.125...
067: dt: 0.2500, sse=1240828.6, rms=2.630 (1.449%)
rms = 2.59, time step reduction 3 of 3 to 0.062...
068: dt: 0.1250, sse=1234868.1, rms=2.586 (1.656%)
positioning took 0.8 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.area.pial
vertex spacing 1.03 +- 0.45 (0.08-->5.93) (max @ vno 105148 --> 105158)
face area 0.43 +- 0.34 (0.00-->5.16)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 148125 vertices processed
25000 of 148125 vertices processed
50000 of 148125 vertices processed
75000 of 148125 vertices processed
100000 of 148125 vertices processed
125000 of 148125 vertices processed
0 of 148125 vertices processed
25000 of 148125 vertices processed
50000 of 148125 vertices processed
75000 of 148125 vertices processed
100000 of 148125 vertices processed
125000 of 148125 vertices processed
thickness calculation complete, 450:2445 truncations.
34427 vertices at 0 distance
107662 vertices at 1 distance
88639 vertices at 2 distance
35381 vertices at 3 distance
11687 vertices at 4 distance
3729 vertices at 5 distance
1278 vertices at 6 distance
482 vertices at 7 distance
182 vertices at 8 distance
116 vertices at 9 distance
74 vertices at 10 distance
36 vertices at 11 distance
36 vertices at 12 distance
41 vertices at 13 distance
27 vertices at 14 distance
28 vertices at 15 distance
8 vertices at 16 distance
5 vertices at 17 distance
10 vertices at 18 distance
7 vertices at 19 distance
9 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.thickness
positioning took 15.9 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050607 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-6.0.0/0050607/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
12985 bright wm thresholded.
2603 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.orig...
computing class statistics...
border white:    287934 voxels (1.72%)
border gray      326636 voxels (1.95%)
WM (96.0): 96.7 +- 7.6 [70.0 --> 110.0]
GM (74.0) : 73.6 +- 9.3 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 60.7 (was 70)
setting MAX_BORDER_WHITE to 106.6 (was 105)
setting MIN_BORDER_WHITE to 70.0 (was 85)
setting MAX_CSF to 51.3 (was 40)
setting MAX_GRAY to 91.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 60.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.0 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=99+-6.1,    GM=70+-7.0
mean inside = 92.8, mean outside = 77.5
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.24 (0.04-->5.19) (max @ vno 97217 --> 98260)
face area 0.34 +- 0.15 (0.00-->3.98)
mean absolute distance = 0.53 +- 0.82
3707 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 2 with 22 points - only 0.00% unknown
deleting segment 3 with 96 points - only 0.00% unknown
deleting segment 4 with 14 points - only 0.00% unknown
deleting segment 5 with 40 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
mean border=81.5, 62 (54) missing vertices, mean dist 0.3 [0.6 (%19.9)->0.5 (%80.1))]
%69 local maxima, %27 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 0.93 +- 0.25 (0.10-->5.02) (max @ vno 99347 --> 98273)
face area 0.34 +- 0.15 (0.00-->3.70)
mean absolute distance = 0.33 +- 0.61
4070 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1916153.0, rms=6.215
001: dt: 0.5000, sse=1213264.0, rms=3.908 (37.110%)
002: dt: 0.5000, sse=1002132.3, rms=2.887 (26.145%)
003: dt: 0.5000, sse=942815.7, rms=2.537 (12.105%)
004: dt: 0.5000, sse=911797.6, rms=2.331 (8.133%)
rms = 2.35, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=847402.9, rms=1.747 (25.036%)
006: dt: 0.2500, sse=820442.8, rms=1.429 (18.208%)
007: dt: 0.2500, sse=812136.0, rms=1.321 (7.540%)
008: dt: 0.2500, sse=808219.5, rms=1.266 (4.201%)
rms = 1.23, time step reduction 2 of 3 to 0.125...
009: dt: 0.2500, sse=806118.5, rms=1.226 (3.163%)
rms = 1.20, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=805630.1, rms=1.199 (2.185%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
deleting segment 1 with 69 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 8 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
mean border=83.3, 40 (10) missing vertices, mean dist -0.2 [0.4 (%64.7)->0.2 (%35.3))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.10-->5.09) (max @ vno 99347 --> 98273)
face area 0.36 +- 0.16 (0.00-->3.98)
mean absolute distance = 0.31 +- 0.49
4808 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1123878.0, rms=3.195
011: dt: 0.5000, sse=928886.1, rms=1.941 (39.244%)
012: dt: 0.5000, sse=911298.3, rms=1.821 (6.220%)
rms = 1.82, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=868929.2, rms=1.358 (25.400%)
014: dt: 0.2500, sse=850446.9, rms=1.087 (19.940%)
015: dt: 0.2500, sse=846252.2, rms=1.029 (5.358%)
rms = 1.01, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=845360.2, rms=1.011 (1.780%)
rms = 1.00, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=844115.2, rms=0.996 (1.469%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
deleting segment 1 with 81 points - only 0.00% unknown
deleting segment 2 with 13 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
mean border=85.0, 25 (5) missing vertices, mean dist -0.1 [0.4 (%64.2)->0.2 (%35.8))]
%81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.04-->4.83) (max @ vno 99347 --> 98273)
face area 0.35 +- 0.16 (0.00-->4.39)
mean absolute distance = 0.28 +- 0.40
4571 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1003635.1, rms=2.665
018: dt: 0.5000, sse=888462.9, rms=1.780 (33.191%)
rms = 1.75, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=883708.2, rms=1.753 (1.512%)
020: dt: 0.2500, sse=824232.8, rms=1.034 (41.035%)
021: dt: 0.2500, sse=819113.3, rms=0.946 (8.492%)
rms = 0.94, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=818912.9, rms=0.939 (0.789%)
rms = 0.92, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=820128.5, rms=0.923 (1.643%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 0.00% unknown
deleting segment 2 with 81 points - only 0.00% unknown
deleting segment 3 with 17 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
mean border=85.9, 45 (3) missing vertices, mean dist -0.1 [0.3 (%55.8)->0.2 (%44.2))]
%85 local maxima, %11 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-6.0.0/0050607/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=847075.1, rms=1.530
024: dt: 0.5000, sse=817392.7, rms=1.135 (25.846%)
rms = 1.37, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=798129.4, rms=0.864 (23.844%)
026: dt: 0.2500, sse=792624.7, rms=0.766 (11.309%)
rms = 0.74, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=791222.3, rms=0.743 (3.076%)
rms = 0.74, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=789696.7, rms=0.741 (0.198%)
positioning took 0.6 minutes
generating cortex label...
17 non-cortical segments detected
only using segment with 7638 vertices
erasing segment 1 (vno[0] = 76913)
erasing segment 2 (vno[0] = 80974)
erasing segment 3 (vno[0] = 98488)
erasing segment 4 (vno[0] = 100716)
erasing segment 5 (vno[0] = 101751)
erasing segment 6 (vno[0] = 107689)
erasing segment 7 (vno[0] = 108659)
erasing segment 8 (vno[0] = 108705)
erasing segment 9 (vno[0] = 110766)
erasing segment 10 (vno[0] = 110918)
erasing segment 11 (vno[0] = 111829)
erasing segment 12 (vno[0] = 111911)
erasing segment 13 (vno[0] = 113838)
erasing segment 14 (vno[0] = 114852)
erasing segment 15 (vno[0] = 115903)
erasing segment 16 (vno[0] = 118277)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.area
vertex spacing 0.90 +- 0.25 (0.05-->5.19) (max @ vno 97217 --> 98260)
face area 0.34 +- 0.16 (0.00-->4.27)
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 2 with 10 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=59.5, 62 (62) missing vertices, mean dist 1.6 [0.0 (%0.0)->2.7 (%100.0))]
%12 local maxima, %44 large gradients and %40 min vals, 826 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=22739978.0, rms=27.084
001: dt: 0.0500, sse=20322168.0, rms=25.551 (5.659%)
002: dt: 0.0500, sse=18583226.0, rms=24.389 (4.548%)
003: dt: 0.0500, sse=17240698.0, rms=23.453 (3.840%)
004: dt: 0.0500, sse=16142536.0, rms=22.658 (3.390%)
005: dt: 0.0500, sse=15207593.0, rms=21.958 (3.088%)
006: dt: 0.0500, sse=14387803.0, rms=21.325 (2.880%)
007: dt: 0.0500, sse=13654507.0, rms=20.743 (2.730%)
008: dt: 0.0500, sse=12988417.0, rms=20.200 (2.620%)
009: dt: 0.0500, sse=12376237.0, rms=19.687 (2.538%)
010: dt: 0.0500, sse=11808610.0, rms=19.200 (2.477%)
positioning took 1.1 minutes
mean border=59.3, 74 (43) missing vertices, mean dist 1.3 [0.2 (%0.0)->2.2 (%100.0))]
%12 local maxima, %44 large gradients and %39 min vals, 781 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=12524817.0, rms=19.812
011: dt: 0.0500, sse=11993214.0, rms=19.359 (2.289%)
012: dt: 0.0500, sse=11495485.0, rms=18.924 (2.244%)
013: dt: 0.0500, sse=11027836.0, rms=18.507 (2.207%)
014: dt: 0.0500, sse=10587956.0, rms=18.105 (2.170%)
015: dt: 0.0500, sse=10173789.0, rms=17.718 (2.135%)
016: dt: 0.0500, sse=9784104.0, rms=17.347 (2.098%)
017: dt: 0.0500, sse=9417573.0, rms=16.990 (2.059%)
018: dt: 0.0500, sse=9072892.0, rms=16.647 (2.019%)
019: dt: 0.0500, sse=8748568.0, rms=16.317 (1.979%)
020: dt: 0.0500, sse=8443313.0, rms=16.001 (1.939%)
positioning took 1.1 minutes
mean border=59.1, 102 (34) missing vertices, mean dist 1.1 [0.1 (%0.7)->1.8 (%99.3))]
%13 local maxima, %44 large gradients and %39 min vals, 757 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=8561497.0, rms=16.128
021: dt: 0.0500, sse=8266185.5, rms=15.818 (1.920%)
022: dt: 0.0500, sse=7989120.0, rms=15.522 (1.873%)
023: dt: 0.0500, sse=7727474.5, rms=15.237 (1.837%)
024: dt: 0.0500, sse=7482202.0, rms=14.965 (1.787%)
025: dt: 0.0500, sse=7252035.0, rms=14.704 (1.739%)
026: dt: 0.0500, sse=7035832.0, rms=14.455 (1.692%)
027: dt: 0.0500, sse=6831798.0, rms=14.216 (1.653%)
028: dt: 0.0500, sse=6637335.5, rms=13.985 (1.630%)
029: dt: 0.0500, sse=6451466.0, rms=13.760 (1.610%)
030: dt: 0.0500, sse=6274048.5, rms=13.541 (1.588%)
positioning took 1.1 minutes
mean border=59.1, 143 (31) missing vertices, mean dist 0.9 [0.1 (%11.5)->1.7 (%88.5))]
%13 local maxima, %45 large gradients and %38 min vals, 734 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=6361301.5, rms=13.647
031: dt: 0.5000, sse=5098428.5, rms=11.992 (12.129%)
032: dt: 0.5000, sse=4231642.5, rms=10.701 (10.767%)
033: dt: 0.5000, sse=3575791.2, rms=9.611 (10.184%)
034: dt: 0.5000, sse=3077036.0, rms=8.684 (9.643%)
035: dt: 0.5000, sse=2672682.5, rms=7.854 (9.555%)
036: dt: 0.5000, sse=2342535.8, rms=7.103 (9.572%)
037: dt: 0.5000, sse=2060296.9, rms=6.395 (9.966%)
038: dt: 0.5000, sse=1843529.8, rms=5.789 (9.468%)
039: dt: 0.5000, sse=1677480.9, rms=5.283 (8.745%)
040: dt: 0.5000, sse=1569048.5, rms=4.920 (6.873%)
041: dt: 0.5000, sse=1492550.2, rms=4.651 (5.475%)
042: dt: 0.5000, sse=1447493.4, rms=4.480 (3.669%)
043: dt: 0.5000, sse=1415141.0, rms=4.357 (2.743%)
044: dt: 0.5000, sse=1396333.4, rms=4.280 (1.777%)
045: dt: 0.5000, sse=1378498.5, rms=4.211 (1.606%)
rms = 4.16, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1367115.5, rms=4.163 (1.140%)
047: dt: 0.2500, sse=1299920.0, rms=3.834 (7.903%)
048: dt: 0.2500, sse=1283401.2, rms=3.758 (1.991%)
rms = 3.75, time step reduction 2 of 3 to 0.125...
049: dt: 0.2500, sse=1282014.5, rms=3.749 (0.237%)
rms = 3.71, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1274814.4, rms=3.712 (0.989%)
positioning took 2.8 minutes
mean border=58.5, 2560 (18) missing vertices, mean dist 0.1 [0.2 (%53.6)->0.6 (%46.4))]
%21 local maxima, %39 large gradients and %34 min vals, 398 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=1467932.1, rms=3.718
051: dt: 0.5000, sse=1393948.0, rms=3.379 (9.110%)
052: dt: 0.5000, sse=1368295.5, rms=3.274 (3.117%)
rms = 3.27, time step reduction 1 of 3 to 0.250...
053: dt: 0.5000, sse=1365192.1, rms=3.270 (0.102%)
054: dt: 0.2500, sse=1296224.2, rms=2.823 (13.683%)
055: dt: 0.2500, sse=1279657.1, rms=2.720 (3.633%)
rms = 2.70, time step reduction 2 of 3 to 0.125...
056: dt: 0.2500, sse=1276783.8, rms=2.701 (0.713%)
057: dt: 0.1250, sse=1268520.0, rms=2.642 (2.177%)
rms = 2.63, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1266775.4, rms=2.632 (0.369%)
positioning took 1.4 minutes
mean border=57.9, 3055 (16) missing vertices, mean dist 0.1 [0.2 (%52.1)->0.5 (%47.9))]
%31 local maxima, %30 large gradients and %33 min vals, 376 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=1308329.1, rms=2.861
rms = 2.88, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1288344.8, rms=2.735 (4.398%)
060: dt: 0.2500, sse=1275364.8, rms=2.657 (2.855%)
rms = 2.63, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1269591.2, rms=2.626 (1.184%)
rms = 2.59, time step reduction 3 of 3 to 0.062...
062: dt: 0.1250, sse=1264427.1, rms=2.588 (1.432%)
positioning took 0.8 minutes
mean border=57.4, 5475 (15) missing vertices, mean dist 0.1 [0.2 (%49.3)->0.4 (%50.7))]
%37 local maxima, %24 large gradients and %32 min vals, 428 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-6.0.0/0050607/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1288296.1, rms=2.720
rms = 2.75, time step reduction 1 of 3 to 0.250...
063: dt: 0.2500, sse=1273644.4, rms=2.625 (3.490%)
064: dt: 0.2500, sse=1261446.9, rms=2.558 (2.556%)
rms = 2.53, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1255359.2, rms=2.526 (1.246%)
rms = 2.48, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1249556.2, rms=2.483 (1.720%)
positioning took 0.8 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.area.pial
vertex spacing 1.02 +- 0.44 (0.05-->8.10) (max @ vno 105487 --> 105486)
face area 0.41 +- 0.32 (0.00-->7.80)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 156423 vertices processed
25000 of 156423 vertices processed
50000 of 156423 vertices processed
75000 of 156423 vertices processed
100000 of 156423 vertices processed
125000 of 156423 vertices processed
150000 of 156423 vertices processed
0 of 156423 vertices processed
25000 of 156423 vertices processed
50000 of 156423 vertices processed
75000 of 156423 vertices processed
100000 of 156423 vertices processed
125000 of 156423 vertices processed
150000 of 156423 vertices processed
thickness calculation complete, 456:1273 truncations.
40456 vertices at 0 distance
115501 vertices at 1 distance
88838 vertices at 2 distance
35968 vertices at 3 distance
12376 vertices at 4 distance
4133 vertices at 5 distance
1393 vertices at 6 distance
487 vertices at 7 distance
211 vertices at 8 distance
113 vertices at 9 distance
83 vertices at 10 distance
69 vertices at 11 distance
45 vertices at 12 distance
25 vertices at 13 distance
20 vertices at 14 distance
16 vertices at 15 distance
18 vertices at 16 distance
15 vertices at 17 distance
8 vertices at 18 distance
8 vertices at 19 distance
17 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.thickness
positioning took 16.7 minutes
PIDs (8232 8235) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 10:14:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/lh.cortex.label
Total face volume 274984
Total vertex volume 271400 (mask=0)
#@# 0050607 lh 271400
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 10:14:41 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/rh.cortex.label
Total face volume 276152
Total vertex volume 273179 (mask=0)
#@# 0050607 rh 273179
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 10:14:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 

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 = 176
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/ribbon.mgz
mris_volmask took 17.79 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 10:32:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 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 0050607 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 10:32:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 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 0050607 rh pial 

Waiting for PID 9895 of (9895 9898 9901 9904) to complete...
Waiting for PID 9898 of (9895 9898 9901 9904) to complete...
Waiting for PID 9901 of (9895 9898 9901 9904) to complete...
Waiting for PID 9904 of (9895 9898 9901 9904) 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 0050607 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 274984
Total vertex volume 271400 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
  997    713   1454  1.989 0.545     0.108     0.018        8     0.6  bankssts
 1036    687   2414  2.905 0.713     0.132     0.021       13     0.9  caudalanteriorcingulate
 3989   2693   8182  2.577 0.716     0.116     0.023       34     3.6  caudalmiddlefrontal
 2263   1649   2924  1.730 0.452     0.163     0.036       34     3.4  cuneus
  560    383   2008  3.556 1.033     0.108     0.025        5     0.4  entorhinal
 4825   3439  10315  2.594 0.680     0.142     0.034       67     7.0  fusiform
 6049   4180  11730  2.503 0.673     0.129     0.030       72     7.3  inferiorparietal
 4210   2958   9147  2.587 0.905     0.138     0.034       58     6.1  inferiortemporal
 1582   1051   3263  2.741 1.013     0.133     0.037       23     2.1  isthmuscingulate
 8754   5861  13580  2.128 0.572     0.141     0.032      110    11.6  lateraloccipital
 4123   2861   9474  2.771 0.794     0.122     0.030       41     4.9  lateralorbitofrontal
 3834   2789   6086  1.995 0.616     0.145     0.032       48     5.2  lingual
 3291   2183   6540  2.597 0.913     0.125     0.033       49     4.1  medialorbitofrontal
 3965   2788  10137  2.542 0.867     0.127     0.029       61     4.7  middletemporal
 1108    721   2336  2.621 0.946     0.072     0.014        4     0.6  parahippocampal
 2590   1702   4138  2.247 0.631     0.118     0.027       22     2.8  paracentral
 3355   2283   7021  2.533 0.618     0.119     0.025       34     3.5  parsopercularis
 1099    741   3056  2.952 0.827     0.135     0.028       16     1.3  parsorbitalis
 2196   1489   4492  2.463 0.638     0.115     0.023       22     1.9  parstriangularis
 1800   1225   1664  1.516 0.365     0.132     0.030       20     2.1  pericalcarine
 6514   4356  10153  2.057 0.678     0.119     0.025       63     6.5  postcentral
 2316   1611   4518  2.561 0.537     0.144     0.036       31     3.4  posteriorcingulate
 8612   5531  15986  2.579 0.719     0.111     0.022       72     7.5  precentral
 7246   5057  12599  2.311 0.560     0.135     0.032       89    10.0  precuneus
 1058    682   2451  2.823 0.859     0.110     0.031       28     1.2  rostralanteriorcingulate
 9612   6305  18067  2.430 0.685     0.126     0.030      112    12.0  rostralmiddlefrontal
13533   8938  29132  2.797 0.714     0.117     0.027      122    14.4  superiorfrontal
 9601   6458  15149  2.125 0.579     0.125     0.025      100     9.9  superiorparietal
 6479   4563  14815  2.821 0.794     0.123     0.026       76     7.1  superiortemporal
 7180   5098  14958  2.497 0.662     0.136     0.028       88     9.0  supramarginal
  398    264    952  2.618 0.852     0.175     0.062       10     1.1  frontalpole
  724    498   2674  3.499 0.913     0.114     0.036        9     1.0  temporalpole
  899    581   1410  2.187 0.469     0.091     0.019        6     0.6  transversetemporal
 4248   2820   8550  3.088 0.746     0.119     0.029       42     4.8  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050607 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 274984
Total vertex volume 271400 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
  997    764   1454  1.989 0.545     0.132     0.026       13     1.2  bankssts
 1036    977   2414  2.905 0.713     0.179     0.043       26     2.0  caudalanteriorcingulate
 3989   3533   8182  2.577 0.716     0.141     0.029       45     5.4  caudalmiddlefrontal
 2263   1867   2924  1.730 0.452     0.153     0.035       32     3.6  cuneus
  560    758   2008  3.556 1.033     0.194     0.042        6     1.1  entorhinal
 4825   4501  10315  2.594 0.680     0.160     0.038       74     8.7  fusiform
 6049   5154  11730  2.503 0.673     0.156     0.037       88    10.4  inferiorparietal
 4210   3990   9147  2.587 0.905     0.176     0.041       63     8.4  inferiortemporal
 1582   1222   3263  2.741 1.013     0.144     0.041       42     2.5  isthmuscingulate
 8754   6999  13580  2.128 0.572     0.133     0.028      119    11.2  lateraloccipital
 4123   3722   9474  2.771 0.794     0.158     0.039       60     7.7  lateralorbitofrontal
 3834   3390   6086  1.995 0.616     0.150     0.035       57     6.2  lingual
 3291   2908   6540  2.597 0.913     0.158     0.038       50     5.7  medialorbitofrontal
 3965   4670  10137  2.542 0.867     0.192     0.038       50     7.5  middletemporal
 1108   1040   2336  2.621 0.946     0.123     0.024        5     1.4  parahippocampal
 2590   2006   4138  2.247 0.631     0.136     0.034       47     3.8  paracentral
 3355   3164   7021  2.533 0.618     0.161     0.031       36     4.9  parsopercularis
 1099   1229   3056  2.952 0.827     0.171     0.032       13     1.6  parsorbitalis
 2196   2054   4492  2.463 0.638     0.154     0.028       25     2.9  parstriangularis
 1800   1080   1664  1.516 0.365     0.112     0.027       31     2.1  pericalcarine
 6514   5445  10153  2.057 0.678     0.133     0.026       61     7.9  postcentral
 2316   1895   4518  2.561 0.537     0.159     0.043       67     4.4  posteriorcingulate
 8612   6592  15986  2.579 0.719     0.116     0.024       85     9.3  precentral
 7246   5918  12599  2.311 0.560     0.148     0.034       96    11.1  precuneus
 1058   1035   2451  2.823 0.859     0.205     0.060       19     3.2  rostralanteriorcingulate
 9612   8229  18067  2.430 0.685     0.149     0.031      114    14.4  rostralmiddlefrontal
13533  11526  29132  2.797 0.714     0.142     0.045      241    33.5  superiorfrontal
 9601   7714  15149  2.125 0.579     0.133     0.027      105    11.8  superiorparietal
 6479   5743  14815  2.821 0.794     0.152     0.033       83     9.9  superiortemporal
 7180   6655  14958  2.497 0.662     0.155     0.034       82    11.3  supramarginal
  398    457    952  2.618 0.852     0.207     0.041        5     0.8  frontalpole
  724   1005   2674  3.499 0.913     0.206     0.042       10     1.6  temporalpole
  899    763   1410  2.187 0.469     0.118     0.028        5     1.0  transversetemporal
 4248   2589   8550  3.088 0.746     0.126     0.036       57     6.7  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 0050607 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 276152
Total vertex volume 273179 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
 1250    896   2130  2.405 0.389     0.101     0.016        6     0.8  bankssts
  852    580   1422  2.299 0.532     0.128     0.014       12     0.5  caudalanteriorcingulate
 3736   2486   7269  2.583 0.709     0.110     0.021       29     3.2  caudalmiddlefrontal
 3053   2054   3956  1.871 0.496     0.148     0.035       42     4.5  cuneus
  554    405   1872  3.436 0.824     0.122     0.035        5     0.7  entorhinal
 4671   3275   9831  2.756 0.630     0.135     0.043       60    10.5  fusiform
 7890   5345  14980  2.433 0.633     0.129     0.032       98    10.1  inferiorparietal
 5007   3442  11490  2.597 0.839     0.131     0.038       75     8.0  inferiortemporal
 1794   1173   3768  2.620 1.007     0.127     0.036       23     2.3  isthmuscingulate
 9850   6473  15130  2.208 0.568     0.146     0.039      137    15.8  lateraloccipital
 4263   3002  10314  2.896 0.776     0.130     0.036       52     6.4  lateralorbitofrontal
 4405   3098   6575  1.993 0.588     0.139     0.037       56     6.7  lingual
 3227   2311   6801  2.561 0.873     0.134     0.030       46     3.9  medialorbitofrontal
 5430   3853  13583  2.716 0.805     0.135     0.032       70     7.6  middletemporal
 1096    721   2146  2.628 0.895     0.102     0.037       27     2.0  parahippocampal
 2865   1828   4398  2.266 0.589     0.115     0.024       25     2.9  paracentral
 2828   1956   5634  2.495 0.679     0.121     0.023       29     2.6  parsopercularis
 1698   1142   4369  2.936 0.894     0.146     0.038       24     2.8  parsorbitalis
 3210   2157   6503  2.512 0.716     0.127     0.027       39     3.4  parstriangularis
 2554   1771   2270  1.485 0.372     0.133     0.030       27     2.9  pericalcarine
 6679   4318   8837  1.861 0.647     0.110     0.023       58     6.1  postcentral
 2005   1401   3576  2.272 0.710     0.145     0.036       30     3.2  posteriorcingulate
 8760   5699  13752  2.285 0.666     0.107     0.022       64     7.8  precentral
 7395   5109  12366  2.361 0.630     0.134     0.032       84     9.5  precuneus
  708    440   1099  2.420 0.667     0.105     0.019        7     0.5  rostralanteriorcingulate
10503   6799  18005  2.291 0.687     0.121     0.030      116    13.1  rostralmiddlefrontal
13159   8778  28111  2.742 0.706     0.119     0.025      128    12.9  superiorfrontal
10234   6655  14849  2.083 0.600     0.121     0.027      108    11.4  superiorparietal
 6402   4395  13353  2.630 0.765     0.116     0.023       66     6.2  superiortemporal
 5786   3909  10716  2.473 0.640     0.131     0.027       68     6.2  supramarginal
  509    359   1403  2.918 0.604     0.182     0.060       10     1.3  frontalpole
  922    666   3061  3.217 0.830     0.132     0.034       12     1.4  temporalpole
  649    416    807  1.820 0.360     0.127     0.022        7     0.5  transversetemporal
 4288   2943   8638  3.013 0.778     0.129     0.034       49     5.9  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 0050607 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 276152
Total vertex volume 273179 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
 1250    853   2130  2.405 0.389     0.115     0.025       14     1.4  bankssts
  852    675   1422  2.299 0.532     0.144     0.027       23     0.9  caudalanteriorcingulate
 3736   3084   7269  2.583 0.709     0.127     0.025       33     4.3  caudalmiddlefrontal
 3053   2367   3956  1.871 0.496     0.137     0.031       35     4.4  cuneus
  554    713   1872  3.436 0.824     0.187     0.046        5     1.2  entorhinal
 4671   3750   9831  2.756 0.630     0.137     0.035      109     7.4  fusiform
 7890   6810  14980  2.433 0.633     0.146     0.031       90    11.5  inferiorparietal
 5007   5000  11490  2.597 0.839     0.167     0.044      154    11.1  inferiortemporal
 1794   1566   3768  2.620 1.007     0.140     0.032       16     2.5  isthmuscingulate
 9850   7317  15130  2.208 0.568     0.127     0.032      156    14.2  lateraloccipital
 4263   4023  10314  2.896 0.776     0.169     0.040       56     8.2  lateralorbitofrontal
 4405   3648   6575  1.993 0.588     0.141     0.035       71     7.2  lingual
 3227   3049   6801  2.561 0.873     0.165     0.037       44     5.5  medialorbitofrontal
 5430   5702  13583  2.716 0.805     0.176     0.039       76    10.4  middletemporal
 1096    894   2146  2.628 0.895     0.133     0.037       21     1.9  parahippocampal
 2865   2079   4398  2.266 0.589     0.120     0.028       40     3.5  paracentral
 2828   2453   5634  2.495 0.679     0.142     0.030       30     3.8  parsopercularis
 1698   1766   4369  2.936 0.894     0.174     0.032       21     2.7  parsorbitalis
 3210   2951   6503  2.512 0.716     0.160     0.034       39     4.6  parstriangularis
 2554   1534   2270  1.485 0.372     0.105     0.026       34     2.9  pericalcarine
 6679   5165   8837  1.861 0.647     0.122     0.023       55     7.0  postcentral
 2005   1679   3576  2.272 0.710     0.151     0.035       24     3.4  posteriorcingulate
 8760   6341  13752  2.285 0.666     0.111     0.022       82     8.6  precentral
 7395   5414  12366  2.361 0.630     0.135     0.033      113    10.9  precuneus
  708    501   1099  2.420 0.667     0.125     0.030        8     0.9  rostralanteriorcingulate
10503   8676  18005  2.291 0.687     0.144     0.030      120    15.2  rostralmiddlefrontal
13159  11181  28111  2.742 0.706     0.138     0.030      156    17.8  superiorfrontal
10234   7648  14849  2.083 0.600     0.125     0.025      109    11.3  superiorparietal
 6402   5575  13353  2.630 0.765     0.143     0.030       74     9.2  superiortemporal
 5786   4628  10716  2.473 0.640     0.142     0.032       68     8.3  supramarginal
  509    567   1403  2.918 0.604     0.187     0.035        5     0.8  frontalpole
  922   1229   3061  3.217 0.830     0.199     0.041        9     2.0  temporalpole
  649    485    807  1.820 0.360     0.127     0.027        5     0.8  transversetemporal
 4288   2829   8638  3.013 0.778     0.134     0.036       64     6.5  insula
PIDs (9895 9898 9901 9904) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 10:34:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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 10:34:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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 10008 of (10008 10011) to complete...
Waiting for PID 10011 of (10008 10011) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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...
55 labels changed using aseg
relabeling using gibbs priors...
000:   9570 changed, 148125 examined...
001:   2171 changed, 37246 examined...
002:    624 changed, 11415 examined...
003:    260 changed, 3516 examined...
004:    109 changed, 1466 examined...
005:     55 changed, 633 examined...
006:     31 changed, 322 examined...
007:     16 changed, 175 examined...
008:     10 changed, 96 examined...
009:      5 changed, 56 examined...
010:      1 changed, 28 examined...
011:      0 changed, 6 examined...
33 labels changed using aseg
000: 271 total segments, 187 labels (2546 vertices) changed
001: 96 total segments, 12 labels (33 vertices) changed
002: 85 total segments, 1 labels (6 vertices) changed
003: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 43 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1548 vertices marked for relabeling...
1548 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 0050607 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...
26 labels changed using aseg
relabeling using gibbs priors...
000:  10054 changed, 156423 examined...
001:   2287 changed, 39377 examined...
002:    711 changed, 12134 examined...
003:    258 changed, 3971 examined...
004:    132 changed, 1491 examined...
005:     64 changed, 765 examined...
006:     27 changed, 361 examined...
007:     13 changed, 154 examined...
008:      8 changed, 74 examined...
009:      4 changed, 52 examined...
010:      2 changed, 30 examined...
011:      2 changed, 8 examined...
012:      1 changed, 11 examined...
013:      0 changed, 7 examined...
24 labels changed using aseg
000: 275 total segments, 192 labels (2985 vertices) changed
001: 91 total segments, 9 labels (26 vertices) changed
002: 82 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 44 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1390 vertices marked for relabeling...
1390 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.
PIDs (10008 10011) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 10:34:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 10:34:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 rh white 

Waiting for PID 10055 of (10055 10058) to complete...
Waiting for PID 10058 of (10055 10058) 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 0050607 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 274984
Total vertex volume 271400 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
 1450    954   2596  2.340 0.602     0.126     0.031       19     1.9  G&S_frontomargin
 1775   1210   2955  2.242 0.550     0.134     0.027       23     1.8  G&S_occipital_inf
 2252   1416   3131  1.956 0.596     0.117     0.025       21     2.4  G&S_paracentral
 1748   1201   3643  2.557 0.519     0.132     0.031       22     2.0  G&S_subcentral
  963    638   2015  2.507 0.771     0.159     0.048       18     2.0  G&S_transv_frontopol
 2204   1505   4811  2.743 0.728     0.108     0.022       15     1.8  G&S_cingul-Ant
 1398    987   2873  2.626 0.592     0.118     0.025       12     1.3  G&S_cingul-Mid-Ant
 1685   1204   3405  2.596 0.545     0.124     0.028       14     2.0  G&S_cingul-Mid-Post
  700    491   1761  2.874 0.588     0.172     0.055       12     1.6  G_cingul-Post-dorsal
  325    211   1040  3.547 0.872     0.133     0.036        4     0.3  G_cingul-Post-ventral
 2185   1575   2982  1.741 0.446     0.172     0.038       36     3.6  G_cuneus
 1986   1348   5118  2.750 0.631     0.132     0.032       27     2.6  G_front_inf-Opercular
  449    306   1000  2.439 0.545     0.141     0.028        8     0.5  G_front_inf-Orbital
 1348    895   3552  2.722 0.677     0.128     0.028       18     1.5  G_front_inf-Triangul
 5618   3523  13765  2.789 0.777     0.132     0.034       76     8.0  G_front_middle
 9906   6405  23978  2.962 0.697     0.125     0.030      114    12.1  G_front_sup
  773    483   1620  3.147 0.675     0.126     0.032        9     0.9  G_Ins_lg&S_cent_ins
  983    605   2577  3.430 0.815     0.129     0.036       16     1.4  G_insular_short
 2622   1749   5659  2.459 0.618     0.155     0.040       42     4.5  G_occipital_middle
 1559   1041   2642  2.174 0.596     0.140     0.037       19     2.4  G_occipital_sup
 2252   1611   5251  2.668 0.637     0.150     0.034       35     3.1  G_oc-temp_lat-fusifor
 2450   1834   4442  2.023 0.698     0.164     0.039       38     4.0  G_oc-temp_med-Lingual
 1306    872   3755  3.131 1.001     0.091     0.020        9     0.9  G_oc-temp_med-Parahip
 2608   1811   8108  3.072 0.816     0.136     0.035       38     3.8  G_orbital
 2507   1780   6263  2.654 0.762     0.153     0.041       46     4.4  G_pariet_inf-Angular
 3873   2727   9525  2.628 0.682     0.141     0.032       58     5.5  G_pariet_inf-Supramar
 3892   2568   6694  2.122 0.619     0.129     0.028       50     4.5  G_parietal_sup
 2365   1529   3940  2.097 0.663     0.125     0.028       25     2.8  G_postcentral
 3156   1840   7406  2.987 0.742     0.109     0.025       30     3.2  G_precentral
 4104   2871   8217  2.294 0.588     0.157     0.042       71     7.8  G_precuneus
  889    561   2095  2.433 0.855     0.139     0.045       16     1.8  G_rectus
 1131    751   2410  3.109 1.088     0.112     0.042       11     1.6  G_subcallosal
  733    471   1279  2.225 0.533     0.094     0.019        6     0.4  G_temp_sup-G_T_transv
 2270   1582   6521  2.938 0.837     0.146     0.035       36     3.4  G_temp_sup-Lateral
  777    555   2538  3.642 0.883     0.094     0.031       13     0.7  G_temp_sup-Plan_polar
 1169    821   2394  2.717 0.570     0.109     0.018        9     0.9  G_temp_sup-Plan_tempo
 2122   1509   5531  2.724 0.982     0.160     0.046       44     4.3  G_temporal_inf
 2149   1488   6294  2.655 0.881     0.148     0.040       49     3.7  G_temporal_middle
  330    227    477  2.280 0.403     0.089     0.015        1     0.1  Lat_Fis-ant-Horizont
  355    260    502  2.125 0.510     0.109     0.019        2     0.3  Lat_Fis-ant-Vertical
 1544   1041   2075  2.398 0.524     0.122     0.024       12     1.5  Lat_Fis-post
 2708   1767   3834  1.987 0.589     0.149     0.036       38     4.0  Pole_occipital
 1542   1127   5799  3.330 0.915     0.154     0.049       26     3.1  Pole_temporal
 2364   1580   2752  1.843 0.729     0.124     0.030       25     2.8  S_calcarine
 3045   2079   3352  1.779 0.525     0.106     0.019       19     2.3  S_central
 1440   1005   2121  2.260 0.571     0.124     0.027       12     1.6  S_cingul-Marginalis
  838    563   1375  2.693 0.678     0.102     0.020        4     0.7  S_circular_insula_ant
 1477   1051   2582  2.969 0.650     0.098     0.016        7     1.1  S_circular_insula_inf
 2225   1523   3492  2.701 0.550     0.101     0.017       11     1.6  S_circular_insula_sup
  753    529   1412  2.959 0.700     0.105     0.021        4     0.4  S_collat_transv_ant
  335    236    471  2.368 0.533     0.146     0.034        4     0.4  S_collat_transv_post
 2650   1844   3932  2.189 0.451     0.120     0.022       23     2.4  S_front_inf
 1720   1194   2434  2.172 0.483     0.112     0.022       13     1.4  S_front_middle
 3124   2190   4722  2.284 0.499     0.101     0.019       19     2.1  S_front_sup
  207    168    426  2.504 0.782     0.149     0.033        2     0.3  S_interm_prim-Jensen
 3349   2307   4656  2.193 0.577     0.108     0.017       23     2.3  S_intrapariet&P_trans
 1135    792   1391  2.016 0.395     0.111     0.023        8     0.9  S_oc_middle&Lunatus
 1526   1042   1891  2.023 0.485     0.114     0.022       10     1.3  S_oc_sup&transversal
  706    491    981  1.965 0.443     0.120     0.027        6     0.8  S_occipital_ant
  779    566   1448  2.210 0.699     0.120     0.025        7     0.9  S_oc-temp_lat
 2633   1800   3540  2.125 0.544     0.112     0.022       20     2.3  S_oc-temp_med&Lingual
  408    278    503  2.152 0.443     0.090     0.018        2     0.2  S_orbital_lateral
  641    424    850  2.342 0.723     0.110     0.022        5     0.4  S_orbital_med-olfact
 1389    946   2766  2.839 0.817     0.107     0.023        8     1.4  S_orbital-H_Shaped
 2286   1565   3077  2.274 0.583     0.115     0.022       15     2.1  S_parieto_occipital
 1331    817   1321  2.179 0.774     0.122     0.024       38     0.9  S_pericallosal
 3305   2299   5002  2.139 0.634     0.121     0.020       28     2.8  S_postcentral
 1818   1232   2890  2.356 0.414     0.105     0.017       12     1.4  S_precentral-inf-part
 1975   1369   2896  2.401 0.524     0.111     0.019       13     1.5  S_precentral-sup-part
  625    426    839  2.258 0.870     0.132     0.018        7     0.5  S_suborbital
 1189    838   1788  2.323 0.451     0.111     0.018        9     0.9  S_subparietal
 1410    983   1869  2.143 0.528     0.110     0.016        9     1.0  S_temporal_inf
 4690   3292   7473  2.319 0.604     0.110     0.019       34     3.5  S_temporal_sup
  525    389    678  2.123 0.365     0.103     0.015        3     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 0050607 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 276152
Total vertex volume 273179 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
 1021    731   2017  2.378 0.656     0.145     0.036       15     1.5  G&S_frontomargin
 1682   1140   3198  2.513 0.578     0.159     0.049       28     3.3  G&S_occipital_inf
 1909   1202   2551  1.967 0.560     0.127     0.027       19     2.1  G&S_paracentral
 1307    905   2755  2.635 0.635     0.139     0.036       16     1.7  G&S_subcentral
 1410    937   3440  2.719 0.688     0.149     0.041       24     2.2  G&S_transv_frontopol
 3589   2410   6472  2.502 0.588     0.121     0.023       43     3.4  G&S_cingul-Ant
 1670   1181   3421  2.680 0.577     0.111     0.017       14     1.1  G&S_cingul-Mid-Ant
 1498   1068   2974  2.491 0.695     0.135     0.036       17     2.3  G&S_cingul-Mid-Post
  832    556   2267  2.958 0.581     0.169     0.062       14     2.2  G_cingul-Post-dorsal
  394    243   1162  3.451 1.031     0.128     0.038        5     0.4  G_cingul-Post-ventral
 2823   1929   3530  1.754 0.464     0.152     0.036       41     4.0  G_cuneus
 1976   1360   5125  2.734 0.643     0.142     0.030       31     2.4  G_front_inf-Opercular
  479    319   1129  2.480 0.571     0.143     0.034        8     0.6  G_front_inf-Orbital
 1488    961   3683  2.917 0.625     0.144     0.035       23     2.1  G_front_inf-Triangul
 5475   3289  12271  2.703 0.762     0.131     0.037       78     8.5  G_front_middle
 8125   5214  19132  2.872 0.727     0.123     0.029       85     9.2  G_front_sup
  680    489   1412  2.822 0.499     0.142     0.036       10     0.8  G_Ins_lg&S_cent_ins
 1274    847   3347  3.473 0.841     0.144     0.040       19     2.1  G_insular_short
 3222   2081   6649  2.489 0.632     0.142     0.040       54     5.4  G_occipital_middle
 1922   1254   2808  2.065 0.544     0.148     0.033       26     2.7  G_occipital_sup
 2240   1565   5298  2.855 0.630     0.152     0.041       32     3.7  G_oc-temp_lat-fusifor
 2590   1795   4083  1.914 0.607     0.150     0.045       40     4.8  G_oc-temp_med-Lingual
 1170    783   3220  3.073 1.034     0.115     0.046       28     2.5  G_oc-temp_med-Parahip
 3509   2447   9826  2.963 0.818     0.149     0.045       57     6.7  G_orbital
 2852   1832   6436  2.599 0.751     0.143     0.039       43     4.7  G_pariet_inf-Angular
 3274   2232   7135  2.559 0.622     0.148     0.033       51     4.5  G_pariet_inf-Supramar
 3459   2166   5774  2.093 0.677     0.113     0.030       39     4.3  G_parietal_sup
 2803   1680   3640  1.848 0.546     0.119     0.025       31     3.0  G_postcentral
 3535   2126   6130  2.300 0.682     0.107     0.024       28     3.7  G_precentral
 3456   2385   6681  2.344 0.606     0.152     0.040       56     5.8  G_precuneus
  840    693   2682  2.776 0.785     0.195     0.051       18     2.0  G_rectus
  682    465   1138  2.590 1.359     0.126     0.059       11     1.8  G_subcallosal
  509    326    715  1.757 0.358     0.117     0.018        5     0.4  G_temp_sup-G_T_transv
 2169   1519   6257  3.095 0.769     0.139     0.027       31     2.3  G_temp_sup-Lateral
 1163    818   2481  2.831 0.925     0.094     0.031        9     1.7  G_temp_sup-Plan_polar
  819    600   1479  2.197 0.503     0.118     0.020        8     0.7  G_temp_sup-Plan_tempo
 2900   1969   7363  2.611 0.855     0.146     0.048       57     6.0  G_temporal_inf
 2961   2151   9332  2.896 0.831     0.162     0.043       52     5.8  G_temporal_middle
  404    284    472  1.979 0.443     0.108     0.015        2     0.3  Lat_Fis-ant-Horizont
  452    327    714  2.255 0.499     0.113     0.016        3     0.3  Lat_Fis-ant-Vertical
 1409    958   1980  2.438 0.601     0.117     0.024       11     1.2  Lat_Fis-post
 4389   2884   5996  1.981 0.598     0.152     0.042       61     7.4  Pole_occipital
 2162   1607   7738  3.260 0.820     0.155     0.041       40     3.8  Pole_temporal
 2803   1948   3259  1.970 0.752     0.123     0.026       27     3.0  S_calcarine
 3247   2218   3255  1.623 0.462     0.089     0.014       15     1.8  S_central
 1605   1080   2298  2.106 0.533     0.112     0.022       12     1.4  S_cingul-Marginalis
  830    569   1394  2.951 0.620     0.092     0.017        3     0.6  S_circular_insula_ant
 1199    830   1701  2.521 0.714     0.093     0.015        5     0.6  S_circular_insula_inf
 1856   1297   2982  2.657 0.667     0.102     0.019        9     1.4  S_circular_insula_sup
  787    526   1382  2.824 0.709     0.095     0.023        4     0.5  S_collat_transv_ant
  561    388    809  2.348 0.496     0.152     0.038        6     1.0  S_collat_transv_post
 2801   1849   3623  2.019 0.519     0.101     0.019       18     2.2  S_front_inf
 2771   1882   3475  2.036 0.503     0.103     0.020       16     2.1  S_front_middle
 3241   2256   5160  2.366 0.570     0.109     0.021       22     2.5  S_front_sup
  365    254    414  1.928 0.420     0.106     0.017        2     0.3  S_interm_prim-Jensen
 4412   3000   5923  2.105 0.551     0.119     0.023       37     4.2  S_intrapariet&P_trans
 1266    869   1511  2.108 0.428     0.120     0.025        9     1.3  S_oc_middle&Lunatus
 1511   1031   2045  2.142 0.426     0.113     0.017       12     1.0  S_oc_sup&transversal
  616    452   1032  2.286 0.536     0.122     0.028        6     0.6  S_occipital_ant
  917    657   1187  2.172 0.368     0.112     0.018        6     0.7  S_oc-temp_lat
 2500   1726   3488  2.319 0.594     0.105     0.040       22     6.3  S_oc-temp_med&Lingual
  641    442    784  1.965 0.526     0.114     0.023        5     0.6  S_orbital_lateral
  568    406   1164  3.180 0.713     0.113     0.025        4     0.5  S_orbital_med-olfact
 1458   1015   2936  2.662 0.892     0.117     0.025       12     1.5  S_orbital-H_Shaped
 2436   1662   3404  2.380 0.667     0.122     0.024       20     2.4  S_parieto_occipital
 1468    927   1181  1.720 0.512     0.116     0.017       22     0.7  S_pericallosal
 2412   1642   2902  2.034 0.523     0.112     0.020       18     2.0  S_postcentral
 1568   1107   2346  2.340 0.520     0.105     0.016        9     1.0  S_precentral-inf-part
 1825   1235   2536  2.381 0.610     0.093     0.014       10     1.0  S_precentral-sup-part
  447    308    718  2.481 0.627     0.122     0.023        5     0.4  S_suborbital
 1556   1105   2354  2.350 0.452     0.124     0.027       13     1.7  S_subparietal
 1583   1062   1899  2.112 0.491     0.096     0.016        8     1.0  S_temporal_inf
 6055   4140   9609  2.406 0.488     0.102     0.018       43     4.2  S_temporal_sup
  475    321    491  1.898 0.249     0.123     0.011        5     0.2  S_temporal_transverse
PIDs (10055 10058) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 10:35:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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 10:35:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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 10128 of (10128 10131) to complete...
Waiting for PID 10131 of (10128 10131) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050607 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...
1381 labels changed using aseg
relabeling using gibbs priors...
000:   2093 changed, 148125 examined...
001:    477 changed, 9633 examined...
002:    137 changed, 2772 examined...
003:     48 changed, 791 examined...
004:     27 changed, 279 examined...
005:     14 changed, 158 examined...
006:     13 changed, 64 examined...
007:     10 changed, 70 examined...
008:      6 changed, 66 examined...
009:      6 changed, 36 examined...
010:      8 changed, 39 examined...
011:      7 changed, 38 examined...
012:      7 changed, 33 examined...
013:      5 changed, 31 examined...
014:      4 changed, 23 examined...
015:      3 changed, 25 examined...
016:      3 changed, 21 examined...
017:      1 changed, 21 examined...
018:      1 changed, 7 examined...
019:      0 changed, 7 examined...
276 labels changed using aseg
000: 60 total segments, 27 labels (186 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...
1004 vertices marked for relabeling...
1004 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 0050607 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...
1522 labels changed using aseg
relabeling using gibbs priors...
000:   2165 changed, 156423 examined...
001:    535 changed, 10214 examined...
002:    152 changed, 3011 examined...
003:     64 changed, 913 examined...
004:     34 changed, 372 examined...
005:     19 changed, 201 examined...
006:     10 changed, 115 examined...
007:      7 changed, 70 examined...
008:      5 changed, 42 examined...
009:      6 changed, 36 examined...
010:     10 changed, 39 examined...
011:      6 changed, 43 examined...
012:      8 changed, 40 examined...
013:      7 changed, 42 examined...
014:      5 changed, 37 examined...
015:      3 changed, 30 examined...
016:      1 changed, 17 examined...
017:      1 changed, 9 examined...
018:      2 changed, 7 examined...
019:      2 changed, 10 examined...
020:      5 changed, 12 examined...
021:      3 changed, 21 examined...
022:      3 changed, 17 examined...
023:      4 changed, 21 examined...
024:      4 changed, 22 examined...
025:      1 changed, 20 examined...
026:      0 changed, 7 examined...
293 labels changed using aseg
000: 56 total segments, 23 labels (223 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...
1063 vertices marked for relabeling...
1063 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.
PIDs (10128 10131) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 10:35:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 10:35:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 rh white 

Waiting for PID 10179 of (10179 10182) to complete...
Waiting for PID 10182 of (10179 10182) 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 0050607 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 274984
Total vertex volume 271400 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
 1694   1141   3514  2.782 0.683     0.126     0.022       19     1.5  caudalanteriorcingulate
 4219   2854   8645  2.572 0.722     0.116     0.022       35     3.7  caudalmiddlefrontal
 3094   2177   4124  1.852 0.520     0.152     0.033       42     4.2  cuneus
  584    400   2017  3.461 1.028     0.102     0.024        5     0.5  entorhinal
 4435   3141   9033  2.519 0.625     0.140     0.032       58     5.6  fusiform
 6174   4289  12162  2.492 0.675     0.132     0.031       77     7.7  inferiorparietal
 4176   2974  10113  2.737 0.947     0.144     0.038       63     6.8  inferiortemporal
 1519   1008   3180  2.770 1.014     0.131     0.037       21     2.0  isthmuscingulate
 8803   5875  13662  2.135 0.580     0.142     0.032      111    11.9  lateraloccipital
 4775   3292  11662  2.898 0.865     0.126     0.035       57     6.6  lateralorbitofrontal
 3918   2860   6204  1.986 0.614     0.143     0.032       48     5.1  lingual
 2522   1668   5200  2.535 0.886     0.126     0.031       41     3.3  medialorbitofrontal
 5139   3610  11936  2.466 0.820     0.127     0.029       73     6.3  middletemporal
 1154    753   2412  2.608 0.928     0.075     0.014        4     0.6  parahippocampal
 3126   2084   5035  2.267 0.610     0.119     0.027       26     3.4  paracentral
 3080   2106   6383  2.521 0.604     0.120     0.025       31     3.3  parsopercularis
 1190    801   2465  2.573 0.571     0.121     0.022       13     1.1  parsorbitalis
 2791   1886   5516  2.434 0.644     0.119     0.024       29     2.6  parstriangularis
 1811   1238   1684  1.520 0.368     0.132     0.029       20     2.1  pericalcarine
 7440   4976  11728  2.098 0.683     0.120     0.025       72     7.5  postcentral
 2476   1709   4739  2.544 0.542     0.144     0.036       33     3.6  posteriorcingulate
 8415   5374  15486  2.579 0.716     0.111     0.022       70     7.5  precentral
 7196   5019  12846  2.331 0.564     0.137     0.032       93    10.1  precuneus
 1562   1022   3097  2.639 0.857     0.114     0.031       33     1.8  rostralanteriorcingulate
 6596   4302  12823  2.489 0.716     0.122     0.030       74     7.8  rostralmiddlefrontal
15075   9941  32570  2.757 0.743     0.120     0.028      148    17.0  superiorfrontal
 7757   5264  11880  2.074 0.558     0.121     0.023       76     7.3  superiorparietal
 8003   5607  18512  2.815 0.852     0.120     0.027       91     8.7  superiortemporal
 6829   4828  14080  2.504 0.660     0.135     0.028       83     8.3  supramarginal
  891    570   1391  2.188 0.471     0.090     0.019        6     0.6  transversetemporal
 3615   2397   7299  3.085 0.696     0.116     0.027       35     3.9  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 0050607 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 276152
Total vertex volume 273179 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
  935    630   1525  2.289 0.522     0.125     0.014       13     0.5  caudalanteriorcingulate
 3865   2568   7470  2.587 0.713     0.109     0.021       30     3.3  caudalmiddlefrontal
 3587   2408   4598  1.909 0.510     0.146     0.035       47     5.1  cuneus
  523    386   1753  3.395 0.867     0.119     0.032        4     0.7  entorhinal
 4271   2964   8486  2.711 0.602     0.132     0.044       51     9.7  fusiform
 7853   5298  14897  2.447 0.637     0.130     0.032       98    10.2  inferiorparietal
 5510   3810  12884  2.638 0.837     0.134     0.038       84     9.0  inferiortemporal
 1776   1160   3731  2.630 1.003     0.127     0.035       22     2.1  isthmuscingulate
10005   6592  15145  2.185 0.567     0.147     0.039      141    15.9  lateraloccipital
 4963   3523  11697  2.847 0.855     0.138     0.041       67     8.7  lateralorbitofrontal
 4405   3088   6583  1.998 0.593     0.138     0.037       56     6.7  lingual
 2185   1600   5225  2.759 0.781     0.144     0.038       30     3.6  medialorbitofrontal
 6497   4603  15621  2.674 0.775     0.128     0.029       74     8.1  middletemporal
 1141    758   2267  2.649 0.891     0.104     0.037       27     2.0  parahippocampal
 2934   1879   4497  2.251 0.589     0.113     0.024       25     2.8  paracentral
 3368   2331   6803  2.497 0.662     0.123     0.024       37     3.2  parsopercularis
 1473    982   3494  2.722 0.821     0.136     0.032       18     2.0  parsorbitalis
 3144   2089   5892  2.461 0.724     0.128     0.028       36     3.6  parstriangularis
 2511   1746   2240  1.491 0.375     0.135     0.030       27     2.9  pericalcarine
 7435   4801   9855  1.883 0.652     0.114     0.023       69     7.0  postcentral
 2104   1472   3716  2.274 0.711     0.144     0.036       31     3.3  posteriorcingulate
 8309   5435  13237  2.274 0.660     0.107     0.022       60     7.4  precentral
 7553   5204  12777  2.360 0.632     0.134     0.032       89     9.9  precuneus
 1101    720   1517  2.240 0.958     0.105     0.022       11     0.9  rostralanteriorcingulate
 7636   4894  12871  2.288 0.699     0.120     0.031       85     9.8  rostralmiddlefrontal
16754  11125  35624  2.705 0.719     0.122     0.026      176    17.6  superiorfrontal
 8489   5508  12651  2.094 0.618     0.118     0.026       85     9.3  superiorparietal
 8206   5711  18057  2.696 0.796     0.119     0.026       89     8.8  superiortemporal
 5468   3716   9899  2.450 0.624     0.129     0.027       62     5.8  supramarginal
  633    405    796  1.792 0.361     0.117     0.021        6     0.5  transversetemporal
 3669   2525   7370  3.012 0.689     0.126     0.028       38     3.9  insula
PIDs (10179 10182) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 10:36:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 pctsurfcon --s 0050607 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 10:36:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts

 pctsurfcon --s 0050607 --rh-only 

Waiting for PID 10255 of (10255 10267) to complete...
Waiting for PID 10267 of (10255 10267) to complete...

 pctsurfcon --s 0050607 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts/pctsurfcon.log
Sun Oct  8 10:36:15 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-6.0.0/0050607/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-388 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-6.0.0/0050607/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10255/lh.wm.mgh --regheader 0050607 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 = 83994
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10255/lh.wm.mgh
Dim: 148125 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10255/lh.gm.mgh --projfrac 0.3 --regheader 0050607 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 = 99416
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10255/lh.gm.mgh
Dim: 148125 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10255/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10255/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.w-g.pct.mgh --annot 0050607 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/lh.w-g.pct.mgh --annot 0050607 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/lh.w-g.pct.mgh
Vertex Area is 0.677733 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 0050607 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/scripts/pctsurfcon.log
Sun Oct  8 10:36:15 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-6.0.0/0050607/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-388 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-6.0.0/0050607/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10267/rh.wm.mgh --regheader 0050607 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 = 88255
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10267/rh.wm.mgh
Dim: 156423 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10267/rh.gm.mgh --projfrac 0.3 --regheader 0050607 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 = 104337
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10267/rh.gm.mgh
Dim: 156423 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10267/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/tmp.pctsurfcon.10267/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.w-g.pct.mgh --annot 0050607 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/rh.w-g.pct.mgh --annot 0050607 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/rh.w-g.pct.mgh
Vertex Area is 0.6733 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 (10255 10267) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 10:36:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
4512 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
3481 voxels changed to hypointensity...
7977 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 10:36:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607

 mri_aparc2aseg --s 0050607 --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 10:36:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607

 mri_aparc2aseg --s 0050607 --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 10:36:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607

 mri_aparc2aseg --s 0050607 --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 10433 of (10433 10436 10439) to complete...
Waiting for PID 10436 of (10433 10436 10439) to complete...
Waiting for PID 10439 of (10433 10436 10439) to complete...

 mri_aparc2aseg --s 0050607 --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 0050607
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/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-6.0.0/0050607/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 8.26
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 109
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 18
rescaling Left_Inf_Lat_Vent from 34 --> 35
rescaling Left_Cerebellum_White_Matter from 86 --> 89
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 81
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 34
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 101
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 14
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 60
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 70
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 88
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 68
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 30
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 541906
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 132 changed.
pass 2: 8 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050607 --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 0050607
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/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-6.0.0/0050607/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 8.26
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 109
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 18
rescaling Left_Inf_Lat_Vent from 34 --> 35
rescaling Left_Cerebellum_White_Matter from 86 --> 89
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 81
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 34
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 101
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 14
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 60
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 70
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 88
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 68
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 30
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 542026
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 132 changed.
pass 2: 8 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050607 --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 0050607
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/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-6.0.0/0050607/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 8.26
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 109
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 18
rescaling Left_Inf_Lat_Vent from 34 --> 35
rescaling Left_Cerebellum_White_Matter from 86 --> 89
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 85
rescaling Left_Caudate from 75 --> 69
rescaling Left_Putamen from 80 --> 79
rescaling Left_Pallidum from 98 --> 94
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 13
rescaling Brain_Stem from 81 --> 81
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 62
rescaling CSF from 32 --> 34
rescaling Left_Accumbens_area from 62 --> 62
rescaling Left_VentralDC from 87 --> 87
rescaling Right_Cerebral_White_Matter from 105 --> 101
rescaling Right_Cerebral_Cortex from 58 --> 60
rescaling Right_Lateral_Ventricle from 13 --> 14
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 86
rescaling Right_Cerebellum_Cortex from 59 --> 60
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 70
rescaling Right_Putamen from 80 --> 77
rescaling Right_Pallidum from 97 --> 88
rescaling Right_Hippocampus from 53 --> 62
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 68
rescaling Right_VentralDC from 86 --> 88
rescaling Fifth_Ventricle from 40 --> 30
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 542026
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 132 changed.
pass 2: 8 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (10433 10436 10439) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 10:44:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri

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

Sun Oct  8 10:44:00 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-6.0.0/0050607/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-388 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-6.0.0/0050607/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-388
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 10:44:00 CEST 2017 
Ended   at Sun Oct  8 10:44:06 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 10:44:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607

 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 0050607 


$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 0050607 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1684585 mm^3    (det: 1.156431 )
Computing euler number
orig.nofix lheno =  -70, rheno = -64
orig.nofix lhholes =   36, rhholes = 33
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
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 10:45:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607

 mri_aparc2aseg --s 0050607 --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 0050607
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-6.0.0/0050607/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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-6.0.0/0050607/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8079 vertices from left hemi
Ripped 8191 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-6.0.0/0050607/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 = 1098918
Used brute-force search on 150 voxels
Fixing Parahip LH WM
  Found 6 clusters
     0 k 1.000000
     1 k 7.000000
     2 k 1.000000
     3 k 6.000000
     4 k 1.000000
     5 k 1613.000000
Fixing Parahip RH WM
  Found 8 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 2.000000
     3 k 2.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1787.000000
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 0050607 --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 0050607 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1684585 mm^3    (det: 1.156431 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
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-6.0.0/0050607/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 10:55:26 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 0050607 --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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11354 of (11354 11360 11366 11371 11378) to complete...
Waiting for PID 11360 of (11354 11360 11366 11371 11378) to complete...
Waiting for PID 11366 of (11354 11360 11366 11371 11378) to complete...
Waiting for PID 11371 of (11354 11360 11366 11371 11378) to complete...
Waiting for PID 11378 of (11354 11360 11366 11371 11378) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 314
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4443
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 630
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8539
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 150
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4227
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 345
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6328
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 830
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6614
mri_label2label: Done

PIDs (11354 11360 11366 11371 11378) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11440 of (11440 11446 11449 11456) to complete...
Waiting for PID 11446 of (11440 11446 11449 11456) to complete...
Waiting for PID 11449 of (11440 11446 11449 11456) to complete...
Waiting for PID 11456 of (11440 11446 11449 11456) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 325
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4395
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 2678
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16267
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 828
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 5009
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 1008
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4430
mri_label2label: Done

PIDs (11440 11446 11449 11456) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 11504 of (11504 11510 11516 11521 11528) to complete...
Waiting for PID 11510 of (11504 11510 11516 11521 11528) to complete...
Waiting for PID 11516 of (11504 11510 11516 11521 11528) to complete...
Waiting for PID 11521 of (11504 11510 11516 11521 11528) to complete...
Waiting for PID 11528 of (11504 11510 11516 11521 11528) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 1430
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6071
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 3117
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11231
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 361
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2379
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 74
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1364
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 96
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1295
mri_label2label: Done

PIDs (11504 11510 11516 11521 11528) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11590 of (11590 11596 11602 11608 11612) to complete...
Waiting for PID 11596 of (11590 11596 11602 11608 11612) to complete...
Waiting for PID 11602 of (11590 11596 11602 11608 11612) to complete...
Waiting for PID 11608 of (11590 11596 11602 11608 11612) to complete...
Waiting for PID 11612 of (11590 11596 11602 11608 11612) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 59
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1073
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 220
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2312
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 49
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1553
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 54
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2050
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 236
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2555
mri_label2label: Done

PIDs (11590 11596 11602 11608 11612) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11659 of (11659 11665 11671 11676) to complete...
Waiting for PID 11665 of (11659 11665 11671 11676) to complete...
Waiting for PID 11671 of (11659 11665 11671 11676) to complete...
Waiting for PID 11676 of (11659 11665 11671 11676) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 84
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1633
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 1455
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8490
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 465
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2377
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 435
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1586
mri_label2label: Done

PIDs (11659 11665 11671 11676) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 11723 of (11723 11729 11735 11741 11746) to complete...
Waiting for PID 11729 of (11723 11729 11735 11741 11746) to complete...
Waiting for PID 11735 of (11723 11729 11735 11741 11746) to complete...
Waiting for PID 11741 of (11723 11729 11735 11741 11746) to complete...
Waiting for PID 11746 of (11723 11729 11735 11741 11746) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 954
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4359
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 1425
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4759
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 76
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 589
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 33
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 503
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 148125
Number of reverse mapping hits = 20
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 470
mri_label2label: Done

PIDs (11723 11729 11735 11741 11746) completed and logs appended.

 mris_label2annot --s 0050607 --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-6.0.0/0050607/label
cmdline mris_label2annot --s 0050607 --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-388
machine  x86_64
user     ntraut

subject 0050607
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-6.0.0/0050607/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 102005 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050607 --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-6.0.0/0050607/label
cmdline mris_label2annot --s 0050607 --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-388
machine  x86_64
user     ntraut

subject 0050607
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-6.0.0/0050607/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 120925 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 274984
Total vertex volume 271400 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
 1149    707   2155  2.248 0.728     0.134     0.035       14     1.6  BA1_exvivo
 4292   2943   7095  2.179 0.643     0.119     0.023       41     3.8  BA2_exvivo
 1086    728    998  1.695 0.386     0.138     0.028       10     1.2  BA3a_exvivo
 2300   1553   3437  1.877 0.707     0.116     0.023       20     2.2  BA3b_exvivo
 1946   1194   3447  2.499 0.699     0.106     0.025       15     1.9  BA4a_exvivo
 1368    930   1942  2.059 0.610     0.100     0.017        8     1.0  BA4p_exvivo
12083   7727  25863  2.809 0.713     0.113     0.024      102    11.5  BA6_exvivo
 3139   2137   6508  2.543 0.581     0.121     0.026       34     3.5  BA44_exvivo
 3492   2375   7363  2.471 0.631     0.127     0.027       39     3.7  BA45_exvivo
 3410   2417   3940  1.629 0.511     0.145     0.034       42     4.9  V1_exvivo
 8667   5971  12732  2.010 0.562     0.151     0.035      120    12.5  V2_exvivo
 1890   1296   3693  2.357 0.663     0.133     0.029       23     2.3  MT_exvivo
  611    405   1750  3.339 0.965     0.110     0.025        7     0.6  perirhinal_exvivo
  687    455   1845  2.959 1.060     0.092     0.020        5     0.5  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 0050607 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 274984
Total vertex volume 271400 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
  656    408   1280  2.278 0.739     0.150     0.034        9     0.9  BA1_exvivo
 1747   1176   2676  2.128 0.642     0.116     0.022       16     1.5  BA2_exvivo
  941    621    786  1.672 0.329     0.144     0.030       10     1.1  BA3a_exvivo
 1231    895   1372  1.460 0.296     0.090     0.012        6     0.6  BA3b_exvivo
 1812   1165   3230  2.519 0.683     0.101     0.022       10     1.6  BA4a_exvivo
 1124    763   1465  1.966 0.502     0.099     0.017        6     0.9  BA4p_exvivo
 7074   4337  14759  2.854 0.710     0.110     0.024       61     6.8  BA6_exvivo
 2061   1426   4570  2.567 0.604     0.130     0.029       26     2.5  BA44_exvivo
 1485   1003   3750  2.657 0.721     0.136     0.031       20     1.8  BA45_exvivo
 3665   2565   4277  1.640 0.510     0.143     0.034       45     5.3  V1_exvivo
 4291   3015   5975  1.936 0.556     0.165     0.038       68     6.7  V2_exvivo
  458    324    939  2.420 0.758     0.151     0.033        6     0.6  MT_exvivo
  309    204   1019  3.544 0.912     0.065     0.011        1     0.1  perirhinal_exvivo
  346    231   1021  3.242 0.821     0.076     0.013        1     0.2  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 10:58:56 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 0050607 --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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 11867 of (11867 11873 11879 11885 11890) to complete...
Waiting for PID 11873 of (11867 11873 11879 11885 11890) to complete...
Waiting for PID 11879 of (11867 11873 11879 11885 11890) to complete...
Waiting for PID 11885 of (11867 11873 11879 11885 11890) to complete...
Waiting for PID 11890 of (11867 11873 11879 11885 11890) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 478
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4440
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 588
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7275
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 236
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4216
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 327
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4849
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 768
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6515
mri_label2label: Done

PIDs (11867 11873 11879 11885 11890) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 11933 of (11933 11939 11945 11951) to complete...
Waiting for PID 11939 of (11933 11939 11945 11951) to complete...
Waiting for PID 11945 of (11933 11939 11945 11951) to complete...
Waiting for PID 11951 of (11933 11939 11945 11951) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 263
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4736
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 2123
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14379
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 1664
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8576
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 2301
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7656
mri_label2label: Done

PIDs (11933 11939 11945 11951) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 12005 of (12005 12011 12017 12023 12029) to complete...
Waiting for PID 12011 of (12005 12011 12017 12023 12029) to complete...
Waiting for PID 12017 of (12005 12011 12017 12023 12029) to complete...
Waiting for PID 12023 of (12005 12011 12017 12023 12029) to complete...
Waiting for PID 12029 of (12005 12011 12017 12023 12029) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 2049
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6776
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 3968
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11984
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 750
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2682
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 92
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1130
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 81
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 833
mri_label2label: Done

PIDs (12005 12011 12017 12023 12029) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12095 of (12095 12101 12107 12113 12119) to complete...
Waiting for PID 12101 of (12095 12101 12107 12113 12119) to complete...
Waiting for PID 12107 of (12095 12101 12107 12113 12119) to complete...
Waiting for PID 12113 of (12095 12101 12107 12113 12119) to complete...
Waiting for PID 12119 of (12095 12101 12107 12113 12119) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 140
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1016
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 247
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2935
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 90
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1788
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 150
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2333
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 168
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1556
mri_label2label: Done

PIDs (12095 12101 12107 12113 12119) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12170 of (12170 12176 12182 12188) to complete...
Waiting for PID 12176 of (12170 12176 12182 12188) to complete...
Waiting for PID 12182 of (12170 12176 12182 12188) to complete...
Waiting for PID 12188 of (12170 12176 12182 12188) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 87
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1576
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 1379
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8338
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 314
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1326
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 626
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1804
mri_label2label: Done

PIDs (12170 12176 12182 12188) 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 0050607 --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 0050607 --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 0050607 --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 0050607 --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 0050607 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 12243 of (12243 12249 12255 12261 12266) to complete...
Waiting for PID 12249 of (12243 12249 12255 12261 12266) to complete...
Waiting for PID 12255 of (12243 12249 12255 12261 12266) to complete...
Waiting for PID 12261 of (12243 12249 12255 12261 12266) to complete...
Waiting for PID 12266 of (12243 12249 12255 12261 12266) 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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 1286
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4518
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 1814
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5251
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 90
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 358
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 47
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 741
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 0050607 --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 = 0050607
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-6.0.0/0050607/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 156423
Number of reverse mapping hits = 13
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 304
mri_label2label: Done

PIDs (12243 12249 12255 12261 12266) completed and logs appended.

 mris_label2annot --s 0050607 --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-6.0.0/0050607/label
cmdline mris_label2annot --s 0050607 --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-388
machine  x86_64
user     ntraut

subject 0050607
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-6.0.0/0050607/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 107104 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050607 --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-6.0.0/0050607/label
cmdline mris_label2annot --s 0050607 --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-388
machine  x86_64
user     ntraut

subject 0050607
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-6.0.0/0050607/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 128429 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/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 0050607 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 276152
Total vertex volume 273179 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
 1133    641   1564  1.971 0.578     0.132     0.031       13     1.6  BA1_exvivo
 3477   2272   4363  1.940 0.554     0.117     0.023       32     3.3  BA2_exvivo
 1204    808   1029  1.515 0.480     0.124     0.021        9     1.1  BA3a_exvivo
 2054   1369   2530  1.635 0.603     0.096     0.017       15     1.4  BA3b_exvivo
 1853   1195   2771  2.165 0.600     0.111     0.024       15     1.8  BA4a_exvivo
 1317    899   1821  2.041 0.473     0.082     0.015        5     0.7  BA4p_exvivo
10671   6855  20846  2.627 0.730     0.110     0.022       87    10.0  BA6_exvivo
 4287   2955   8051  2.489 0.645     0.124     0.024       42     4.1  BA44_exvivo
 5903   3915  11655  2.457 0.733     0.125     0.028       67     6.3  BA45_exvivo
 4408   3096   5137  1.648 0.511     0.145     0.034       56     6.1  V1_exvivo
 9613   6383  12883  2.008 0.548     0.149     0.039      134    15.4  V2_exvivo
 2464   1665   4381  2.458 0.545     0.133     0.034       31     3.2  MT_exvivo
  575    406   2041  3.608 0.722     0.118     0.031        5     0.7  perirhinal_exvivo
  360    256    933  2.958 0.597     0.128     0.030        4     0.5  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050607 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050607/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 276152
Total vertex volume 273179 (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) = 1684585 mm^3    (det: 1.156431 )
lhCtxGM: 270615.081 270417.000  diff=  198.1  pctdiff= 0.073
rhCtxGM: 271816.655 271715.000  diff=  101.7  pctdiff= 0.037
lhCtxWM: 277248.240 276946.500  diff=  301.7  pctdiff= 0.109
rhCtxWM: 282774.066 283364.500  diff= -590.4  pctdiff=-0.209
SubCortGMVol  69826.000
SupraTentVol  1182484.043 (1179779.000) diff=2705.043 pctdiff=0.229
SupraTentVolNotVent  1174995.043 (1172290.000) diff=2705.043 pctdiff=0.230
BrainSegVol  1324315.000 (1322316.000) diff=1999.000 pctdiff=0.151
BrainSegVolNotVent  1313719.000 (1313526.043) diff=192.957 pctdiff=0.015
BrainSegVolNotVent  1313719.000
CerebellumVol 141225.000
VentChorVol    7489.000
3rd4th5thCSF   3107.000
CSFVol  1108.000, OptChiasmVol   204.000
MaskVol 1845838.000
  780    431    989  1.841 0.467     0.124     0.029        9     1.0  BA1_exvivo
 2040   1292   2624  1.935 0.549     0.114     0.023       18     2.0  BA2_exvivo
 1097    732    801  1.441 0.270     0.127     0.020        9     1.0  BA3a_exvivo
 1616   1084   1610  1.443 0.394     0.083     0.013        8     0.8  BA3b_exvivo
 1230    765   1816  2.340 0.595     0.110     0.026        9     1.3  BA4a_exvivo
 1111    773   1519  2.053 0.423     0.073     0.013        3     0.6  BA4p_exvivo
 7083   4429  12768  2.570 0.695     0.108     0.023       56     6.8  BA6_exvivo
 1228    884   2922  2.581 0.659     0.136     0.025       16     1.2  BA44_exvivo
 1733   1156   3976  2.685 0.675     0.144     0.033       26     2.3  BA45_exvivo
 4210   2953   4797  1.633 0.500     0.141     0.034       51     5.7  V1_exvivo
 4982   3285   6396  1.920 0.551     0.154     0.042       77     8.4  V2_exvivo
  328    225    633  2.501 0.428     0.148     0.037        5     0.4  MT_exvivo
  352    239   1236  3.724 0.657     0.105     0.024        2     0.4  perirhinal_exvivo
  204    161    644  3.096 0.584     0.147     0.035        2     0.4  entorhinal_exvivo

Started at Sun Oct 8 01:38:35 CEST 2017 
Ended   at Sun Oct 8 11:02:31 CEST 2017
#@#%# recon-all-run-time-hours 9.399
recon-all -s 0050607 finished without error at Sun Oct  8 11:02:31 CEST 2017