ABIDE_fs-6.0.0/0050244/scripts/recon-all.log

Sat Oct  7 19:38:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050244 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050244/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050244
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-951 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:      66074800   52647868   13426932    1745616          0   48039440
-/+ buffers/cache:    4608428   61466372
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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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: 2017/10/07-17:38:39-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-951  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-6.0.0/0050244

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050244/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050244/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050244/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-6.0.0/0050244/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 19:38:42 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, 1, 0)
k_ras = (-0, -0, 1)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 19:38:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/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-951 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 19:38:53 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.28429
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28429/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.28429/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.28429/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 19:38:56 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.28429/nu0.mnc ./tmp.mri_nu_correct.mni.28429/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28429/0/ -iterations 1000 -distance 50
[ntraut@tars-951:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/] [2017-10-07 19:38:56] 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.28429/0/ ./tmp.mri_nu_correct.mni.28429/nu0.mnc ./tmp.mri_nu_correct.mni.28429/nu1.imp

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Number of iterations: 68 
CV of field change: 0.000984483
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.28429/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.28429/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.28429/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 19:40:31 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 19:40:31 CEST 2017
Ended   at Sat Oct  7 19:41:13 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 19:41:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4681, pval=0.1049 >= 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-6.0.0/0050244/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/transforms/talairach_avi.log 

TalAviQA: 0.97275
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 19:41:15 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-6.0.0/0050244/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-951 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 19:41:15 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.29565
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29565/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.29565/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.29565/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 19:41:18 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.29565/nu0.mnc ./tmp.mri_nu_correct.mni.29565/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29565/0/
[ntraut@tars-951:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/] [2017-10-07 19:41:18] 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.29565/0/ ./tmp.mri_nu_correct.mni.29565/nu0.mnc ./tmp.mri_nu_correct.mni.29565/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00110433
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 19:42:15 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.29565/nu1.mnc ./tmp.mri_nu_correct.mni.29565/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.29565/1/
[ntraut@tars-951:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/] [2017-10-07 19:42:15] 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.29565/1/ ./tmp.mri_nu_correct.mni.29565/nu1.mnc ./tmp.mri_nu_correct.mni.29565/nu2.imp

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Number of iterations: 18 
CV of field change: 0.000985942
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.29565/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.29565/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-6.0.0/0050244/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.29565/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.29565/ones.mgz 
sysname  Linux
hostname tars-951
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.29565/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.29565/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.29565/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.29565/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29565/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.29565/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.29565/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29565/input.mean.dat 
sysname  Linux
hostname tars-951
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.29565/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.29565/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.29565/ones.mgz --i ./tmp.mri_nu_correct.mni.29565/nu2.mnc --sum ./tmp.mri_nu_correct.mni.29565/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29565/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.29565/ones.mgz --i ./tmp.mri_nu_correct.mni.29565/nu2.mnc --sum ./tmp.mri_nu_correct.mni.29565/sum.junk --avgwf ./tmp.mri_nu_correct.mni.29565/output.mean.dat 
sysname  Linux
hostname tars-951
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.29565/ones.mgz
Loading ./tmp.mri_nu_correct.mni.29565/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.29565/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.29565/nu2.mnc ./tmp.mri_nu_correct.mni.29565/nu2.mnc mul .88742115381434789902
Saving result to './tmp.mri_nu_correct.mni.29565/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.29565/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.29565/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.29565/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 ( 7, 159) to ( 3, 110)
 
 
Sat Oct  7 19:43:38 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 19:43:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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
 1.03944  -0.00561  -0.01137   5.56966;
 0.00062   0.87630   0.40644   2.73689;
 0.01815  -0.34312   0.91156  -2.83250;
 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 = 22
Starting OpenSpline(): npoints = 22
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 74 (74), valley at 38 (38)
csf peak at 24, 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 74 (74), valley at 37 (37)
csf peak at 24, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 9 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 19:45:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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=10.0
skull bounding box = (45, 26, 0) --> (209, 206, 224)
using (100, 86, 112) as brain centroid...
mean wm in atlas = 108, using box (80,64,84) --> (120, 108,139) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 107 +- 4.5
after smoothing, mri peak at 108, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.228
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.227596 @ (0.000, 0.000, 0.000)
max log p =    -4.146818 @ (-4.545, 4.545, 4.545)
max log p =    -4.130344 @ (2.273, -2.273, -6.818)
max log p =    -4.091577 @ (-1.136, 1.136, 3.409)
max log p =    -4.087385 @ (0.568, 0.568, -0.568)
max log p =    -4.085418 @ (-0.284, 0.852, -0.852)
Found translation: (-3.1, 4.8, -0.3): log p = -4.085
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.916, old_max_log_p =-4.085 (thresh=-4.1)
 1.00000   0.00000   0.00000  -3.12500;
 0.00000   0.92388   0.38268  -27.27289;
 0.00000  -0.38268   0.92388   60.74058;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.916, old_max_log_p =-3.916 (thresh=-3.9)
 1.00000   0.00000   0.00000  -3.12500;
 0.00000   0.92388   0.38268  -27.27289;
 0.00000  -0.38268   0.92388   60.74058;
 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=-3.824, old_max_log_p =-3.916 (thresh=-3.9)
 0.97956  -0.04049   0.01903   2.93562;
 0.02942   0.93552   0.35182  -27.33053;
-0.03087  -0.33365   0.88306   62.49606;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.822, old_max_log_p =-3.824 (thresh=-3.8)
 0.97956  -0.04049   0.01903   2.93562;
 0.02997   0.95306   0.35842  -30.50873;
-0.03029  -0.32739   0.86650   61.52906;
 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=-3.798, old_max_log_p =-3.822 (thresh=-3.8)
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01399  -0.32061   0.87060   58.99863;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.797, old_max_log_p =-3.798 (thresh=-3.8)
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01398  -0.32024   0.86958   59.05948;
 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
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01398  -0.32024   0.86958   59.05948;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01398  -0.32024   0.86958   59.05948;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01398  -0.32024   0.86958   59.05948;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.797 (old=-4.228)
transform before final EM align:
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01398  -0.32024   0.86958   59.05948;
 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
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01398  -0.32024   0.86958   59.05948;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01398  -0.32024   0.86958   59.05948;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.2  tol 0.000000
final transform:
 0.97878  -0.03497   0.00492   3.89220;
 0.02988   0.95349   0.35046  -30.13708;
-0.01398  -0.32024   0.86958   59.05948;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1159.205773
mri_em_register stimesec    1.121829
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   157589
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    97
mri_em_register ru_nivcsw   1935
registration took 10 minutes and 8 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=128 y=109 z=105 r=79
      first estimation of the main basin volume: 2085467 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=151, y=89, z=67, Imax=255
      CSF=15, 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=9700807327 voxels, voxel volume =1.000 
                     = 9700807327 mmm3 = 9700807.680 cm3
done.
PostAnalyze...Basin Prior
 154 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=128,y=117, z=98, r=11159 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=39 , nb = 45300
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=34 , nb = -1028801456
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=30 , nb = -1040932141
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=36 , nb = -1059729707
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 1074441696
    OTHER      CSF_MIN=0, CSF_intensity=23, CSF_MAX=52 , nb = 1082665542
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    39,      47,        52,   70
  after  analyzing :    39,      50,        52,   55
   RIGHT_CER   
  before analyzing :    34,      44,        51,   72
  after  analyzing :    34,      48,        51,   54
   LEFT_CER    
  before analyzing :    30,      41,        50,   71
  after  analyzing :    30,      47,        50,   53
  RIGHT_BRAIN  
  before analyzing :    36,      45,        52,   70
  after  analyzing :    36,      49,        52,   54
  LEFT_BRAIN   
  before analyzing :    37,      44,        50,   70
  after  analyzing :    37,      48,        50,   53
     OTHER     
  before analyzing :    52,      65,        74,   92
  after  analyzing :    52,      71,        74,   76
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...66 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.011
curvature mean = 75.523, std = 8.501

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.51, sigma = 6.09
      after  rotation: sse = 3.51, sigma = 6.09
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  4.72, its var is  8.71   
      before Erosion-Dilatation  2.98% of inacurate vertices
      after  Erosion-Dilatation  2.08% 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...52 iterations

      mri_strip_skull: done peeling brain

Brain Size = 2198941 voxels, voxel volume = 1.000 mm3
           = 2198941 mmm3 = 2198.941 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    28.756628
mri_watershed stimesec    0.423935
mri_watershed ru_maxrss   829444
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   214700
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  3376
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1524
mri_watershed ru_nivcsw   51
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 19:56:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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=26.1
skull bounding box = (59, 43, 18) --> (197, 205, 194)
using (105, 97, 106) as brain centroid...
mean wm in atlas = 107, using box (88,77,84) --> (121, 116,127) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 107 +- 4.5
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.078
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.073797 @ (-9.091, 9.091, 9.091)
max log p =    -3.976011 @ (4.545, -4.545, -4.545)
max log p =    -3.938955 @ (2.273, -2.273, 6.818)
max log p =    -3.920183 @ (-1.136, -1.136, -5.682)
max log p =    -3.910015 @ (0.568, 0.568, 3.977)
max log p =    -3.910015 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, 1.7, 9.7): log p = -3.910
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.563, old_max_log_p =-3.910 (thresh=-3.9)
 1.00000   0.00000   0.00000  -2.84091;
 0.00000   0.90348   0.20035  -6.13719;
 0.00000  -0.27051   0.87553   45.88964;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.532, old_max_log_p =-3.563 (thresh=-3.6)
 1.00000   0.00000   0.00000  -2.84091;
 0.00000   0.92498   0.33639  -22.74717;
 0.00000  -0.38612   0.84188   62.77068;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.532, old_max_log_p =-3.532 (thresh=-3.5)
 1.00000   0.00000   0.00000  -2.84091;
 0.00000   0.92498   0.33639  -22.74717;
 0.00000  -0.38612   0.84188   62.77068;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.394, old_max_log_p =-3.532 (thresh=-3.5)
 1.01750  -0.02882  -0.01254  -0.46873;
 0.03395   0.89726   0.39052  -29.55533;
 0.00000  -0.43712   0.80217   76.61968;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.394, old_max_log_p =-3.394 (thresh=-3.4)
 1.01750  -0.02882  -0.01254  -0.46873;
 0.03395   0.89726   0.39052  -29.55533;
 0.00000  -0.43712   0.80217   76.61968;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.342, old_max_log_p =-3.394 (thresh=-3.4)
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.342, old_max_log_p =-3.342 (thresh=-3.3)
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 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
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.342 (old=-4.078)
transform before final EM align:
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 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
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    3.9  tol 0.000000
final transform:
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1180.757497
mri_em_register stimesec    1.293803
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   159498
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    139
mri_em_register ru_nivcsw   1967
registration took 10 minutes and 9 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 20:06:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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=26.1
skull bounding box = (59, 43, 18) --> (197, 205, 194)
using (105, 97, 106) as brain centroid...
mean wm in atlas = 107, using box (88,77,84) --> (121, 116,127) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 107 +- 4.5
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246344 sample points...
INFO: compute sample coordinates transform
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51012;
 0.00000   0.00000   0.00000   1.00000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 49, 18) --> (193, 177, 199)
Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0
1 of 3212 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 49, 19) --> (130, 169, 198)
Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 2770 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 147, 61) --> (178, 190, 120)
Left_Cerebellum_White_Matter: limiting intensities to 104.0 --> 132.0
2 of 14 (14.3%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 147, 57) --> (129, 189, 120)
Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 132.0
0 of 12 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 128, 93) --> (146, 196, 130)
Brain_Stem: limiting intensities to 89.0 --> 132.0
0 of 76 (0.0%) samples deleted
using 6084 total control points for intensity normalization...
bias field = 0.968 +- 0.043
60 of 6081 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 49, 18) --> (193, 177, 199)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 4033 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 49, 19) --> (130, 169, 198)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
2 of 3492 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 147, 61) --> (178, 190, 120)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 94 (1.1%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 147, 57) --> (129, 189, 120)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
7 of 76 (9.2%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 128, 93) --> (146, 196, 130)
Brain_Stem: limiting intensities to 88.0 --> 132.0
6 of 149 (4.0%) samples deleted
using 7844 total control points for intensity normalization...
bias field = 1.027 +- 0.046
65 of 7761 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (129, 49, 18) --> (193, 177, 199)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
6 of 4065 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (66, 49, 19) --> (130, 169, 198)
Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
15 of 3454 (0.4%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (131, 147, 61) --> (178, 190, 120)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
5 of 74 (6.8%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 147, 57) --> (129, 189, 120)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
23 of 80 (28.8%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 128, 93) --> (146, 196, 130)
Brain_Stem: limiting intensities to 88.0 --> 132.0
49 of 204 (24.0%) samples deleted
using 7877 total control points for intensity normalization...
bias field = 1.025 +- 0.042
49 of 7632 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 43 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 20:08:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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) = 0.91 (predicted orig area = 8.8)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.794, neg=0, invalid=762
0001: dt=189.137888, rms=0.742 (6.655%), neg=0, invalid=762
0002: dt=234.905028, rms=0.723 (2.439%), neg=0, invalid=762
0003: dt=140.026846, rms=0.714 (1.364%), neg=0, invalid=762
0004: dt=443.904000, rms=0.706 (1.003%), neg=0, invalid=762
0005: dt=129.472000, rms=0.701 (0.703%), neg=0, invalid=762
0006: dt=517.888000, rms=0.697 (0.599%), neg=0, invalid=762
0007: dt=129.472000, rms=0.694 (0.453%), neg=0, invalid=762
0008: dt=517.888000, rms=0.692 (0.370%), neg=0, invalid=762
0009: dt=129.472000, rms=0.689 (0.337%), neg=0, invalid=762
0010: dt=369.920000, rms=0.688 (0.199%), neg=0, invalid=762
0011: dt=369.920000, rms=0.688 (-0.081%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.688, neg=0, invalid=762
0012: dt=221.952000, rms=0.685 (0.441%), neg=0, invalid=762
0013: dt=295.936000, rms=0.684 (0.241%), neg=0, invalid=762
0014: dt=295.936000, rms=0.683 (0.147%), neg=0, invalid=762
0015: dt=295.936000, rms=0.680 (0.386%), neg=0, invalid=762
0016: dt=295.936000, rms=0.678 (0.266%), neg=0, invalid=762
0017: dt=295.936000, rms=0.675 (0.410%), neg=0, invalid=762
0018: dt=295.936000, rms=0.674 (0.205%), neg=0, invalid=762
0019: dt=295.936000, rms=0.672 (0.318%), neg=0, invalid=762
0020: dt=295.936000, rms=0.670 (0.203%), neg=0, invalid=762
0021: dt=295.936000, rms=0.669 (0.232%), neg=0, invalid=762
0022: dt=295.936000, rms=0.668 (0.196%), neg=0, invalid=762
0023: dt=295.936000, rms=0.667 (0.143%), neg=0, invalid=762
0024: dt=295.936000, rms=0.665 (0.200%), neg=0, invalid=762
0025: dt=295.936000, rms=0.665 (0.095%), neg=0, invalid=762
0026: dt=295.936000, rms=0.663 (0.221%), neg=0, invalid=762
0027: dt=295.936000, rms=0.662 (0.129%), neg=0, invalid=762
0028: dt=295.936000, rms=0.662 (0.078%), neg=0, invalid=762
0029: dt=295.936000, rms=0.661 (0.109%), neg=0, invalid=762
0030: dt=295.936000, rms=0.661 (0.079%), neg=0, invalid=762
0031: dt=129.472000, rms=0.660 (0.046%), neg=0, invalid=762
0032: dt=129.472000, rms=0.660 (0.019%), neg=0, invalid=762
0033: dt=129.472000, rms=0.660 (0.028%), neg=0, invalid=762
0034: dt=129.472000, rms=0.660 (0.044%), neg=0, invalid=762
0035: dt=129.472000, rms=0.659 (0.035%), neg=0, invalid=762
0036: dt=129.472000, rms=0.659 (0.037%), neg=0, invalid=762
0037: dt=129.472000, rms=0.659 (0.032%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.665, neg=0, invalid=762
0038: dt=119.757576, rms=0.661 (0.604%), neg=0, invalid=762
0039: dt=331.776000, rms=0.650 (1.703%), neg=0, invalid=762
0040: dt=36.288000, rms=0.648 (0.336%), neg=0, invalid=762
0041: dt=68.923077, rms=0.647 (0.162%), neg=0, invalid=762
0042: dt=68.923077, rms=0.645 (0.221%), neg=0, invalid=762
0043: dt=68.923077, rms=0.643 (0.382%), neg=0, invalid=762
0044: dt=68.923077, rms=0.640 (0.489%), neg=0, invalid=762
0045: dt=68.923077, rms=0.636 (0.533%), neg=0, invalid=762
0046: dt=68.923077, rms=0.633 (0.519%), neg=0, invalid=762
0047: dt=68.923077, rms=0.630 (0.471%), neg=0, invalid=762
0048: dt=68.923077, rms=0.628 (0.404%), neg=0, invalid=762
0049: dt=68.923077, rms=0.626 (0.324%), neg=0, invalid=762
0050: dt=68.923077, rms=0.624 (0.286%), neg=0, invalid=762
0051: dt=68.923077, rms=0.622 (0.284%), neg=0, invalid=762
0052: dt=68.923077, rms=0.620 (0.274%), neg=0, invalid=762
0053: dt=68.923077, rms=0.619 (0.250%), neg=0, invalid=762
0054: dt=68.923077, rms=0.618 (0.195%), neg=0, invalid=762
0055: dt=68.923077, rms=0.616 (0.181%), neg=0, invalid=762
0056: dt=68.923077, rms=0.615 (0.162%), neg=0, invalid=762
0057: dt=68.923077, rms=0.615 (0.150%), neg=0, invalid=762
0058: dt=68.923077, rms=0.614 (0.152%), neg=0, invalid=762
0059: dt=68.923077, rms=0.613 (0.136%), neg=0, invalid=762
0060: dt=68.923077, rms=0.612 (0.103%), neg=0, invalid=762
0061: dt=68.923077, rms=0.611 (0.104%), neg=0, invalid=762
0062: dt=68.923077, rms=0.611 (0.114%), neg=0, invalid=762
0063: dt=68.923077, rms=0.610 (0.092%), neg=0, invalid=762
0064: dt=36.288000, rms=0.610 (0.014%), neg=0, invalid=762
0065: dt=36.288000, rms=0.610 (0.005%), neg=0, invalid=762
0066: dt=36.288000, rms=0.610 (0.009%), neg=0, invalid=762
0067: dt=36.288000, rms=0.610 (0.006%), neg=0, invalid=762
0068: dt=36.288000, rms=0.610 (0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.611, neg=0, invalid=762
0069: dt=145.152000, rms=0.608 (0.477%), neg=0, invalid=762
0070: dt=62.208000, rms=0.608 (0.048%), neg=0, invalid=762
0071: dt=62.208000, rms=0.607 (0.032%), neg=0, invalid=762
0072: dt=62.208000, rms=0.607 (0.023%), neg=0, invalid=762
0073: dt=62.208000, rms=0.607 (0.012%), neg=0, invalid=762
0074: dt=145.152000, rms=0.607 (0.023%), neg=0, invalid=762
0075: dt=62.208000, rms=0.607 (0.016%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.634, neg=0, invalid=762
0076: dt=8.000000, rms=0.633 (0.185%), neg=0, invalid=762
0077: dt=2.800000, rms=0.633 (0.005%), neg=0, invalid=762
0078: dt=2.800000, rms=0.633 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.633, neg=0, invalid=762
0079: dt=2.400000, rms=0.633 (0.102%), neg=0, invalid=762
0080: dt=0.175000, rms=0.633 (0.001%), neg=0, invalid=762
0081: dt=0.175000, rms=0.633 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.699, neg=0, invalid=762
0082: dt=6.524823, rms=0.675 (3.359%), neg=0, invalid=762
0083: dt=5.297297, rms=0.673 (0.287%), neg=0, invalid=762
0084: dt=1.728000, rms=0.673 (0.009%), neg=0, invalid=762
0085: dt=1.728000, rms=0.673 (0.000%), neg=0, invalid=762
0086: dt=1.728000, rms=0.673 (-0.033%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.674, neg=0, invalid=762
0087: dt=0.000000, rms=0.673 (0.074%), neg=0, invalid=762
0088: dt=0.000000, rms=0.673 (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=0.718, neg=0, invalid=762
0089: dt=0.256000, rms=0.717 (0.086%), neg=0, invalid=762
0090: dt=0.256000, rms=0.717 (0.013%), neg=0, invalid=762
0091: dt=0.256000, rms=0.717 (0.014%), neg=0, invalid=762
0092: dt=0.256000, rms=0.717 (0.001%), neg=0, invalid=762
0093: dt=0.256000, rms=0.717 (-0.032%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.717, neg=0, invalid=762
0094: dt=1.280000, rms=0.715 (0.294%), neg=0, invalid=762
0095: dt=1.792000, rms=0.714 (0.198%), neg=0, invalid=762
0096: dt=1.792000, rms=0.713 (0.133%), neg=0, invalid=762
0097: dt=1.792000, rms=0.713 (0.042%), neg=0, invalid=762
0098: dt=1.792000, rms=0.713 (-0.253%), neg=0, invalid=762
0099: dt=1.792000, rms=0.712 (0.088%), neg=0, invalid=762
0100: dt=1.024000, rms=0.712 (0.028%), 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=0.685, neg=0, invalid=762
0101: dt=0.720149, rms=0.670 (2.105%), neg=0, invalid=762
0102: dt=0.064000, rms=0.670 (0.079%), neg=0, invalid=762
0103: dt=0.064000, rms=0.670 (-0.057%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.670, neg=0, invalid=762
0104: dt=0.028000, rms=0.670 (0.078%), neg=0, invalid=762
0105: dt=0.004000, rms=0.670 (-0.003%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.13830 (26)
Left_Lateral_Ventricle (4): linear fit = 1.43 x + 0.0 (1423 voxels, overlap=0.379)
Left_Lateral_Ventricle (4): linear fit = 1.43 x + 0.0 (1423 voxels, peak = 29), gca=28.7
gca peak = 0.15565 (16)
mri peak = 0.15055 (26)
Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (1127 voxels, overlap=0.207)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1127 voxels, peak = 26), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.11095 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1415 voxels, overlap=0.999)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1415 voxels, peak = 96), gca=96.0
gca peak = 0.20183 (93)
mri peak = 0.07869 (95)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (1156 voxels, overlap=1.011)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (1156 voxels, peak = 94), gca=94.4
gca peak = 0.21683 (55)
mri peak = 0.08803 (70)
Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1504 voxels, overlap=0.027)
Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1504 voxels, peak = 67), gca=67.4
gca peak = 0.30730 (58)
mri peak = 0.08403 (67)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (1322 voxels, overlap=0.182)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (1322 voxels, peak = 68), gca=67.6
gca peak = 0.11430 (101)
mri peak = 0.11288 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (89006 voxels, overlap=0.619)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (89006 voxels, peak = 106), gca=105.5
gca peak = 0.12076 (102)
mri peak = 0.11696 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (94571 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (94571 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.04303 (69)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (41484 voxels, overlap=0.684)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (41484 voxels, peak = 69), gca=69.3
gca peak = 0.15082 (58)
mri peak = 0.04493 (70)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (42428 voxels, overlap=0.536)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (42428 voxels, peak = 69), gca=69.3
gca peak = 0.14161 (67)
mri peak = 0.13217 (80)
Right_Caudate (50): linear fit = 1.16 x + 0.0 (630 voxels, overlap=0.049)
Right_Caudate (50): linear fit = 1.16 x + 0.0 (630 voxels, peak = 78), gca=78.1
gca peak = 0.15243 (71)
mri peak = 0.07683 (84)
Left_Caudate (11): linear fit = 1.15 x + 0.0 (1590 voxels, overlap=0.149)
Left_Caudate (11): linear fit = 1.15 x + 0.0 (1590 voxels, peak = 82), gca=82.0
gca peak = 0.13336 (57)
mri peak = 0.03459 (65)
Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (26254 voxels, overlap=0.647)
Left_Cerebellum_Cortex (8): linear fit = 1.16 x + 0.0 (26254 voxels, peak = 66), gca=66.4
gca peak = 0.13252 (56)
mri peak = 0.03407 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.16 x + 0.0 (29149 voxels, overlap=0.442)
Right_Cerebellum_Cortex (47): linear fit = 1.16 x + 0.0 (29149 voxels, peak = 65), gca=65.2
gca peak = 0.18181 (84)
mri peak = 0.09733 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (11419 voxels, overlap=0.253)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (11419 voxels, peak = 91), gca=91.1
gca peak = 0.20573 (83)
mri peak = 0.07094 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (10039 voxels, overlap=0.457)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (10039 voxels, peak = 90), gca=90.1
gca peak = 0.21969 (57)
mri peak = 0.08019 (67)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (619 voxels, overlap=0.044)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (619 voxels, peak = 70), gca=69.8
gca peak = 0.39313 (56)
mri peak = 0.11955 (67)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (772 voxels, overlap=0.056)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (772 voxels, peak = 67), gca=67.5
gca peak = 0.14181 (85)
mri peak = 0.08274 (92)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (7487 voxels, overlap=0.627)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (7487 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.07051 (90)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (6207 voxels, overlap=0.693)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (6207 voxels, peak = 90), gca=90.1
gca peak = 0.13399 (79)
mri peak = 0.06373 (89)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (3358 voxels, overlap=0.490)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (3358 voxels, peak = 88), gca=88.1
gca peak = 0.14159 (79)
mri peak = 0.08376 (89)
Right_Putamen (51): linear fit = 1.14 x + 0.0 (3366 voxels, overlap=0.198)
Right_Putamen (51): linear fit = 1.14 x + 0.0 (3366 voxels, peak = 90), gca=90.5
gca peak = 0.10025 (80)
mri peak = 0.09599 (90)
Brain_Stem (16): linear fit = 1.14 x + 0.0 (14735 voxels, overlap=0.203)
Brain_Stem (16): linear fit = 1.14 x + 0.0 (14735 voxels, peak = 92), gca=91.6
gca peak = 0.13281 (86)
mri peak = 0.09045 (92)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1816 voxels, overlap=0.554)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1816 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.08134 (92)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (2215 voxels, overlap=0.427)
Left_VentralDC (28): linear fit = 1.10 x + 0.0 (2215 voxels, peak = 97), gca=97.5
gca peak = 0.20494 (23)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.15061 (21)
mri peak = 0.16254 (24)
Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (542 voxels, overlap=0.629)
Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (542 voxels, peak = 23), gca=23.0
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 1.20 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 1.34 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=0.662, neg=0, invalid=762
0106: dt=112.041995, rms=0.652 (1.489%), neg=0, invalid=762
0107: dt=129.472000, rms=0.650 (0.373%), neg=0, invalid=762
0108: dt=517.888000, rms=0.646 (0.582%), neg=0, invalid=762
0109: dt=369.920000, rms=0.643 (0.546%), neg=0, invalid=762
0110: dt=110.976000, rms=0.641 (0.249%), neg=0, invalid=762
0111: dt=129.472000, rms=0.641 (0.083%), neg=0, invalid=762
0112: dt=517.888000, rms=0.639 (0.224%), neg=0, invalid=762
0113: dt=92.480000, rms=0.638 (0.116%), neg=0, invalid=762
0114: dt=2071.552000, rms=0.635 (0.513%), neg=0, invalid=762
0115: dt=73.984000, rms=0.634 (0.227%), neg=0, invalid=762
0116: dt=92.480000, rms=0.634 (0.014%), neg=0, invalid=762
0117: dt=92.480000, rms=0.633 (0.019%), neg=0, invalid=762
0118: dt=92.480000, rms=0.633 (0.024%), neg=0, invalid=762
0119: dt=92.480000, rms=0.633 (0.037%), neg=0, invalid=762
0120: dt=92.480000, rms=0.633 (0.058%), neg=0, invalid=762
0121: dt=92.480000, rms=0.632 (0.085%), neg=0, invalid=762
0122: dt=92.480000, rms=0.632 (0.101%), neg=0, invalid=762
0123: dt=92.480000, rms=0.631 (0.109%), neg=0, invalid=762
0124: dt=92.480000, rms=0.630 (0.106%), neg=0, invalid=762
0125: dt=92.480000, rms=0.630 (0.092%), neg=0, invalid=762
0126: dt=92.480000, rms=0.629 (0.076%), neg=0, invalid=762
0127: dt=92.480000, rms=0.629 (0.074%), neg=0, invalid=762
0128: dt=92.480000, rms=0.628 (0.061%), neg=0, invalid=762
0129: dt=92.480000, rms=0.628 (0.059%), neg=0, invalid=762
0130: dt=92.480000, rms=0.627 (0.063%), neg=0, invalid=762
0131: dt=92.480000, rms=0.627 (0.060%), neg=0, invalid=762
0132: dt=92.480000, rms=0.627 (0.066%), neg=0, invalid=762
0133: dt=92.480000, rms=0.626 (0.068%), neg=0, invalid=762
0134: dt=92.480000, rms=0.626 (0.067%), neg=0, invalid=762
0135: dt=92.480000, rms=0.625 (0.062%), neg=0, invalid=762
0136: dt=92.480000, rms=0.625 (0.052%), neg=0, invalid=762
0137: dt=92.480000, rms=0.625 (0.054%), neg=0, invalid=762
0138: dt=92.480000, rms=0.624 (0.051%), neg=0, invalid=762
0139: dt=92.480000, rms=0.624 (0.051%), neg=0, invalid=762
0140: dt=92.480000, rms=0.624 (0.050%), neg=0, invalid=762
0141: dt=92.480000, rms=0.624 (0.046%), neg=0, invalid=762
0142: dt=92.480000, rms=0.623 (0.046%), neg=0, invalid=762
0143: dt=92.480000, rms=0.623 (0.045%), neg=0, invalid=762
0144: dt=92.480000, rms=0.623 (0.046%), neg=0, invalid=762
0145: dt=92.480000, rms=0.622 (0.045%), neg=0, invalid=762
0146: dt=92.480000, rms=0.622 (0.040%), neg=0, invalid=762
0147: dt=92.480000, rms=0.622 (0.042%), neg=0, invalid=762
0148: dt=92.480000, rms=0.622 (0.042%), neg=0, invalid=762
0149: dt=92.480000, rms=0.621 (0.039%), neg=0, invalid=762
0150: dt=92.480000, rms=0.621 (0.041%), neg=0, invalid=762
0151: dt=92.480000, rms=0.621 (0.036%), neg=0, invalid=762
0152: dt=92.480000, rms=0.621 (0.034%), neg=0, invalid=762
0153: dt=92.480000, rms=0.621 (0.028%), neg=0, invalid=762
0154: dt=92.480000, rms=0.620 (0.035%), neg=0, invalid=762
0155: dt=92.480000, rms=0.620 (0.032%), neg=0, invalid=762
0156: dt=92.480000, rms=0.620 (0.037%), neg=0, invalid=762
0157: dt=92.480000, rms=0.620 (0.036%), neg=0, invalid=762
0158: dt=92.480000, rms=0.619 (0.029%), neg=0, invalid=762
0159: dt=92.480000, rms=0.619 (0.033%), neg=0, invalid=762
0160: dt=92.480000, rms=0.619 (0.034%), neg=0, invalid=762
0161: dt=92.480000, rms=0.619 (0.024%), neg=0, invalid=762
0162: dt=92.480000, rms=0.619 (0.027%), neg=0, invalid=762
0163: dt=92.480000, rms=0.619 (0.034%), neg=0, invalid=762
0164: dt=92.480000, rms=0.618 (0.031%), neg=0, invalid=762
0165: dt=92.480000, rms=0.618 (0.030%), neg=0, invalid=762
0166: dt=92.480000, rms=0.618 (0.028%), neg=0, invalid=762
0167: dt=92.480000, rms=0.618 (0.027%), neg=0, invalid=762
0168: dt=92.480000, rms=0.618 (0.026%), neg=0, invalid=762
0169: dt=92.480000, rms=0.618 (0.025%), neg=0, invalid=762
0170: dt=92.480000, rms=0.617 (0.024%), neg=0, invalid=762
0171: dt=517.888000, rms=0.617 (0.017%), neg=0, invalid=762
0172: dt=517.888000, rms=0.617 (-0.091%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.618, neg=0, invalid=762
0173: dt=369.920000, rms=0.616 (0.265%), neg=0, invalid=762
0174: dt=129.472000, rms=0.616 (0.052%), neg=0, invalid=762
0175: dt=517.888000, rms=0.615 (0.036%), neg=0, invalid=762
0176: dt=517.888000, rms=0.615 (0.008%), neg=0, invalid=762
0177: dt=517.888000, rms=0.615 (-0.353%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.617, neg=0, invalid=762
0178: dt=102.966790, rms=0.614 (0.550%), neg=0, invalid=762
0179: dt=166.956522, rms=0.609 (0.779%), neg=0, invalid=762
0180: dt=62.208000, rms=0.606 (0.557%), neg=0, invalid=762
0181: dt=248.832000, rms=0.601 (0.757%), neg=0, invalid=762
0182: dt=77.837838, rms=0.598 (0.463%), neg=0, invalid=762
0183: dt=88.324723, rms=0.596 (0.322%), neg=0, invalid=762
0184: dt=98.698795, rms=0.595 (0.278%), neg=0, invalid=762
0185: dt=84.516746, rms=0.593 (0.241%), neg=0, invalid=762
0186: dt=103.680000, rms=0.592 (0.252%), neg=0, invalid=762
0187: dt=82.944000, rms=0.591 (0.195%), neg=0, invalid=762
0188: dt=103.680000, rms=0.589 (0.215%), neg=0, invalid=762
0189: dt=68.072727, rms=0.588 (0.174%), neg=0, invalid=762
0190: dt=145.152000, rms=0.587 (0.212%), neg=0, invalid=762
0191: dt=36.288000, rms=0.586 (0.132%), neg=0, invalid=762
0192: dt=145.152000, rms=0.585 (0.199%), neg=0, invalid=762
0193: dt=82.944000, rms=0.584 (0.167%), neg=0, invalid=762
0194: dt=82.944000, rms=0.583 (0.108%), neg=0, invalid=762
0195: dt=103.680000, rms=0.583 (0.150%), neg=0, invalid=762
0196: dt=69.900709, rms=0.582 (0.101%), neg=0, invalid=762
0197: dt=145.152000, rms=0.581 (0.144%), neg=0, invalid=762
0198: dt=36.288000, rms=0.581 (0.095%), neg=0, invalid=762
0199: dt=145.152000, rms=0.580 (0.149%), neg=0, invalid=762
0200: dt=82.944000, rms=0.579 (0.101%), neg=0, invalid=762
0201: dt=82.944000, rms=0.579 (0.090%), neg=0, invalid=762
0202: dt=82.944000, rms=0.578 (0.089%), neg=0, invalid=762
0203: dt=82.944000, rms=0.578 (0.081%), neg=0, invalid=762
0204: dt=82.944000, rms=0.577 (0.085%), neg=0, invalid=762
0205: dt=82.944000, rms=0.577 (0.082%), neg=0, invalid=762
0206: dt=103.680000, rms=0.576 (0.080%), neg=0, invalid=762
0207: dt=82.944000, rms=0.576 (0.081%), neg=0, invalid=762
0208: dt=62.208000, rms=0.575 (0.065%), neg=0, invalid=762
0209: dt=145.152000, rms=0.575 (0.082%), neg=0, invalid=762
0210: dt=36.288000, rms=0.575 (0.065%), neg=0, invalid=762
0211: dt=145.152000, rms=0.574 (0.088%), neg=0, invalid=762
0212: dt=36.288000, rms=0.574 (0.043%), neg=0, invalid=762
0213: dt=36.288000, rms=0.574 (0.036%), neg=0, invalid=762
0214: dt=36.288000, rms=0.573 (0.046%), neg=0, invalid=762
0215: dt=36.288000, rms=0.573 (0.071%), neg=0, invalid=762
0216: dt=36.288000, rms=0.572 (0.089%), neg=0, invalid=762
0217: dt=36.288000, rms=0.572 (0.102%), neg=0, invalid=762
0218: dt=36.288000, rms=0.571 (0.109%), neg=0, invalid=762
0219: dt=36.288000, rms=0.570 (0.118%), neg=0, invalid=762
0220: dt=36.288000, rms=0.570 (0.117%), neg=0, invalid=762
0221: dt=36.288000, rms=0.569 (0.123%), neg=0, invalid=762
0222: dt=36.288000, rms=0.568 (0.122%), neg=0, invalid=762
0223: dt=36.288000, rms=0.568 (0.117%), neg=0, invalid=762
0224: dt=36.288000, rms=0.567 (0.116%), neg=0, invalid=762
0225: dt=36.288000, rms=0.566 (0.120%), neg=0, invalid=762
0226: dt=36.288000, rms=0.566 (0.123%), neg=0, invalid=762
0227: dt=36.288000, rms=0.565 (0.123%), neg=0, invalid=762
0228: dt=36.288000, rms=0.564 (0.113%), neg=0, invalid=762
0229: dt=36.288000, rms=0.564 (0.111%), neg=0, invalid=762
0230: dt=36.288000, rms=0.563 (0.099%), neg=0, invalid=762
0231: dt=36.288000, rms=0.563 (0.088%), neg=0, invalid=762
0232: dt=36.288000, rms=0.563 (0.010%), neg=0, invalid=762
0233: dt=36.288000, rms=0.563 (0.016%), neg=0, invalid=762
0234: dt=36.288000, rms=0.562 (0.022%), neg=0, invalid=762
0235: dt=36.288000, rms=0.562 (0.029%), neg=0, invalid=762
0236: dt=36.288000, rms=0.562 (0.038%), neg=0, invalid=762
0237: dt=36.288000, rms=0.562 (0.043%), neg=0, invalid=762
0238: dt=36.288000, rms=0.562 (0.045%), neg=0, invalid=762
0239: dt=36.288000, rms=0.561 (0.053%), neg=0, invalid=762
0240: dt=36.288000, rms=0.561 (0.052%), neg=0, invalid=762
0241: dt=36.288000, rms=0.561 (0.057%), neg=0, invalid=762
0242: dt=36.288000, rms=0.560 (0.053%), neg=0, invalid=762
0243: dt=36.288000, rms=0.560 (0.056%), neg=0, invalid=762
0244: dt=36.288000, rms=0.560 (0.056%), neg=0, invalid=762
0245: dt=36.288000, rms=0.559 (0.058%), neg=0, invalid=762
0246: dt=36.288000, rms=0.559 (0.062%), neg=0, invalid=762
0247: dt=36.288000, rms=0.559 (0.074%), neg=0, invalid=762
0248: dt=36.288000, rms=0.558 (0.074%), neg=0, invalid=762
0249: dt=36.288000, rms=0.558 (0.004%), neg=0, invalid=762
0250: dt=36.288000, rms=0.558 (0.011%), neg=0, invalid=762
0251: dt=36.288000, rms=0.558 (0.013%), neg=0, invalid=762
0252: dt=9.072000, rms=0.558 (0.006%), neg=0, invalid=762
0253: dt=2.268000, rms=0.558 (0.000%), neg=0, invalid=762
0254: dt=0.283500, rms=0.558 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.558, neg=0, invalid=762
0255: dt=145.152000, rms=0.556 (0.512%), neg=0, invalid=762
0256: dt=103.680000, rms=0.555 (0.071%), neg=0, invalid=762
0257: dt=248.832000, rms=0.554 (0.163%), neg=0, invalid=762
0258: dt=62.208000, rms=0.554 (0.077%), neg=0, invalid=762
0259: dt=145.152000, rms=0.554 (0.041%), neg=0, invalid=762
0260: dt=145.152000, rms=0.553 (0.050%), neg=0, invalid=762
0261: dt=145.152000, rms=0.553 (0.072%), neg=0, invalid=762
0262: dt=145.152000, rms=0.552 (0.187%), neg=0, invalid=762
0263: dt=145.152000, rms=0.551 (0.150%), neg=0, invalid=762
0264: dt=145.152000, rms=0.551 (0.061%), neg=0, invalid=762
0265: dt=145.152000, rms=0.550 (0.147%), neg=0, invalid=762
0266: dt=145.152000, rms=0.549 (0.137%), neg=0, invalid=762
0267: dt=145.152000, rms=0.549 (0.120%), neg=0, invalid=762
0268: dt=145.152000, rms=0.548 (0.177%), neg=0, invalid=762
0269: dt=145.152000, rms=0.547 (0.097%), neg=0, invalid=762
0270: dt=145.152000, rms=0.546 (0.144%), neg=0, invalid=762
0271: dt=145.152000, rms=0.546 (0.129%), neg=0, invalid=762
0272: dt=145.152000, rms=0.545 (0.126%), neg=0, invalid=762
0273: dt=145.152000, rms=0.544 (0.101%), neg=0, invalid=762
0274: dt=145.152000, rms=0.544 (0.095%), neg=0, invalid=762
0275: dt=145.152000, rms=0.543 (0.123%), neg=0, invalid=762
0276: dt=145.152000, rms=0.543 (0.095%), neg=0, invalid=762
0277: dt=145.152000, rms=0.542 (0.066%), neg=0, invalid=762
0278: dt=145.152000, rms=0.542 (0.120%), neg=0, invalid=762
0279: dt=145.152000, rms=0.541 (0.069%), neg=0, invalid=762
0280: dt=145.152000, rms=0.541 (0.107%), neg=0, invalid=762
0281: dt=145.152000, rms=0.540 (0.081%), neg=0, invalid=762
0282: dt=145.152000, rms=0.540 (0.065%), neg=0, invalid=762
0283: dt=145.152000, rms=0.539 (0.095%), neg=0, invalid=762
0284: dt=145.152000, rms=0.539 (-0.095%), neg=0, invalid=762
0285: dt=36.288000, rms=0.539 (0.013%), neg=0, invalid=762
0286: dt=36.288000, rms=0.539 (0.004%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.550, neg=0, invalid=762
0287: dt=25.600000, rms=0.548 (0.275%), neg=0, invalid=762
0288: dt=44.800000, rms=0.546 (0.274%), neg=0, invalid=762
0289: dt=128.000000, rms=0.542 (0.747%), neg=0, invalid=762
0290: dt=44.800000, rms=0.540 (0.401%), neg=0, invalid=762
0291: dt=44.800000, rms=0.538 (0.327%), neg=0, invalid=762
0292: dt=32.000000, rms=0.537 (0.282%), neg=0, invalid=762
0293: dt=44.800000, rms=0.536 (0.199%), neg=0, invalid=762
0294: dt=38.400000, rms=0.535 (0.227%), neg=0, invalid=762
0295: dt=32.000000, rms=0.534 (0.150%), neg=0, invalid=762
0296: dt=44.800000, rms=0.533 (0.187%), neg=0, invalid=762
0297: dt=32.000000, rms=0.532 (0.125%), neg=0, invalid=762
0298: dt=44.800000, rms=0.531 (0.179%), neg=0, invalid=762
0299: dt=32.000000, rms=0.531 (0.095%), neg=0, invalid=762
0300: dt=38.400000, rms=0.530 (0.153%), neg=0, invalid=762
0301: dt=25.600000, rms=0.530 (0.076%), neg=0, invalid=762
0302: dt=44.800000, rms=0.529 (0.141%), neg=0, invalid=762
0303: dt=25.600000, rms=0.528 (0.063%), neg=0, invalid=762
0304: dt=44.800000, rms=0.528 (0.113%), neg=0, invalid=762
0305: dt=25.600000, rms=0.528 (0.057%), neg=0, invalid=762
0306: dt=44.800000, rms=0.527 (0.114%), neg=0, invalid=762
0307: dt=25.600000, rms=0.527 (0.048%), neg=0, invalid=762
0308: dt=25.600000, rms=0.526 (0.086%), neg=0, invalid=762
0309: dt=25.600000, rms=0.526 (0.091%), neg=0, invalid=762
0310: dt=25.600000, rms=0.525 (0.135%), neg=0, invalid=762
0311: dt=25.600000, rms=0.525 (0.059%), neg=0, invalid=762
0312: dt=25.600000, rms=0.524 (0.078%), neg=0, invalid=762
0313: dt=25.600000, rms=0.524 (0.119%), neg=0, invalid=762
0314: dt=25.600000, rms=0.523 (0.042%), neg=0, invalid=762
0315: dt=25.600000, rms=0.523 (0.072%), neg=0, invalid=762
0316: dt=25.600000, rms=0.523 (0.034%), neg=0, invalid=762
0317: dt=25.600000, rms=0.523 (0.039%), neg=0, invalid=762
0318: dt=0.800000, rms=0.523 (0.001%), neg=0, invalid=762
0319: dt=0.400000, rms=0.523 (-0.001%), neg=0, invalid=762
0320: dt=0.175000, rms=0.523 (0.000%), neg=0, invalid=762
0321: dt=0.175000, rms=0.523 (0.001%), neg=0, invalid=762
0322: dt=0.043750, rms=0.523 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.523, neg=0, invalid=762
0323: dt=44.800000, rms=0.520 (0.505%), neg=0, invalid=762
0324: dt=38.400000, rms=0.520 (0.095%), neg=0, invalid=762
0325: dt=25.600000, rms=0.520 (0.061%), neg=0, invalid=762
0326: dt=38.400000, rms=0.519 (0.070%), neg=0, invalid=762
0327: dt=25.600000, rms=0.519 (0.030%), neg=0, invalid=762
0328: dt=25.600000, rms=0.519 (0.042%), neg=0, invalid=762
0329: dt=25.600000, rms=0.519 (0.049%), neg=0, invalid=762
0330: dt=25.600000, rms=0.518 (0.052%), neg=0, invalid=762
0331: dt=25.600000, rms=0.518 (0.053%), neg=0, invalid=762
0332: dt=25.600000, rms=0.518 (0.058%), neg=0, invalid=762
0333: dt=25.600000, rms=0.517 (0.069%), neg=0, invalid=762
0334: dt=25.600000, rms=0.517 (0.087%), neg=0, invalid=762
0335: dt=25.600000, rms=0.516 (0.121%), neg=0, invalid=762
0336: dt=25.600000, rms=0.516 (0.133%), neg=0, invalid=762
0337: dt=25.600000, rms=0.515 (0.148%), neg=0, invalid=762
0338: dt=25.600000, rms=0.514 (0.160%), neg=0, invalid=762
0339: dt=25.600000, rms=0.513 (0.181%), neg=0, invalid=762
0340: dt=25.600000, rms=0.512 (0.166%), neg=0, invalid=762
0341: dt=25.600000, rms=0.512 (0.159%), neg=0, invalid=762
0342: dt=25.600000, rms=0.511 (0.156%), neg=0, invalid=762
0343: dt=25.600000, rms=0.510 (0.141%), neg=0, invalid=762
0344: dt=25.600000, rms=0.509 (0.135%), neg=0, invalid=762
0345: dt=25.600000, rms=0.509 (0.100%), neg=0, invalid=762
0346: dt=25.600000, rms=0.508 (0.109%), neg=0, invalid=762
0347: dt=25.600000, rms=0.508 (0.067%), neg=0, invalid=762
0348: dt=25.600000, rms=0.508 (0.073%), neg=0, invalid=762
0349: dt=25.600000, rms=0.507 (0.058%), neg=0, invalid=762
0350: dt=25.600000, rms=0.507 (0.074%), neg=0, invalid=762
0351: dt=25.600000, rms=0.507 (0.058%), neg=0, invalid=762
0352: dt=25.600000, rms=0.507 (0.017%), neg=0, invalid=762
0353: dt=25.600000, rms=0.506 (0.015%), neg=0, invalid=762
0354: dt=25.600000, rms=0.506 (0.036%), neg=0, invalid=762
0355: dt=11.200000, rms=0.506 (0.000%), neg=0, invalid=762
0356: dt=11.200000, rms=0.506 (0.002%), neg=0, invalid=762
0357: dt=11.200000, rms=0.506 (0.007%), neg=0, invalid=762
0358: dt=11.200000, rms=0.506 (0.006%), neg=0, invalid=762
0359: dt=11.200000, rms=0.506 (0.008%), neg=0, invalid=762
0360: dt=11.200000, rms=0.506 (0.007%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.528, neg=0, invalid=762
0361: dt=0.000000, rms=0.528 (0.069%), neg=0, invalid=762
0362: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=762
0363: dt=0.150000, rms=0.528 (-0.016%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.528, neg=0, invalid=762
0364: dt=0.000000, rms=0.528 (0.069%), neg=0, invalid=762
0365: dt=0.000000, rms=0.528 (0.000%), neg=0, invalid=762
0366: dt=0.150000, rms=0.528 (-0.016%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.571, neg=0, invalid=762
0367: dt=1.536000, rms=0.567 (0.661%), neg=0, invalid=762
0368: dt=0.112000, rms=0.567 (0.008%), neg=0, invalid=762
0369: dt=0.112000, rms=0.567 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.567, neg=0, invalid=762
0370: dt=0.768000, rms=0.566 (0.160%), neg=0, invalid=762
0371: dt=0.256000, rms=0.566 (0.009%), neg=0, invalid=762
0372: dt=0.256000, rms=0.566 (-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=0.519, neg=0, invalid=762
0373: dt=0.448000, rms=0.507 (2.383%), neg=0, invalid=762
0374: dt=0.448000, rms=0.504 (0.540%), neg=0, invalid=762
0375: dt=0.448000, rms=0.502 (0.316%), neg=0, invalid=762
0376: dt=0.448000, rms=0.501 (0.197%), neg=0, invalid=762
0377: dt=0.448000, rms=0.500 (0.141%), neg=0, invalid=762
0378: dt=0.448000, rms=0.500 (0.110%), neg=0, invalid=762
0379: dt=0.448000, rms=0.500 (0.082%), neg=0, invalid=762
0380: dt=0.448000, rms=0.499 (0.071%), neg=0, invalid=762
0381: dt=0.448000, rms=0.499 (0.054%), neg=0, invalid=762
0382: dt=0.448000, rms=0.499 (0.050%), neg=0, invalid=762
0383: dt=0.448000, rms=0.498 (0.036%), neg=0, invalid=762
0384: dt=0.448000, rms=0.498 (0.040%), neg=0, invalid=762
0385: dt=0.448000, rms=0.498 (0.054%), neg=0, invalid=762
0386: dt=0.448000, rms=0.498 (0.074%), neg=0, invalid=762
0387: dt=0.448000, rms=0.497 (0.078%), neg=0, invalid=762
0388: dt=0.448000, rms=0.497 (0.005%), neg=0, invalid=762
0389: dt=0.448000, rms=0.497 (0.007%), neg=0, invalid=762
0390: dt=0.448000, rms=0.497 (0.011%), neg=0, invalid=762
0391: dt=0.448000, rms=0.497 (0.010%), neg=0, invalid=762
0392: dt=0.448000, rms=0.497 (0.006%), neg=0, invalid=762
0393: dt=0.448000, rms=0.497 (0.009%), neg=0, invalid=762
0394: dt=0.448000, rms=0.497 (0.007%), neg=0, invalid=762
0395: dt=0.448000, rms=0.497 (0.009%), neg=0, invalid=762
0396: dt=0.448000, rms=0.497 (0.009%), neg=0, invalid=762
0397: dt=0.448000, rms=0.497 (0.010%), neg=0, invalid=762
0398: dt=0.448000, rms=0.497 (0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.497, neg=0, invalid=762
0399: dt=0.448000, rms=0.492 (1.081%), neg=0, invalid=762
0400: dt=0.500000, rms=0.491 (0.170%), neg=0, invalid=762
0401: dt=0.448000, rms=0.491 (0.030%), neg=0, invalid=762
0402: dt=0.448000, rms=0.491 (0.008%), neg=0, invalid=762
0403: dt=0.448000, rms=0.491 (0.008%), neg=0, invalid=762
0404: dt=0.448000, rms=0.491 (0.002%), neg=0, invalid=762
0405: dt=0.000000, rms=0.491 (-0.001%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.489, neg=0, invalid=762
0406: dt=0.000000, rms=0.489 (0.085%), neg=0, invalid=762
0407: dt=0.000000, rms=0.489 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.489, neg=0, invalid=762
0408: dt=129.472000, rms=0.488 (0.131%), neg=0, invalid=762
0409: dt=369.920000, rms=0.488 (0.057%), neg=0, invalid=762
0410: dt=369.920000, rms=0.488 (-0.715%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.488, neg=0, invalid=762
0411: dt=25.920000, rms=0.488 (0.137%), neg=0, invalid=762
0412: dt=15.552000, rms=0.488 (0.007%), neg=0, invalid=762
0413: dt=15.552000, rms=0.488 (0.006%), neg=0, invalid=762
0414: dt=15.552000, rms=0.488 (-0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.488, neg=0, invalid=762
0415: dt=124.416000, rms=0.486 (0.461%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0416: dt=36.288000, rms=0.485 (0.100%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0417: dt=36.288000, rms=0.485 (0.047%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0418: dt=36.288000, rms=0.485 (0.064%), neg=0, invalid=762
0419: dt=36.288000, rms=0.484 (0.091%), neg=0, invalid=762
0420: dt=36.288000, rms=0.484 (0.107%), neg=0, invalid=762
0421: dt=36.288000, rms=0.483 (0.112%), neg=0, invalid=762
0422: dt=36.288000, rms=0.483 (0.108%), neg=0, invalid=762
0423: dt=36.288000, rms=0.483 (0.077%), neg=0, invalid=762
0424: dt=124.416000, rms=0.482 (0.029%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0425: dt=31.587983, rms=0.481 (0.445%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0426: dt=44.800000, rms=0.479 (0.355%), neg=0, invalid=762
0427: dt=25.600000, rms=0.478 (0.223%), neg=0, invalid=762
0428: dt=25.600000, rms=0.477 (0.198%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
0429: dt=25.600000, rms=0.476 (0.209%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0430: dt=25.600000, rms=0.475 (0.221%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 4 iterations, nbhd size=0, neg = 0
0431: dt=25.600000, rms=0.474 (0.172%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 4 iterations, nbhd size=0, neg = 0
0432: dt=25.600000, rms=0.474 (0.108%), neg=0, invalid=762
iter 0, gcam->neg = 17
after 13 iterations, nbhd size=1, neg = 0
0433: dt=25.600000, rms=0.473 (0.116%), neg=0, invalid=762
iter 0, gcam->neg = 16
after 13 iterations, nbhd size=1, neg = 0
0434: dt=25.600000, rms=0.473 (0.131%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 12 iterations, nbhd size=1, neg = 0
0435: dt=25.600000, rms=0.472 (0.135%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 6 iterations, nbhd size=0, neg = 0
0436: dt=25.600000, rms=0.472 (0.108%), neg=0, invalid=762
iter 0, gcam->neg = 13
after 7 iterations, nbhd size=0, neg = 0
0437: dt=25.600000, rms=0.471 (0.116%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 5 iterations, nbhd size=0, neg = 0
0438: dt=25.600000, rms=0.470 (0.117%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 3 iterations, nbhd size=0, neg = 0
0439: dt=25.600000, rms=0.470 (0.091%), neg=0, invalid=762
0440: dt=44.800000, rms=0.470 (0.092%), neg=0, invalid=762
0441: dt=25.600000, rms=0.469 (0.040%), neg=0, invalid=762
0442: dt=25.600000, rms=0.469 (0.042%), neg=0, invalid=762
0443: dt=25.600000, rms=0.469 (0.052%), neg=0, invalid=762
0444: dt=25.600000, rms=0.469 (0.060%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0445: dt=25.600000, rms=0.468 (0.066%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0446: dt=25.600000, rms=0.468 (0.039%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0447: dt=25.600000, rms=0.468 (0.017%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
0448: dt=54.832432, rms=0.464 (0.931%), neg=0, invalid=762
0449: dt=25.600000, rms=0.463 (0.290%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0450: dt=32.000000, rms=0.462 (0.200%), neg=0, invalid=762
0451: dt=32.000000, rms=0.462 (0.077%), neg=0, invalid=762
0452: dt=32.000000, rms=0.461 (0.249%), neg=0, invalid=762
0453: dt=32.000000, rms=0.460 (0.102%), neg=0, invalid=762
0454: dt=32.000000, rms=0.459 (0.178%), neg=0, invalid=762
0455: dt=32.000000, rms=0.459 (-0.092%), neg=0, invalid=762
0456: dt=11.200000, rms=0.459 (0.038%), neg=0, invalid=762
0457: dt=44.800000, rms=0.459 (0.062%), neg=0, invalid=762
0458: dt=25.600000, rms=0.459 (0.029%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.466, neg=0, invalid=762
0459: dt=2.000000, rms=0.465 (0.106%), neg=0, invalid=762
0460: dt=0.252000, rms=0.465 (0.001%), neg=0, invalid=762
0461: dt=0.252000, rms=0.465 (0.001%), neg=0, invalid=762
0462: dt=0.252000, rms=0.465 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.466, neg=0, invalid=762
0463: dt=8.000000, rms=0.465 (0.228%), neg=0, invalid=762
0464: dt=8.000000, rms=0.464 (0.053%), neg=0, invalid=762
0465: dt=8.000000, rms=0.464 (0.064%), neg=0, invalid=762
0466: dt=8.000000, rms=0.464 (0.022%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
0467: dt=8.000000, rms=0.464 (-0.032%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
0468: dt=0.000000, rms=0.469 (0.090%), neg=0, invalid=762
0469: dt=0.000000, rms=0.469 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.469, neg=0, invalid=762
0470: dt=0.000000, rms=0.469 (0.090%), neg=0, invalid=762
0471: dt=0.000000, rms=0.469 (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=0.461, neg=0, invalid=762
iter 0, gcam->neg = 373
after 14 iterations, nbhd size=1, neg = 0
0472: dt=2.066333, rms=0.436 (5.446%), neg=0, invalid=762
0473: dt=0.064000, rms=0.436 (0.039%), neg=0, invalid=762
0474: dt=0.064000, rms=0.436 (-0.031%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.436, neg=0, invalid=762
0475: dt=0.096000, rms=0.436 (0.183%), neg=0, invalid=762
0476: dt=0.001750, rms=0.436 (-0.005%), 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=0.423, neg=0, invalid=762
0477: dt=0.000000, rms=0.423 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.423, neg=0, invalid=762
0478: dt=32.368000, rms=0.423 (0.002%), neg=0, invalid=762
0479: dt=32.368000, rms=0.423 (0.001%), neg=0, invalid=762
0480: dt=32.368000, rms=0.423 (0.000%), neg=0, invalid=762
0481: dt=32.368000, rms=0.423 (-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=0.423, neg=0, invalid=762
0482: dt=0.000000, rms=0.423 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.423, neg=0, invalid=762
0483: dt=82.944000, rms=0.423 (0.045%), neg=0, invalid=762
0484: dt=145.152000, rms=0.423 (0.044%), neg=0, invalid=762
0485: dt=145.152000, rms=0.423 (-0.039%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.423, neg=0, invalid=762
0486: dt=8.000000, rms=0.423 (0.036%), neg=0, invalid=762
0487: dt=2.800000, rms=0.423 (0.005%), neg=0, invalid=762
0488: dt=2.800000, rms=0.423 (0.002%), neg=0, invalid=762
0489: dt=2.800000, rms=0.423 (-0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.423, neg=0, invalid=762
0490: dt=81.411765, rms=0.420 (0.635%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0491: dt=24.513208, rms=0.419 (0.298%), neg=0, invalid=762
0492: dt=44.800000, rms=0.419 (0.132%), neg=0, invalid=762
0493: dt=44.800000, rms=0.418 (0.097%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0494: dt=44.800000, rms=0.417 (0.251%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0495: dt=44.800000, rms=0.416 (0.192%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0496: dt=44.800000, rms=0.416 (0.213%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
0497: dt=44.800000, rms=0.415 (0.178%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 10 iterations, nbhd size=1, neg = 0
0498: dt=44.800000, rms=0.414 (0.137%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0499: dt=44.800000, rms=0.414 (0.148%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0500: dt=44.800000, rms=0.413 (0.074%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0501: dt=44.800000, rms=0.413 (0.087%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0502: dt=44.800000, rms=0.413 (0.075%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0503: dt=25.600000, rms=0.413 (0.019%), neg=0, invalid=762
0504: dt=25.600000, rms=0.413 (0.016%), neg=0, invalid=762
0505: dt=25.600000, rms=0.412 (0.017%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0506: dt=25.600000, rms=0.412 (0.017%), neg=0, invalid=762
0507: dt=25.600000, rms=0.412 (0.007%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.417, neg=0, invalid=762
0508: dt=0.000000, rms=0.417 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.417, neg=0, invalid=762
0509: dt=4.032000, rms=0.417 (0.032%), neg=0, invalid=762
0510: dt=2.304000, rms=0.417 (0.007%), neg=0, invalid=762
0511: dt=2.304000, rms=0.417 (0.001%), neg=0, invalid=762
0512: dt=2.304000, rms=0.417 (-0.016%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.424, neg=0, invalid=762
0513: dt=0.000000, rms=0.424 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.424, neg=0, invalid=762
0514: dt=0.000000, rms=0.424 (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=0.411, neg=0, invalid=762
iter 0, gcam->neg = 386
after 12 iterations, nbhd size=1, neg = 0
0515: dt=1.340194, rms=0.402 (2.363%), neg=0, invalid=762
0516: dt=0.000013, rms=0.402 (0.000%), neg=0, invalid=762
0517: dt=0.000013, rms=0.402 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.402, neg=0, invalid=762
0518: dt=0.112000, rms=0.401 (0.055%), neg=0, invalid=762
0519: dt=0.064000, rms=0.401 (0.009%), neg=0, invalid=762
0520: dt=0.064000, rms=0.401 (0.001%), neg=0, invalid=762
0521: dt=0.064000, rms=0.401 (-0.030%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 36 minutes and 55 seconds.
mri_ca_register utimesec    10337.722427
mri_ca_register stimesec    9.350578
mri_ca_register ru_maxrss   1349404
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   5386001
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63496
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    4369
mri_ca_register ru_nivcsw   13862
FSRUNTIME@ mri_ca_register  2.6152 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 22:45:12 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-951
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-6.0.0/0050244/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 8.78
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 = 0.14588 (26)
Left_Lateral_Ventricle (4): linear fit = 1.37 x + 0.0 (1177 voxels, overlap=0.256)
Left_Lateral_Ventricle (4): linear fit = 1.37 x + 0.0 (1177 voxels, peak = 27), gca=27.3
gca peak = 0.17677 (13)
mri peak = 0.13026 (26)
Right_Lateral_Ventricle (43): linear fit = 1.88 x + 0.0 (1950 voxels, overlap=0.282)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1950 voxels, peak = 25), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.12772 (95)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1102 voxels, overlap=1.006)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1102 voxels, peak = 96), gca=96.4
gca peak = 0.16930 (96)
mri peak = 0.12254 (99)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1056 voxels, overlap=0.863)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (1056 voxels, peak = 98), gca=98.4
gca peak = 0.24553 (55)
mri peak = 0.08674 (70)
Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1596 voxels, overlap=0.020)
Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1596 voxels, peak = 67), gca=67.4
gca peak = 0.30264 (59)
mri peak = 0.08679 (68)
Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (1578 voxels, overlap=0.136)
Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (1578 voxels, peak = 68), gca=67.6
gca peak = 0.07580 (103)
mri peak = 0.12632 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (62868 voxels, overlap=0.597)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (62868 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.12500 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (69022 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (69022 voxels, peak = 105), gca=104.5
gca peak = 0.09712 (58)
mri peak = 0.04634 (68)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (56607 voxels, overlap=0.545)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (56607 voxels, peak = 69), gca=68.7
gca peak = 0.11620 (58)
mri peak = 0.04783 (72)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (55960 voxels, overlap=0.548)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (55960 voxels, peak = 69), gca=69.3
gca peak = 0.30970 (66)
mri peak = 0.11556 (82)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1549 voxels, overlap=0.023)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1549 voxels, peak = 80), gca=79.5
gca peak = 0.15280 (69)
mri peak = 0.10440 (84)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (1587 voxels, overlap=0.214)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (1587 voxels, peak = 78), gca=77.6
gca peak = 0.13902 (56)
mri peak = 0.04822 (63)
Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (28250 voxels, overlap=0.721)
Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (28250 voxels, peak = 65), gca=64.7
gca peak = 0.14777 (55)
mri peak = 0.04866 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (27855 voxels, overlap=0.721)
Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (27855 voxels, peak = 64), gca=63.5
gca peak = 0.16765 (84)
mri peak = 0.11762 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9298 voxels, overlap=0.405)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9298 voxels, peak = 89), gca=89.5
gca peak = 0.18739 (84)
mri peak = 0.11414 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (8950 voxels, overlap=0.466)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (8950 voxels, peak = 90), gca=90.3
gca peak = 0.29869 (57)
mri peak = 0.10516 (70)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (1053 voxels, overlap=0.061)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (1053 voxels, peak = 68), gca=67.5
gca peak = 0.33601 (57)
mri peak = 0.09787 (67)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (1032 voxels, overlap=0.057)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (1032 voxels, peak = 68), gca=67.5
gca peak = 0.11131 (90)
mri peak = 0.07771 (92)
Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (7578 voxels, overlap=0.833)
Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (7578 voxels, peak = 93), gca=93.1
gca peak = 0.11793 (83)
mri peak = 0.07767 (92)
Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (6957 voxels, overlap=0.680)
Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (6957 voxels, peak = 91), gca=90.9
gca peak = 0.08324 (81)
mri peak = 0.08791 (89)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (2966 voxels, overlap=0.428)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (2966 voxels, peak = 90), gca=90.3
gca peak = 0.10360 (77)
mri peak = 0.09372 (89)
Right_Putamen (51): linear fit = 1.12 x + 0.0 (3099 voxels, overlap=0.377)
Right_Putamen (51): linear fit = 1.12 x + 0.0 (3099 voxels, peak = 87), gca=86.6
gca peak = 0.08424 (78)
mri peak = 0.09955 (88)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (19294 voxels, overlap=0.414)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (19294 voxels, peak = 86), gca=86.2
gca peak = 0.12631 (89)
mri peak = 0.09150 (92)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (2608 voxels, overlap=0.561)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (2608 voxels, peak = 97), gca=96.6
gca peak = 0.14500 (87)
mri peak = 0.09054 (94)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2534 voxels, overlap=0.584)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2534 voxels, peak = 93), gca=92.7
gca peak = 0.14975 (24)
mri peak = 0.14405 (26)
gca peak = 0.19357 (14)
mri peak = 0.17500 (24)
Fourth_Ventricle (15): linear fit = 1.46 x + 0.0 (160 voxels, overlap=0.280)
Fourth_Ventricle (15): linear fit = 1.46 x + 0.0 (160 voxels, peak = 20), gca=20.4
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak 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 1.19 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 1.44 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16119 (25)
mri peak = 0.14588 (26)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1177 voxels, overlap=0.765)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (1177 voxels, peak = 25), gca=25.4
gca peak = 0.13997 (19)
mri peak = 0.13026 (26)
Right_Lateral_Ventricle (43): linear fit = 1.24 x + 0.0 (1950 voxels, overlap=0.552)
Right_Lateral_Ventricle (43): linear fit = 1.24 x + 0.0 (1950 voxels, peak = 23), gca=23.5
gca peak = 0.25969 (97)
mri peak = 0.12772 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1102 voxels, overlap=1.004)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1102 voxels, peak = 97), gca=96.5
gca peak = 0.16585 (97)
mri peak = 0.12254 (99)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1056 voxels, overlap=1.000)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1056 voxels, peak = 97), gca=97.5
gca peak = 0.25345 (68)
mri peak = 0.08674 (70)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1596 voxels, overlap=0.979)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (1596 voxels, peak = 67), gca=67.0
gca peak = 0.22435 (64)
mri peak = 0.08679 (68)
Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1578 voxels, overlap=1.007)
Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1578 voxels, peak = 65), gca=65.0
gca peak = 0.07767 (104)
mri peak = 0.12632 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (62868 voxels, overlap=0.662)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (62868 voxels, peak = 104), gca=104.0
gca peak = 0.07908 (105)
mri peak = 0.12500 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (69022 voxels, overlap=0.636)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (69022 voxels, peak = 105), gca=105.0
gca peak = 0.08216 (69)
mri peak = 0.04634 (68)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (56607 voxels, overlap=0.946)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (56607 voxels, peak = 68), gca=68.0
gca peak = 0.09972 (69)
mri peak = 0.04783 (72)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (55960 voxels, overlap=0.935)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (55960 voxels, peak = 68), gca=68.0
gca peak = 0.21551 (80)
mri peak = 0.11556 (82)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1549 voxels, overlap=1.004)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1549 voxels, peak = 80), gca=80.0
gca peak = 0.16640 (87)
mri peak = 0.10440 (84)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (1587 voxels, overlap=0.977)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (1587 voxels, peak = 88), gca=88.3
gca peak = 0.12579 (65)
mri peak = 0.04822 (63)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (28250 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (28250 voxels, peak = 64), gca=64.0
gca peak = 0.13054 (63)
mri peak = 0.04866 (63)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27855 voxels, overlap=0.995)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (27855 voxels, peak = 62), gca=62.1
gca peak = 0.15888 (90)
mri peak = 0.11762 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (9298 voxels, overlap=0.865)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (9298 voxels, peak = 91), gca=91.3
gca peak = 0.14842 (90)
mri peak = 0.11414 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8950 voxels, overlap=0.893)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8950 voxels, peak = 90), gca=89.6
gca peak = 0.29148 (69)
mri peak = 0.10516 (70)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (1053 voxels, overlap=1.024)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (1053 voxels, peak = 69), gca=69.0
gca peak = 0.32128 (68)
mri peak = 0.09787 (67)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (1032 voxels, overlap=1.015)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (1032 voxels, peak = 68), gca=68.0
gca peak = 0.11142 (93)
mri peak = 0.07771 (92)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (7578 voxels, overlap=0.941)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (7578 voxels, peak = 93), gca=92.5
gca peak = 0.09484 (88)
mri peak = 0.07767 (92)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (6957 voxels, overlap=0.928)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (6957 voxels, peak = 87), gca=86.7
gca peak = 0.08274 (92)
mri peak = 0.08791 (89)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2966 voxels, overlap=0.861)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2966 voxels, peak = 91), gca=90.6
gca peak = 0.08246 (88)
mri peak = 0.09372 (89)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (3099 voxels, overlap=0.855)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (3099 voxels, peak = 88), gca=87.6
gca peak = 0.07221 (90)
mri peak = 0.09955 (88)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (19294 voxels, overlap=0.756)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (19294 voxels, peak = 90), gca=89.6
gca peak = 0.11733 (95)
mri peak = 0.09150 (92)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2608 voxels, overlap=0.826)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2608 voxels, peak = 95), gca=94.5
gca peak = 0.14580 (92)
mri peak = 0.09054 (94)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (2534 voxels, overlap=0.877)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (2534 voxels, peak = 93), gca=93.4
gca peak = 0.12333 (37)
mri peak = 0.14405 (26)
gca peak = 0.15108 (21)
mri peak = 0.17500 (24)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (160 voxels, overlap=0.694)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (160 voxels, peak = 22), gca=21.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16611 (31)
gca peak Left_Thalamus = 0.36646 (102)
gca peak Third_Ventricle = 0.12333 (37)
gca peak CSF = 0.17785 (52)
gca peak Left_Accumbens_area = 0.77242 (70)
gca peak Left_undetermined = 0.95280 (31)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12536 (35)
gca peak Right_Inf_Lat_Vent = 0.20093 (28)
gca peak Right_Accumbens_area = 0.29889 (78)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14504 (37)
gca peak Fifth_Ventricle = 0.51780 (44)
gca peak WM_hypointensities = 0.08488 (77)
gca peak non_WM_hypointensities = 0.12165 (55)
gca peak Optic_Chiasm = 0.70875 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.09 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
93542 voxels changed in iteration 0 of unlikely voxel relabeling
270 voxels changed in iteration 1 of unlikely voxel relabeling
6 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
64649 gm and wm labels changed (%25 to gray, %75 to white out of all changed labels)
478 hippocampal voxels changed.
2 amygdala voxels changed.
pass 1: 89200 changed. image ll: -2.176, PF=0.500
pass 2: 24818 changed. image ll: -2.175, PF=0.500
pass 3: 7479 changed.
pass 4: 2715 changed.
68751 voxels changed in iteration 0 of unlikely voxel relabeling
413 voxels changed in iteration 1 of unlikely voxel relabeling
28 voxels changed in iteration 2 of unlikely voxel relabeling
8 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
8415 voxels changed in iteration 0 of unlikely voxel relabeling
100 voxels changed in iteration 1 of unlikely voxel relabeling
5 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
7357 voxels changed in iteration 0 of unlikely voxel relabeling
72 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
6923 voxels changed in iteration 0 of unlikely voxel relabeling
40 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
1 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    4530.647236
mri_ca_label stimesec    1.320799
mri_ca_label ru_maxrss   2108436
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   691439
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  568
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    284
mri_ca_label ru_nivcsw   5717
auto-labeling took 74 minutes and 44 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/transforms/cc_up.lta 0050244 

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-6.0.0/0050244/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/norm.mgz
38029 voxels in left wm, 47184 in right wm, xrange [124, 131]
searching rotation angles z=[-6  8], y=[-6  8]

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 127.5, rotations (0.50, 1.13)
final transformation (x=127.5, yr=0.500, zr=1.129):
 0.99977  -0.01971   0.00873   1.72571;
 0.01971   0.99981   0.00017   24.49142;
-0.00873   0.00000   0.99996   35.11672;
 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 128 101 94
eigenvectors:
-0.00164   0.00249   1.00000;
-0.19991  -0.97981   0.00211;
 0.97981  -0.19991   0.00211;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.7 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 00:00:39 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 00:00:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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...
1024 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 75 (75), valley at 33 (33)
csf peak at 37, setting threshold to 62
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 75 (75), valley at 33 (33)
csf peak at 38, setting threshold to 62
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 15 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 00:03:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri

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

threshold mask volume at 5
DoAbs = 0
Found 2154358 voxels in mask (pct= 12.84)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 00:03:58 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 103.6 +- 6.9 [79.0 --> 125.0]
GM (74.0) : 73.3 +- 9.9 [30.0 --> 95.0]
setting bottom of white matter range to 83.3
setting top of gray matter range to 93.2
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...
10142 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5990 filled
3582 bright non-wm voxels segmented.
4385 diagonally connected voxels added...
white matter segmentation took 1.9 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 0.53 minutes
reading wm segmentation from wm.seg.mgz...
119 voxels added to wm to prevent paths from MTL structures to cortex
3236 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 46946 voxels turned on, 59147 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 98   new 98
115,126,128 old 98   new 98
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  34 found -  34 modified     |    TOTAL:  34
pass   2 (xy+):   0 found -  34 modified     |    TOTAL:  34
pass   1 (xy-):  32 found -  32 modified     |    TOTAL:  66
pass   2 (xy-):   0 found -  32 modified     |    TOTAL:  66
pass   1 (yz+):  42 found -  42 modified     |    TOTAL: 108
pass   2 (yz+):   0 found -  42 modified     |    TOTAL: 108
pass   1 (yz-):  40 found -  40 modified     |    TOTAL: 148
pass   2 (yz-):   0 found -  40 modified     |    TOTAL: 148
pass   1 (xz+):  33 found -  33 modified     |    TOTAL: 181
pass   2 (xz+):   0 found -  33 modified     |    TOTAL: 181
pass   1 (xz-):  26 found -  26 modified     |    TOTAL: 207
pass   2 (xz-):   0 found -  26 modified     |    TOTAL: 207
Iteration Number : 1
pass   1 (+++):  17 found -  17 modified     |    TOTAL:  17
pass   2 (+++):   0 found -  17 modified     |    TOTAL:  17
pass   1 (+++):  30 found -  30 modified     |    TOTAL:  47
pass   2 (+++):   0 found -  30 modified     |    TOTAL:  47
pass   1 (+++):  26 found -  26 modified     |    TOTAL:  73
pass   2 (+++):   0 found -  26 modified     |    TOTAL:  73
pass   1 (+++):  14 found -  14 modified     |    TOTAL:  87
pass   2 (+++):   0 found -  14 modified     |    TOTAL:  87
Iteration Number : 1
pass   1 (++): 272 found - 272 modified     |    TOTAL: 272
pass   2 (++):   0 found - 272 modified     |    TOTAL: 272
pass   1 (+-): 209 found - 209 modified     |    TOTAL: 481
pass   2 (+-):   0 found - 209 modified     |    TOTAL: 481
pass   1 (--): 185 found - 185 modified     |    TOTAL: 666
pass   2 (--):   0 found - 185 modified     |    TOTAL: 666
pass   1 (-+): 175 found - 175 modified     |    TOTAL: 841
pass   2 (-+):   0 found - 175 modified     |    TOTAL: 841
Iteration Number : 2
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   8 found -   8 modified     |    TOTAL:  12
pass   2 (xy-):   0 found -   8 modified     |    TOTAL:  12
pass   1 (yz+):   7 found -   7 modified     |    TOTAL:  19
pass   2 (yz+):   0 found -   7 modified     |    TOTAL:  19
pass   1 (yz-):   8 found -   8 modified     |    TOTAL:  27
pass   2 (yz-):   0 found -   8 modified     |    TOTAL:  27
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  30
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  30
pass   1 (xz-):   7 found -   7 modified     |    TOTAL:  37
pass   2 (xz-):   0 found -   7 modified     |    TOTAL:  37
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   4
pass   1 (+++):   3 found -   3 modified     |    TOTAL:   7
pass   2 (+++):   0 found -   3 modified     |    TOTAL:   7
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   7
Iteration Number : 2
pass   1 (++):   5 found -   5 modified     |    TOTAL:   5
pass   2 (++):   0 found -   5 modified     |    TOTAL:   5
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   6
pass   1 (--):   0 found -   0 modified     |    TOTAL:   6
pass   1 (-+):   4 found -   4 modified     |    TOTAL:  10
pass   2 (-+):   0 found -   4 modified     |    TOTAL:  10
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   5
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   5
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 = 1194 (out of 760677: 0.156965)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 00:06:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51013;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.02028  -0.01394   0.01014  -4.36719;
 0.00913   0.90352   0.38473  -25.56552;
-0.01651  -0.42921   0.80544   77.51013;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2477 (min = 350, max = 1400), aspect = 1.15 (min = 0.10, max = 0.75)
need search nearby
using seed (124, 123, 150), TAL = (4.0, 22.0, 5.0)
talairach voxel to voxel transform
 0.97980   0.00755  -0.01594   5.70722;
-0.01503   0.90197  -0.43065   56.37318;
 0.01207   0.48081   1.01174  -66.07553;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (124,  123,  150) --> (4.0, 22.0, 5.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (4.00, 22.00, 5.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(22.00, 22.00, 5.00) SRC: (108.10, 101.13, 146.10)
search lh wm seed point around talairach space (-14.00, 22.00, 5.00), SRC: (143.38, 100.58, 146.54)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sun Oct  8 00:07:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   5
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   7
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  10
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  10
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  11
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  11
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   2
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 = 13 (out of 366329: 0.003549)
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 20: 24 vertices, 34 faces
slice 30: 3873 vertices, 4133 faces
slice 40: 14643 vertices, 15083 faces
slice 50: 28546 vertices, 29071 faces
slice 60: 43442 vertices, 43945 faces
slice 70: 58243 vertices, 58708 faces
slice 80: 72635 vertices, 73146 faces
slice 90: 87026 vertices, 87534 faces
slice 100: 100597 vertices, 101068 faces
slice 110: 113651 vertices, 114111 faces
slice 120: 126063 vertices, 126506 faces
slice 130: 138424 vertices, 138942 faces
slice 140: 150513 vertices, 150936 faces
slice 150: 161262 vertices, 161747 faces
slice 160: 170784 vertices, 171133 faces
slice 170: 178485 vertices, 178813 faces
slice 180: 185001 vertices, 185266 faces
slice 190: 189900 vertices, 190082 faces
slice 200: 191234 vertices, 191298 faces
slice 210: 191234 vertices, 191298 faces
slice 220: 191234 vertices, 191298 faces
slice 230: 191234 vertices, 191298 faces
slice 240: 191234 vertices, 191298 faces
slice 250: 191234 vertices, 191298 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...
   191234 voxel in cpt #1: X=-64 [v=191234,e=573894,f=382596] located at (-28.395060, -29.327583, 18.587421)
For the whole surface: X=-64 [v=191234,e=573894,f=382596]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 00:07:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   4
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   6
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   8
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   8
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 9 (out of 363948: 0.002473)
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 20: 49 vertices, 67 faces
slice 30: 4293 vertices, 4561 faces
slice 40: 14635 vertices, 15064 faces
slice 50: 29230 vertices, 29706 faces
slice 60: 43875 vertices, 44374 faces
slice 70: 58689 vertices, 59187 faces
slice 80: 73020 vertices, 73497 faces
slice 90: 86882 vertices, 87361 faces
slice 100: 99955 vertices, 100395 faces
slice 110: 112474 vertices, 112926 faces
slice 120: 124620 vertices, 125090 faces
slice 130: 136677 vertices, 137166 faces
slice 140: 149113 vertices, 149582 faces
slice 150: 159290 vertices, 159747 faces
slice 160: 168314 vertices, 168679 faces
slice 170: 176262 vertices, 176590 faces
slice 180: 182597 vertices, 182854 faces
slice 190: 187365 vertices, 187559 faces
slice 200: 188370 vertices, 188448 faces
slice 210: 188370 vertices, 188448 faces
slice 220: 188370 vertices, 188448 faces
slice 230: 188370 vertices, 188448 faces
slice 240: 188370 vertices, 188448 faces
slice 250: 188370 vertices, 188448 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...
   188370 voxel in cpt #1: X=-78 [v=188370,e=565344,f=376896] located at (29.194696, -29.936514, 17.683393)
For the whole surface: X=-78 [v=188370,e=565344,f=376896]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 00:07:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 00:07:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

Waiting for PID 10351 of (10351 10354) to complete...
Waiting for PID 10354 of (10351 10354) 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 (10351 10354) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 00:07:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 00:07:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

Waiting for PID 10401 of (10401 10404) to complete...
Waiting for PID 10404 of (10401 10404) 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 = 53.1 mm, total surface area = 101679 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 1.0 minutes

step 000: RMS=0.153 (target=0.015)   
step 005: RMS=0.117 (target=0.015)   
step 010: RMS=0.089 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.064 (target=0.015)   
step 025: RMS=0.057 (target=0.015)   
step 030: RMS=0.051 (target=0.015)   
step 035: RMS=0.047 (target=0.015)   
step 040: RMS=0.044 (target=0.015)   
step 045: RMS=0.043 (target=0.015)   
step 050: RMS=0.041 (target=0.015)   
step 055: RMS=0.042 (target=0.015)   
step 060: RMS=0.041 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    58.666081
mris_inflate stimesec    0.149977
mris_inflate ru_maxrss   277752
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   39736
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  13456
mris_inflate ru_oublock  13472
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2326
mris_inflate ru_nivcsw   4254

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 53.1 mm, total surface area = 99975 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 1.0 minutes

step 000: RMS=0.153 (target=0.015)   
step 005: RMS=0.116 (target=0.015)   
step 010: RMS=0.088 (target=0.015)   
step 015: RMS=0.073 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.054 (target=0.015)   
step 030: RMS=0.049 (target=0.015)   
step 035: RMS=0.044 (target=0.015)   
step 040: RMS=0.041 (target=0.015)   
step 045: RMS=0.038 (target=0.015)   
step 050: RMS=0.038 (target=0.015)   
step 055: RMS=0.037 (target=0.015)   
step 060: RMS=0.036 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    57.551250
mris_inflate stimesec    0.150977
mris_inflate ru_maxrss   273948
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   39295
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  13256
mris_inflate ru_oublock  13272
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2292
mris_inflate ru_nivcsw   4340
PIDs (10401 10404) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 00:08:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 00:08:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

Waiting for PID 10473 of (10473 10477) to complete...
Waiting for PID 10477 of (10473 10477) 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 0.84 +- 0.54 (0.00-->6.08) (max @ vno 117818 --> 119231)
face area 0.02 +- 0.03 (-0.16-->0.61)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.276...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.825, avgs=0
005/300: dt: 0.9000, rms radial error=175.568, avgs=0
010/300: dt: 0.9000, rms radial error=175.015, avgs=0
015/300: dt: 0.9000, rms radial error=174.290, avgs=0
020/300: dt: 0.9000, rms radial error=173.465, avgs=0
025/300: dt: 0.9000, rms radial error=172.579, avgs=0
030/300: dt: 0.9000, rms radial error=171.660, avgs=0
035/300: dt: 0.9000, rms radial error=170.723, avgs=0
040/300: dt: 0.9000, rms radial error=169.778, avgs=0
045/300: dt: 0.9000, rms radial error=168.829, avgs=0
050/300: dt: 0.9000, rms radial error=167.880, avgs=0
055/300: dt: 0.9000, rms radial error=166.934, avgs=0
060/300: dt: 0.9000, rms radial error=165.990, avgs=0
065/300: dt: 0.9000, rms radial error=165.049, avgs=0
070/300: dt: 0.9000, rms radial error=164.113, avgs=0
075/300: dt: 0.9000, rms radial error=163.181, avgs=0
080/300: dt: 0.9000, rms radial error=162.255, avgs=0
085/300: dt: 0.9000, rms radial error=161.333, avgs=0
090/300: dt: 0.9000, rms radial error=160.428, avgs=0
095/300: dt: 0.9000, rms radial error=159.530, avgs=0
100/300: dt: 0.9000, rms radial error=158.637, avgs=0
105/300: dt: 0.9000, rms radial error=157.749, avgs=0
110/300: dt: 0.9000, rms radial error=156.866, avgs=0
115/300: dt: 0.9000, rms radial error=155.988, avgs=0
120/300: dt: 0.9000, rms radial error=155.115, avgs=0
125/300: dt: 0.9000, rms radial error=154.247, avgs=0
130/300: dt: 0.9000, rms radial error=153.383, avgs=0
135/300: dt: 0.9000, rms radial error=152.525, avgs=0
140/300: dt: 0.9000, rms radial error=151.671, avgs=0
145/300: dt: 0.9000, rms radial error=150.822, avgs=0
150/300: dt: 0.9000, rms radial error=149.978, avgs=0
155/300: dt: 0.9000, rms radial error=149.138, avgs=0
160/300: dt: 0.9000, rms radial error=148.303, avgs=0
165/300: dt: 0.9000, rms radial error=147.472, avgs=0
170/300: dt: 0.9000, rms radial error=146.646, avgs=0
175/300: dt: 0.9000, rms radial error=145.825, avgs=0
180/300: dt: 0.9000, rms radial error=145.008, avgs=0
185/300: dt: 0.9000, rms radial error=144.196, avgs=0
190/300: dt: 0.9000, rms radial error=143.388, avgs=0
195/300: dt: 0.9000, rms radial error=142.585, avgs=0
200/300: dt: 0.9000, rms radial error=141.786, avgs=0
205/300: dt: 0.9000, rms radial error=140.992, avgs=0
210/300: dt: 0.9000, rms radial error=140.202, avgs=0
215/300: dt: 0.9000, rms radial error=139.416, avgs=0
220/300: dt: 0.9000, rms radial error=138.635, avgs=0
225/300: dt: 0.9000, rms radial error=137.858, avgs=0
230/300: dt: 0.9000, rms radial error=137.086, avgs=0
235/300: dt: 0.9000, rms radial error=136.318, avgs=0
240/300: dt: 0.9000, rms radial error=135.554, avgs=0
245/300: dt: 0.9000, rms radial error=134.794, avgs=0
250/300: dt: 0.9000, rms radial error=134.039, avgs=0
255/300: dt: 0.9000, rms radial error=133.288, avgs=0
260/300: dt: 0.9000, rms radial error=132.541, avgs=0
265/300: dt: 0.9000, rms radial error=131.798, avgs=0
270/300: dt: 0.9000, rms radial error=131.059, avgs=0
275/300: dt: 0.9000, rms radial error=130.324, avgs=0
280/300: dt: 0.9000, rms radial error=129.594, avgs=0
285/300: dt: 0.9000, rms radial error=128.867, avgs=0
290/300: dt: 0.9000, rms radial error=128.144, avgs=0
295/300: dt: 0.9000, rms radial error=127.426, avgs=0
300/300: dt: 0.9000, rms radial error=126.711, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 23238.97
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
epoch 2 (K=40.0), pass 1, starting sse = 4295.66
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
epoch 3 (K=160.0), pass 1, starting sse = 513.56
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00336
epoch 4 (K=640.0), pass 1, starting sse = 36.49
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/12 = 0.00667
final distance error %29.83
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    346.562314
mris_sphere stimesec    0.243962
mris_sphere ru_maxrss   277956
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   39279
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  13456
mris_sphere ru_oublock  13496
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8404
mris_sphere ru_nivcsw   24980
FSRUNTIME@ mris_sphere  0.0961 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 0.85 +- 0.54 (0.00-->6.70) (max @ vno 137444 --> 137470)
face area 0.02 +- 0.03 (-0.13-->0.57)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.278...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.608, avgs=0
005/300: dt: 0.9000, rms radial error=175.350, avgs=0
010/300: dt: 0.9000, rms radial error=174.796, avgs=0
015/300: dt: 0.9000, rms radial error=174.068, avgs=0
020/300: dt: 0.9000, rms radial error=173.238, avgs=0
025/300: dt: 0.9000, rms radial error=172.350, avgs=0
030/300: dt: 0.9000, rms radial error=171.429, avgs=0
035/300: dt: 0.9000, rms radial error=170.491, avgs=0
040/300: dt: 0.9000, rms radial error=169.545, avgs=0
045/300: dt: 0.9000, rms radial error=168.596, avgs=0
050/300: dt: 0.9000, rms radial error=167.647, avgs=0
055/300: dt: 0.9000, rms radial error=166.705, avgs=0
060/300: dt: 0.9000, rms radial error=165.768, avgs=0
065/300: dt: 0.9000, rms radial error=164.835, avgs=0
070/300: dt: 0.9000, rms radial error=163.907, avgs=0
075/300: dt: 0.9000, rms radial error=162.984, avgs=0
080/300: dt: 0.9000, rms radial error=162.067, avgs=0
085/300: dt: 0.9000, rms radial error=161.160, avgs=0
090/300: dt: 0.9000, rms radial error=160.258, avgs=0
095/300: dt: 0.9000, rms radial error=159.362, avgs=0
100/300: dt: 0.9000, rms radial error=158.470, avgs=0
105/300: dt: 0.9000, rms radial error=157.583, avgs=0
110/300: dt: 0.9000, rms radial error=156.702, avgs=0
115/300: dt: 0.9000, rms radial error=155.825, avgs=0
120/300: dt: 0.9000, rms radial error=154.952, avgs=0
125/300: dt: 0.9000, rms radial error=154.084, avgs=0
130/300: dt: 0.9000, rms radial error=153.221, avgs=0
135/300: dt: 0.9000, rms radial error=152.363, avgs=0
140/300: dt: 0.9000, rms radial error=151.509, avgs=0
145/300: dt: 0.9000, rms radial error=150.661, avgs=0
150/300: dt: 0.9000, rms radial error=149.816, avgs=0
155/300: dt: 0.9000, rms radial error=148.976, avgs=0
160/300: dt: 0.9000, rms radial error=148.142, avgs=0
165/300: dt: 0.9000, rms radial error=147.312, avgs=0
170/300: dt: 0.9000, rms radial error=146.487, avgs=0
175/300: dt: 0.9000, rms radial error=145.666, avgs=0
180/300: dt: 0.9000, rms radial error=144.850, avgs=0
185/300: dt: 0.9000, rms radial error=144.038, avgs=0
190/300: dt: 0.9000, rms radial error=143.231, avgs=0
195/300: dt: 0.9000, rms radial error=142.428, avgs=0
200/300: dt: 0.9000, rms radial error=141.629, avgs=0
205/300: dt: 0.9000, rms radial error=140.835, avgs=0
210/300: dt: 0.9000, rms radial error=140.045, avgs=0
215/300: dt: 0.9000, rms radial error=139.259, avgs=0
220/300: dt: 0.9000, rms radial error=138.478, avgs=0
225/300: dt: 0.9000, rms radial error=137.701, avgs=0
230/300: dt: 0.9000, rms radial error=136.929, avgs=0
235/300: dt: 0.9000, rms radial error=136.160, avgs=0
240/300: dt: 0.9000, rms radial error=135.396, avgs=0
245/300: dt: 0.9000, rms radial error=134.636, avgs=0
250/300: dt: 0.9000, rms radial error=133.880, avgs=0
255/300: dt: 0.9000, rms radial error=133.128, avgs=0
260/300: dt: 0.9000, rms radial error=132.381, avgs=0
265/300: dt: 0.9000, rms radial error=131.638, avgs=0
270/300: dt: 0.9000, rms radial error=130.898, avgs=0
275/300: dt: 0.9000, rms radial error=130.163, avgs=0
280/300: dt: 0.9000, rms radial error=129.432, avgs=0
285/300: dt: 0.9000, rms radial error=128.705, avgs=0
290/300: dt: 0.9000, rms radial error=127.982, avgs=0
295/300: dt: 0.9000, rms radial error=127.264, avgs=0
300/300: dt: 0.9000, rms radial error=126.549, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 22847.22
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
epoch 2 (K=40.0), pass 1, starting sse = 4186.06
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
epoch 3 (K=160.0), pass 1, starting sse = 494.66
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00401
epoch 4 (K=640.0), pass 1, starting sse = 34.22
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/12 = 0.00520
final distance error %29.53
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    343.479783
mris_sphere stimesec    0.269958
mris_sphere ru_maxrss   274152
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   39344
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  13296
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8181
mris_sphere ru_nivcsw   24959
FSRUNTIME@ mris_sphere  0.0956 hours 1 threads
PIDs (10473 10477) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 00:14:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 00:14:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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


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

#@# Fix Topology lh Sun Oct  8 00:14:16 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050244 lh 

#@# Fix Topology rh Sun Oct  8 00:14:16 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050244 rh 

Waiting for PID 10732 of (10732 10735) to complete...
Waiting for PID 10735 of (10732 10735) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050244 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=-64 (nv=191234, nf=382596, ne=573894, 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...
8103 ambiguous faces found in tessellation
segmenting defects...
40 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 26 into 21
39 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.1452  (-4.5726)
      -vertex     loglikelihood: -6.0609  (-3.0304)
      -normal dot loglikelihood: -3.5628  (-3.5628)
      -quad curv  loglikelihood: -6.4661  (-3.2330)
      Total Loglikelihood : -25.2350

CORRECTING DEFECT 0 (vertices=17, convex hull=18, v0=11880)
After retessellation of defect 0 (v0=11880), euler #=-34 (186383,557536,371119) : difference with theory (-36) = -2 

CORRECTING DEFECT 1 (vertices=55, convex hull=79, v0=30028)
After retessellation of defect 1 (v0=30028), euler #=-33 (186416,557671,371222) : difference with theory (-35) = -2 

CORRECTING DEFECT 2 (vertices=24, convex hull=56, v0=32685)
After retessellation of defect 2 (v0=32685), euler #=-32 (186425,557722,371265) : difference with theory (-34) = -2 

CORRECTING DEFECT 3 (vertices=15, convex hull=35, v0=41570)
After retessellation of defect 3 (v0=41570), euler #=-31 (186428,557742,371283) : difference with theory (-33) = -2 

CORRECTING DEFECT 4 (vertices=136, convex hull=58, v0=66410)
After retessellation of defect 4 (v0=66410), euler #=-30 (186437,557792,371325) : difference with theory (-32) = -2 

CORRECTING DEFECT 5 (vertices=1235, convex hull=506, v0=67792)
XL defect detected...
After retessellation of defect 5 (v0=67792), euler #=-32 (186885,559438,372521) : difference with theory (-31) = 1 

CORRECTING DEFECT 6 (vertices=17, convex hull=47, v0=79796)
After retessellation of defect 6 (v0=79796), euler #=-31 (186893,559476,372552) : difference with theory (-30) = 1 

CORRECTING DEFECT 7 (vertices=20, convex hull=40, v0=83508)
After retessellation of defect 7 (v0=83508), euler #=-30 (186899,559512,372583) : difference with theory (-29) = 1 

CORRECTING DEFECT 8 (vertices=280, convex hull=247, v0=84973)
After retessellation of defect 8 (v0=84973), euler #=-29 (187026,560038,372983) : difference with theory (-28) = 1 

CORRECTING DEFECT 9 (vertices=25, convex hull=57, v0=88409)
After retessellation of defect 9 (v0=88409), euler #=-28 (187034,560087,373025) : difference with theory (-27) = 1 

CORRECTING DEFECT 10 (vertices=21, convex hull=38, v0=100035)
After retessellation of defect 10 (v0=100035), euler #=-27 (187036,560103,373040) : difference with theory (-26) = 1 

CORRECTING DEFECT 11 (vertices=31, convex hull=24, v0=102634)
After retessellation of defect 11 (v0=102634), euler #=-26 (187041,560124,373057) : difference with theory (-25) = 1 

CORRECTING DEFECT 12 (vertices=21, convex hull=24, v0=109877)
After retessellation of defect 12 (v0=109877), euler #=-25 (187043,560140,373072) : difference with theory (-24) = 1 

CORRECTING DEFECT 13 (vertices=25, convex hull=43, v0=115553)
After retessellation of defect 13 (v0=115553), euler #=-24 (187049,560169,373096) : difference with theory (-23) = 1 

CORRECTING DEFECT 14 (vertices=805, convex hull=539, v0=117076)
L defect detected...
After retessellation of defect 14 (v0=117076), euler #=-23 (187289,561163,373851) : difference with theory (-22) = 1 

CORRECTING DEFECT 15 (vertices=8, convex hull=25, v0=117162)
After retessellation of defect 15 (v0=117162), euler #=-22 (187291,561176,373863) : difference with theory (-21) = 1 

CORRECTING DEFECT 16 (vertices=34, convex hull=80, v0=123294)
After retessellation of defect 16 (v0=123294), euler #=-21 (187314,561275,373940) : difference with theory (-20) = 1 

CORRECTING DEFECT 17 (vertices=132, convex hull=50, v0=125539)
After retessellation of defect 17 (v0=125539), euler #=-20 (187328,561334,373986) : difference with theory (-19) = 1 

CORRECTING DEFECT 18 (vertices=17, convex hull=19, v0=127888)
After retessellation of defect 18 (v0=127888), euler #=-19 (187331,561347,373997) : difference with theory (-18) = 1 

CORRECTING DEFECT 19 (vertices=74, convex hull=54, v0=130200)
After retessellation of defect 19 (v0=130200), euler #=-18 (187343,561406,374045) : difference with theory (-17) = 1 

CORRECTING DEFECT 20 (vertices=115, convex hull=30, v0=132579)
After retessellation of defect 20 (v0=132579), euler #=-17 (187357,561459,374085) : difference with theory (-16) = 1 

CORRECTING DEFECT 21 (vertices=445, convex hull=326, v0=134144)
After retessellation of defect 21 (v0=134144), euler #=-15 (187556,562232,374661) : difference with theory (-15) = 0 

CORRECTING DEFECT 22 (vertices=82, convex hull=74, v0=135416)
After retessellation of defect 22 (v0=135416), euler #=-14 (187595,562384,374775) : difference with theory (-14) = 0 

CORRECTING DEFECT 23 (vertices=104, convex hull=49, v0=135687)
After retessellation of defect 23 (v0=135687), euler #=-13 (187606,562431,374812) : difference with theory (-13) = 0 

CORRECTING DEFECT 24 (vertices=32, convex hull=26, v0=138326)
After retessellation of defect 24 (v0=138326), euler #=-12 (187608,562444,374824) : difference with theory (-12) = 0 

CORRECTING DEFECT 25 (vertices=116, convex hull=83, v0=140417)
After retessellation of defect 25 (v0=140417), euler #=-11 (187628,562535,374896) : difference with theory (-11) = 0 

CORRECTING DEFECT 26 (vertices=26, convex hull=72, v0=142909)
After retessellation of defect 26 (v0=142909), euler #=-10 (187639,562596,374947) : difference with theory (-10) = 0 

CORRECTING DEFECT 27 (vertices=322, convex hull=75, v0=143216)
After retessellation of defect 27 (v0=143216), euler #=-9 (187650,562665,375006) : difference with theory (-9) = 0 

CORRECTING DEFECT 28 (vertices=44, convex hull=34, v0=144797)
After retessellation of defect 28 (v0=144797), euler #=-8 (187655,562692,375029) : difference with theory (-8) = 0 

CORRECTING DEFECT 29 (vertices=15, convex hull=19, v0=145644)
After retessellation of defect 29 (v0=145644), euler #=-7 (187658,562706,375041) : difference with theory (-7) = 0 

CORRECTING DEFECT 30 (vertices=6, convex hull=19, v0=145726)
After retessellation of defect 30 (v0=145726), euler #=-6 (187658,562711,375047) : difference with theory (-6) = 0 

CORRECTING DEFECT 31 (vertices=6, convex hull=28, v0=148022)
After retessellation of defect 31 (v0=148022), euler #=-5 (187659,562724,375060) : difference with theory (-5) = 0 

CORRECTING DEFECT 32 (vertices=45, convex hull=98, v0=148207)
After retessellation of defect 32 (v0=148207), euler #=-4 (187683,562832,375145) : difference with theory (-4) = 0 

CORRECTING DEFECT 33 (vertices=304, convex hull=211, v0=152502)
After retessellation of defect 33 (v0=152502), euler #=-3 (187752,563147,375392) : difference with theory (-3) = 0 

CORRECTING DEFECT 34 (vertices=16, convex hull=46, v0=153742)
After retessellation of defect 34 (v0=153742), euler #=-2 (187760,563188,375426) : difference with theory (-2) = 0 

CORRECTING DEFECT 35 (vertices=64, convex hull=80, v0=158407)
After retessellation of defect 35 (v0=158407), euler #=-1 (187781,563285,375503) : difference with theory (-1) = 0 

CORRECTING DEFECT 36 (vertices=60, convex hull=58, v0=161158)
After retessellation of defect 36 (v0=161158), euler #=0 (187789,563330,375541) : difference with theory (0) = 0 

CORRECTING DEFECT 37 (vertices=20, convex hull=22, v0=167214)
After retessellation of defect 37 (v0=167214), euler #=1 (187793,563349,375557) : difference with theory (1) = 0 

CORRECTING DEFECT 38 (vertices=26, convex hull=57, v0=168045)
After retessellation of defect 38 (v0=168045), euler #=2 (187799,563391,375594) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.03-->10.64) (max @ vno 91186 --> 186950)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.03-->10.64) (max @ vno 91186 --> 186950)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
134 mutations (36.2%), 236 crossovers (63.8%), 135 vertices were eliminated
building final representation...
3435 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=187799, nf=375594, ne=563391, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 31.9 minutes
0 defective edges
removing intersecting faces
000: 492 intersecting
001: 26 intersecting
002: 7 intersecting
003: 2 intersecting
expanding nbhd size to 2
004: 6 intersecting
005: 4 intersecting
mris_fix_topology utimesec    1915.715766
mris_fix_topology stimesec    0.252961
mris_fix_topology ru_maxrss   595768
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   65009
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  36496
mris_fix_topology ru_oublock  17928
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    487
mris_fix_topology ru_nivcsw   5523
FSRUNTIME@ mris_fix_topology lh  0.5322 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050244 rh

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

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

*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
before topology correction, eno=-78 (nv=188370, nf=376896, ne=565344, g=40)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 12 iterations
marking ambiguous vertices...
7827 ambiguous faces found in tessellation
segmenting defects...
47 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 10 into 8
      -merging segment 9 into 11
      -merging segment 18 into 16
      -merging segment 25 into 23
43 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2328  (-4.6164)
      -vertex     loglikelihood: -6.0193  (-3.0097)
      -normal dot loglikelihood: -3.6146  (-3.6146)
      -quad curv  loglikelihood: -6.4364  (-3.2182)
      Total Loglikelihood : -25.3032

CORRECTING DEFECT 0 (vertices=28, convex hull=58, v0=13152)
After retessellation of defect 0 (v0=13152), euler #=-42 (183797,550007,366168) : difference with theory (-40) = 2 

CORRECTING DEFECT 1 (vertices=5, convex hull=31, v0=16835)
After retessellation of defect 1 (v0=16835), euler #=-41 (183797,550014,366176) : difference with theory (-39) = 2 

CORRECTING DEFECT 2 (vertices=37, convex hull=45, v0=21346)
After retessellation of defect 2 (v0=21346), euler #=-40 (183803,550051,366208) : difference with theory (-38) = 2 

CORRECTING DEFECT 3 (vertices=94, convex hull=93, v0=30300)
After retessellation of defect 3 (v0=30300), euler #=-39 (183820,550142,366283) : difference with theory (-37) = 2 

CORRECTING DEFECT 4 (vertices=148, convex hull=79, v0=39198)
After retessellation of defect 4 (v0=39198), euler #=-38 (183848,550259,366373) : difference with theory (-36) = 2 

CORRECTING DEFECT 5 (vertices=6, convex hull=25, v0=46231)
After retessellation of defect 5 (v0=46231), euler #=-37 (183850,550271,366384) : difference with theory (-35) = 2 

CORRECTING DEFECT 6 (vertices=48, convex hull=64, v0=46291)
After retessellation of defect 6 (v0=46291), euler #=-36 (183864,550339,366439) : difference with theory (-34) = 2 

CORRECTING DEFECT 7 (vertices=32, convex hull=43, v0=55379)
After retessellation of defect 7 (v0=55379), euler #=-35 (183869,550369,366465) : difference with theory (-33) = 2 

CORRECTING DEFECT 8 (vertices=177, convex hull=89, v0=64168)
After retessellation of defect 8 (v0=64168), euler #=-33 (183899,550497,366565) : difference with theory (-32) = 1 

CORRECTING DEFECT 9 (vertices=951, convex hull=375, v0=73999)
After retessellation of defect 9 (v0=73999), euler #=-31 (184114,551334,367189) : difference with theory (-31) = 0 

CORRECTING DEFECT 10 (vertices=37, convex hull=36, v0=75167)
After retessellation of defect 10 (v0=75167), euler #=-30 (184118,551357,367209) : difference with theory (-30) = 0 

CORRECTING DEFECT 11 (vertices=29, convex hull=43, v0=82657)
After retessellation of defect 11 (v0=82657), euler #=-29 (184128,551404,367247) : difference with theory (-29) = 0 

CORRECTING DEFECT 12 (vertices=30, convex hull=42, v0=88404)
After retessellation of defect 12 (v0=88404), euler #=-28 (184137,551447,367282) : difference with theory (-28) = 0 

CORRECTING DEFECT 13 (vertices=34, convex hull=66, v0=94953)
After retessellation of defect 13 (v0=94953), euler #=-27 (184156,551532,367349) : difference with theory (-27) = 0 

CORRECTING DEFECT 14 (vertices=19, convex hull=51, v0=96014)
After retessellation of defect 14 (v0=96014), euler #=-25 (184163,551572,367384) : difference with theory (-26) = -1 

CORRECTING DEFECT 15 (vertices=14, convex hull=23, v0=98244)
After retessellation of defect 15 (v0=98244), euler #=-24 (184168,551592,367400) : difference with theory (-25) = -1 

CORRECTING DEFECT 16 (vertices=22, convex hull=47, v0=99421)
After retessellation of defect 16 (v0=99421), euler #=-23 (184177,551634,367434) : difference with theory (-24) = -1 

CORRECTING DEFECT 17 (vertices=26, convex hull=49, v0=100490)
After retessellation of defect 17 (v0=100490), euler #=-22 (184190,551691,367479) : difference with theory (-23) = -1 

CORRECTING DEFECT 18 (vertices=6, convex hull=16, v0=104924)
After retessellation of defect 18 (v0=104924), euler #=-21 (184191,551698,367486) : difference with theory (-22) = -1 

CORRECTING DEFECT 19 (vertices=25, convex hull=60, v0=108437)
After retessellation of defect 19 (v0=108437), euler #=-20 (184204,551757,367533) : difference with theory (-21) = -1 

CORRECTING DEFECT 20 (vertices=1411, convex hull=593, v0=112155)
XL defect detected...
After retessellation of defect 20 (v0=112155), euler #=-20 (184280,552310,368010) : difference with theory (-20) = 0 

CORRECTING DEFECT 21 (vertices=12, convex hull=20, v0=116861)
After retessellation of defect 21 (v0=116861), euler #=-19 (184283,552327,368025) : difference with theory (-19) = 0 

CORRECTING DEFECT 22 (vertices=11, convex hull=38, v0=126581)
After retessellation of defect 22 (v0=126581), euler #=-18 (184285,552346,368043) : difference with theory (-18) = 0 

CORRECTING DEFECT 23 (vertices=117, convex hull=114, v0=130245)
After retessellation of defect 23 (v0=130245), euler #=-17 (184356,552619,368246) : difference with theory (-17) = 0 

CORRECTING DEFECT 24 (vertices=333, convex hull=214, v0=130387)
After retessellation of defect 24 (v0=130387), euler #=-16 (184393,552849,368440) : difference with theory (-16) = 0 

CORRECTING DEFECT 25 (vertices=22, convex hull=28, v0=132467)
After retessellation of defect 25 (v0=132467), euler #=-15 (184398,552873,368460) : difference with theory (-15) = 0 

CORRECTING DEFECT 26 (vertices=27, convex hull=27, v0=135462)
After retessellation of defect 26 (v0=135462), euler #=-14 (184401,552890,368475) : difference with theory (-14) = 0 

CORRECTING DEFECT 27 (vertices=30, convex hull=56, v0=136168)
After retessellation of defect 27 (v0=136168), euler #=-13 (184417,552962,368532) : difference with theory (-13) = 0 

CORRECTING DEFECT 28 (vertices=327, convex hull=62, v0=141351)
After retessellation of defect 28 (v0=141351), euler #=-12 (184441,553057,368604) : difference with theory (-12) = 0 

CORRECTING DEFECT 29 (vertices=21, convex hull=27, v0=143730)
After retessellation of defect 29 (v0=143730), euler #=-11 (184445,553078,368622) : difference with theory (-11) = 0 

CORRECTING DEFECT 30 (vertices=148, convex hull=56, v0=146394)
After retessellation of defect 30 (v0=146394), euler #=-10 (184454,553130,368666) : difference with theory (-10) = 0 

CORRECTING DEFECT 31 (vertices=46, convex hull=38, v0=147934)
After retessellation of defect 31 (v0=147934), euler #=-9 (184459,553158,368690) : difference with theory (-9) = 0 

CORRECTING DEFECT 32 (vertices=30, convex hull=56, v0=151924)
After retessellation of defect 32 (v0=151924), euler #=-8 (184472,553217,368737) : difference with theory (-8) = 0 

CORRECTING DEFECT 33 (vertices=44, convex hull=83, v0=152926)
After retessellation of defect 33 (v0=152926), euler #=-7 (184490,553310,368813) : difference with theory (-7) = 0 

CORRECTING DEFECT 34 (vertices=37, convex hull=49, v0=153228)
After retessellation of defect 34 (v0=153228), euler #=-6 (184510,553391,368875) : difference with theory (-6) = 0 

CORRECTING DEFECT 35 (vertices=78, convex hull=84, v0=154034)
After retessellation of defect 35 (v0=154034), euler #=-5 (184538,553513,368970) : difference with theory (-5) = 0 

CORRECTING DEFECT 36 (vertices=17, convex hull=51, v0=163294)
After retessellation of defect 36 (v0=163294), euler #=-4 (184547,553557,369006) : difference with theory (-4) = 0 

CORRECTING DEFECT 37 (vertices=5, convex hull=33, v0=164210)
After retessellation of defect 37 (v0=164210), euler #=-3 (184548,553570,369019) : difference with theory (-3) = 0 

CORRECTING DEFECT 38 (vertices=6, convex hull=21, v0=166678)
After retessellation of defect 38 (v0=166678), euler #=-2 (184548,553575,369025) : difference with theory (-2) = 0 

CORRECTING DEFECT 39 (vertices=24, convex hull=60, v0=174800)
After retessellation of defect 39 (v0=174800), euler #=-1 (184564,553647,369082) : difference with theory (-1) = 0 

CORRECTING DEFECT 40 (vertices=6, convex hull=14, v0=181512)
After retessellation of defect 40 (v0=181512), euler #=0 (184565,553653,369088) : difference with theory (0) = 0 

CORRECTING DEFECT 41 (vertices=33, convex hull=69, v0=186241)
After retessellation of defect 41 (v0=186241), euler #=1 (184578,553716,369139) : difference with theory (1) = 0 

CORRECTING DEFECT 42 (vertices=25, convex hull=27, v0=188277)
After retessellation of defect 42 (v0=188277), euler #=2 (184579,553731,369154) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.23 (0.02-->13.39) (max @ vno 81395 --> 185035)
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 (0.02-->13.39) (max @ vno 81395 --> 185035)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
161 mutations (35.4%), 294 crossovers (64.6%), 501 vertices were eliminated
building final representation...
3791 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=184579, nf=369154, ne=553731, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 32.4 minutes
0 defective edges
removing intersecting faces
000: 467 intersecting
001: 29 intersecting
002: 8 intersecting
mris_fix_topology utimesec    1944.815343
mris_fix_topology stimesec    0.238963
mris_fix_topology ru_maxrss   579156
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   62274
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  24776
mris_fix_topology ru_oublock  17640
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    551
mris_fix_topology ru_nivcsw   3806
FSRUNTIME@ mris_fix_topology rh  0.5402 hours 1 threads
PIDs (10732 10735) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 187799 - 563391 + 375594 = 2 --> 0 holes
      F =2V-4:          375594 = 375598-4 (0)
      2E=3F:            1126782 = 1126782 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 184579 - 553731 + 369154 = 2 --> 0 holes
      F =2V-4:          369154 = 369158-4 (0)
      2E=3F:            1107462 = 1107462 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 162 intersecting
001: 5 intersecting
expanding nbhd size to 2
002: 7 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 116 intersecting
001: 10 intersecting
002: 4 intersecting
expanding nbhd size to 2
003: 7 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 00:47:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050244 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 00:47:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050244 rh 

Waiting for PID 13725 of (13725 13728) to complete...
Waiting for PID 13728 of (13725 13728) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050244 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-6.0.0/0050244/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
42076 bright wm thresholded.
3645 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.orig...
computing class statistics...
border white:    343001 voxels (2.04%)
border gray      395990 voxels (2.36%)
WM (101.0): 101.0 +- 7.5 [70.0 --> 110.0]
GM (77.0) : 76.7 +- 9.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 64.3 (was 70)
setting MAX_BORDER_WHITE to 113.5 (was 105)
setting MIN_BORDER_WHITE to 74.0 (was 85)
setting MAX_CSF to 54.7 (was 40)
setting MAX_GRAY to 98.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 64.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 45.0 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->6.13) (max @ vno 91186 --> 186509)
face area 0.28 +- 0.12 (0.00-->4.09)
mean absolute distance = 0.69 +- 0.86
6393 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=74+-7.0
mean inside = 97.2, mean outside = 80.0
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=84.0, 64 (64) missing vertices, mean dist 0.3 [0.5 (%35.6)->0.8 (%64.4))]
%71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.09-->7.65) (max @ vno 91186 --> 186470)
face area 0.28 +- 0.13 (0.00-->5.33)
mean absolute distance = 0.38 +- 0.52
6593 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3859596.8, rms=9.220
001: dt: 0.5000, sse=2223361.5, rms=6.381 (30.795%)
002: dt: 0.5000, sse=1576083.5, rms=4.794 (24.868%)
003: dt: 0.5000, sse=1290709.4, rms=3.894 (18.761%)
004: dt: 0.5000, sse=1148409.1, rms=3.344 (14.144%)
005: dt: 0.5000, sse=1097922.2, rms=3.108 (7.056%)
006: dt: 0.5000, sse=1060290.5, rms=2.950 (5.080%)
rms = 2.93, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=1059123.0, rms=2.927 (0.784%)
008: dt: 0.2500, sse=886206.7, rms=1.843 (37.014%)
009: dt: 0.2500, sse=856051.6, rms=1.596 (13.403%)
010: dt: 0.2500, sse=848945.1, rms=1.526 (4.401%)
rms = 1.48, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=844412.1, rms=1.480 (3.010%)
rms = 1.45, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=841814.1, rms=1.447 (2.256%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=87.8, 76 (15) missing vertices, mean dist -0.3 [0.4 (%81.5)->0.3 (%18.5))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.08-->7.81) (max @ vno 91186 --> 186470)
face area 0.35 +- 0.16 (0.00-->7.61)
mean absolute distance = 0.22 +- 0.34
5479 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1808124.8, rms=4.898
013: dt: 0.5000, sse=1275250.2, rms=3.037 (37.993%)
014: dt: 0.5000, sse=1224161.5, rms=2.810 (7.480%)
015: dt: 0.5000, sse=1207750.6, rms=2.743 (2.377%)
rms = 2.93, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=1070367.8, rms=1.885 (31.293%)
017: dt: 0.2500, sse=1020652.5, rms=1.454 (22.841%)
018: dt: 0.2500, sse=1006873.2, rms=1.313 (9.745%)
rms = 1.27, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=1003803.0, rms=1.269 (3.339%)
rms = 1.23, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=1000102.2, rms=1.228 (3.214%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=89.8, 81 (7) missing vertices, mean dist -0.1 [0.2 (%74.1)->0.2 (%25.9))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.02-->7.96) (max @ vno 91186 --> 186470)
face area 0.33 +- 0.16 (0.00-->8.09)
mean absolute distance = 0.18 +- 0.28
4914 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1192319.1, rms=2.807
021: dt: 0.5000, sse=1097208.6, rms=2.235 (20.365%)
rms = 2.48, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=999426.2, rms=1.541 (31.054%)
023: dt: 0.2500, sse=965956.8, rms=1.196 (22.381%)
024: dt: 0.2500, sse=956209.3, rms=1.103 (7.829%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=954198.4, rms=1.090 (1.168%)
rms = 1.06, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=953590.8, rms=1.060 (2.693%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=90.3, 85 (5) missing vertices, mean dist -0.0 [0.2 (%56.5)->0.2 (%43.5))]
%92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=961571.7, rms=1.278
rms = 1.25, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=959128.4, rms=1.250 (2.219%)
028: dt: 0.2500, sse=935157.5, rms=0.998 (20.142%)
029: dt: 0.2500, sse=923904.2, rms=0.854 (14.435%)
rms = 0.90, time step reduction 2 of 3 to 0.125...
rms = 0.83, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=921515.1, rms=0.835 (2.243%)
positioning took 0.7 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 9156 vertices
erasing segment 1 (vno[0] = 133873)
erasing segment 2 (vno[0] = 139515)
erasing segment 3 (vno[0] = 139581)
erasing segment 4 (vno[0] = 140666)
erasing segment 5 (vno[0] = 142788)
erasing segment 6 (vno[0] = 143968)
erasing segment 7 (vno[0] = 144138)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.02-->7.88) (max @ vno 91186 --> 186470)
face area 0.33 +- 0.15 (0.00-->8.32)
refinement took 7.3 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050244 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-6.0.0/0050244/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
42076 bright wm thresholded.
3645 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.orig...
computing class statistics...
border white:    343001 voxels (2.04%)
border gray      395990 voxels (2.36%)
WM (101.0): 101.0 +- 7.5 [70.0 --> 110.0]
GM (77.0) : 76.7 +- 9.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 64.3 (was 70)
setting MAX_BORDER_WHITE to 113.5 (was 105)
setting MIN_BORDER_WHITE to 74.0 (was 85)
setting MAX_CSF to 54.7 (was 40)
setting MAX_GRAY to 98.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 64.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 45.0 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->9.25) (max @ vno 81395 --> 184006)
face area 0.28 +- 0.13 (0.00-->11.10)
mean absolute distance = 0.69 +- 0.86
6649 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=74+-7.8
mean inside = 97.4, mean outside = 80.5
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=84.4, 40 (40) missing vertices, mean dist 0.3 [0.5 (%36.4)->0.8 (%63.6))]
%73 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.10-->11.63) (max @ vno 184006 --> 81395)
face area 0.28 +- 0.13 (0.00-->13.11)
mean absolute distance = 0.38 +- 0.53
7006 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3778486.0, rms=9.181
001: dt: 0.5000, sse=2200558.8, rms=6.405 (30.241%)
002: dt: 0.5000, sse=1560799.4, rms=4.820 (24.745%)
003: dt: 0.5000, sse=1271327.2, rms=3.890 (19.289%)
004: dt: 0.5000, sse=1127101.9, rms=3.328 (14.454%)
005: dt: 0.5000, sse=1070745.1, rms=3.078 (7.499%)
006: dt: 0.5000, sse=1038163.4, rms=2.913 (5.383%)
rms = 2.89, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=1032737.1, rms=2.886 (0.922%)
008: dt: 0.2500, sse=868524.2, rms=1.814 (37.154%)
009: dt: 0.2500, sse=840177.5, rms=1.570 (13.407%)
010: dt: 0.2500, sse=834648.6, rms=1.515 (3.545%)
rms = 1.47, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=830603.8, rms=1.470 (2.970%)
rms = 1.45, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=829195.9, rms=1.451 (1.309%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=88.1, 92 (8) missing vertices, mean dist -0.3 [0.4 (%81.6)->0.3 (%18.4))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.24 (0.04-->11.90) (max @ vno 184006 --> 81395)
face area 0.35 +- 0.17 (0.00-->19.29)
mean absolute distance = 0.22 +- 0.32
4850 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1783014.8, rms=4.887
013: dt: 0.5000, sse=1267866.5, rms=3.072 (37.135%)
014: dt: 0.5000, sse=1217413.1, rms=2.848 (7.281%)
015: dt: 0.5000, sse=1195686.4, rms=2.754 (3.316%)
rms = 2.93, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=1068045.0, rms=1.950 (29.184%)
017: dt: 0.2500, sse=1020400.1, rms=1.537 (21.174%)
018: dt: 0.2500, sse=1003361.4, rms=1.371 (10.822%)
019: dt: 0.2500, sse=1000344.6, rms=1.312 (4.261%)
020: dt: 0.2500, sse=994403.2, rms=1.257 (4.230%)
rms = 1.23, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=993258.4, rms=1.234 (1.852%)
rms = 1.21, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=989748.7, rms=1.208 (2.041%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=90.1, 81 (5) missing vertices, mean dist -0.1 [0.2 (%73.8)->0.2 (%26.2))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.04-->11.90) (max @ vno 184006 --> 81395)
face area 0.34 +- 0.16 (0.00-->19.72)
mean absolute distance = 0.18 +- 0.28
4796 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1176574.0, rms=2.791
023: dt: 0.5000, sse=1080770.6, rms=2.170 (22.246%)
rms = 2.39, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=987034.2, rms=1.517 (30.102%)
025: dt: 0.2500, sse=959923.6, rms=1.194 (21.268%)
026: dt: 0.2500, sse=946473.8, rms=1.102 (7.755%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=946267.4, rms=1.088 (1.245%)
rms = 1.06, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=945821.6, rms=1.060 (2.627%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=90.6, 88 (3) missing vertices, mean dist -0.0 [0.2 (%56.6)->0.2 (%43.4))]
%93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=952544.6, rms=1.273
rms = 1.23, time step reduction 1 of 3 to 0.250...
029: dt: 0.5000, sse=955246.5, rms=1.227 (3.591%)
030: dt: 0.2500, sse=927359.1, rms=0.991 (19.255%)
031: dt: 0.2500, sse=914601.8, rms=0.852 (14.044%)
rms = 0.90, time step reduction 2 of 3 to 0.125...
rms = 0.84, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=912713.9, rms=0.836 (1.860%)
positioning took 0.7 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 8786 vertices
erasing segment 1 (vno[0] = 106174)
erasing segment 2 (vno[0] = 108767)
erasing segment 3 (vno[0] = 125320)
erasing segment 4 (vno[0] = 136584)
erasing segment 5 (vno[0] = 136609)
erasing segment 6 (vno[0] = 136621)
erasing segment 7 (vno[0] = 137818)
erasing segment 8 (vno[0] = 140051)
erasing segment 9 (vno[0] = 141255)
erasing segment 10 (vno[0] = 142382)
erasing segment 11 (vno[0] = 143485)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.02-->11.82) (max @ vno 81395 --> 184006)
face area 0.33 +- 0.16 (0.00-->20.56)
refinement took 7.6 minutes
PIDs (13725 13728) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 00:54:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 00:54:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

Waiting for PID 14029 of (14029 14032) to complete...
Waiting for PID 14032 of (14029 14032) 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 (14029 14032) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 00:54:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 00:54:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 14077 of (14077 14080) to complete...
Waiting for PID 14080 of (14077 14080) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 53.4 mm, total surface area = 113283 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.172 (target=0.015)   
step 005: RMS=0.122 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.052 (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=0.026 (target=0.015)   
step 055: RMS=0.023 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
inflation took 1.2 minutes
mris_inflate utimesec    69.077498
mris_inflate stimesec    0.172973
mris_inflate ru_maxrss   273120
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   39218
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  14704
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2032
mris_inflate ru_nivcsw   5346

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 53.4 mm, total surface area = 111573 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.172 (target=0.015)   
step 005: RMS=0.121 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.061 (target=0.015)   
step 025: RMS=0.051 (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=0.026 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.021 (target=0.015)   
step 060: RMS=0.020 (target=0.015)   
inflation complete.
inflation took 1.1 minutes
mris_inflate utimesec    68.120644
mris_inflate stimesec    0.159975
mris_inflate ru_maxrss   268608
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   38600
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  14448
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2072
mris_inflate ru_nivcsw   5221
PIDs (14077 14080) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 00:55:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf

 mris_curvature -w lh.white.preaparc 

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

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

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct  8 00:55:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 14187 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14190 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14193 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14196 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14199 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14202 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14205 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14208 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14211 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14214 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14217 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...
Waiting for PID 14220 of (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 2.951*4pi (37.080) --> -2 handles
ICI = 202.0, FI = 2483.3, variation=37857.010
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
270 vertices thresholded to be in k1 ~ [-0.29 0.28], k2 ~ [-0.12 0.13]
total integrated curvature = 0.511*4pi (6.416) --> 0 handles
ICI = 1.6, FI = 12.3, variation=201.602
221 vertices thresholded to be in [-0.02 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
185 vertices thresholded to be in [-0.13 0.13]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.014, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 15.760*4pi (198.049) --> -15 handles
ICI = 215.1, FI = 3036.2, variation=44959.149
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
252 vertices thresholded to be in k1 ~ [-0.21 0.29], k2 ~ [-0.10 0.06]
total integrated curvature = 0.534*4pi (6.714) --> 0 handles
ICI = 1.6, FI = 11.5, variation=189.298
177 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
191 vertices thresholded to be in [-0.11 0.15]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.021
done.
PIDs (14187 14190 14193 14196 14199 14202 14205 14208 14211 14214 14217 14220) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 00:57:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050244 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      [ 0050244/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                      [ 362 ]
Gb_filter = 0

WARN:   k2 lookup   min:                          -27.357197
WARN:   k2 explicit min:                          -16.439270	vertex = 126992

WARN:    S lookup   min:                          -3.680295
WARN:    S explicit min:                          0.000000	vertex = 2152

WARN:    C lookup   max:                          560.595642
WARN:    C explicit max:                          79.067062	vertex = 187563

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 00:57:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050244 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      [ 0050244/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                      [ 366 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.168595
WARN:    S explicit min:                          0.000000	vertex = 128
#--------------------------------------------
#@# Sphere lh Sun Oct  8 00:58:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 00:58:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 14501 of (14501 14504) to complete...
Waiting for PID 14504 of (14501 14504) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0.259...
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 %20.01
pass 1: epoch 2 of 3 starting distance error %19.97
unfolding complete - removing small folds...
starting distance error %19.89
removing remaining folds...
final distance error %19.90
MRISunfold() return, current seed 1234
-01: dt=0.0000, 294 negative triangles
178: dt=0.9900, 294 negative triangles
179: dt=0.9900, 164 negative triangles
180: dt=0.9900, 149 negative triangles
181: dt=0.9900, 130 negative triangles
182: dt=0.9900, 109 negative triangles
183: dt=0.9900, 106 negative triangles
184: dt=0.9900, 85 negative triangles
185: dt=0.9900, 71 negative triangles
186: dt=0.9900, 78 negative triangles
187: dt=0.9900, 62 negative triangles
188: dt=0.9900, 56 negative triangles
189: dt=0.9900, 49 negative triangles
190: dt=0.9900, 45 negative triangles
191: dt=0.9900, 45 negative triangles
192: dt=0.9900, 32 negative triangles
193: dt=0.9900, 39 negative triangles
194: dt=0.9900, 35 negative triangles
195: dt=0.9900, 34 negative triangles
196: dt=0.9900, 24 negative triangles
197: dt=0.9900, 34 negative triangles
198: dt=0.9900, 23 negative triangles
199: dt=0.9900, 29 negative triangles
200: dt=0.9900, 30 negative triangles
201: dt=0.9900, 25 negative triangles
202: dt=0.9900, 27 negative triangles
203: dt=0.9900, 25 negative triangles
204: dt=0.9900, 19 negative triangles
205: dt=0.9900, 21 negative triangles
206: dt=0.9900, 16 negative triangles
207: dt=0.9900, 19 negative triangles
208: dt=0.9900, 17 negative triangles
209: dt=0.9900, 17 negative triangles
210: dt=0.9900, 12 negative triangles
211: dt=0.9900, 17 negative triangles
212: dt=0.9900, 12 negative triangles
213: dt=0.9900, 15 negative triangles
214: dt=0.9900, 13 negative triangles
215: dt=0.9900, 15 negative triangles
216: dt=0.9900, 15 negative triangles
217: dt=0.9900, 16 negative triangles
218: dt=0.9900, 14 negative triangles
219: dt=0.9900, 11 negative triangles
220: dt=0.9900, 9 negative triangles
221: dt=0.9900, 9 negative triangles
222: dt=0.9900, 11 negative triangles
223: dt=0.9900, 10 negative triangles
224: dt=0.9900, 6 negative triangles
225: dt=0.9900, 9 negative triangles
226: dt=0.9900, 7 negative triangles
227: dt=0.9900, 7 negative triangles
228: dt=0.9900, 10 negative triangles
229: dt=0.9900, 7 negative triangles
230: dt=0.9900, 5 negative triangles
231: dt=0.9900, 5 negative triangles
232: dt=0.9900, 1 negative triangles
233: dt=0.9900, 2 negative triangles
234: dt=0.9900, 4 negative triangles
235: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.52 hours
mris_sphere utimesec    5551.632023
mris_sphere stimesec    2.804573
mris_sphere ru_maxrss   380616
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   66224
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  13264
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    153930
mris_sphere ru_nivcsw   450986
FSRUNTIME@ mris_sphere  1.5160 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0.260...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.54
pass 1: epoch 2 of 3 starting distance error %20.47
unfolding complete - removing small folds...
starting distance error %20.36
removing remaining folds...
final distance error %20.37
MRISunfold() return, current seed 1234
-01: dt=0.0000, 222 negative triangles
200: dt=0.9900, 222 negative triangles
201: dt=0.9900, 135 negative triangles
202: dt=0.9900, 125 negative triangles
203: dt=0.9900, 104 negative triangles
204: dt=0.9900, 108 negative triangles
205: dt=0.9900, 99 negative triangles
206: dt=0.9900, 102 negative triangles
207: dt=0.9900, 92 negative triangles
208: dt=0.9900, 101 negative triangles
209: dt=0.9900, 95 negative triangles
210: dt=0.9900, 87 negative triangles
211: dt=0.9900, 84 negative triangles
212: dt=0.9900, 76 negative triangles
213: dt=0.9900, 73 negative triangles
214: dt=0.9900, 74 negative triangles
215: dt=0.9900, 63 negative triangles
216: dt=0.9900, 63 negative triangles
217: dt=0.9900, 59 negative triangles
218: dt=0.9900, 60 negative triangles
219: dt=0.9900, 53 negative triangles
220: dt=0.9900, 38 negative triangles
221: dt=0.9900, 47 negative triangles
222: dt=0.9900, 43 negative triangles
223: dt=0.9900, 34 negative triangles
224: dt=0.9900, 34 negative triangles
225: dt=0.9900, 32 negative triangles
226: dt=0.9900, 24 negative triangles
227: dt=0.9900, 26 negative triangles
228: dt=0.9900, 22 negative triangles
229: dt=0.9900, 22 negative triangles
230: dt=0.9900, 20 negative triangles
231: dt=0.9900, 20 negative triangles
232: dt=0.9900, 17 negative triangles
233: dt=0.9900, 20 negative triangles
234: dt=0.9900, 19 negative triangles
235: dt=0.9900, 18 negative triangles
236: dt=0.9900, 18 negative triangles
237: dt=0.9900, 20 negative triangles
238: dt=0.9900, 17 negative triangles
239: dt=0.9900, 19 negative triangles
240: dt=0.9900, 20 negative triangles
241: dt=0.9900, 18 negative triangles
242: dt=0.9900, 15 negative triangles
243: dt=0.9900, 19 negative triangles
244: dt=0.9900, 17 negative triangles
245: dt=0.9900, 17 negative triangles
246: dt=0.9900, 15 negative triangles
247: dt=0.9900, 17 negative triangles
248: dt=0.9900, 16 negative triangles
249: dt=0.9900, 19 negative triangles
250: dt=0.9900, 16 negative triangles
251: dt=0.9900, 15 negative triangles
252: dt=0.9405, 19 negative triangles
253: dt=0.9405, 17 negative triangles
254: dt=0.9405, 17 negative triangles
255: dt=0.9405, 21 negative triangles
256: dt=0.9405, 16 negative triangles
257: dt=0.9405, 12 negative triangles
258: dt=0.9405, 17 negative triangles
259: dt=0.9405, 16 negative triangles
260: dt=0.9405, 15 negative triangles
261: dt=0.9405, 18 negative triangles
262: dt=0.9405, 18 negative triangles
263: dt=0.9405, 17 negative triangles
264: dt=0.9405, 14 negative triangles
265: dt=0.9405, 15 negative triangles
266: dt=0.9405, 9 negative triangles
267: dt=0.9405, 14 negative triangles
268: dt=0.9405, 15 negative triangles
269: dt=0.9405, 13 negative triangles
270: dt=0.9405, 9 negative triangles
271: dt=0.9405, 13 negative triangles
272: dt=0.9405, 10 negative triangles
273: dt=0.9405, 11 negative triangles
274: dt=0.9405, 8 negative triangles
275: dt=0.9405, 10 negative triangles
276: dt=0.9405, 11 negative triangles
277: dt=0.9405, 12 negative triangles
278: dt=0.9405, 8 negative triangles
279: dt=0.9405, 11 negative triangles
280: dt=0.9405, 11 negative triangles
281: dt=0.9405, 9 negative triangles
282: dt=0.9405, 5 negative triangles
283: dt=0.9405, 6 negative triangles
284: dt=0.9405, 2 negative triangles
285: dt=0.9405, 1 negative triangles
286: dt=0.9405, 2 negative triangles
287: dt=0.9405, 3 negative triangles
288: dt=0.9405, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.49 hours
mris_sphere utimesec    5352.171346
mris_sphere stimesec    2.752581
mris_sphere ru_maxrss   374456
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   65211
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  13088
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    151783
mris_sphere ru_nivcsw   448141
FSRUNTIME@ mris_sphere  1.4852 hours 1 threads
PIDs (14501 14504) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 02:29:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 02:29:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 17412 of (17412 17415) to complete...
Waiting for PID 17415 of (17412 17415) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 = 5.529
curvature mean = 0.033, std = 0.817
curvature mean = 0.026, std = 0.820
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, -16.00) sse = 475438.4, tmin=1.4572
  d=32.00 min @ (-8.00, -8.00, 8.00) sse = 343096.5, tmin=2.9318
  d=16.00 min @ (0.00, 4.00, 0.00) sse = 334264.3, tmin=4.4071
  d=8.00 min @ (0.00, -2.00, 0.00) sse = 326010.6, tmin=5.8685
  d=4.00 min @ (1.00, 1.00, -1.00) sse = 325033.2, tmin=7.3306
  d=2.00 min @ (-0.50, -0.50, 0.50) sse = 324168.8, tmin=8.8019
  d=0.50 min @ (0.12, 0.00, 0.00) sse = 324146.8, tmin=11.7690
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  11.77 min
curvature mean = 0.005, std = 0.808
curvature mean = 0.009, std = 0.924
curvature mean = -0.002, std = 0.811
curvature mean = 0.004, std = 0.965
curvature mean = -0.004, std = 0.810
curvature mean = 0.001, std = 0.983
2 Reading smoothwm
curvature mean = -0.028, std = 0.305
curvature mean = 0.039, std = 0.244
curvature mean = 0.074, std = 0.294
curvature mean = 0.035, std = 0.301
curvature mean = 0.046, std = 0.466
curvature mean = 0.034, std = 0.329
curvature mean = 0.027, std = 0.607
curvature mean = 0.033, std = 0.340
curvature mean = 0.010, std = 0.725
MRISregister() return, current seed 0
-01: dt=0.0000, 132 negative triangles
138: dt=0.9900, 132 negative triangles
139: dt=0.9900, 94 negative triangles
140: dt=0.9900, 66 negative triangles
141: dt=0.9900, 45 negative triangles
142: dt=0.9900, 45 negative triangles
143: dt=0.9900, 41 negative triangles
144: dt=0.9900, 29 negative triangles
145: dt=0.9900, 39 negative triangles
146: dt=0.9900, 35 negative triangles
147: dt=0.9900, 32 negative triangles
148: dt=0.9900, 25 negative triangles
149: dt=0.9900, 22 negative triangles
150: dt=0.9900, 25 negative triangles
151: dt=0.9900, 17 negative triangles
152: dt=0.9900, 19 negative triangles
153: dt=0.9900, 16 negative triangles
154: dt=0.9900, 15 negative triangles
155: dt=0.9900, 10 negative triangles
156: dt=0.9900, 11 negative triangles
157: dt=0.9900, 13 negative triangles
158: dt=0.9900, 11 negative triangles
159: dt=0.9900, 14 negative triangles
160: dt=0.9900, 11 negative triangles
161: dt=0.9900, 12 negative triangles
162: dt=0.9900, 13 negative triangles
163: dt=0.9900, 7 negative triangles
164: dt=0.9900, 11 negative triangles
165: dt=0.9900, 9 negative triangles
166: dt=0.9900, 14 negative triangles
167: dt=0.9900, 11 negative triangles
168: dt=0.9900, 9 negative triangles
169: dt=0.9900, 5 negative triangles
170: dt=0.9900, 7 negative triangles
171: dt=0.9900, 7 negative triangles
172: dt=0.9900, 8 negative triangles
173: dt=0.9900, 6 negative triangles
174: dt=0.9900, 3 negative triangles
175: dt=0.9900, 3 negative triangles
176: dt=0.9900, 3 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.69 hours
mris_register utimesec    6090.529098
mris_register stimesec    5.351186
mris_register ru_maxrss   327604
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   46284
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  13312
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    358045
mris_register ru_nivcsw   273194
FSRUNTIME@ mris_register  1.6931 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 = 5.598
curvature mean = 0.014, std = 0.811
curvature mean = 0.027, std = 0.825
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, -8.00) sse = 383110.8, tmin=2.8472
  d=16.00 min @ (0.00, 0.00, 4.00) sse = 365532.1, tmin=4.2834
  d=8.00 min @ (0.00, 2.00, 0.00) sse = 358573.2, tmin=5.7104
  d=2.00 min @ (-0.50, -0.50, 0.00) sse = 357801.0, tmin=8.5686
  d=0.50 min @ (0.00, 0.00, -0.12) sse = 357795.9, tmin=11.4364
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  11.44 min
curvature mean = -0.019, std = 0.794
curvature mean = 0.010, std = 0.927
curvature mean = -0.031, std = 0.791
curvature mean = 0.004, std = 0.968
curvature mean = -0.033, std = 0.789
curvature mean = 0.001, std = 0.985
2 Reading smoothwm
curvature mean = -0.028, std = 0.453
curvature mean = 0.028, std = 0.236
curvature mean = 0.048, std = 0.200
curvature mean = 0.025, std = 0.294
curvature mean = 0.030, std = 0.317
curvature mean = 0.024, std = 0.321
curvature mean = 0.017, std = 0.418
curvature mean = 0.024, std = 0.332
curvature mean = 0.006, std = 0.512
MRISregister() return, current seed 0
-01: dt=0.0000, 78 negative triangles
144: dt=0.9900, 78 negative triangles
145: dt=0.9900, 76 negative triangles
146: dt=0.9900, 73 negative triangles
147: dt=0.9900, 69 negative triangles
148: dt=0.9900, 65 negative triangles
149: dt=0.9900, 64 negative triangles
150: dt=0.9900, 61 negative triangles
151: dt=0.9900, 53 negative triangles
152: dt=0.9900, 58 negative triangles
153: dt=0.9900, 48 negative triangles
154: dt=0.9900, 43 negative triangles
155: dt=0.9900, 42 negative triangles
156: dt=0.9900, 45 negative triangles
157: dt=0.9900, 40 negative triangles
158: dt=0.9900, 35 negative triangles
159: dt=0.9900, 33 negative triangles
160: dt=0.9900, 29 negative triangles
161: dt=0.9900, 28 negative triangles
162: dt=0.9900, 27 negative triangles
163: dt=0.9900, 25 negative triangles
164: dt=0.9900, 22 negative triangles
165: dt=0.9900, 16 negative triangles
166: dt=0.9900, 14 negative triangles
167: dt=0.9900, 17 negative triangles
168: dt=0.9900, 13 negative triangles
169: dt=0.9900, 10 negative triangles
170: dt=0.9900, 11 negative triangles
171: dt=0.9900, 7 negative triangles
172: dt=0.9900, 5 negative triangles
173: dt=0.9900, 8 negative triangles
174: dt=0.9900, 5 negative triangles
175: dt=0.9900, 6 negative triangles
176: dt=0.9900, 3 negative triangles
177: dt=0.9900, 4 negative triangles
178: dt=0.9900, 2 negative triangles
179: dt=0.9900, 3 negative triangles
180: dt=0.9900, 3 negative triangles
181: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.91 hours
mris_register utimesec    7327.402065
mris_register stimesec    5.977091
mris_register ru_maxrss   321300
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   45396
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  13064
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    432057
mris_register ru_nivcsw   267699
FSRUNTIME@ mris_register  1.9106 hours 1 threads
PIDs (17412 17415) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 04:23:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 04:23:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

Waiting for PID 24069 of (24069 24072) to complete...
Waiting for PID 24072 of (24069 24072) 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 (24069 24072) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 04:23:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

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

#--------------------------------------------
#@# AvgCurv rh Sun Oct  8 04:23:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 24115 of (24115 24118) to complete...
Waiting for PID 24118 of (24115 24118) 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 (24115 24118) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 04:23:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

#-----------------------------------------
#@# Cortical Parc rh Sun Oct  8 04:23:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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 24163 of (24163 24166) to complete...
Waiting for PID 24166 of (24163 24166) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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...
2606 labels changed using aseg
relabeling using gibbs priors...
000:   4123 changed, 187799 examined...
001:   1003 changed, 17127 examined...
002:    263 changed, 5538 examined...
003:     92 changed, 1584 examined...
004:     40 changed, 531 examined...
005:     15 changed, 236 examined...
006:      9 changed, 89 examined...
007:      4 changed, 57 examined...
008:      3 changed, 28 examined...
009:      3 changed, 19 examined...
010:      6 changed, 21 examined...
011:      1 changed, 28 examined...
012:      1 changed, 7 examined...
013:      1 changed, 7 examined...
014:      2 changed, 7 examined...
015:      3 changed, 13 examined...
016:      1 changed, 13 examined...
017:      1 changed, 7 examined...
018:      1 changed, 7 examined...
019:      1 changed, 7 examined...
020:      1 changed, 7 examined...
021:      0 changed, 7 examined...
375 labels changed using aseg
000: 165 total segments, 123 labels (632 vertices) changed
001: 41 total segments, 3 labels (9 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
3114 vertices marked for relabeling...
3114 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 19 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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...
2127 labels changed using aseg
relabeling using gibbs priors...
000:   3526 changed, 184579 examined...
001:    810 changed, 15008 examined...
002:    227 changed, 4631 examined...
003:     73 changed, 1269 examined...
004:     27 changed, 427 examined...
005:      7 changed, 159 examined...
006:      2 changed, 35 examined...
007:      2 changed, 15 examined...
008:      2 changed, 14 examined...
009:      2 changed, 12 examined...
010:      0 changed, 11 examined...
168 labels changed using aseg
000: 125 total segments, 81 labels (437 vertices) changed
001: 47 total segments, 3 labels (4 vertices) changed
002: 44 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 10 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2628 vertices marked for relabeling...
2628 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 18 seconds.
PIDs (24163 24166) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 04:24:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050244 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 04:24:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050244 rh 

Waiting for PID 24220 of (24220 24223) to complete...
Waiting for PID 24223 of (24220 24223) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050244 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-6.0.0/0050244/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
42076 bright wm thresholded.
3645 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.orig...
computing class statistics...
border white:    343001 voxels (2.04%)
border gray      395990 voxels (2.36%)
WM (101.0): 101.0 +- 7.5 [70.0 --> 110.0]
GM (77.0) : 76.7 +- 9.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 64.3 (was 70)
setting MAX_BORDER_WHITE to 113.5 (was 105)
setting MIN_BORDER_WHITE to 74.0 (was 85)
setting MAX_CSF to 54.7 (was 40)
setting MAX_GRAY to 98.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 64.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 45.0 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=74+-7.0
mean inside = 97.2, mean outside = 80.0
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.02-->7.88) (max @ vno 91186 --> 186470)
face area 0.33 +- 0.15 (0.00-->8.28)
mean absolute distance = 0.66 +- 0.82
4785 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 143 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 214 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 13 points - only 0.00% unknown
mean border=83.8, 100 (100) missing vertices, mean dist 0.5 [0.9 (%10.5)->0.6 (%89.5))]
%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 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.25 (0.04-->7.98) (max @ vno 91186 --> 186470)
face area 0.33 +- 0.15 (0.00-->7.14)
mean absolute distance = 0.37 +- 0.48
6191 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3164665.0, rms=7.938
001: dt: 0.5000, sse=1657494.8, rms=4.611 (41.907%)
002: dt: 0.5000, sse=1249811.2, rms=3.182 (31.001%)
003: dt: 0.5000, sse=1178912.0, rms=2.868 (9.865%)
004: dt: 0.5000, sse=1125731.8, rms=2.613 (8.900%)
rms = 2.73, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=1021644.7, rms=1.925 (26.306%)
006: dt: 0.2500, sse=982272.5, rms=1.588 (17.514%)
007: dt: 0.2500, sse=973474.6, rms=1.478 (6.941%)
rms = 1.44, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=969770.1, rms=1.436 (2.807%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=964607.1, rms=1.399 (2.630%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 133 points - only 0.00% unknown
deleting segment 1 with 179 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
mean border=87.7, 96 (31) missing vertices, mean dist -0.3 [0.4 (%82.5)->0.3 (%17.5))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.06-->7.98) (max @ vno 91186 --> 186470)
face area 0.35 +- 0.17 (0.00-->8.53)
mean absolute distance = 0.22 +- 0.33
4955 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1825073.4, rms=4.912
010: dt: 0.5000, sse=1281133.5, rms=2.988 (39.176%)
011: dt: 0.5000, sse=1214786.6, rms=2.691 (9.941%)
012: dt: 0.5000, sse=1198769.8, rms=2.628 (2.326%)
rms = 2.83, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=1064235.5, rms=1.739 (33.848%)
014: dt: 0.2500, sse=1020992.1, rms=1.291 (25.758%)
015: dt: 0.2500, sse=1011194.4, rms=1.169 (9.410%)
rms = 1.15, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=1010312.1, rms=1.150 (1.687%)
rms = 1.12, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=1008262.8, rms=1.118 (2.792%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 124 points - only 0.00% unknown
deleting segment 1 with 227 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
mean border=89.7, 102 (16) missing vertices, mean dist -0.1 [0.2 (%74.4)->0.2 (%25.6))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.06-->7.98) (max @ vno 91186 --> 186470)
face area 0.34 +- 0.16 (0.00-->8.26)
mean absolute distance = 0.18 +- 0.28
4671 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1200267.4, rms=2.785
018: dt: 0.5000, sse=1101606.2, rms=2.201 (20.970%)
rms = 2.44, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=1002913.1, rms=1.500 (31.878%)
020: dt: 0.2500, sse=970392.1, rms=1.149 (23.400%)
021: dt: 0.2500, sse=961239.2, rms=1.059 (7.824%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=960975.9, rms=1.052 (0.619%)
rms = 1.02, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=957194.0, rms=1.022 (2.892%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 126 points - only 0.00% unknown
deleting segment 1 with 222 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
deleting segment 4 with 12 points - only 0.00% unknown
mean border=90.3, 105 (15) missing vertices, mean dist -0.0 [0.2 (%56.6)->0.2 (%43.4))]
%93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=964717.3, rms=1.249
rms = 1.24, time step reduction 1 of 3 to 0.250...
024: dt: 0.5000, sse=965505.1, rms=1.235 (1.074%)
025: dt: 0.2500, sse=940986.8, rms=0.971 (21.437%)
026: dt: 0.2500, sse=930879.4, rms=0.831 (14.411%)
rms = 0.88, time step reduction 2 of 3 to 0.125...
rms = 0.81, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=928371.2, rms=0.811 (2.358%)
positioning took 0.6 minutes
generating cortex label...
7 non-cortical segments detected
only using segment with 9162 vertices
erasing segment 1 (vno[0] = 139515)
erasing segment 2 (vno[0] = 139581)
erasing segment 3 (vno[0] = 140666)
erasing segment 4 (vno[0] = 142788)
erasing segment 5 (vno[0] = 143968)
erasing segment 6 (vno[0] = 187469)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.02-->7.98) (max @ vno 91186 --> 186470)
face area 0.33 +- 0.16 (0.00-->7.99)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 11 points - only 0.00% unknown
deleting segment 1 with 18 points - only 0.00% unknown
deleting segment 3 with 81 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=62.7, 146 (146) missing vertices, mean dist 1.6 [0.2 (%0.0)->3.0 (%100.0))]
%13 local maxima, %39 large gradients and %43 min vals, 446 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=29569696.0, rms=28.217
001: dt: 0.0500, sse=26023508.0, rms=26.415 (6.386%)
002: dt: 0.0500, sse=23517618.0, rms=25.064 (5.117%)
003: dt: 0.0500, sse=21625024.0, rms=23.992 (4.274%)
004: dt: 0.0500, sse=20118284.0, rms=23.104 (3.703%)
005: dt: 0.0500, sse=18870494.0, rms=22.341 (3.301%)
006: dt: 0.0500, sse=17807692.0, rms=21.670 (3.002%)
007: dt: 0.0500, sse=16882478.0, rms=21.069 (2.775%)
008: dt: 0.0500, sse=16064107.0, rms=20.522 (2.595%)
009: dt: 0.0500, sse=15331704.0, rms=20.020 (2.446%)
010: dt: 0.0500, sse=14669046.0, rms=19.555 (2.324%)
positioning took 1.3 minutes
mean border=62.5, 105 (69) missing vertices, mean dist 1.4 [0.2 (%0.1)->2.5 (%99.9))]
%15 local maxima, %39 large gradients and %42 min vals, 434 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=15596740.0, rms=20.205
011: dt: 0.0500, sse=14990138.0, rms=19.784 (2.086%)
012: dt: 0.0500, sse=14435823.0, rms=19.391 (1.987%)
013: dt: 0.0500, sse=13926265.0, rms=19.022 (1.901%)
014: dt: 0.0500, sse=13456710.0, rms=18.676 (1.820%)
015: dt: 0.0500, sse=13022976.0, rms=18.350 (1.744%)
016: dt: 0.0500, sse=12621530.0, rms=18.044 (1.672%)
017: dt: 0.0500, sse=12249146.0, rms=17.754 (1.604%)
018: dt: 0.0500, sse=11903546.0, rms=17.481 (1.537%)
019: dt: 0.0500, sse=11581967.0, rms=17.223 (1.475%)
020: dt: 0.0500, sse=11281861.0, rms=16.979 (1.419%)
positioning took 1.3 minutes
mean border=62.4, 125 (55) missing vertices, mean dist 1.2 [0.1 (%0.4)->2.1 (%99.6))]
%15 local maxima, %39 large gradients and %42 min vals, 409 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=11377657.0, rms=17.064
021: dt: 0.0500, sse=11093896.0, rms=16.831 (1.367%)
022: dt: 0.0500, sse=10827935.0, rms=16.609 (1.317%)
023: dt: 0.0500, sse=10577286.0, rms=16.398 (1.274%)
024: dt: 0.0500, sse=10340558.0, rms=16.195 (1.235%)
025: dt: 0.0500, sse=10116106.0, rms=16.001 (1.201%)
026: dt: 0.0500, sse=9902000.0, rms=15.813 (1.174%)
027: dt: 0.0500, sse=9696903.0, rms=15.631 (1.152%)
028: dt: 0.0500, sse=9499123.0, rms=15.453 (1.137%)
029: dt: 0.0500, sse=9307453.0, rms=15.279 (1.128%)
030: dt: 0.0500, sse=9120865.0, rms=15.107 (1.124%)
positioning took 1.3 minutes
mean border=62.3, 135 (41) missing vertices, mean dist 1.0 [0.1 (%3.1)->1.9 (%96.9))]
%15 local maxima, %39 large gradients and %42 min vals, 353 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=9200691.0, rms=15.182
031: dt: 0.5000, sse=7822281.5, rms=13.855 (8.746%)
032: dt: 0.5000, sse=6682468.5, rms=12.646 (8.720%)
033: dt: 0.5000, sse=5685277.0, rms=11.487 (9.172%)
034: dt: 0.5000, sse=4803516.0, rms=10.350 (9.893%)
035: dt: 0.5000, sse=4024174.2, rms=9.232 (10.802%)
036: dt: 0.5000, sse=3366889.8, rms=8.168 (11.523%)
037: dt: 0.5000, sse=2810432.2, rms=7.149 (12.483%)
038: dt: 0.5000, sse=2387680.8, rms=6.262 (12.405%)
039: dt: 0.5000, sse=2086820.1, rms=5.549 (11.388%)
040: dt: 0.5000, sse=1908335.1, rms=5.074 (8.556%)
041: dt: 0.5000, sse=1803431.1, rms=4.777 (5.847%)
042: dt: 0.5000, sse=1754439.1, rms=4.628 (3.123%)
043: dt: 0.5000, sse=1720174.5, rms=4.524 (2.254%)
rms = 4.48, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1706480.8, rms=4.480 (0.979%)
045: dt: 0.2500, sse=1559584.5, rms=3.939 (12.056%)
046: dt: 0.2500, sse=1519156.5, rms=3.792 (3.756%)
rms = 3.78, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1517359.5, rms=3.781 (0.289%)
048: dt: 0.1250, sse=1488363.6, rms=3.666 (3.043%)
rms = 3.65, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1483939.4, rms=3.649 (0.454%)
positioning took 3.3 minutes
mean border=61.3, 3722 (7) missing vertices, mean dist 0.1 [0.2 (%45.2)->0.5 (%54.8))]
%28 local maxima, %28 large gradients and %38 min vals, 215 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=1881648.8, rms=4.157
050: dt: 0.5000, sse=1830292.0, rms=3.992 (3.971%)
051: dt: 0.5000, sse=1803034.4, rms=3.931 (1.527%)
rms = 4.04, time step reduction 1 of 3 to 0.250...
052: dt: 0.2500, sse=1655356.0, rms=3.312 (15.753%)
053: dt: 0.2500, sse=1618125.1, rms=3.128 (5.559%)
rms = 3.10, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1611602.8, rms=3.097 (0.974%)
055: dt: 0.1250, sse=1582357.0, rms=2.951 (4.722%)
rms = 2.92, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1576210.5, rms=2.923 (0.959%)
positioning took 1.7 minutes
mean border=60.5, 3925 (5) missing vertices, mean dist 0.1 [0.2 (%42.1)->0.3 (%57.9))]
%41 local maxima, %16 large gradients and %37 min vals, 206 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=1648528.2, rms=3.250
rms = 3.65, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1602416.2, rms=3.035 (6.600%)
058: dt: 0.2500, sse=1589242.9, rms=2.975 (1.986%)
rms = 2.96, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1584541.4, rms=2.961 (0.470%)
060: dt: 0.1250, sse=1566436.0, rms=2.868 (3.129%)
rms = 2.84, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1561053.0, rms=2.844 (0.845%)
positioning took 1.4 minutes
mean border=59.9, 7582 (4) missing vertices, mean dist 0.0 [0.2 (%45.4)->0.2 (%54.6))]
%44 local maxima, %13 large gradients and %36 min vals, 208 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-6.0.0/0050244/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1585110.9, rms=2.950
rms = 3.22, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1565467.1, rms=2.852 (3.325%)
063: dt: 0.2500, sse=1550655.5, rms=2.793 (2.064%)
rms = 2.78, time step reduction 2 of 3 to 0.125...
064: dt: 0.2500, sse=1546113.2, rms=2.777 (0.567%)
065: dt: 0.1250, sse=1527925.1, rms=2.680 (3.501%)
rms = 2.66, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1522669.0, rms=2.656 (0.883%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.area.pial
vertex spacing 1.01 +- 0.44 (0.06-->8.79) (max @ vno 186675 --> 186540)
face area 0.40 +- 0.32 (0.00-->10.88)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 187799 vertices processed
25000 of 187799 vertices processed
50000 of 187799 vertices processed
75000 of 187799 vertices processed
100000 of 187799 vertices processed
125000 of 187799 vertices processed
150000 of 187799 vertices processed
175000 of 187799 vertices processed
0 of 187799 vertices processed
25000 of 187799 vertices processed
50000 of 187799 vertices processed
75000 of 187799 vertices processed
100000 of 187799 vertices processed
125000 of 187799 vertices processed
150000 of 187799 vertices processed
175000 of 187799 vertices processed
thickness calculation complete, 454:1216 truncations.
40655 vertices at 0 distance
128873 vertices at 1 distance
118014 vertices at 2 distance
49476 vertices at 3 distance
15848 vertices at 4 distance
4793 vertices at 5 distance
1592 vertices at 6 distance
597 vertices at 7 distance
213 vertices at 8 distance
79 vertices at 9 distance
61 vertices at 10 distance
27 vertices at 11 distance
31 vertices at 12 distance
25 vertices at 13 distance
21 vertices at 14 distance
29 vertices at 15 distance
22 vertices at 16 distance
20 vertices at 17 distance
18 vertices at 18 distance
26 vertices at 19 distance
28 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.thickness
positioning took 20.8 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050244 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-6.0.0/0050244/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
42076 bright wm thresholded.
3645 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.orig...
computing class statistics...
border white:    343001 voxels (2.04%)
border gray      395990 voxels (2.36%)
WM (101.0): 101.0 +- 7.5 [70.0 --> 110.0]
GM (77.0) : 76.7 +- 9.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 64.3 (was 70)
setting MAX_BORDER_WHITE to 113.5 (was 105)
setting MIN_BORDER_WHITE to 74.0 (was 85)
setting MAX_CSF to 54.7 (was 40)
setting MAX_GRAY to 98.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 64.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 45.0 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-4.3,    GM=74+-7.8
mean inside = 97.4, mean outside = 80.5
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 0.89 +- 0.25 (0.02-->11.82) (max @ vno 81395 --> 184006)
face area 0.33 +- 0.16 (0.00-->20.44)
mean absolute distance = 0.67 +- 0.83
5502 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 2 with 201 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 5 with 8 points - only 0.00% unknown
deleting segment 7 with 42 points - only 0.00% unknown
deleting segment 8 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 19 points - only 0.00% unknown
deleting segment 14 with 71 points - only 0.00% unknown
mean border=84.1, 90 (90) missing vertices, mean dist 0.5 [0.9 (%10.3)->0.6 (%89.7))]
%71 local maxima, %25 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-->12.00) (max @ vno 184006 --> 81395)
face area 0.33 +- 0.16 (0.00-->19.38)
mean absolute distance = 0.38 +- 0.49
6002 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3114724.2, rms=7.924
001: dt: 0.5000, sse=1656931.5, rms=4.676 (40.994%)
002: dt: 0.5000, sse=1248021.5, rms=3.227 (30.976%)
003: dt: 0.5000, sse=1164879.6, rms=2.880 (10.759%)
004: dt: 0.5000, sse=1110623.6, rms=2.610 (9.374%)
rms = 2.72, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=1011164.6, rms=1.943 (25.546%)
006: dt: 0.2500, sse=974625.6, rms=1.619 (16.672%)
007: dt: 0.2500, sse=961922.3, rms=1.508 (6.850%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=957462.4, rms=1.459 (3.276%)
rms = 1.42, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=954330.9, rms=1.424 (2.398%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 1 with 180 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 37 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 72 points - only 0.00% unknown
removing 2 vertex label from ripped group
mean border=88.0, 82 (20) missing vertices, mean dist -0.3 [0.4 (%83.1)->0.3 (%16.9))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.04-->12.03) (max @ vno 184006 --> 81395)
face area 0.35 +- 0.18 (0.00-->22.56)
mean absolute distance = 0.22 +- 0.32
4693 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1796176.8, rms=4.894
010: dt: 0.5000, sse=1269398.0, rms=3.019 (38.324%)
011: dt: 0.5000, sse=1206018.0, rms=2.718 (9.969%)
012: dt: 0.5000, sse=1185210.2, rms=2.630 (3.211%)
rms = 2.79, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=1059859.5, rms=1.792 (31.884%)
014: dt: 0.2500, sse=1012949.3, rms=1.338 (25.305%)
015: dt: 0.2500, sse=999832.2, rms=1.195 (10.695%)
rms = 1.16, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=997354.9, rms=1.160 (2.964%)
rms = 1.13, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=995823.1, rms=1.127 (2.793%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 1 with 192 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 40 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 16 points - only 0.00% unknown
deleting segment 9 with 69 points - only 0.00% unknown
mean border=90.1, 101 (11) missing vertices, mean dist -0.1 [0.2 (%74.6)->0.2 (%25.4))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.05-->12.05) (max @ vno 184006 --> 81395)
face area 0.34 +- 0.17 (0.00-->22.20)
mean absolute distance = 0.18 +- 0.27
4559 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1183063.8, rms=2.788
018: dt: 0.5000, sse=1091248.0, rms=2.148 (22.946%)
rms = 2.36, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=989944.1, rms=1.483 (30.983%)
020: dt: 0.2500, sse=962063.1, rms=1.144 (22.829%)
021: dt: 0.2500, sse=950838.6, rms=1.060 (7.347%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=950379.1, rms=1.051 (0.849%)
rms = 1.02, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=948835.1, rms=1.023 (2.701%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 1 with 209 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 4 with 39 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 16 points - only 0.00% unknown
deleting segment 9 with 69 points - only 0.00% unknown
removing 2 vertex label from ripped group
mean border=90.6, 103 (11) missing vertices, mean dist -0.0 [0.2 (%56.8)->0.2 (%43.2))]
%93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=955225.2, rms=1.245
rms = 1.21, time step reduction 1 of 3 to 0.250...
024: dt: 0.5000, sse=963990.6, rms=1.214 (2.541%)
025: dt: 0.2500, sse=932840.2, rms=0.972 (19.952%)
026: dt: 0.2500, sse=920449.5, rms=0.831 (14.477%)
rms = 0.87, time step reduction 2 of 3 to 0.125...
rms = 0.81, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=918085.9, rms=0.815 (1.969%)
positioning took 0.6 minutes
generating cortex label...
15 non-cortical segments detected
only using segment with 8769 vertices
erasing segment 1 (vno[0] = 108767)
erasing segment 2 (vno[0] = 119811)
erasing segment 3 (vno[0] = 125320)
erasing segment 4 (vno[0] = 125600)
erasing segment 5 (vno[0] = 136584)
erasing segment 6 (vno[0] = 136609)
erasing segment 7 (vno[0] = 136621)
erasing segment 8 (vno[0] = 137818)
erasing segment 9 (vno[0] = 140051)
erasing segment 10 (vno[0] = 141255)
erasing segment 11 (vno[0] = 142382)
erasing segment 12 (vno[0] = 143485)
erasing segment 13 (vno[0] = 150232)
erasing segment 14 (vno[0] = 184330)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.area
vertex spacing 0.89 +- 0.26 (0.02-->12.10) (max @ vno 81395 --> 184006)
face area 0.33 +- 0.17 (0.00-->22.31)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=62.9, 84 (84) missing vertices, mean dist 1.6 [0.9 (%0.0)->3.0 (%100.0))]
%13 local maxima, %38 large gradients and %45 min vals, 391 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=29439994.0, rms=28.387
001: dt: 0.0500, sse=25999080.0, rms=26.622 (6.217%)
002: dt: 0.0500, sse=23563308.0, rms=25.298 (4.972%)
003: dt: 0.0500, sse=21721522.0, rms=24.249 (4.147%)
004: dt: 0.0500, sse=20255174.0, rms=23.380 (3.583%)
005: dt: 0.0500, sse=19039984.0, rms=22.635 (3.188%)
006: dt: 0.0500, sse=18002462.0, rms=21.978 (2.900%)
007: dt: 0.0500, sse=17099090.0, rms=21.390 (2.676%)
008: dt: 0.0500, sse=16299137.0, rms=20.856 (2.499%)
009: dt: 0.0500, sse=15581823.0, rms=20.364 (2.356%)
010: dt: 0.0500, sse=14932686.0, rms=19.909 (2.235%)
positioning took 1.2 minutes
mean border=62.7, 66 (38) missing vertices, mean dist 1.4 [0.2 (%0.0)->2.5 (%100.0))]
%14 local maxima, %38 large gradients and %44 min vals, 354 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=15886345.0, rms=20.578
011: dt: 0.0500, sse=15290194.0, rms=20.165 (2.008%)
012: dt: 0.0500, sse=14743590.0, rms=19.779 (1.917%)
013: dt: 0.0500, sse=14240140.0, rms=19.416 (1.834%)
014: dt: 0.0500, sse=13775067.0, rms=19.074 (1.758%)
015: dt: 0.0500, sse=13344307.0, rms=18.753 (1.687%)
016: dt: 0.0500, sse=12944967.0, rms=18.449 (1.618%)
017: dt: 0.0500, sse=12573457.0, rms=18.162 (1.555%)
018: dt: 0.0500, sse=12228115.0, rms=17.891 (1.492%)
019: dt: 0.0500, sse=11905878.0, rms=17.635 (1.434%)
020: dt: 0.0500, sse=11605164.0, rms=17.392 (1.378%)
positioning took 1.2 minutes
mean border=62.6, 69 (28) missing vertices, mean dist 1.2 [0.1 (%0.3)->2.2 (%99.7))]
%15 local maxima, %38 large gradients and %44 min vals, 343 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=11721855.0, rms=17.494
021: dt: 0.0500, sse=11436306.0, rms=17.261 (1.330%)
022: dt: 0.0500, sse=11168454.0, rms=17.040 (1.281%)
023: dt: 0.0500, sse=10915449.0, rms=16.828 (1.242%)
024: dt: 0.0500, sse=10676433.0, rms=16.626 (1.203%)
025: dt: 0.0500, sse=10449937.0, rms=16.432 (1.168%)
026: dt: 0.0500, sse=10234168.0, rms=16.244 (1.140%)
027: dt: 0.0500, sse=10027656.0, rms=16.063 (1.117%)
028: dt: 0.0500, sse=9828443.0, rms=15.886 (1.102%)
029: dt: 0.0500, sse=9636065.0, rms=15.713 (1.089%)
030: dt: 0.0500, sse=9448916.0, rms=15.543 (1.083%)
positioning took 1.2 minutes
mean border=62.5, 81 (22) missing vertices, mean dist 1.0 [0.1 (%2.8)->1.9 (%97.2))]
%15 local maxima, %38 large gradients and %43 min vals, 330 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=9541131.0, rms=15.629
031: dt: 0.5000, sse=8170376.0, rms=14.328 (8.324%)
032: dt: 0.5000, sse=7041757.0, rms=13.156 (8.181%)
033: dt: 0.5000, sse=6033816.0, rms=12.012 (8.692%)
034: dt: 0.5000, sse=5113755.5, rms=10.862 (9.574%)
035: dt: 0.5000, sse=4275120.0, rms=9.697 (10.724%)
036: dt: 0.5000, sse=3549074.0, rms=8.562 (11.714%)
037: dt: 0.5000, sse=2937916.2, rms=7.475 (12.688%)
038: dt: 0.5000, sse=2471090.5, rms=6.524 (12.729%)
039: dt: 0.5000, sse=2140710.2, rms=5.758 (11.731%)
040: dt: 0.5000, sse=1937402.5, rms=5.231 (9.163%)
041: dt: 0.5000, sse=1816216.2, rms=4.890 (6.515%)
042: dt: 0.5000, sse=1755083.6, rms=4.707 (3.734%)
043: dt: 0.5000, sse=1716159.0, rms=4.588 (2.531%)
044: dt: 0.5000, sse=1696575.9, rms=4.526 (1.353%)
rms = 4.48, time step reduction 1 of 3 to 0.250...
045: dt: 0.5000, sse=1683153.2, rms=4.484 (0.939%)
046: dt: 0.2500, sse=1540246.0, rms=3.948 (11.938%)
047: dt: 0.2500, sse=1500463.1, rms=3.801 (3.728%)
rms = 3.79, time step reduction 2 of 3 to 0.125...
048: dt: 0.2500, sse=1499607.9, rms=3.794 (0.200%)
049: dt: 0.1250, sse=1470689.5, rms=3.677 (3.074%)
rms = 3.66, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1466479.1, rms=3.661 (0.445%)
positioning took 3.5 minutes
mean border=61.5, 3605 (7) missing vertices, mean dist 0.1 [0.2 (%46.3)->0.5 (%53.7))]
%27 local maxima, %28 large gradients and %39 min vals, 160 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=1826720.0, rms=4.057
051: dt: 0.5000, sse=1794951.4, rms=3.954 (2.527%)
052: dt: 0.5000, sse=1766610.1, rms=3.889 (1.660%)
rms = 4.03, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1625640.6, rms=3.280 (15.654%)
054: dt: 0.2500, sse=1592051.0, rms=3.109 (5.206%)
rms = 3.09, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1589129.2, rms=3.095 (0.456%)
056: dt: 0.1250, sse=1560230.0, rms=2.948 (4.759%)
rms = 2.92, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1554856.4, rms=2.922 (0.855%)
positioning took 1.7 minutes
mean border=60.8, 3956 (7) missing vertices, mean dist 0.1 [0.2 (%43.6)->0.3 (%56.4))]
%39 local maxima, %16 large gradients and %38 min vals, 169 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=1616174.8, rms=3.221
rms = 3.64, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1576581.2, rms=3.034 (5.825%)
rms = 3.00, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1568757.6, rms=3.001 (1.086%)
060: dt: 0.1250, sse=1556631.6, rms=2.938 (2.095%)
rms = 2.91, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1550487.1, rms=2.911 (0.907%)
positioning took 1.1 minutes
mean border=60.3, 7897 (7) missing vertices, mean dist 0.0 [0.2 (%45.2)->0.2 (%54.8))]
%42 local maxima, %13 large gradients and %37 min vals, 147 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-6.0.0/0050244/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1575946.8, rms=3.031
rms = 3.28, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1556998.4, rms=2.938 (3.060%)
063: dt: 0.2500, sse=1542190.0, rms=2.882 (1.903%)
rms = 2.86, time step reduction 2 of 3 to 0.125...
064: dt: 0.2500, sse=1535479.8, rms=2.858 (0.853%)
065: dt: 0.1250, sse=1515921.1, rms=2.755 (3.585%)
rms = 2.73, time step reduction 3 of 3 to 0.062...
066: dt: 0.1250, sse=1510133.8, rms=2.730 (0.926%)
positioning took 1.4 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.area.pial
vertex spacing 1.01 +- 0.44 (0.04-->13.30) (max @ vno 184006 --> 81395)
face area 0.40 +- 0.32 (0.00-->18.20)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 184579 vertices processed
25000 of 184579 vertices processed
50000 of 184579 vertices processed
75000 of 184579 vertices processed
100000 of 184579 vertices processed
125000 of 184579 vertices processed
150000 of 184579 vertices processed
175000 of 184579 vertices processed
0 of 184579 vertices processed
25000 of 184579 vertices processed
50000 of 184579 vertices processed
75000 of 184579 vertices processed
100000 of 184579 vertices processed
125000 of 184579 vertices processed
150000 of 184579 vertices processed
175000 of 184579 vertices processed
thickness calculation complete, 368:1267 truncations.
39741 vertices at 0 distance
123916 vertices at 1 distance
115231 vertices at 2 distance
50514 vertices at 3 distance
16803 vertices at 4 distance
5265 vertices at 5 distance
1833 vertices at 6 distance
598 vertices at 7 distance
218 vertices at 8 distance
98 vertices at 9 distance
80 vertices at 10 distance
46 vertices at 11 distance
33 vertices at 12 distance
37 vertices at 13 distance
27 vertices at 14 distance
23 vertices at 15 distance
20 vertices at 16 distance
19 vertices at 17 distance
17 vertices at 18 distance
10 vertices at 19 distance
25 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.thickness
positioning took 20.5 minutes
PIDs (24220 24223) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 04:44:55 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/lh.cortex.label
Total face volume 372420
Total vertex volume 368593 (mask=0)
#@# 0050244 lh 368593
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 04:44:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/rh.cortex.label
Total face volume 371207
Total vertex volume 367470 (mask=0)
#@# 0050244 rh 367470
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 04:45:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 

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 = 251
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/ribbon.mgz
mris_volmask took 25.02 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 05:10:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 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 0050244 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 05:10:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 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 0050244 rh pial 

Waiting for PID 26444 of (26444 26447 26450 26453) to complete...
Waiting for PID 26447 of (26444 26447 26450 26453) to complete...
Waiting for PID 26450 of (26444 26447 26450 26453) to complete...
Waiting for PID 26453 of (26444 26447 26450 26453) 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 0050244 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 372420
Total vertex volume 368593 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1877   1312   3452  2.860 0.430     0.093     0.015       12     1.1  bankssts
 1824   1174   3931  3.068 0.611     0.125     0.019       32     1.4  caudalanteriorcingulate
 4845   3236  10474  2.924 0.499     0.109     0.020       47     4.0  caudalmiddlefrontal
 2658   1703   5033  2.580 0.527     0.131     0.024       36     2.6  cuneus
 1003    716   3142  3.144 0.996     0.114     0.029       10     1.5  entorhinal
 6589   4445  15446  2.930 0.520     0.124     0.026       93     7.0  fusiform
 9776   6488  20057  2.750 0.478     0.119     0.022      127     8.4  inferiorparietal
 6205   4236  13952  2.747 0.654     0.129     0.030      108     7.9  inferiortemporal
 2881   1871   5684  2.573 1.049     0.122     0.028       45     3.0  isthmuscingulate
 8706   5776  16273  2.422 0.529     0.131     0.029      125     9.9  lateraloccipital
 5760   3787  11875  2.877 0.660     0.131     0.034       90     7.7  lateralorbitofrontal
 6242   3991   9921  2.288 0.672     0.133     0.033       89     8.2  lingual
 3939   2561   7369  2.527 0.766     0.115     0.032       61     5.1  medialorbitofrontal
 6206   4275  16505  3.032 0.613     0.127     0.028      110     7.2  middletemporal
 1359    929   3285  3.208 0.714     0.092     0.014        9     0.8  parahippocampal
 3214   1763   5326  2.851 0.580     0.092     0.032       54     3.2  paracentral
 2822   1917   6520  2.998 0.489     0.125     0.025       37     2.7  parsopercularis
 1582   1047   3872  2.863 0.646     0.155     0.038       36     2.4  parsorbitalis
 2591   1766   5695  2.769 0.498     0.122     0.027       35     2.8  parstriangularis
 2889   1916   3857  2.064 0.492     0.130     0.033       30     3.7  pericalcarine
 9070   5563  15705  2.528 0.656     0.105     0.021       90     7.4  postcentral
 2239   1456   4345  2.708 0.759     0.122     0.021       34     1.7  posteriorcingulate
10247   6322  19992  2.930 0.635     0.115     0.028      105    12.4  precentral
 7995   5293  16031  2.858 0.465     0.121     0.024       98     7.5  precuneus
 2148   1426   4996  3.108 0.647     0.139     0.037       49     2.9  rostralanteriorcingulate
12807   8610  25732  2.625 0.525     0.129     0.028      195    15.0  rostralmiddlefrontal
16600  11114  37554  2.963 0.571     0.120     0.026      199    17.7  superiorfrontal
11490   7446  22413  2.615 0.510     0.112     0.020      128     9.2  superiorparietal
 7367   4922  17033  3.055 0.657     0.102     0.020       79     5.6  superiortemporal
 8594   5765  17329  2.825 0.470     0.110     0.019      102     6.5  supramarginal
  392    273   1124  2.713 0.614     0.181     0.045       13     0.7  frontalpole
  741    556   3279  3.591 1.005     0.149     0.045       15     1.5  temporalpole
 1002    593   1656  2.525 0.629     0.127     0.049       21     1.8  transversetemporal
 4486   2995   9708  3.250 0.800     0.114     0.032       49     5.4  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 0050244 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 372420
Total vertex volume 368593 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1877   1134   3452  2.860 0.430     0.116     0.029       21     2.6  bankssts
 1824   1436   3931  3.068 0.611     0.140     0.032       51     2.3  caudalanteriorcingulate
 4845   3772  10474  2.924 0.499     0.120     0.025       53     5.3  caudalmiddlefrontal
 2658   2238   5033  2.580 0.527     0.143     0.035       31     4.1  cuneus
 1003   1246   3142  3.144 0.996     0.186     0.044       11     2.2  entorhinal
 6589   5893  15446  2.930 0.520     0.150     0.036       91    10.9  fusiform
 9776   8024  20057  2.750 0.478     0.139     0.028      177    12.6  inferiorparietal
 6205   5647  13952  2.747 0.654     0.165     0.039      102    11.6  inferiortemporal
 2881   2384   5684  2.573 1.049     0.136     0.032       41     3.8  isthmuscingulate
 8706   7539  16273  2.422 0.529     0.148     0.031      114    12.6  lateraloccipital
 5760   4394  11875  2.877 0.660     0.137     0.038       94     9.6  lateralorbitofrontal
 6242   4651   9921  2.288 0.672     0.130     0.032       78     9.3  lingual
 3939   3195   7369  2.527 0.766     0.147     0.038       55     6.6  medialorbitofrontal
 6206   6274  16505  3.032 0.613     0.163     0.033       85     9.3  middletemporal
 1359   1158   3285  3.208 0.714     0.121     0.027       13     1.7  parahippocampal
 3214   2026   5326  2.851 0.580     0.088     0.019       37     2.6  paracentral
 2822   2375   6520  2.998 0.489     0.154     0.038       54     4.7  parsopercularis
 1582   1617   3872  2.863 0.646     0.174     0.040       23     3.0  parsorbitalis
 2591   2239   5695  2.769 0.498     0.155     0.034       35     4.1  parstriangularis
 2889   1789   3857  2.064 0.492     0.125     0.034       38     4.4  pericalcarine
 9070   6799  15705  2.528 0.656     0.115     0.023       94     9.1  postcentral
 2239   1729   4345  2.708 0.759     0.147     0.037       82     3.3  posteriorcingulate
10247   7254  19992  2.930 0.635     0.110     0.024      115    10.6  precentral
 7995   5801  16031  2.858 0.465     0.126     0.030      107    10.3  precuneus
 2148   1882   4996  3.108 0.647     0.161     0.043       34     4.1  rostralanteriorcingulate
12807  10609  25732  2.625 0.525     0.148     0.031      170    18.0  rostralmiddlefrontal
16600  13417  37554  2.963 0.571     0.135     0.029      216    21.4  superiorfrontal
11490   9265  22413  2.615 0.510     0.126     0.025      127    12.4  superiorparietal
 7367   6092  17033  3.055 0.657     0.140     0.033      114    11.4  superiortemporal
 8594   6442  17329  2.825 0.470     0.125     0.027      119    10.0  supramarginal
  392    514   1124  2.713 0.614     0.239     0.041        8     0.8  frontalpole
  741   1194   3279  3.591 1.005     0.244     0.049       10     1.7  temporalpole
 1002    756   1656  2.525 0.629     0.141     0.048       16     1.8  transversetemporal
 4486   2947   9708  3.250 0.800     0.152     0.051       94    10.3  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 0050244 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 371207
Total vertex volume 367470 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1801   1273   3419  2.713 0.431     0.098     0.016       13     1.0  bankssts
 1271    848   2432  2.542 0.787     0.137     0.025       25     1.0  caudalanteriorcingulate
 5860   3856  13095  3.000 0.497     0.111     0.022       63     4.9  caudalmiddlefrontal
 2171   1400   4198  2.601 0.480     0.135     0.034       28     2.8  cuneus
  891    586   2875  3.304 0.903     0.137     0.058       13     2.1  entorhinal
 6292   4264  14543  2.905 0.580     0.123     0.025       85     6.2  fusiform
10764   7268  22770  2.716 0.547     0.121     0.022      140     9.4  inferiorparietal
 7226   4895  16293  2.802 0.672     0.134     0.034      137    10.2  inferiortemporal
 2106   1345   4277  2.612 1.011     0.117     0.027       27     2.2  isthmuscingulate
 9230   6242  17223  2.381 0.593     0.135     0.026      131     9.8  lateraloccipital
 6582   4347  12904  2.813 0.637     0.125     0.033       89     8.4  lateralorbitofrontal
 5015   3291   9003  2.451 0.606     0.137     0.036       76     7.0  lingual
 3731   2500   7529  2.744 0.638     0.123     0.031       63     5.0  medialorbitofrontal
 7451   5249  18893  3.051 0.606     0.131     0.025      115     7.5  middletemporal
 1304    869   2999  3.068 0.652     0.085     0.022        9     1.2  parahippocampal
 4048   2329   7306  2.888 0.491     0.102     0.023       32     4.0  paracentral
 2335   1513   5673  3.212 0.572     0.111     0.021       28     2.0  parsopercularis
 1936   1232   4953  3.060 0.529     0.143     0.036       39     2.5  parsorbitalis
 2693   1794   5451  2.935 0.482     0.125     0.025       33     2.8  parstriangularis
 2508   1697   2970  1.956 0.464     0.142     0.031       28     3.4  pericalcarine
 9016   5543  15160  2.477 0.740     0.107     0.021       87     7.7  postcentral
 2631   1724   5625  2.929 0.675     0.143     0.031       47     3.2  posteriorcingulate
 9676   5908  18323  2.951 0.711     0.108     0.024       82     9.8  precentral
 8120   5370  15561  2.730 0.505     0.125     0.025      105     7.8  precuneus
 1629   1060   3507  2.940 0.442     0.126     0.032       39     1.8  rostralanteriorcingulate
13630   9046  27423  2.702 0.486     0.130     0.029      205    15.3  rostralmiddlefrontal
15778  10459  37504  3.104 0.540     0.118     0.024      178    15.1  superiorfrontal
10401   6784  19982  2.559 0.509     0.118     0.022      132     9.1  superiorparietal
 6127   4060  15263  3.314 0.587     0.103     0.018       57     4.6  superiortemporal
 6793   4518  14139  2.896 0.526     0.114     0.021       74     5.7  supramarginal
  592    383   1532  3.011 0.474     0.167     0.045       14     1.0  frontalpole
 1005    732   4383  3.805 0.838     0.140     0.038       18     1.7  temporalpole
  689    367    954  2.591 0.600     0.123     0.061       11     2.0  transversetemporal
 4107   2842   9287  3.194 0.805     0.124     0.037       48     6.5  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 0050244 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 371207
Total vertex volume 367470 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1801   1195   3419  2.713 0.431     0.111     0.027       20     2.1  bankssts
 1271   1025   2432  2.542 0.787     0.147     0.041       33     1.8  caudalanteriorcingulate
 5860   4695  13095  3.000 0.497     0.129     0.026       69     6.9  caudalmiddlefrontal
 2171   1835   4198  2.601 0.480     0.147     0.036       31     3.5  cuneus
  891   1109   2875  3.304 0.903     0.191     0.038       11     1.8  entorhinal
 6292   5553  14543  2.905 0.580     0.146     0.033       85     9.8  fusiform
10764   8965  22770  2.716 0.547     0.135     0.027      129    13.1  inferiorparietal
 7226   6538  16293  2.802 0.672     0.161     0.038      101    13.5  inferiortemporal
 2106   1777   4277  2.612 1.011     0.150     0.044       40     3.7  isthmuscingulate
 9230   7926  17223  2.381 0.593     0.148     0.030      126    12.7  lateraloccipital
 6582   4866  12904  2.813 0.637     0.140     0.042      133    11.4  lateralorbitofrontal
 5015   4096   9003  2.451 0.606     0.146     0.039       84     8.4  lingual
 3731   3042   7529  2.744 0.638     0.139     0.032       46     5.5  medialorbitofrontal
 7451   6765  18893  3.051 0.606     0.147     0.030       98    10.3  middletemporal
 1304   1096   2999  3.068 0.652     0.134     0.035       17     2.0  parahippocampal
 4048   2736   7306  2.888 0.491     0.109     0.025       52     4.5  paracentral
 2335   1998   5673  3.212 0.572     0.143     0.031       23     3.5  parsopercularis
 1936   1966   4953  3.060 0.529     0.158     0.030       35     2.6  parsorbitalis
 2693   1946   5451  2.935 0.482     0.141     0.033       40     4.2  parstriangularis
 2508   1451   2970  1.956 0.464     0.112     0.031       52     3.5  pericalcarine
 9016   6713  15160  2.477 0.740     0.114     0.022       78     8.9  postcentral
 2631   2098   5625  2.929 0.675     0.154     0.042       57     5.0  posteriorcingulate
 9676   6610  18323  2.951 0.711     0.105     0.024      109    10.5  precentral
 8120   5911  15561  2.730 0.505     0.131     0.031      116    11.7  precuneus
 1629   1413   3507  2.940 0.442     0.161     0.041       37     3.0  rostralanteriorcingulate
13630  10891  27423  2.702 0.486     0.144     0.031      204    19.2  rostralmiddlefrontal
15778  13122  37504  3.104 0.540     0.134     0.029      193    19.9  superiorfrontal
10401   8397  19982  2.559 0.509     0.134     0.027      130    12.5  superiorparietal
 6127   5131  15263  3.314 0.587     0.140     0.032       90     9.1  superiortemporal
 6793   5127  14139  2.896 0.526     0.129     0.030      106     8.5  supramarginal
  592    614   1532  3.011 0.474     0.181     0.040        8     1.0  frontalpole
 1005   1499   4383  3.805 0.838     0.233     0.044       18     2.4  temporalpole
  689    402    954  2.591 0.600     0.125     0.038        8     1.2  transversetemporal
 4107   2799   9287  3.194 0.805     0.153     0.047       79     8.5  insula
PIDs (26444 26447 26450 26453) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 05:12:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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 05:12:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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 26559 of (26559 26562) to complete...
Waiting for PID 26562 of (26559 26562) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 2.9   using min determinant for regularization = 0.086
0 singular and 762 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
24 labels changed using aseg
relabeling using gibbs priors...
000:  12141 changed, 187799 examined...
001:   2859 changed, 47531 examined...
002:    812 changed, 14887 examined...
003:    308 changed, 4587 examined...
004:    160 changed, 1800 examined...
005:     91 changed, 859 examined...
006:     46 changed, 514 examined...
007:     27 changed, 266 examined...
008:     12 changed, 160 examined...
009:      7 changed, 66 examined...
010:      4 changed, 47 examined...
011:      1 changed, 26 examined...
012:      0 changed, 7 examined...
0 labels changed using aseg
000: 334 total segments, 238 labels (3593 vertices) changed
001: 108 total segments, 17 labels (173 vertices) changed
002: 91 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 46 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1918 vertices marked for relabeling...
1918 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 25 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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...
3 labels changed using aseg
relabeling using gibbs priors...
000:  11487 changed, 184579 examined...
001:   2662 changed, 45152 examined...
002:    751 changed, 13969 examined...
003:    295 changed, 4323 examined...
004:    147 changed, 1767 examined...
005:     67 changed, 840 examined...
006:     24 changed, 389 examined...
007:     14 changed, 136 examined...
008:     11 changed, 85 examined...
009:      6 changed, 53 examined...
010:      1 changed, 37 examined...
011:      0 changed, 6 examined...
2 labels changed using aseg
000: 334 total segments, 247 labels (3735 vertices) changed
001: 110 total segments, 24 labels (166 vertices) changed
002: 86 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 69 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1654 vertices marked for relabeling...
1654 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 25 seconds.
PIDs (26559 26562) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 05:12:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 05:12:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 rh white 

Waiting for PID 26614 of (26614 26617) to complete...
Waiting for PID 26617 of (26614 26617) 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 0050244 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 372420
Total vertex volume 368593 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1414    977   2689  2.490 0.499     0.140     0.031       23     2.0  G&S_frontomargin
 2302   1584   4773  2.509 0.639     0.137     0.030       37     2.7  G&S_occipital_inf
 2448   1206   4274  2.869 0.563     0.091     0.022       22     2.2  G&S_paracentral
 1924   1305   5003  3.175 0.490     0.119     0.021       26     1.7  G&S_subcentral
 1010    645   2346  2.599 0.583     0.178     0.058       40     3.0  G&S_transv_frontopol
 3401   2300   7059  2.921 0.551     0.117     0.028       56     3.4  G&S_cingul-Ant
 2522   1696   5033  2.934 0.451     0.107     0.018       27     1.8  G&S_cingul-Mid-Ant
 1605   1096   3259  2.839 0.460     0.116     0.018       20     1.1  G&S_cingul-Mid-Post
 1212    790   3716  3.386 0.545     0.145     0.032       22     1.6  G_cingul-Post-dorsal
  512    324   1232  3.017 1.095     0.129     0.042        9     0.8  G_cingul-Post-ventral
 2547   1577   5170  2.538 0.568     0.132     0.030       41     2.9  G_cuneus
 1503   1004   4538  3.299 0.464     0.135     0.032       25     1.9  G_front_inf-Opercular
  627    376   1570  2.906 0.402     0.147     0.034       16     0.8  G_front_inf-Orbital
 1358    919   3644  2.877 0.508     0.138     0.036       25     1.8  G_front_inf-Triangul
 6578   4348  17435  2.953 0.551     0.135     0.031      120     8.3  G_front_middle
11707   7511  29764  3.110 0.596     0.128     0.034      197    14.5  G_front_sup
 1086    724   2461  3.181 0.840     0.129     0.041       16     1.6  G_Ins_lg&S_cent_ins
  988    625   3064  3.613 0.871     0.136     0.046       20     1.7  G_insular_short
 2816   1844   6529  2.699 0.510     0.141     0.026       55     3.2  G_occipital_middle
 1860   1139   3801  2.671 0.553     0.121     0.028       30     2.0  G_occipital_sup
 3037   1976   7746  3.055 0.458     0.128     0.028       53     3.3  G_oc-temp_lat-fusifor
 4397   2675   7243  2.218 0.711     0.141     0.042       74     6.9  G_oc-temp_med-Lingual
 1792   1227   5508  3.322 0.854     0.103     0.021       15     1.6  G_oc-temp_med-Parahip
 4008   2540   9778  2.877 0.756     0.147     0.044       93     6.8  G_orbital
 3509   2205   8641  2.980 0.485     0.133     0.029       65     3.5  G_pariet_inf-Angular
 3855   2589   9331  2.966 0.541     0.121     0.025       63     3.4  G_pariet_inf-Supramar
 4283   2729   9766  2.737 0.518     0.118     0.021       59     3.7  G_parietal_sup
 3663   1893   6208  2.593 0.584     0.105     0.025       43     3.6  G_postcentral
 4181   2283   9434  3.082 0.654     0.112     0.031       54     5.6  G_precentral
 4201   2660  10616  3.038 0.505     0.134     0.030       74     4.8  G_precuneus
 1282    790   3022  2.618 0.787     0.139     0.043       34     2.4  G_rectus
 1140    736   2013  2.536 1.057     0.107     0.052       16     1.8  G_subcallosal
  750    435   1402  2.508 0.647     0.128     0.053       19     1.5  G_temp_sup-G_T_transv
 2337   1509   7358  3.231 0.758     0.127     0.031       46     2.4  G_temp_sup-Lateral
 1083    777   3094  3.688 0.662     0.078     0.012        4     0.6  G_temp_sup-Plan_polar
 1215    822   2572  2.891 0.485     0.076     0.010        6     0.5  G_temp_sup-Plan_tempo
 3243   2179   8654  2.857 0.693     0.147     0.039       87     5.3  G_temporal_inf
 3576   2466  11548  3.272 0.571     0.145     0.035       87     5.1  G_temporal_middle
  367    254    533  2.474 0.349     0.089     0.017        1     0.2  Lat_Fis-ant-Horizont
  523    369    935  2.880 0.437     0.109     0.015        6     0.3  Lat_Fis-ant-Vertical
 1376    901   1915  2.741 0.392     0.106     0.023        9     1.3  Lat_Fis-post
 2141   1386   3671  2.261 0.568     0.139     0.035       31     2.9  Pole_occipital
 2071   1449   7339  3.013 0.978     0.145     0.049       44     4.2  Pole_temporal
 3422   2353   4688  2.215 0.521     0.123     0.028       33     3.8  S_calcarine
 4151   2967   5699  2.255 0.659     0.112     0.022       25     4.1  S_central
 1278    881   2057  2.658 0.344     0.096     0.014        7     0.7  S_cingul-Marginalis
  647    447   1181  3.169 0.462     0.105     0.021        3     0.5  S_circular_insula_ant
 1504   1053   2635  3.195 0.764     0.088     0.015        7     0.9  S_circular_insula_inf
 2230   1492   3476  2.961 0.454     0.099     0.018       10     1.7  S_circular_insula_sup
 1101    760   1949  2.689 0.563     0.107     0.017        8     0.8  S_collat_transv_ant
  614    416    972  2.418 0.558     0.129     0.025        6     0.6  S_collat_transv_post
 3407   2350   5189  2.475 0.352     0.111     0.019       30     2.7  S_front_inf
 2709   1846   3862  2.411 0.424     0.121     0.023       24     2.6  S_front_middle
 4820   3291   8755  2.742 0.436     0.102     0.017       35     3.4  S_front_sup
  549    378    803  2.553 0.267     0.103     0.010        3     0.3  S_interm_prim-Jensen
 3862   2654   6170  2.577 0.365     0.091     0.013       20     2.1  S_intrapariet&P_trans
  820    585   1331  2.261 0.380     0.125     0.022        9     0.7  S_oc_middle&Lunatus
 1991   1370   2929  2.327 0.332     0.103     0.016       15     1.2  S_oc_sup&transversal
 1091    762   1825  2.370 0.443     0.107     0.019        9     0.8  S_occipital_ant
 1152    815   2299  2.726 0.478     0.128     0.023       13     1.1  S_oc-temp_lat
 3249   2265   5307  2.660 0.490     0.104     0.015       24     2.2  S_oc-temp_med&Lingual
  587    420    821  2.191 0.391     0.120     0.020        4     0.6  S_orbital_lateral
  957    667   1384  2.577 0.529     0.096     0.012        5     0.5  S_orbital_med-olfact
 1973   1346   3761  2.912 0.546     0.131     0.029       23     2.3  S_orbital-H_Shaped
 2632   1753   4288  2.727 0.430     0.110     0.018       22     1.9  S_parieto_occipital
 2269   1391   2658  2.178 1.090     0.119     0.020       33     1.4  S_pericallosal
 5473   3653   8753  2.510 0.416     0.106     0.017       51     3.7  S_postcentral
 2022   1363   3296  2.819 0.353     0.117     0.022       17     1.9  S_precentral-inf-part
 1845   1284   3128  2.809 0.448     0.103     0.019       10     1.4  S_precentral-sup-part
 1000    677   1469  2.504 0.550     0.112     0.018        9     0.8  S_suborbital
 1940   1345   3031  2.705 0.343     0.118     0.023       19     1.8  S_subparietal
 2265   1565   3569  2.656 0.478     0.112     0.018       13     1.8  S_temporal_inf
 8552   5849  14803  2.700 0.409     0.101     0.017       64     6.0  S_temporal_sup
  577    395    818  2.668 0.450     0.113     0.017        4     0.5  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 0050244 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 371207
Total vertex volume 367470 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1259    863   2431  2.486 0.528     0.139     0.040       21     1.9  G&S_frontomargin
 1868   1262   3500  2.384 0.570     0.136     0.027       30     2.0  G&S_occipital_inf
 2279   1262   4099  2.689 0.544     0.108     0.026       21     2.7  G&S_paracentral
 1840   1230   4507  3.413 0.413     0.138     0.028       25     2.2  G&S_subcentral
 1653   1070   4077  2.941 0.548     0.156     0.035       37     2.4  G&S_transv_frontopol
 4761   3180  10111  2.946 0.481     0.115     0.024       68     4.4  G&S_cingul-Ant
 1776   1219   3717  3.043 0.422     0.115     0.025       21     1.6  G&S_cingul-Mid-Ant
 2030   1377   4184  2.911 0.505     0.124     0.024       27     1.9  G&S_cingul-Mid-Post
  905    585   2825  3.379 0.497     0.150     0.039       17     1.3  G_cingul-Post-dorsal
  499    315   1380  3.249 0.757     0.114     0.033        8     0.6  G_cingul-Post-ventral
 2074   1351   4037  2.528 0.553     0.155     0.039       33     3.2  G_cuneus
 1838   1151   5249  3.390 0.551     0.124     0.025       28     1.8  G_front_inf-Opercular
  460    284   1359  3.266 0.382     0.146     0.033        9     0.6  G_front_inf-Orbital
 1100    702   2608  3.011 0.420     0.142     0.032       21     1.3  G_front_inf-Triangul
 6856   4290  17989  3.037 0.506     0.132     0.030      124     7.8  G_front_middle
10945   6827  28135  3.199 0.563     0.125     0.028      149    12.6  G_front_sup
  923    680   2400  3.390 0.858     0.151     0.042       14     1.9  G_Ins_lg&S_cent_ins
 1131    721   3164  3.184 1.011     0.138     0.062       23     2.5  G_insular_short
 3030   1987   7747  2.829 0.594     0.139     0.029       63     3.4  G_occipital_middle
 1935   1186   3647  2.429 0.443     0.117     0.029       35     2.1  G_occipital_sup
 3200   2119   7824  2.909 0.545     0.126     0.025       55     3.1  G_oc-temp_lat-fusifor
 2988   1847   5839  2.522 0.667     0.143     0.043       53     4.9  G_oc-temp_med-Lingual
 1649   1067   4812  3.227 0.871     0.116     0.048       21     3.2  G_oc-temp_med-Parahip
 4461   2868  11213  2.961 0.645     0.142     0.039       91     6.2  G_orbital
 4334   2886  11613  2.978 0.578     0.137     0.026       79     4.5  G_pariet_inf-Angular
 3229   2125   8333  3.118 0.552     0.130     0.026       50     3.3  G_pariet_inf-Supramar
 3019   1905   7743  2.881 0.545     0.127     0.024       50     3.0  G_parietal_sup
 3659   1969   6524  2.553 0.603     0.109     0.024       42     3.5  G_postcentral
 4193   2058   8973  3.229 0.659     0.094     0.024       41     4.3  G_precentral
 3657   2337   8686  2.871 0.539     0.136     0.030       65     4.0  G_precuneus
 1028    669   2707  2.690 0.692     0.144     0.054       29     2.3  G_rectus
  724    489   1379  2.859 0.928     0.079     0.026        5     0.4  G_subcallosal
  552    260    824  2.624 0.728     0.127     0.079       12     2.2  G_temp_sup-G_T_transv
 1987   1298   6454  3.459 0.591     0.123     0.024       32     1.8  G_temp_sup-Lateral
 1243    849   3466  3.600 0.828     0.095     0.020        7     1.2  G_temp_sup-Plan_polar
 1055    731   2275  3.001 0.516     0.098     0.013        8     0.5  G_temp_sup-Plan_tempo
 3898   2564  10172  2.860 0.736     0.159     0.050      114     7.8  G_temporal_inf
 4424   3123  13216  3.135 0.629     0.143     0.031       92     5.2  G_temporal_middle
  385    266    652  3.072 0.545     0.104     0.018        2     0.2  Lat_Fis-ant-Horizont
  188    132    345  3.315 0.353     0.094     0.013        1     0.1  Lat_Fis-ant-Vertical
 1530   1015   2419  2.951 0.403     0.097     0.017        7     1.1  Lat_Fis-post
 3775   2502   6854  2.291 0.604     0.145     0.032       56     5.0  Pole_occipital
 2402   1681   8998  3.487 0.898     0.140     0.033       40     3.6  Pole_temporal
 2439   1697   3249  2.250 0.635     0.129     0.026       23     2.7  S_calcarine
 3325   2528   4069  1.932 0.655     0.125     0.026       22     3.6  S_central
 1917   1283   3141  2.728 0.412     0.115     0.022       18     1.7  S_cingul-Marginalis
  705    481   1153  3.159 0.429     0.102     0.019        3     0.6  S_circular_insula_ant
 1313    892   2310  3.290 0.527     0.082     0.010        4     0.5  S_circular_insula_inf
 1627   1092   2745  2.957 0.462     0.100     0.018        7     1.3  S_circular_insula_sup
 1127    813   1999  2.861 0.420     0.099     0.013        6     0.6  S_collat_transv_ant
  568    403    887  2.283 0.429     0.148     0.034        6     0.9  S_collat_transv_post
 3036   2063   5260  2.664 0.445     0.109     0.019       27     2.3  S_front_inf
 3769   2614   6467  2.587 0.392     0.127     0.025       43     3.8  S_front_middle
 4236   2949   7399  2.759 0.416     0.105     0.019       30     3.3  S_front_sup
  474    328    625  2.439 0.332     0.107     0.018        3     0.4  S_interm_prim-Jensen
 4356   2976   6448  2.367 0.339     0.098     0.014       29     2.4  S_intrapariet&P_trans
 1387    933   1719  2.051 0.369     0.109     0.019        8     1.1  S_oc_middle&Lunatus
 1959   1351   2881  2.293 0.399     0.123     0.022       18     1.8  S_oc_sup&transversal
  859    629   1478  2.422 0.471     0.128     0.021       10     0.8  S_occipital_ant
 1342    962   2303  2.623 0.519     0.116     0.017       11     1.1  S_oc-temp_lat
 2934   2081   5036  2.584 0.502     0.109     0.023       24     2.6  S_oc-temp_med&Lingual
  873    611   1311  2.506 0.408     0.130     0.030        8     1.1  S_orbital_lateral
 1155    809   1724  2.630 0.645     0.105     0.019        8     1.2  S_orbital_med-olfact
 2462   1656   4375  2.724 0.464     0.123     0.029       25     3.0  S_orbital-H_Shaped
 2570   1724   3988  2.561 0.441     0.091     0.013       15     1.4  S_parieto_occipital
 2205   1387   2349  2.046 0.824     0.126     0.020       38     1.5  S_pericallosal
 4077   2701   5690  2.382 0.357     0.095     0.015       27     2.6  S_postcentral
 2596   1762   4227  2.902 0.420     0.100     0.018       16     1.8  S_precentral-inf-part
 1777   1204   2865  2.827 0.367     0.089     0.015        9     1.0  S_precentral-sup-part
  510    354    785  3.020 0.620     0.126     0.017        4     0.4  S_suborbital
 2232   1520   3909  2.704 0.479     0.140     0.029       26     2.8  S_subparietal
 2595   1807   4124  2.756 0.430     0.106     0.016       16     1.8  S_temporal_inf
 7973   5495  13934  2.728 0.449     0.102     0.016       59     5.2  S_temporal_sup
  284    199    532  2.832 0.514     0.112     0.028        2     0.3  S_temporal_transverse
PIDs (26614 26617) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 05:13:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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 05:13:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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 26684 of (26684 26687) to complete...
Waiting for PID 26687 of (26684 26687) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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...
2146 labels changed using aseg
relabeling using gibbs priors...
000:   2691 changed, 187799 examined...
001:    615 changed, 12289 examined...
002:    196 changed, 3466 examined...
003:     66 changed, 1156 examined...
004:     37 changed, 403 examined...
005:     16 changed, 215 examined...
006:      9 changed, 91 examined...
007:      8 changed, 64 examined...
008:      5 changed, 52 examined...
009:      3 changed, 22 examined...
010:      0 changed, 17 examined...
212 labels changed using aseg
000: 64 total segments, 31 labels (274 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1610 vertices marked for relabeling...
1610 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 20 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050244 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...
2150 labels changed using aseg
relabeling using gibbs priors...
000:   2507 changed, 184579 examined...
001:    600 changed, 11490 examined...
002:    171 changed, 3405 examined...
003:     70 changed, 998 examined...
004:     34 changed, 421 examined...
005:     15 changed, 177 examined...
006:      6 changed, 92 examined...
007:      4 changed, 37 examined...
008:      2 changed, 22 examined...
009:      3 changed, 16 examined...
010:      0 changed, 10 examined...
161 labels changed using aseg
000: 55 total segments, 22 labels (194 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 7 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1397 vertices marked for relabeling...
1397 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 19 seconds.
PIDs (26684 26687) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 05:13:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 05:13:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 rh white 

Waiting for PID 26739 of (26739 26742) to complete...
Waiting for PID 26742 of (26739 26742) 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 0050244 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 372420
Total vertex volume 368593 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 2795   1837   5645  2.967 0.561     0.114     0.018       39     1.9  caudalanteriorcingulate
 5356   3548  11506  2.915 0.504     0.109     0.021       53     4.5  caudalmiddlefrontal
 3707   2360   7060  2.614 0.550     0.126     0.027       51     3.7  cuneus
  898    640   2965  3.196 1.024     0.113     0.029        9     1.4  entorhinal
 6297   4230  14074  2.918 0.463     0.124     0.026       89     6.4  fusiform
 9670   6394  19681  2.747 0.475     0.118     0.022      125     8.1  inferiorparietal
 6111   4172  15017  2.797 0.700     0.133     0.032      113     8.3  inferiortemporal
 2866   1864   5600  2.572 1.035     0.123     0.028       46     3.0  isthmuscingulate
 8729   5808  16413  2.425 0.533     0.132     0.029      127     9.9  lateraloccipital
 6469   4267  13380  2.837 0.680     0.137     0.037      112     9.4  lateralorbitofrontal
 6381   4076  10211  2.291 0.663     0.133     0.033       90     8.4  lingual
 3200   2064   6273  2.529 0.799     0.117     0.035       57     4.6  medialorbitofrontal
 8445   5862  20647  2.953 0.605     0.122     0.026      127     8.9  middletemporal
 1421    972   3463  3.229 0.714     0.094     0.015       10     0.9  parahippocampal
 3880   2152   6827  2.882 0.586     0.095     0.032       62     4.0  paracentral
 2640   1782   6101  3.023 0.499     0.126     0.028       38     2.8  parsopercularis
 1306    858   2930  2.821 0.487     0.119     0.024       17     1.1  parsorbitalis
 3260   2211   6664  2.724 0.464     0.129     0.026       44     3.5  parstriangularis
 2838   1879   3764  2.055 0.496     0.132     0.033       31     3.9  pericalcarine
10459   6472  18118  2.535 0.636     0.107     0.021      104     8.6  postcentral
 2461   1609   4708  2.697 0.741     0.122     0.021       37     1.9  posteriorcingulate
 9981   6201  19323  2.926 0.635     0.114     0.027       97    11.8  precentral
 7778   5146  16020  2.870 0.470     0.122     0.024       97     7.3  precuneus
 2902   1934   6084  2.990 0.657     0.130     0.032       55     3.3  rostralanteriorcingulate
 9487   6360  19414  2.662 0.567     0.130     0.030      143    11.6  rostralmiddlefrontal
17699  11893  40727  2.912 0.591     0.125     0.028      242    20.0  superiorfrontal
 9362   6088  18104  2.610 0.490     0.108     0.018      100     6.8  superiorparietal
 9321   6300  22000  3.050 0.691     0.104     0.021      102     7.9  superiortemporal
 7616   5130  15559  2.844 0.473     0.112     0.020       92     5.9  supramarginal
  968    571   1607  2.524 0.645     0.128     0.051       21     1.8  transversetemporal
 3836   2551   8708  3.349 0.775     0.109     0.029       39     4.3  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 0050244 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 371207
Total vertex volume 367470 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1476    985   2793  2.582 0.775     0.139     0.025       27     1.3  caudalanteriorcingulate
 6074   4007  13453  2.981 0.509     0.112     0.022       65     5.1  caudalmiddlefrontal
 2839   1841   5419  2.586 0.467     0.127     0.030       33     3.3  cuneus
  858    566   2684  3.271 0.914     0.136     0.058       13     2.0  entorhinal
 5690   3892  12628  2.852 0.533     0.122     0.024       77     5.3  fusiform
10623   7168  22309  2.709 0.560     0.121     0.021      136     9.3  inferiorparietal
 7744   5218  18118  2.851 0.707     0.135     0.035      146    11.0  inferiortemporal
 2131   1363   4272  2.615 0.999     0.117     0.028       28     2.2  isthmuscingulate
 9177   6167  17089  2.386 0.592     0.133     0.026      130     9.8  lateraloccipital
 6945   4618  13954  2.755 0.645     0.133     0.036      103     9.9  lateralorbitofrontal
 4826   3182   8729  2.447 0.595     0.137     0.036       73     6.8  lingual
 2840   1888   6107  2.811 0.695     0.123     0.033       46     3.8  medialorbitofrontal
 9054   6385  22093  2.986 0.597     0.127     0.024      130     8.7  middletemporal
 1337    895   3106  3.067 0.662     0.085     0.022        9     1.2  parahippocampal
 4240   2445   7784  2.904 0.503     0.099     0.022       32     3.9  paracentral
 2811   1812   6714  3.185 0.555     0.117     0.022       35     2.5  parsopercularis
 1463    950   3452  3.064 0.472     0.126     0.029       24     1.5  parsorbitalis
 2819   1874   5670  2.882 0.476     0.128     0.027       39     3.1  parstriangularis
 2529   1698   3018  1.956 0.465     0.142     0.031       30     3.3  pericalcarine
 9877   6071  16518  2.490 0.723     0.109     0.021       96     8.5  postcentral
 2646   1733   5602  2.922 0.677     0.142     0.030       46     3.1  posteriorcingulate
 9232   5613  17749  2.966 0.720     0.108     0.025       80     9.6  precentral
 8252   5474  15953  2.727 0.516     0.125     0.025      108     8.2  precuneus
 2113   1389   4384  2.893 0.494     0.124     0.029       47     2.2  rostralanteriorcingulate
10460   6855  21257  2.739 0.488     0.129     0.028      154    11.4  rostralmiddlefrontal
19390  12903  44527  3.021 0.554     0.121     0.025      239    19.7  superiorfrontal
 8833   5763  17134  2.565 0.510     0.119     0.023      117     7.7  superiorparietal
 8321   5628  21774  3.283 0.686     0.108     0.021       86     7.4  superiortemporal
 6409   4284  13489  2.894 0.521     0.113     0.021       70     5.4  supramarginal
  680    353    940  2.595 0.604     0.120     0.062       11     2.0  transversetemporal
 3735   2584   8750  3.311 0.715     0.119     0.034       41     5.4  insula
PIDs (26739 26742) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 05:14:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 pctsurfcon --s 0050244 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 05:14:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts

 pctsurfcon --s 0050244 --rh-only 

Waiting for PID 26811 of (26811 26819) to complete...
Waiting for PID 26819 of (26811 26819) to complete...

 pctsurfcon --s 0050244 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts/pctsurfcon.log
Sun Oct  8 05:14:51 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-6.0.0/0050244/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-951 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-6.0.0/0050244/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26811/lh.wm.mgh --regheader 0050244 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 = 100634
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26811/lh.wm.mgh
Dim: 187799 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26811/lh.gm.mgh --projfrac 0.3 --regheader 0050244 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 = 124830
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26811/lh.gm.mgh
Dim: 187799 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26811/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26811/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.w-g.pct.mgh --annot 0050244 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/lh.w-g.pct.mgh --annot 0050244 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-951
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/lh.w-g.pct.mgh
Vertex Area is 0.659317 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 0050244 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/scripts/pctsurfcon.log
Sun Oct  8 05:14:51 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-6.0.0/0050244/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-951 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-6.0.0/0050244/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26819/rh.wm.mgh --regheader 0050244 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 = 99390
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26819/rh.wm.mgh
Dim: 184579 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26819/rh.gm.mgh --projfrac 0.3 --regheader 0050244 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 = 122031
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26819/rh.gm.mgh
Dim: 184579 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26819/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/tmp.pctsurfcon.26819/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.w-g.pct.mgh --annot 0050244 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/rh.w-g.pct.mgh --annot 0050244 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-951
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/rh.w-g.pct.mgh
Vertex Area is 0.661538 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 (26811 26819) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 05:14:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2833 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
3122 voxels changed to hypointensity...
5915 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 05:15:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244

 mri_aparc2aseg --s 0050244 --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 05:15:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244

 mri_aparc2aseg --s 0050244 --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 05:15:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244

 mri_aparc2aseg --s 0050244 --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 26987 of (26987 26990 26993) to complete...
Waiting for PID 26990 of (26987 26990 26993) to complete...
Waiting for PID 26993 of (26987 26990 26993) to complete...

 mri_aparc2aseg --s 0050244 --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 0050244
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/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-6.0.0/0050244/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 8.78
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 64
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 91
rescaling Left_Pallidum from 98 --> 97
rescaling Third_Ventricle from 25 --> 40
rescaling Fourth_Ventricle from 22 --> 22
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 87
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 88
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 68
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 48
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 55
  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 = 730817
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 114 changed.
pass 2: 2 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050244 --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 0050244
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/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-6.0.0/0050244/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 8.78
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 64
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 91
rescaling Left_Pallidum from 98 --> 97
rescaling Third_Ventricle from 25 --> 40
rescaling Fourth_Ventricle from 22 --> 22
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 87
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 88
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 68
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 48
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 55
  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 = 730783
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 114 changed.
pass 2: 2 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050244 --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 0050244
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/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-6.0.0/0050244/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 8.78
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 105
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 64
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 91
rescaling Left_Pallidum from 98 --> 97
rescaling Third_Ventricle from 25 --> 40
rescaling Fourth_Ventricle from 22 --> 22
rescaling Brain_Stem from 81 --> 90
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 57
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 93
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 62
rescaling Right_Thalamus_Proper from 85 --> 87
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 88
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 68
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 48
rescaling WM_hypointensities from 78 --> 77
rescaling non_WM_hypointensities from 40 --> 55
  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 = 730783
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 114 changed.
pass 2: 2 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (26987 26990 26993) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 05:23:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri

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

Sun Oct  8 05:23:58 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-6.0.0/0050244/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-951 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-6.0.0/0050244/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-951
machine  x86_64
user     ntraut

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done
 
Started at Sun Oct 8 05:23:58 CEST 2017 
Ended   at Sun Oct  8 05:24:04 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 05:24:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244

 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 0050244 


$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 0050244 
sysname  Linux
hostname tars-951
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1997233 mm^3    (det: 0.975402 )
Computing euler number
orig.nofix lheno =  -64, rheno = -78
orig.nofix lhholes =   33, rhholes = 40
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
Loading mri/norm.mgz
Loading mri/norm.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found  50 segmentations
Computing statistics for each segmentation

Reporting on  45 segmentations
Using PrintSegStat
mri_segstats done
#-----------------------------------------
#@# WMParc Sun Oct  8 05:26:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244

 mri_aparc2aseg --s 0050244 --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 0050244
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-6.0.0/0050244/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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-6.0.0/0050244/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 9653 vertices from left hemi
Ripped 9170 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-6.0.0/0050244/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 = 1339382
Used brute-force search on 1099 voxels
Fixing Parahip LH WM
  Found 8 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 2708.000000
     5 k 31.000000
     6 k 2.000000
     7 k 1.000000
Fixing Parahip RH WM
  Found 10 clusters
     0 k 10.000000
     1 k 1.000000
     2 k 2279.000000
     3 k 1.000000
     4 k 26.000000
     5 k 2.000000
     6 k 3.000000
     7 k 1.000000
     8 k 1.000000
     9 k 1.000000
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 0050244 --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 0050244 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-951
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1997233 mm^3    (det: 0.975402 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
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-6.0.0/0050244/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 05:37:12 CEST 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050244 --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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 28735 of (28735 28741 28747 28752 28757) to complete...
Waiting for PID 28741 of (28735 28741 28747 28752 28757) to complete...
Waiting for PID 28747 of (28735 28741 28747 28752 28757) to complete...
Waiting for PID 28752 of (28735 28741 28747 28752 28757) to complete...
Waiting for PID 28757 of (28735 28741 28747 28752 28757) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 1456
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 5585
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 2310
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 10219
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 304
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4381
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 1282
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 7265
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 1853
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 7637
mri_label2label: Done

PIDs (28735 28741 28747 28752 28757) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 28815 of (28815 28821 28827 28833) to complete...
Waiting for PID 28821 of (28815 28821 28827 28833) to complete...
Waiting for PID 28827 of (28815 28821 28827 28833) to complete...
Waiting for PID 28833 of (28815 28821 28827 28833) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 709
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4779
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 4698
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 18287
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 582
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4763
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 1736
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 5158
mri_label2label: Done

PIDs (28815 28821 28827 28833) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 28891 of (28891 28897 28903 28908 28915) to complete...
Waiting for PID 28897 of (28891 28897 28903 28908 28915) to complete...
Waiting for PID 28903 of (28891 28897 28903 28908 28915) to complete...
Waiting for PID 28908 of (28891 28897 28903 28908 28915) to complete...
Waiting for PID 28915 of (28891 28897 28903 28908 28915) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 2464
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 7105
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 3832
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11946
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 1263
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 3281
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 243
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1533
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 242
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1441
mri_label2label: Done

PIDs (28891 28897 28903 28908 28915) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 29014 of (29014 29020 29026 29031 29038) to complete...
Waiting for PID 29020 of (29014 29020 29026 29031 29038) to complete...
Waiting for PID 29026 of (29014 29020 29026 29031 29038) to complete...
Waiting for PID 29031 of (29014 29020 29026 29031 29038) to complete...
Waiting for PID 29038 of (29014 29020 29026 29031 29038) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 483
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1497
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 720
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2812
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 111
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1615
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 263
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2259
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 899
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 3218
mri_label2label: Done

PIDs (29014 29020 29026 29031 29038) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 29088 of (29088 29094 29100 29105) to complete...
Waiting for PID 29094 of (29088 29094 29100 29105) to complete...
Waiting for PID 29100 of (29088 29094 29100 29105) to complete...
Waiting for PID 29105 of (29088 29094 29100 29105) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 192
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1741
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 2251
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 9286
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 211
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2123
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 582
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1733
mri_label2label: Done

PIDs (29088 29094 29100 29105) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 29191 of (29191 29197 29203 29208 29215) to complete...
Waiting for PID 29197 of (29191 29197 29203 29208 29215) to complete...
Waiting for PID 29203 of (29191 29197 29203 29208 29215) to complete...
Waiting for PID 29208 of (29191 29197 29203 29208 29215) to complete...
Waiting for PID 29215 of (29191 29197 29203 29208 29215) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 1975
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 5380
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 1655
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4989
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 393
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 906
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 83
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 553
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 187799
Number of reverse mapping hits = 100
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 550
mri_label2label: Done

PIDs (29191 29197 29203 29208 29215) completed and logs appended.

 mris_label2annot --s 0050244 --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-6.0.0/0050244/label
cmdline mris_label2annot --s 0050244 --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-951
machine  x86_64
user     ntraut

subject 0050244
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-6.0.0/0050244/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 129943 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050244 --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-6.0.0/0050244/label
cmdline mris_label2annot --s 0050244 --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-951
machine  x86_64
user     ntraut

subject 0050244
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-6.0.0/0050244/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 153985 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 372420
Total vertex volume 368593 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1895    958   3395  2.702 0.561     0.108     0.027       24     2.0  BA1_exvivo
 6255   4048  10795  2.581 0.451     0.105     0.018       59     4.5  BA2_exvivo
 1227    907   1565  2.165 0.505     0.128     0.025        9     1.2  BA3a_exvivo
 3215   2045   5174  2.303 0.696     0.104     0.019       32     2.5  BA3b_exvivo
 2957   1489   5043  2.996 0.727     0.099     0.038       51     4.0  BA4a_exvivo
 1657   1161   2766  2.669 0.705     0.123     0.030       13     2.2  BA4p_exvivo
14651   9334  33707  3.054 0.532     0.115     0.026      168    14.8  BA6_exvivo
 2609   1736   5812  3.017 0.471     0.127     0.026       31     2.7  BA44_exvivo
 4305   2930   8742  2.672 0.499     0.123     0.027       58     4.5  BA45_exvivo
 4892   3204   6838  2.047 0.500     0.135     0.035       63     6.9  V1_exvivo
 9408   6017  16469  2.390 0.599     0.132     0.032      136    11.6  V2_exvivo
 3155   2188   5926  2.493 0.489     0.130     0.025       42     3.2  MT_exvivo
  766    536   2877  3.712 0.657     0.087     0.017        4     0.6  perirhinal_exvivo
  864    618   1937  2.744 0.814     0.125     0.033       11     1.4  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 0050244 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 372420
Total vertex volume 368593 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1372    620   2232  2.618 0.555     0.112     0.029       19     1.7  BA1_exvivo
 2475   1520   4223  2.609 0.497     0.106     0.019       24     1.7  BA2_exvivo
 1079    805   1315  2.117 0.493     0.132     0.026        8     1.1  BA3a_exvivo
 1754   1150   2180  1.887 0.526     0.090     0.015        9     1.1  BA3b_exvivo
 2791   1472   4716  2.950 0.746     0.102     0.040       50     3.7  BA4a_exvivo
 1317    932   2212  2.657 0.756     0.125     0.031       10     1.9  BA4p_exvivo
 8200   5014  18312  3.071 0.568     0.114     0.027       92     9.1  BA6_exvivo
 1627   1102   3897  3.098 0.480     0.137     0.028       22     1.9  BA44_exvivo
 1623   1129   4020  2.794 0.510     0.141     0.035       31     2.3  BA45_exvivo
 5178   3389   7173  2.032 0.507     0.136     0.035       67     7.3  V1_exvivo
 4655   2930   8117  2.343 0.626     0.136     0.036       70     6.5  V2_exvivo
  895    604   1909  2.620 0.506     0.128     0.028       13     1.0  MT_exvivo
  368    262   1404  3.735 0.624     0.073     0.012        1     0.2  perirhinal_exvivo
  480    335   1058  2.690 0.766     0.121     0.038        7     1.0  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 05:41:08 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 0050244 --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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29354 of (29354 29360 29366 29371 29378) to complete...
Waiting for PID 29360 of (29354 29360 29366 29371 29378) to complete...
Waiting for PID 29366 of (29354 29360 29366 29371 29378) to complete...
Waiting for PID 29371 of (29354 29360 29366 29371 29378) to complete...
Waiting for PID 29378 of (29354 29360 29366 29371 29378) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1127
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 5089
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1743
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 8430
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 222
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4202
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 677
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5199
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1670
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 7417
mri_label2label: Done

PIDs (29354 29360 29366 29371 29378) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29435 of (29435 29441 29447 29452) to complete...
Waiting for PID 29441 of (29435 29441 29447 29452) to complete...
Waiting for PID 29447 of (29435 29441 29447 29452) to complete...
Waiting for PID 29452 of (29435 29441 29447 29452) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 578
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 5051
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 3859
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 16115
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1504
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8416
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1968
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7323
mri_label2label: Done

PIDs (29435 29441 29447 29452) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29534 of (29534 29540 29546 29551 29556) to complete...
Waiting for PID 29540 of (29534 29540 29546 29551 29556) to complete...
Waiting for PID 29546 of (29534 29540 29546 29551 29556) to complete...
Waiting for PID 29551 of (29534 29540 29546 29551 29556) to complete...
Waiting for PID 29556 of (29534 29540 29546 29551 29556) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1802
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6529
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 2914
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10930
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 841
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2773
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 234
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1272
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 178
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 930
mri_label2label: Done

PIDs (29534 29540 29546 29551 29556) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 29618 of (29618 29624 29630 29636 29642) to complete...
Waiting for PID 29624 of (29618 29624 29630 29636 29642) to complete...
Waiting for PID 29630 of (29618 29624 29630 29636 29642) to complete...
Waiting for PID 29636 of (29618 29624 29630 29636 29642) to complete...
Waiting for PID 29642 of (29618 29624 29630 29636 29642) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 402
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1278
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 800
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 3488
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 98
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1796
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 216
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2399
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 537
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1925
mri_label2label: Done

PIDs (29618 29624 29630 29636 29642) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 29690 of (29690 29696 29702 29707) to complete...
Waiting for PID 29696 of (29690 29696 29702 29707) to complete...
Waiting for PID 29702 of (29690 29696 29702 29707) to complete...
Waiting for PID 29707 of (29690 29696 29702 29707) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 132
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1621
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1912
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8871
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 243
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1255
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 234
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1412
mri_label2label: Done

PIDs (29690 29696 29702 29707) 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 0050244 --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 0050244 --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 0050244 --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 0050244 --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 0050244 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 29757 of (29757 29763 29769 29774 29780) to complete...
Waiting for PID 29763 of (29757 29763 29769 29774 29780) to complete...
Waiting for PID 29769 of (29757 29763 29769 29774 29780) to complete...
Waiting for PID 29774 of (29757 29763 29769 29774 29780) to complete...
Waiting for PID 29780 of (29757 29763 29769 29774 29780) 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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1245
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4477
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 1266
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4703
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 104
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 372
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 174
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 868
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 0050244 --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 = 0050244
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-6.0.0/0050244/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 184579
Number of reverse mapping hits = 65
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 356
mri_label2label: Done

PIDs (29757 29763 29769 29774 29780) completed and logs appended.

 mris_label2annot --s 0050244 --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-6.0.0/0050244/label
cmdline mris_label2annot --s 0050244 --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-951
machine  x86_64
user     ntraut

subject 0050244
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-6.0.0/0050244/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 131479 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050244 --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-6.0.0/0050244/label
cmdline mris_label2annot --s 0050244 --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-951
machine  x86_64
user     ntraut

subject 0050244
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-6.0.0/0050244/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 154990 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/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 0050244 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 371207
Total vertex volume 367470 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1508    747   2867  2.798 0.570     0.103     0.023       15     1.4  BA1_exvivo
 5330   3411   8693  2.491 0.430     0.101     0.017       46     3.8  BA2_exvivo
 1163    875   1260  1.990 0.534     0.150     0.031       12     1.4  BA3a_exvivo
 2439   1514   3323  1.977 0.733     0.110     0.022       23     2.3  BA3b_exvivo
 2437   1315   4264  2.900 0.687     0.100     0.029       19     3.2  BA4a_exvivo
 1396   1049   2226  2.313 0.778     0.127     0.032        9     2.0  BA4p_exvivo
12556   7554  28003  3.157 0.527     0.103     0.021      113    10.7  BA6_exvivo
 4308   2838   9167  3.096 0.559     0.115     0.022       47     3.9  BA44_exvivo
 5544   3631  11881  2.903 0.535     0.126     0.028       78     5.8  BA45_exvivo
 4301   2811   6145  2.099 0.519     0.139     0.031       53     5.6  V1_exvivo
 8250   5493  15364  2.457 0.590     0.142     0.035      124    11.5  V2_exvivo
 2643   1799   4737  2.466 0.546     0.123     0.021       35     2.1  MT_exvivo
  792    515   2502  3.303 0.914     0.107     0.046        7     1.6  perirhinal_exvivo
  433    313   1361  3.382 0.626     0.112     0.027        3     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 0050244 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050244/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 371207
Total vertex volume 367470 (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) = 1997233 mm^3    (det: 0.975402 )
lhCtxGM: 366895.767 366136.000  diff=  759.8  pctdiff= 0.207
rhCtxGM: 364563.275 363868.000  diff=  695.3  pctdiff= 0.191
lhCtxWM: 308459.939 308974.500  diff= -514.6  pctdiff=-0.167
rhCtxWM: 303686.824 304441.500  diff= -754.7  pctdiff=-0.249
SubCortGMVol  88138.000
SupraTentVol  1452974.806 (1448201.000) diff=4773.806 pctdiff=0.329
SupraTentVolNotVent  1436392.806 (1431619.000) diff=4773.806 pctdiff=0.332
BrainSegVol  1635911.000 (1633484.000) diff=2427.000 pctdiff=0.148
BrainSegVolNotVent  1615820.000 (1615846.806) diff=-26.806 pctdiff=-0.002
BrainSegVolNotVent  1615820.000
CerebellumVol 184042.000
VentChorVol   16582.000
3rd4th5thCSF   3509.000
CSFVol  1082.000, OptChiasmVol   159.000
MaskVol 2189490.000
 1176    555   1881  2.502 0.638     0.103     0.026       12     1.3  BA1_exvivo
 3220   1992   5672  2.527 0.470     0.094     0.015       29     2.1  BA2_exvivo
 1069    800   1014  1.917 0.447     0.162     0.036       12     1.4  BA3a_exvivo
 1826   1200   2000  1.678 0.487     0.100     0.020       12     1.5  BA3b_exvivo
 1685    845   2956  3.052 0.597     0.097     0.028       13     2.0  BA4a_exvivo
 1140    859   1886  2.471 0.876     0.123     0.029        7     1.6  BA4p_exvivo
 7709   4573  16495  3.078 0.548     0.097     0.020       62     5.9  BA6_exvivo
 1121    724   2965  3.444 0.498     0.132     0.028       17     1.3  BA44_exvivo
 1173    775   2996  3.200 0.513     0.135     0.030       18     1.3  BA45_exvivo
 4078   2666   5722  2.098 0.519     0.139     0.031       51     5.4  V1_exvivo
 4248   2783   7781  2.366 0.601     0.143     0.039       64     6.6  V2_exvivo
  357    247    904  2.768 0.741     0.165     0.025        8     0.4  MT_exvivo
  480    310   1443  3.320 0.933     0.098     0.041        4     0.9  perirhinal_exvivo
  307    208    769  3.054 0.657     0.128     0.044        3     0.6  entorhinal_exvivo

Started at Sat Oct 7 19:38:39 CEST 2017 
Ended   at Sun Oct 8 05:44:58 CEST 2017
#@#%# recon-all-run-time-hours 10.105
recon-all -s 0050244 finished without error at Sun Oct  8 05:44:58 CEST 2017