cortical-surfaces-freesurfer/sub-05/scripts/recon-all.log

Thu Aug  8 10:53:42 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005
/opt/freesurfer/5.3.0/bin/recon-all
-i /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz -T2pial -subjid sub005 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subjid sub005
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Actual FREESURFER_HOME /opt/freesurfer/5.3.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    unlimited
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      unlimited
maxlocks     unlimited
maxsignal    16382 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:      99201692   96396048    2805644          0     188520   94505440
-/+ buffers/cache:    1702088   97499604
Swap:     25165780        532   25165248

########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:42-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:43-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:43-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:43-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:43-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:44-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:44-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:44-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:44-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:44-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $

ProgramName: mri_robust_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:49-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $  User: fkaule  Machine: snake4  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /opt/freesurfer/5.3.0/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /opt/freesurfer/5.3.0/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
-cw256 option is now persistent (remove with -clean-cw256)
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/highres001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998148, -0.0400878, -0.0457496)
j_ras = (-0.0459461, 0.989757, 0.135168)
k_ras = (-0.0398624, -0.13702, 0.989766)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Thu Aug  8 10:54:07 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/sub005/anatomy/other/t2w001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998148, -0.0400878, -0.0457496)
j_ras = (-0.0459461, 0.989757, 0.135168)
k_ras = (-0.0398624, -0.13702, 0.989766)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Thu Aug  8 10:54:24 CEST 2013
Found 1 runs
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz 

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz --conform --cw256 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz --conform --cw256 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998148, -0.0400878, -0.0457496)
j_ras = (-0.0459461, 0.989757, 0.135168)
k_ras = (-0.0398624, -0.13702, 0.989766)
Original Data has (0.699913, 0.666667, 0.666667) mm size and (274, 384, 384) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz...

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Aug  8 10:55:05 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz 


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


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

#--------------------------------------------
#@# Talairach Failure Detection Thu Aug  8 10:58:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5432, pval=0.2115 >= threshold=0.0050)

 awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach_avi.log 


 tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach_avi.log 

TalAviQA: 0.96657
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Thu Aug  8 10:58:01 CEST 2013

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
/opt/freesurfer/5.3.0/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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
Thu Aug  8 10:58:01 CEST 2013
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
tmpdir is ./tmp.mri_nu_correct.mni.20260
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20260/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20260/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 4.19095e-09, 3.72529e-09)
j_ras = (7.45058e-09, 1.49012e-08, -1)
k_ras = (-6.0536e-09, 1, -1.49012e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.20260/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Thu Aug  8 10:58:04 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20260/0/
[fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:58:04] running:
  /opt/freesurfer/5.3.0/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20260/0/ ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00140342
[fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:59:11] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20260/nu0.mnc ./tmp.mri_nu_correct.mni.20260/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Thu Aug  8 10:59:18 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.20260/1/
[fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 10:59:18] running:
  /opt/freesurfer/5.3.0/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20260/1/ ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/nu2.imp

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Number of iterations: 50 
CV of field change: 0.00110121
[fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/] [2013-08-08 11:00:10] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20260/nu1.mnc ./tmp.mri_nu_correct.mni.20260/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20260/ones.mgz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20260/ones.mgz 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule

input      ./tmp.mri_nu_correct.mni.20260/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.20260/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
Found 16777216 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20260/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/input.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20260/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/input.mean.dat 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.20260/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                     16777216  16777216.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.20260/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20260/ones.mgz --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/output.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20260/ones.mgz --i ./tmp.mri_nu_correct.mni.20260/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20260/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20260/output.mean.dat 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.20260/ones.mgz
Loading ./tmp.mri_nu_correct.mni.20260/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                     16777216  16777216.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.20260/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.20260/nu2.mnc ./tmp.mri_nu_correct.mni.20260/nu2.mnc mul .93128273976889651174
Saving result to './tmp.mri_nu_correct.mni.20260/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.20260/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.20260/nu2.mnc nu.mgz --like orig.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.20260/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 4.19095e-09, 3.72529e-09)
j_ras = (7.45058e-09, 1.49012e-08, -1)
k_ras = (-6.0536e-09, 1, -1.49012e-08)
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 7 seconds.
mapping (14, 160) to ( 3, 110)
 
 
Thu Aug  8 11:00:56 CEST 2013
mri_nu_correct.mni done

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Aug  8 11:00:58 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mri_normalize -g 1 nu.mgz T1.mgz 

using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
 1.191   0.081   0.051   3.985;
-0.133   1.061   0.435  -29.785;
 0.011  -0.481   1.181  -2.834;
 0.000   0.000   0.000   1.000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 17
Starting OpenSpline(): npoints = 17
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 108
gm peak at 56 (56), valley at 42 (42)
csf peak at 28, setting threshold to 46
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 56 (56), valley at 41 (41)
csf peak at 28, setting threshold to 46
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 48 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Aug  8 11:03:46 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta 



 ======= NUMBER OF OPENMP THREADS = 1 ======= 
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
average std = 23.1   using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7 
total sample mean = 92.0 (1443 zeros)
************************************************
spacing=8, using 3481 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=8.0
skull bounding box = (52, 13, 10) --> (201, 255, 209)
using (102, 94, 110) as brain centroid...
mean wm in atlas = 126, using box (84,64,85) --> (120, 123,134) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 108, scaling input intensities by 1.167
scaling channel 0 by 1.16667
initial log_p = -4.8
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.553914 @ (-9.091, 27.273, -9.091)
max log p =    -4.487499 @ (4.545, -4.545, -4.545)
max log p =    -4.483190 @ (2.273, -6.818, 6.818)
max log p =    -4.472748 @ (1.136, 1.136, -3.409)
max log p =    -4.469653 @ (0.568, -0.568, 0.568)
max log p =    -4.464366 @ (-1.420, 0.284, 2.557)
Found translation: (-2.0, 16.8, -7.1): log p = -4.464
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.5 (thresh=-4.5)
 1.140   0.057  -0.139  -9.943;
 0.000   1.142   0.473  -43.109;
 0.161  -0.469   1.132   4.165;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.226   0.062  -0.149  -20.121;
 0.000   1.228   0.509  -55.426;
 0.149  -0.434   1.047   11.805;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.226   0.062  -0.149  -20.121;
 0.000   1.228   0.509  -55.426;
 0.149  -0.434   1.047   11.805;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
 1.184   0.047  -0.110  -19.960;
-0.012   1.242   0.390  -40.153;
 0.105  -0.320   1.116   0.548;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.184   0.047  -0.110  -19.960;
-0.012   1.242   0.390  -40.153;
 0.105  -0.320   1.116   0.548;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.180   0.063  -0.125  -19.391;
-0.021   1.243   0.402  -40.394;
 0.124  -0.329   1.111  -0.027;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.180   0.063  -0.125  -19.391;
-0.021   1.243   0.402  -40.394;
 0.124  -0.329   1.111  -0.027;
 0.000   0.000   0.000   1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3481 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.18046   0.06254  -0.12483  -19.39090;
-0.02094   1.24275   0.40179  -40.39419;
 0.12427  -0.32903   1.11130  -0.02731;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.18046   0.06254  -0.12483  -19.39090;
-0.02094   1.24275   0.40179  -40.39419;
 0.12427  -0.32903   1.11130  -0.02731;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.180   0.063  -0.125  -19.391;
-0.021   1.243   0.402  -40.394;
 0.124  -0.329   1.111  -0.027;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.8)
transform before final EM align:
 1.180   0.063  -0.125  -19.391;
-0.021   1.243   0.402  -40.394;
 0.124  -0.329   1.111  -0.027;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 382743 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.18046   0.06254  -0.12483  -19.39090;
-0.02094   1.24275   0.40179  -40.39419;
 0.12427  -0.32903   1.11130  -0.02731;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.18046   0.06254  -0.12483  -19.39090;
-0.02094   1.24275   0.40179  -40.39419;
 0.12427  -0.32903   1.11130  -0.02731;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =    4.4  tol 0.000000
final transform:
 1.180   0.063  -0.125  -19.391;
-0.021   1.243   0.402  -40.394;
 0.124  -0.329   1.111  -0.027;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 33 minutes and 41 seconds.

 mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.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=131 y=83 z=112 r=103
      first estimation of the main basin volume: 4591295 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        14 found in the rest of the brain 
      global maximum in x=157, y=91, z=82, Imax=255
      CSF=12, 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=18116230071 voxels, voxel volume =1.000 
                     = 18116230071 mmm3 = 18116229.120 cm3
done.
PostAnalyze...Basin Prior
 70 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=129,y=94, z=108, r=10265 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45567
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1032253284
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1083673940
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1065167473
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1061764480
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=18 , nb = 1080145814
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    4,      6,        30,   50
  after  analyzing :    4,      22,        30,   29
   RIGHT_CER   
  before analyzing :    4,      4,        24,   64
  after  analyzing :    4,      18,        25,   29
   LEFT_CER    
  before analyzing :    5,      6,        25,   59
  after  analyzing :    5,      18,        25,   28
  RIGHT_BRAIN  
  before analyzing :    4,      6,        30,   50
  after  analyzing :    4,      22,        30,   29
  LEFT_BRAIN   
  before analyzing :    4,      6,        29,   50
  after  analyzing :    4,      21,        29,   28
     OTHER     
  before analyzing :    18,      23,        30,   50
  after  analyzing :    18,      27,        30,   32
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...66 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.012
curvature mean = 69.916, std = 7.602

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.44, sigma = 7.07
      after  rotation: sse = 3.44, sigma = 7.07
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  4.27, its var is 10.70   
      before Erosion-Dilatation  2.14% 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...31 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1621646 voxels, voxel volume = 1.000 mm3
           = 1621646 mmm3 = 1621.646 cm3


******************************
Saving brainmask.auto.mgz
done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Thu Aug  8 11:37:54 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta 



 ======= NUMBER OF OPENMP THREADS = 1 ======= 
aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'...
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 14.9 or > 790.2 
total sample mean = 84.4 (994 zeros)
************************************************
spacing=8, using 2772 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2772, passno 0, spacing 8
resetting wm mean[0]: 102 --> 107
resetting gm mean[0]: 64 --> 64
input volume #1 is the most T1-like
using real data threshold=21.0
skull bounding box = (65, 37, 29) --> (193, 173, 196)
using (108, 82, 113) as brain centroid...
mean wm in atlas = 107, using box (92,65,92) --> (123, 98,133) to find MRI wm
before smoothing, mri peak at 107
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.5
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.085262 @ (-9.091, 27.273, -9.091)
max log p =    -4.023158 @ (4.545, -4.545, -4.545)
max log p =    -4.007773 @ (2.273, -2.273, 2.273)
max log p =    -3.975749 @ (-1.136, 1.136, -1.136)
max log p =    -3.940902 @ (-0.568, 0.568, 1.705)
max log p =    -3.933861 @ (-0.284, 2.557, 0.852)
Found translation: (-4.3, 24.7, -9.9): log p = -3.934
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.9 (thresh=-3.9)
 1.150   0.000   0.000  -23.922;
 0.000   1.111   0.298  -20.026;
 0.000  -0.236   0.883   25.853;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6)
 1.150   0.000   0.000  -23.922;
 0.000   1.111   0.298  -20.026;
 0.000  -0.236   0.883   25.853;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.6)
 1.101   0.054  -0.075  -14.044;
-0.045   1.144   0.243  -11.221;
 0.111  -0.172   0.947  -0.263;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
 1.104   0.046  -0.045  -17.138;
-0.038   1.152   0.310  -18.537;
 0.079  -0.253   0.949   13.278;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
 1.101   0.055  -0.075  -14.198;
-0.036   1.143   0.341  -21.475;
 0.116  -0.289   0.936   13.160;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
 1.101   0.055  -0.075  -14.198;
-0.036   1.143   0.341  -21.475;
 0.116  -0.289   0.936   13.160;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5)
 1.102   0.041  -0.062  -15.344;
-0.028   1.147   0.324  -20.465;
 0.098  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 1.098   0.041  -0.062  -14.845;
-0.028   1.149   0.325  -20.792;
 0.098  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 1.098   0.041  -0.062  -14.845;
-0.028   1.149   0.325  -20.792;
 0.098  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2772 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.09796   0.04098  -0.06217  -14.84461;
-0.02848   1.14937   0.32503  -20.79175;
 0.09809  -0.27194   0.94600   13.81043;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2772
Quasinewton: input matrix
 1.09796   0.04098  -0.06217  -14.84461;
-0.02848   1.14937   0.32503  -20.79175;
 0.09809  -0.27194   0.94600   13.81043;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.098   0.041  -0.062  -14.845;
-0.028   1.149   0.325  -20.792;
 0.098  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.4 (old=-4.5)
transform before final EM align:
 1.098   0.041  -0.062  -14.845;
-0.028   1.149   0.325  -20.792;
 0.098  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 312841 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.09796   0.04098  -0.06217  -14.84461;
-0.02848   1.14937   0.32503  -20.79175;
 0.09809  -0.27194   0.94600   13.81043;
 0.00000   0.00000   0.00000   1.00000;
nsamples 312841
Quasinewton: input matrix
 1.09796   0.04098  -0.06217  -14.84461;
-0.02848   1.14937   0.32503  -20.79175;
 0.09809  -0.27194   0.94600   13.81043;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 012: -log(p) = 4.0
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
dfp_em_step_func: 013: -log(p) = 3.9
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
dfp_em_step_func: 014: -log(p) = 3.9
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
dfp_em_step_func: 015: -log(p) = 3.9
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
dfp_em_step_func: 016: -log(p) = 3.9
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
dfp_em_step_func: 017: -log(p) = 3.9
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
dfp_em_step_func: 018: -log(p) = 3.9
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
dfp_em_step_func: 019: -log(p) = 3.9
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
dfp_em_step_func: 020: -log(p) = 3.9
after pass:transform: ( 1.10, 0.04, -0.06, -14.84)
                      ( -0.03, 1.15, 0.33, -20.79)
                      ( 0.10, -0.27, 0.95, 13.81)
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 022: -log(p) =    3.9  tol 0.000000
final transform:
 1.099   0.042  -0.061  -14.845;
-0.028   1.149   0.325  -20.792;
 0.099  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 34 minutes and 1 seconds.
#--------------------------------------
#@# CA Normalize Thu Aug  8 12:11:54 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.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 '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 102 --> 107
resetting gm mean[0]: 64 --> 64
input volume #1 is the most T1-like
using real data threshold=21.0
skull bounding box = (65, 37, 29) --> (193, 173, 197)
using (108, 82, 113) as brain centroid...
mean wm in atlas = 107, using box (92,65,92) --> (123, 98,133) to find MRI wm
before smoothing, mri peak at 107
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
using 244171 sample points...
INFO: compute sample coordinates transform
 1.099   0.042  -0.061  -14.845;
-0.028   1.149   0.325  -20.792;
 0.099  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (124, 38, 34) --> (189, 140, 197)
Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 153.0
0 of 10 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (71, 36, 35) --> (134, 131, 200)
Right_Cerebral_White_Matter: limiting intensities to 103.0 --> 153.0
0 of 14 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (129, 114, 62) --> (173, 154, 115)
Left_Cerebellum_White_Matter: limiting intensities to 89.0 --> 153.0
0 of 9 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (86, 114, 62) --> (129, 151, 119)
Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 153.0
0 of 14 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (115, 103, 97) --> (145, 163, 128)
Brain_Stem: limiting intensities to 83.0 --> 153.0
3 of 8 (37.5%) samples deleted
using 55 total control points for intensity normalization...
bias field = 0.932 +- 0.060
0 of 52 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (124, 38, 34) --> (189, 140, 197)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 144.0
0 of 89 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (71, 36, 35) --> (134, 131, 200)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 144.0
2 of 88 (2.3%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (129, 114, 62) --> (173, 154, 115)
Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 144.0
0 of 9 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (86, 114, 62) --> (129, 151, 119)
Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 144.0
0 of 9 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (115, 103, 97) --> (145, 163, 128)
Brain_Stem: limiting intensities to 88.0 --> 144.0
43 of 50 (86.0%) samples deleted
using 245 total control points for intensity normalization...
bias field = 0.982 +- 0.048
0 of 200 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (124, 38, 34) --> (189, 140, 197)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 135.0
0 of 213 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (71, 36, 35) --> (134, 131, 200)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 135.0
0 of 160 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (129, 114, 62) --> (173, 154, 115)
Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 135.0
13 of 16 (81.2%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (86, 114, 62) --> (129, 151, 119)
Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 135.0
0 of 8 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (115, 103, 97) --> (145, 163, 128)
Brain_Stem: limiting intensities to 61.0 --> 135.0
1 of 71 (1.4%) samples deleted
using 468 total control points for intensity normalization...
bias field = 1.028 +- 0.070
1 of 454 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 2 minutes and 3 seconds.
#--------------------------------------
#@# CA Reg Thu Aug  8 12:13:57 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.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...
reading 1 input volumes...
logging results to talairach.log


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
reading input volume 'norm.mgz'...
reading GCA '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.30 (predicted orig area = 6.1)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.901, neg=0, invalid=96777
0001: dt=129.472000, rms=0.801 (11.014%), neg=0, invalid=96777
0002: dt=129.472000, rms=0.774 (3.392%), neg=0, invalid=96777
0003: dt=129.472000, rms=0.764 (1.329%), neg=0, invalid=96777
0004: dt=129.472000, rms=0.757 (0.886%), neg=0, invalid=96777
0005: dt=129.472000, rms=0.752 (0.654%), neg=0, invalid=96777
0006: dt=129.472000, rms=0.748 (0.571%), neg=0, invalid=96777
0007: dt=129.472000, rms=0.745 (0.443%), neg=0, invalid=96777
0008: dt=129.472000, rms=0.741 (0.425%), neg=0, invalid=96777
0009: dt=129.472000, rms=0.739 (0.356%), neg=0, invalid=96777
0010: dt=129.472000, rms=0.736 (0.332%), neg=0, invalid=96777
0011: dt=129.472000, rms=0.734 (0.284%), neg=0, invalid=96777
0012: dt=129.472000, rms=0.732 (0.247%), neg=0, invalid=96777
0013: dt=129.472000, rms=0.731 (0.237%), neg=0, invalid=96777
0014: dt=129.472000, rms=0.728 (0.420%), neg=0, invalid=96777
0015: dt=129.472000, rms=0.724 (0.497%), neg=0, invalid=96777
0016: dt=129.472000, rms=0.720 (0.592%), neg=0, invalid=96777
0017: dt=129.472000, rms=0.716 (0.505%), neg=0, invalid=96777
0018: dt=129.472000, rms=0.714 (0.345%), neg=0, invalid=96777
0019: dt=129.472000, rms=0.712 (0.241%), neg=0, invalid=96777
0020: dt=129.472000, rms=0.710 (0.294%), neg=0, invalid=96777
0021: dt=129.472000, rms=0.708 (0.310%), neg=0, invalid=96777
0022: dt=129.472000, rms=0.705 (0.419%), neg=0, invalid=96777
0023: dt=129.472000, rms=0.702 (0.323%), neg=0, invalid=96777
0024: dt=129.472000, rms=0.700 (0.276%), neg=0, invalid=96777
0025: dt=129.472000, rms=0.699 (0.241%), neg=0, invalid=96777
0026: dt=129.472000, rms=0.697 (0.265%), neg=0, invalid=96777
0027: dt=129.472000, rms=0.695 (0.203%), neg=0, invalid=96777
0028: dt=129.472000, rms=0.694 (0.180%), neg=0, invalid=96777
0029: dt=129.472000, rms=0.693 (0.191%), neg=0, invalid=96777
0030: dt=129.472000, rms=0.691 (0.191%), neg=0, invalid=96777
0031: dt=129.472000, rms=0.690 (0.181%), neg=0, invalid=96777
0032: dt=129.472000, rms=0.689 (0.164%), neg=0, invalid=96777
0033: dt=129.472000, rms=0.688 (0.157%), neg=0, invalid=96777
0034: dt=129.472000, rms=0.687 (0.170%), neg=0, invalid=96777
0035: dt=129.472000, rms=0.686 (0.180%), neg=0, invalid=96777
0036: dt=129.472000, rms=0.684 (0.173%), neg=0, invalid=96777
0037: dt=129.472000, rms=0.683 (0.166%), neg=0, invalid=96777
0038: dt=129.472000, rms=0.682 (0.140%), neg=0, invalid=96777
0039: dt=129.472000, rms=0.682 (0.117%), neg=0, invalid=96777
0040: dt=129.472000, rms=0.681 (0.106%), neg=0, invalid=96777
0041: dt=129.472000, rms=0.681 (0.033%), neg=0, invalid=96777
0042: dt=129.472000, rms=0.681 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.681, neg=0, invalid=96777
0043: dt=92.480000, rms=0.680 (0.038%), neg=0, invalid=96777
0044: dt=369.920000, rms=0.679 (0.171%), neg=0, invalid=96777
0045: dt=32.368000, rms=0.679 (0.020%), neg=0, invalid=96777
0046: dt=32.368000, rms=0.679 (0.014%), neg=0, invalid=96777
0047: dt=32.368000, rms=0.679 (0.016%), neg=0, invalid=96777
0048: dt=32.368000, rms=0.679 (0.018%), neg=0, invalid=96777
0049: dt=32.368000, rms=0.679 (0.031%), neg=0, invalid=96777
0050: dt=32.368000, rms=0.678 (0.042%), neg=0, invalid=96777
0051: dt=32.368000, rms=0.678 (0.046%), neg=0, invalid=96777
0052: dt=32.368000, rms=0.678 (0.038%), neg=0, invalid=96777
0053: dt=32.368000, rms=0.677 (0.028%), neg=0, invalid=96777
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.685, neg=0, invalid=96777
0054: dt=145.152000, rms=0.676 (1.407%), neg=0, invalid=96777
0055: dt=103.680000, rms=0.670 (0.904%), neg=0, invalid=96777
0056: dt=36.288000, rms=0.665 (0.762%), neg=0, invalid=96777
0057: dt=36.288000, rms=0.664 (0.117%), neg=0, invalid=96777
0058: dt=36.288000, rms=0.661 (0.392%), neg=0, invalid=96777
0059: dt=36.288000, rms=0.658 (0.488%), neg=0, invalid=96777
0060: dt=36.288000, rms=0.654 (0.561%), neg=0, invalid=96777
0061: dt=36.288000, rms=0.650 (0.689%), neg=0, invalid=96777
0062: dt=36.288000, rms=0.644 (0.841%), neg=0, invalid=96777
0063: dt=36.288000, rms=0.640 (0.720%), neg=0, invalid=96777
0064: dt=36.288000, rms=0.636 (0.553%), neg=0, invalid=96777
0065: dt=36.288000, rms=0.633 (0.455%), neg=0, invalid=96777
0066: dt=36.288000, rms=0.630 (0.529%), neg=0, invalid=96777
0067: dt=36.288000, rms=0.627 (0.404%), neg=0, invalid=96777
0068: dt=36.288000, rms=0.625 (0.338%), neg=0, invalid=96777
0069: dt=36.288000, rms=0.624 (0.253%), neg=0, invalid=96777
0070: dt=36.288000, rms=0.622 (0.307%), neg=0, invalid=96777
0071: dt=36.288000, rms=0.620 (0.251%), neg=0, invalid=96777
0072: dt=36.288000, rms=0.619 (0.212%), neg=0, invalid=96777
0073: dt=36.288000, rms=0.618 (0.166%), neg=0, invalid=96777
0074: dt=36.288000, rms=0.617 (0.128%), neg=0, invalid=96777
0075: dt=36.288000, rms=0.616 (0.156%), neg=0, invalid=96777
0076: dt=36.288000, rms=0.615 (0.103%), neg=0, invalid=96777
0077: dt=36.288000, rms=0.615 (0.087%), neg=0, invalid=96777
0078: dt=145.152000, rms=0.614 (0.126%), neg=0, invalid=96777
0079: dt=9.072000, rms=0.614 (0.003%), neg=0, invalid=96777
0080: dt=9.072000, rms=0.614 (0.006%), neg=0, invalid=96777
0081: dt=9.072000, rms=0.614 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.614, neg=0, invalid=96777
0082: dt=20.736000, rms=0.614 (0.015%), neg=0, invalid=96777
0083: dt=36.288000, rms=0.614 (0.028%), neg=0, invalid=96777
0084: dt=15.552000, rms=0.614 (0.002%), neg=0, invalid=96777
0085: dt=15.552000, rms=0.614 (0.005%), neg=0, invalid=96777
0086: dt=15.552000, rms=0.614 (0.001%), neg=0, invalid=96777
0087: dt=15.552000, rms=0.614 (-0.010%), neg=0, invalid=96777
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.643, neg=0, invalid=96777
0088: dt=5.423729, rms=0.643 (0.056%), neg=0, invalid=96777
0089: dt=1.600000, rms=0.643 (0.006%), neg=0, invalid=96777
0090: dt=1.600000, rms=0.643 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.643, neg=0, invalid=96777
0091: dt=0.000000, rms=0.643 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.723, neg=0, invalid=96777
0092: dt=5.319372, rms=0.702 (2.891%), neg=0, invalid=96777
0093: dt=3.194030, rms=0.700 (0.187%), neg=0, invalid=96777
0094: dt=3.194030, rms=0.700 (-0.021%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.700, neg=0, invalid=96777
0095: dt=0.000000, rms=0.700 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.779, neg=0, invalid=96777
0096: dt=1.111639, rms=0.775 (0.523%), neg=0, invalid=96777
0097: dt=2.377246, rms=0.767 (0.938%), neg=0, invalid=96777
0098: dt=0.448000, rms=0.767 (0.069%), neg=0, invalid=96777
0099: dt=0.448000, rms=0.767 (0.029%), neg=0, invalid=96777
0100: dt=0.448000, rms=0.766 (0.037%), neg=0, invalid=96777
0101: dt=0.448000, rms=0.766 (0.032%), neg=0, invalid=96777
0102: dt=0.448000, rms=0.766 (0.010%), neg=0, invalid=96777
0103: dt=2.227273, rms=0.765 (0.133%), neg=0, invalid=96777
0104: dt=0.000000, rms=0.765 (0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.765, neg=0, invalid=96777
0105: dt=0.544118, rms=0.764 (0.081%), neg=0, invalid=96777
0106: dt=0.080000, rms=0.764 (-0.002%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.716, neg=0, invalid=96777
0107: dt=0.154661, rms=0.708 (1.114%), neg=0, invalid=96777
0108: dt=0.000000, rms=0.708 (0.002%), neg=0, invalid=96777
0109: dt=0.050000, rms=0.708 (-0.013%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.708, neg=0, invalid=96777
0110: dt=0.347584, rms=0.704 (0.542%), neg=0, invalid=96777
0111: dt=0.064000, rms=0.703 (0.118%), neg=0, invalid=96777
0112: dt=0.064000, rms=0.703 (-0.007%), neg=0, invalid=96777
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.11725 (24)
mri peak = 0.14301 (55)
Left_Lateral_Ventricle (4): linear fit = 2.20 x + 0.0 (1178 voxels, overlap=0.005)
Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1178 voxels, peak = 53), gca=36.0
gca peak = 0.14022 (22)
mri peak = 0.10960 ( 7)
Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (604 voxels, overlap=0.005)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (604 voxels, peak =  5), gca=8.8
gca peak = 0.24234 (100)
mri peak = 0.12385 (75)
Right_Pallidum (52): linear fit = 0.80 x + 0.0 (357 voxels, overlap=0.032)
Right_Pallidum (52): linear fit = 0.80 x + 0.0 (357 voxels, peak = 80), gca=79.5
gca peak = 0.19192 (97)
mri peak = 0.18787 (75)
Left_Pallidum (13): linear fit = 0.77 x + 0.0 (315 voxels, overlap=0.484)
Left_Pallidum (13): linear fit = 0.77 x + 0.0 (315 voxels, peak = 75), gca=75.2
gca peak = 0.24007 (63)
mri peak = 0.08999 (56)
Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (418 voxels, overlap=0.201)
Right_Hippocampus (53): linear fit = 0.85 x + 0.0 (418 voxels, peak = 53), gca=53.2
gca peak = 0.29892 (64)
mri peak = 0.09388 (58)
Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (485 voxels, overlap=0.142)
Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (485 voxels, peak = 54), gca=54.1
gca peak = 0.12541 (104)
mri peak = 0.06489 (107)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56578 voxels, overlap=0.897)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56578 voxels, peak = 107), gca=106.6
gca peak = 0.13686 (104)
mri peak = 0.07498 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57418 voxels, overlap=0.772)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (57418 voxels, peak = 108), gca=107.6
gca peak = 0.11691 (63)
mri peak = 0.05213 (50)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (14833 voxels, overlap=0.119)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (14833 voxels, peak = 50), gca=50.1
gca peak = 0.13270 (63)
mri peak = 0.06223 (51)
Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (15455 voxels, overlap=0.110)
Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (15455 voxels, peak = 50), gca=50.1
gca peak = 0.15182 (70)
mri peak = 0.10308 (56)
Right_Caudate (50): linear fit = 0.79 x + 0.0 (462 voxels, overlap=0.011)
Right_Caudate (50): linear fit = 0.79 x + 0.0 (462 voxels, peak = 55), gca=55.0
gca peak = 0.14251 (76)
mri peak = 0.11050 (58)
Left_Caudate (11): linear fit = 0.75 x + 0.0 (568 voxels, overlap=0.021)
Left_Caudate (11): linear fit = 0.75 x + 0.0 (568 voxels, peak = 57), gca=57.4
gca peak = 0.12116 (60)
mri peak = 0.05451 (59)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (9961 voxels, overlap=0.989)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (9961 voxels, peak = 58), gca=57.9
gca peak = 0.12723 (61)
mri peak = 0.05544 (58)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (11865 voxels, overlap=0.991)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (11865 voxels, peak = 60), gca=60.1
gca peak = 0.22684 (88)
mri peak = 0.05818 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5713 voxels, overlap=0.949)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5713 voxels, peak = 89), gca=89.3
gca peak = 0.21067 (87)
mri peak = 0.05650 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5353 voxels, overlap=0.982)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5353 voxels, peak = 87), gca=86.6
gca peak = 0.25455 (62)
mri peak = 0.08370 (58)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (258 voxels, overlap=0.694)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (258 voxels, peak = 54), gca=54.2
gca peak = 0.39668 (62)
mri peak = 0.12756 (53)
Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, overlap=0.055)
Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, peak = 52), gca=52.4
gca peak = 0.10129 (93)
mri peak = 0.04906 (85)
Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4675 voxels, overlap=0.919)
Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4675 voxels, peak = 85), gca=85.1
gca peak = 0.12071 (89)
mri peak = 0.10826 (77)
Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3726 voxels, overlap=0.445)
Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3726 voxels, peak = 83), gca=83.2
gca peak = 0.13716 (82)
mri peak = 0.05377 (75)
Left_Putamen (12): linear fit = 0.88 x + 0.0 (1483 voxels, overlap=0.416)
Left_Putamen (12): linear fit = 0.88 x + 0.0 (1483 voxels, peak = 73), gca=72.6
gca peak = 0.15214 (84)
mri peak = 0.07704 (65)
Right_Putamen (51): linear fit = 0.81 x + 0.0 (1907 voxels, overlap=0.013)
Right_Putamen (51): linear fit = 0.81 x + 0.0 (1907 voxels, peak = 68), gca=67.6
gca peak = 0.08983 (85)
mri peak = 0.10973 (80)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (8634 voxels, overlap=0.767)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (8634 voxels, peak = 84), gca=83.7
gca peak = 0.11809 (92)
mri peak = 0.13966 (83)
Right_VentralDC (60): linear fit = 0.90 x + 0.0 (805 voxels, overlap=0.345)
Right_VentralDC (60): linear fit = 0.90 x + 0.0 (805 voxels, peak = 83), gca=83.3
gca peak = 0.12914 (94)
mri peak = 0.10058 (83)
Left_VentralDC (28): linear fit = 0.89 x + 0.0 (928 voxels, overlap=0.419)
Left_VentralDC (28): linear fit = 0.89 x + 0.0 (928 voxels, peak = 84), gca=84.1
gca peak = 0.21100 (36)
mri peak = 0.12694 (54)
Third_Ventricle (14): linear fit = 1.46 x + 0.0 (71 voxels, overlap=0.081)
Third_Ventricle (14): linear fit = 1.46 x + 0.0 (71 voxels, peak = 52), gca=52.4
gca peak = 0.13542 (27)
mri peak = 0.18125 ( 8)
Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (210 voxels, overlap=0.020)
Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (210 voxels, peak =  6), gca=6.1
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.21802 (40)
gca peak Fourth_Ventricle = 0.13542 (27)
gca peak CSF = 0.17123 (45)
gca peak Left_Accumbens_area = 0.25875 (69)
gca peak Left_undetermined = 0.96240 (36)
gca peak Left_vessel = 0.33262 (65)
gca peak Left_choroid_plexus = 0.09846 (46)
gca peak Right_Inf_Lat_Vent = 0.28113 (34)
gca peak Right_Accumbens_area = 0.27120 (72)
gca peak Right_vessel = 0.61915 (60)
gca peak Right_choroid_plexus = 0.12775 (51)
gca peak Fifth_Ventricle = 0.45329 (44)
gca peak WM_hypointensities = 0.11729 (81)
gca peak non_WM_hypointensities = 0.10912 (56)
gca peak Optic_Chiasm = 0.33287 (75)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 0.83 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.12 x + 0.0
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.737, neg=0, invalid=96777
0113: dt=129.472000, rms=0.727 (1.399%), neg=0, invalid=96777
0114: dt=110.976000, rms=0.723 (0.515%), neg=0, invalid=96777
0115: dt=129.472000, rms=0.720 (0.375%), neg=0, invalid=96777
0116: dt=73.984000, rms=0.719 (0.263%), neg=0, invalid=96777
0117: dt=295.936000, rms=0.716 (0.292%), neg=0, invalid=96777
0118: dt=55.488000, rms=0.715 (0.255%), neg=0, invalid=96777
0119: dt=1479.680000, rms=0.709 (0.823%), neg=0, invalid=96777
0120: dt=295.936000, rms=0.707 (0.202%), neg=0, invalid=96777
0121: dt=32.368000, rms=0.707 (0.049%), neg=0, invalid=96777
0122: dt=32.368000, rms=0.707 (0.019%), neg=0, invalid=96777
0123: dt=32.368000, rms=0.707 (0.020%), neg=0, invalid=96777
0124: dt=32.368000, rms=0.707 (0.022%), neg=0, invalid=96777
0125: dt=32.368000, rms=0.706 (0.041%), neg=0, invalid=96777
0126: dt=32.368000, rms=0.706 (0.067%), neg=0, invalid=96777
0127: dt=32.368000, rms=0.705 (0.083%), neg=0, invalid=96777
0128: dt=32.368000, rms=0.705 (0.082%), neg=0, invalid=96777
0129: dt=32.368000, rms=0.704 (0.073%), neg=0, invalid=96777
0130: dt=32.368000, rms=0.704 (0.070%), neg=0, invalid=96777
0131: dt=32.368000, rms=0.703 (0.066%), neg=0, invalid=96777
0132: dt=32.368000, rms=0.703 (0.063%), neg=0, invalid=96777
0133: dt=32.368000, rms=0.702 (0.063%), neg=0, invalid=96777
0134: dt=32.368000, rms=0.702 (0.072%), neg=0, invalid=96777
0135: dt=32.368000, rms=0.701 (0.072%), neg=0, invalid=96777
0136: dt=32.368000, rms=0.701 (0.071%), neg=0, invalid=96777
0137: dt=32.368000, rms=0.700 (0.064%), neg=0, invalid=96777
0138: dt=32.368000, rms=0.700 (0.056%), neg=0, invalid=96777
0139: dt=32.368000, rms=0.700 (0.046%), neg=0, invalid=96777
0140: dt=32.368000, rms=0.699 (0.046%), neg=0, invalid=96777
0141: dt=32.368000, rms=0.699 (0.045%), neg=0, invalid=96777
0142: dt=32.368000, rms=0.699 (0.048%), neg=0, invalid=96777
0143: dt=32.368000, rms=0.698 (0.043%), neg=0, invalid=96777
0144: dt=32.368000, rms=0.698 (0.040%), neg=0, invalid=96777
0145: dt=32.368000, rms=0.698 (0.039%), neg=0, invalid=96777
0146: dt=32.368000, rms=0.698 (0.033%), neg=0, invalid=96777
0147: dt=32.368000, rms=0.697 (0.030%), neg=0, invalid=96777
0148: dt=32.368000, rms=0.697 (0.031%), neg=0, invalid=96777
0149: dt=32.368000, rms=0.697 (0.033%), neg=0, invalid=96777
0150: dt=32.368000, rms=0.697 (0.035%), neg=0, invalid=96777
0151: dt=32.368000, rms=0.696 (0.037%), neg=0, invalid=96777
0152: dt=32.368000, rms=0.696 (0.035%), neg=0, invalid=96777
0153: dt=32.368000, rms=0.696 (0.033%), neg=0, invalid=96777
0154: dt=32.368000, rms=0.696 (0.033%), neg=0, invalid=96777
0155: dt=32.368000, rms=0.695 (0.035%), neg=0, invalid=96777
0156: dt=32.368000, rms=0.695 (0.034%), neg=0, invalid=96777
0157: dt=32.368000, rms=0.695 (0.034%), neg=0, invalid=96777
0158: dt=32.368000, rms=0.695 (0.033%), neg=0, invalid=96777
0159: dt=32.368000, rms=0.695 (0.030%), neg=0, invalid=96777
0160: dt=32.368000, rms=0.694 (0.026%), neg=0, invalid=96777
0161: dt=32.368000, rms=0.694 (0.025%), neg=0, invalid=96777
0162: dt=32.368000, rms=0.694 (0.025%), neg=0, invalid=96777
0163: dt=32.368000, rms=0.694 (0.027%), neg=0, invalid=96777
0164: dt=32.368000, rms=0.694 (0.028%), neg=0, invalid=96777
0165: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777
0166: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777
0167: dt=32.368000, rms=0.693 (0.030%), neg=0, invalid=96777
0168: dt=32.368000, rms=0.693 (0.022%), neg=0, invalid=96777
0169: dt=32.368000, rms=0.693 (0.021%), neg=0, invalid=96777
0170: dt=32.368000, rms=0.693 (0.001%), neg=0, invalid=96777
0171: dt=32.368000, rms=0.693 (0.001%), neg=0, invalid=96777
0172: dt=32.368000, rms=0.693 (0.003%), neg=0, invalid=96777
0173: dt=32.368000, rms=0.693 (0.003%), neg=0, invalid=96777
0174: dt=32.368000, rms=0.693 (0.008%), neg=0, invalid=96777
0175: dt=32.368000, rms=0.693 (0.009%), neg=0, invalid=96777
0176: dt=32.368000, rms=0.692 (0.011%), neg=0, invalid=96777
0177: dt=32.368000, rms=0.692 (0.014%), neg=0, invalid=96777
0178: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777
0179: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777
0180: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777
0181: dt=32.368000, rms=0.692 (0.015%), neg=0, invalid=96777
0182: dt=32.368000, rms=0.692 (0.014%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.692, neg=0, invalid=96777
0183: dt=295.936000, rms=0.690 (0.328%), neg=0, invalid=96777
0184: dt=73.984000, rms=0.689 (0.043%), neg=0, invalid=96777
0185: dt=73.984000, rms=0.689 (0.021%), neg=0, invalid=96777
0186: dt=73.984000, rms=0.689 (0.040%), neg=0, invalid=96777
0187: dt=73.984000, rms=0.689 (0.051%), neg=0, invalid=96777
0188: dt=73.984000, rms=0.688 (0.061%), neg=0, invalid=96777
0189: dt=73.984000, rms=0.688 (0.071%), neg=0, invalid=96777
0190: dt=73.984000, rms=0.687 (0.071%), neg=0, invalid=96777
0191: dt=73.984000, rms=0.687 (0.061%), neg=0, invalid=96777
0192: dt=73.984000, rms=0.686 (0.050%), neg=0, invalid=96777
0193: dt=73.984000, rms=0.686 (0.045%), neg=0, invalid=96777
0194: dt=73.984000, rms=0.686 (0.039%), neg=0, invalid=96777
0195: dt=73.984000, rms=0.686 (0.039%), neg=0, invalid=96777
0196: dt=73.984000, rms=0.685 (0.042%), neg=0, invalid=96777
0197: dt=73.984000, rms=0.685 (0.046%), neg=0, invalid=96777
0198: dt=73.984000, rms=0.685 (0.049%), neg=0, invalid=96777
0199: dt=73.984000, rms=0.684 (0.053%), neg=0, invalid=96777
0200: dt=73.984000, rms=0.684 (0.050%), neg=0, invalid=96777
0201: dt=73.984000, rms=0.684 (0.045%), neg=0, invalid=96777
0202: dt=73.984000, rms=0.683 (0.041%), neg=0, invalid=96777
0203: dt=73.984000, rms=0.683 (0.035%), neg=0, invalid=96777
0204: dt=73.984000, rms=0.683 (0.036%), neg=0, invalid=96777
0205: dt=73.984000, rms=0.683 (0.036%), neg=0, invalid=96777
0206: dt=73.984000, rms=0.682 (0.040%), neg=0, invalid=96777
0207: dt=73.984000, rms=0.682 (0.038%), neg=0, invalid=96777
0208: dt=73.984000, rms=0.682 (0.035%), neg=0, invalid=96777
0209: dt=73.984000, rms=0.682 (0.032%), neg=0, invalid=96777
0210: dt=73.984000, rms=0.681 (0.027%), neg=0, invalid=96777
0211: dt=73.984000, rms=0.681 (0.025%), neg=0, invalid=96777
0212: dt=73.984000, rms=0.681 (0.023%), neg=0, invalid=96777
0213: dt=1479.680000, rms=0.681 (0.059%), neg=0, invalid=96777
0214: dt=73.984000, rms=0.681 (0.027%), neg=0, invalid=96777
0215: dt=73.984000, rms=0.680 (-0.004%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.681, neg=0, invalid=96777
0216: dt=124.416000, rms=0.675 (0.873%), neg=0, invalid=96777
0217: dt=82.944000, rms=0.670 (0.693%), neg=0, invalid=96777
0218: dt=36.288000, rms=0.667 (0.581%), neg=0, invalid=96777
0219: dt=25.920000, rms=0.665 (0.205%), neg=0, invalid=96777
0220: dt=145.152000, rms=0.660 (0.744%), neg=0, invalid=96777
0221: dt=20.736000, rms=0.658 (0.388%), neg=0, invalid=96777
0222: dt=580.608000, rms=0.647 (1.701%), neg=0, invalid=96777
0223: dt=20.025157, rms=0.642 (0.715%), neg=0, invalid=96777
0224: dt=145.152000, rms=0.640 (0.361%), neg=0, invalid=96777
0225: dt=36.288000, rms=0.638 (0.169%), neg=0, invalid=96777
0226: dt=145.152000, rms=0.637 (0.280%), neg=0, invalid=96777
0227: dt=31.104000, rms=0.636 (0.163%), neg=0, invalid=96777
0228: dt=36.288000, rms=0.635 (0.037%), neg=0, invalid=96777
0229: dt=36.288000, rms=0.635 (0.096%), neg=0, invalid=96777
0230: dt=36.288000, rms=0.634 (0.129%), neg=0, invalid=96777
0231: dt=36.288000, rms=0.633 (0.159%), neg=0, invalid=96777
0232: dt=36.288000, rms=0.632 (0.214%), neg=0, invalid=96777
0233: dt=36.288000, rms=0.630 (0.265%), neg=0, invalid=96777
0234: dt=36.288000, rms=0.628 (0.266%), neg=0, invalid=96777
0235: dt=36.288000, rms=0.627 (0.269%), neg=0, invalid=96777
0236: dt=36.288000, rms=0.625 (0.272%), neg=0, invalid=96777
0237: dt=36.288000, rms=0.623 (0.294%), neg=0, invalid=96777
0238: dt=36.288000, rms=0.621 (0.268%), neg=0, invalid=96777
0239: dt=36.288000, rms=0.620 (0.246%), neg=0, invalid=96777
0240: dt=36.288000, rms=0.618 (0.223%), neg=0, invalid=96777
0241: dt=36.288000, rms=0.617 (0.229%), neg=0, invalid=96777
0242: dt=36.288000, rms=0.616 (0.206%), neg=0, invalid=96777
0243: dt=36.288000, rms=0.615 (0.191%), neg=0, invalid=96777
0244: dt=36.288000, rms=0.613 (0.188%), neg=0, invalid=96777
0245: dt=36.288000, rms=0.612 (0.180%), neg=0, invalid=96777
0246: dt=36.288000, rms=0.611 (0.180%), neg=0, invalid=96777
0247: dt=36.288000, rms=0.610 (0.164%), neg=0, invalid=96777
0248: dt=36.288000, rms=0.609 (0.166%), neg=0, invalid=96777
0249: dt=36.288000, rms=0.608 (0.152%), neg=0, invalid=96777
0250: dt=36.288000, rms=0.607 (0.154%), neg=0, invalid=96777
0251: dt=36.288000, rms=0.607 (0.137%), neg=0, invalid=96777
0252: dt=36.288000, rms=0.606 (0.142%), neg=0, invalid=96777
0253: dt=36.288000, rms=0.605 (0.127%), neg=0, invalid=96777
0254: dt=36.288000, rms=0.604 (0.113%), neg=0, invalid=96777
0255: dt=36.288000, rms=0.604 (0.089%), neg=0, invalid=96777
0256: dt=36.288000, rms=0.603 (0.097%), neg=0, invalid=96777
0257: dt=36.288000, rms=0.602 (0.102%), neg=0, invalid=96777
0258: dt=36.288000, rms=0.602 (0.095%), neg=0, invalid=96777
0259: dt=36.288000, rms=0.601 (0.078%), neg=0, invalid=96777
0260: dt=36.288000, rms=0.601 (0.069%), neg=0, invalid=96777
0261: dt=36.288000, rms=0.601 (0.072%), neg=0, invalid=96777
0262: dt=36.288000, rms=0.600 (0.076%), neg=0, invalid=96777
0263: dt=36.288000, rms=0.600 (0.074%), neg=0, invalid=96777
0264: dt=36.288000, rms=0.599 (0.063%), neg=0, invalid=96777
0265: dt=36.288000, rms=0.599 (0.060%), neg=0, invalid=96777
0266: dt=36.288000, rms=0.599 (0.049%), neg=0, invalid=96777
0267: dt=36.288000, rms=0.598 (0.063%), neg=0, invalid=96777
0268: dt=36.288000, rms=0.598 (0.064%), neg=0, invalid=96777
0269: dt=36.288000, rms=0.598 (0.064%), neg=0, invalid=96777
0270: dt=36.288000, rms=0.597 (0.057%), neg=0, invalid=96777
0271: dt=36.288000, rms=0.597 (0.048%), neg=0, invalid=96777
0272: dt=36.288000, rms=0.597 (0.041%), neg=0, invalid=96777
0273: dt=36.288000, rms=0.596 (0.050%), neg=0, invalid=96777
0274: dt=36.288000, rms=0.596 (0.054%), neg=0, invalid=96777
0275: dt=36.288000, rms=0.596 (0.048%), neg=0, invalid=96777
0276: dt=36.288000, rms=0.595 (0.043%), neg=0, invalid=96777
0277: dt=36.288000, rms=0.595 (0.039%), neg=0, invalid=96777
0278: dt=36.288000, rms=0.595 (0.044%), neg=0, invalid=96777
0279: dt=36.288000, rms=0.595 (0.054%), neg=0, invalid=96777
0280: dt=36.288000, rms=0.594 (0.047%), neg=0, invalid=96777
0281: dt=36.288000, rms=0.594 (0.037%), neg=0, invalid=96777
0282: dt=36.288000, rms=0.594 (0.029%), neg=0, invalid=96777
0283: dt=36.288000, rms=0.594 (0.035%), neg=0, invalid=96777
0284: dt=36.288000, rms=0.594 (0.036%), neg=0, invalid=96777
0285: dt=36.288000, rms=0.593 (0.045%), neg=0, invalid=96777
0286: dt=36.288000, rms=0.593 (0.040%), neg=0, invalid=96777
0287: dt=36.288000, rms=0.593 (0.040%), neg=0, invalid=96777
0288: dt=36.288000, rms=0.593 (0.032%), neg=0, invalid=96777
0289: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=96777
0290: dt=36.288000, rms=0.592 (0.024%), neg=0, invalid=96777
0291: dt=36.288000, rms=0.592 (0.029%), neg=0, invalid=96777
0292: dt=36.288000, rms=0.592 (0.030%), neg=0, invalid=96777
0293: dt=36.288000, rms=0.592 (0.032%), neg=0, invalid=96777
0294: dt=36.288000, rms=0.592 (0.027%), neg=0, invalid=96777
0295: dt=36.288000, rms=0.591 (0.027%), neg=0, invalid=96777
0296: dt=36.288000, rms=0.591 (0.037%), neg=0, invalid=96777
0297: dt=36.288000, rms=0.591 (0.027%), neg=0, invalid=96777
0298: dt=36.288000, rms=0.591 (0.036%), neg=0, invalid=96777
0299: dt=36.288000, rms=0.591 (0.024%), neg=0, invalid=96777
0300: dt=36.288000, rms=0.591 (0.026%), neg=0, invalid=96777
0301: dt=36.288000, rms=0.590 (0.026%), neg=0, invalid=96777
0302: dt=36.288000, rms=0.590 (0.037%), neg=0, invalid=96777
0303: dt=36.288000, rms=0.590 (0.035%), neg=0, invalid=96777
0304: dt=36.288000, rms=0.590 (0.031%), neg=0, invalid=96777
0305: dt=36.288000, rms=0.590 (0.026%), neg=0, invalid=96777
0306: dt=36.288000, rms=0.590 (0.019%), neg=0, invalid=96777
0307: dt=36.288000, rms=0.589 (0.020%), neg=0, invalid=96777
0308: dt=36.288000, rms=0.589 (0.031%), neg=0, invalid=96777
0309: dt=36.288000, rms=0.589 (0.031%), neg=0, invalid=96777
0310: dt=36.288000, rms=0.589 (0.032%), neg=0, invalid=96777
0311: dt=36.288000, rms=0.589 (0.020%), neg=0, invalid=96777
0312: dt=36.288000, rms=0.589 (0.013%), neg=0, invalid=96777
0313: dt=145.152000, rms=0.588 (0.031%), neg=0, invalid=96777
0314: dt=2.268000, rms=0.588 (0.000%), neg=0, invalid=96777
0315: dt=2.268000, rms=0.588 (0.000%), neg=0, invalid=96777
0316: dt=2.268000, rms=0.589 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.589, neg=0, invalid=96777
0317: dt=103.680000, rms=0.587 (0.247%), neg=0, invalid=96777
0318: dt=31.104000, rms=0.586 (0.133%), neg=0, invalid=96777
0319: dt=31.104000, rms=0.586 (0.049%), neg=0, invalid=96777
0320: dt=31.104000, rms=0.586 (0.057%), neg=0, invalid=96777
0321: dt=31.104000, rms=0.585 (0.070%), neg=0, invalid=96777
0322: dt=31.104000, rms=0.585 (0.090%), neg=0, invalid=96777
0323: dt=31.104000, rms=0.584 (0.069%), neg=0, invalid=96777
0324: dt=31.104000, rms=0.584 (0.087%), neg=0, invalid=96777
0325: dt=31.104000, rms=0.583 (0.081%), neg=0, invalid=96777
0326: dt=31.104000, rms=0.583 (0.079%), neg=0, invalid=96777
0327: dt=31.104000, rms=0.582 (0.063%), neg=0, invalid=96777
0328: dt=31.104000, rms=0.582 (0.056%), neg=0, invalid=96777
0329: dt=31.104000, rms=0.582 (0.069%), neg=0, invalid=96777
0330: dt=31.104000, rms=0.581 (0.059%), neg=0, invalid=96777
0331: dt=31.104000, rms=0.581 (0.057%), neg=0, invalid=96777
0332: dt=31.104000, rms=0.581 (0.042%), neg=0, invalid=96777
0333: dt=31.104000, rms=0.581 (0.055%), neg=0, invalid=96777
0334: dt=31.104000, rms=0.580 (0.049%), neg=0, invalid=96777
0335: dt=31.104000, rms=0.580 (0.047%), neg=0, invalid=96777
0336: dt=31.104000, rms=0.580 (0.033%), neg=0, invalid=96777
0337: dt=31.104000, rms=0.580 (0.035%), neg=0, invalid=96777
0338: dt=31.104000, rms=0.579 (0.048%), neg=0, invalid=96777
0339: dt=31.104000, rms=0.579 (0.042%), neg=0, invalid=96777
0340: dt=31.104000, rms=0.579 (0.049%), neg=0, invalid=96777
0341: dt=31.104000, rms=0.579 (0.028%), neg=0, invalid=96777
0342: dt=31.104000, rms=0.578 (0.047%), neg=0, invalid=96777
0343: dt=31.104000, rms=0.578 (0.037%), neg=0, invalid=96777
0344: dt=31.104000, rms=0.578 (0.034%), neg=0, invalid=96777
0345: dt=31.104000, rms=0.578 (0.042%), neg=0, invalid=96777
0346: dt=31.104000, rms=0.577 (0.033%), neg=0, invalid=96777
0347: dt=31.104000, rms=0.577 (0.036%), neg=0, invalid=96777
0348: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777
0349: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777
0350: dt=31.104000, rms=0.577 (0.031%), neg=0, invalid=96777
0351: dt=31.104000, rms=0.577 (0.019%), neg=0, invalid=96777
0352: dt=31.104000, rms=0.576 (0.032%), neg=0, invalid=96777
0353: dt=31.104000, rms=0.576 (0.027%), neg=0, invalid=96777
0354: dt=31.104000, rms=0.576 (0.026%), neg=0, invalid=96777
0355: dt=31.104000, rms=0.576 (0.028%), neg=0, invalid=96777
0356: dt=31.104000, rms=0.576 (0.029%), neg=0, invalid=96777
0357: dt=31.104000, rms=0.576 (0.031%), neg=0, invalid=96777
0358: dt=31.104000, rms=0.575 (0.024%), neg=0, invalid=96777
0359: dt=31.104000, rms=0.575 (0.020%), neg=0, invalid=96777
0360: dt=82.944000, rms=0.575 (0.011%), neg=0, invalid=96777
0361: dt=82.944000, rms=0.575 (-0.046%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.585, neg=0, invalid=96777
0362: dt=25.600000, rms=0.583 (0.206%), neg=0, invalid=96777
0363: dt=25.600000, rms=0.582 (0.207%), neg=0, invalid=96777
0364: dt=8.622222, rms=0.581 (0.138%), neg=0, invalid=96777
0365: dt=32.000000, rms=0.580 (0.214%), neg=0, invalid=96777
0366: dt=8.000000, rms=0.579 (0.173%), neg=0, invalid=96777
0367: dt=38.400000, rms=0.578 (0.202%), neg=0, invalid=96777
0368: dt=7.439252, rms=0.577 (0.233%), neg=0, invalid=96777
0369: dt=128.000000, rms=0.574 (0.510%), neg=0, invalid=96777
0370: dt=9.182266, rms=0.572 (0.315%), neg=0, invalid=96777
0371: dt=11.200000, rms=0.571 (0.166%), neg=0, invalid=96777
0372: dt=19.200000, rms=0.570 (0.168%), neg=0, invalid=96777
0373: dt=10.295652, rms=0.569 (0.201%), neg=0, invalid=96777
0374: dt=11.200000, rms=0.568 (0.170%), neg=0, invalid=96777
0375: dt=11.200000, rms=0.567 (0.094%), neg=0, invalid=96777
0376: dt=11.200000, rms=0.567 (0.100%), neg=0, invalid=96777
0377: dt=25.600000, rms=0.566 (0.090%), neg=0, invalid=96777
0378: dt=9.600000, rms=0.566 (0.130%), neg=0, invalid=96777
0379: dt=11.200000, rms=0.565 (0.069%), neg=0, invalid=96777
0380: dt=19.200000, rms=0.565 (0.102%), neg=0, invalid=96777
0381: dt=8.000000, rms=0.564 (0.076%), neg=0, invalid=96777
0382: dt=44.800000, rms=0.563 (0.142%), neg=0, invalid=96777
0383: dt=6.925373, rms=0.563 (0.137%), neg=0, invalid=96777
0384: dt=153.600000, rms=0.561 (0.251%), neg=0, invalid=96777
0385: dt=8.075829, rms=0.559 (0.406%), neg=0, invalid=96777
0386: dt=9.600000, rms=0.558 (0.162%), neg=0, invalid=96777
0387: dt=11.200000, rms=0.558 (0.063%), neg=0, invalid=96777
0388: dt=32.000000, rms=0.557 (0.070%), neg=0, invalid=96777
0389: dt=8.000000, rms=0.557 (0.070%), neg=0, invalid=96777
0390: dt=19.200000, rms=0.557 (0.048%), neg=0, invalid=96777
0391: dt=19.200000, rms=0.557 (0.004%), neg=0, invalid=96777
0392: dt=19.200000, rms=0.556 (0.132%), neg=0, invalid=96777
0393: dt=19.200000, rms=0.555 (0.224%), neg=0, invalid=96777
0394: dt=19.200000, rms=0.553 (0.195%), neg=0, invalid=96777
0395: dt=19.200000, rms=0.552 (0.210%), neg=0, invalid=96777
0396: dt=19.200000, rms=0.551 (0.259%), neg=0, invalid=96777
0397: dt=19.200000, rms=0.549 (0.320%), neg=0, invalid=96777
0398: dt=19.200000, rms=0.548 (0.234%), neg=0, invalid=96777
0399: dt=19.200000, rms=0.547 (0.227%), neg=0, invalid=96777
0400: dt=19.200000, rms=0.545 (0.294%), neg=0, invalid=96777
0401: dt=19.200000, rms=0.544 (0.233%), neg=0, invalid=96777
0402: dt=19.200000, rms=0.542 (0.237%), neg=0, invalid=96777
0403: dt=19.200000, rms=0.541 (0.204%), neg=0, invalid=96777
0404: dt=19.200000, rms=0.540 (0.171%), neg=0, invalid=96777
0405: dt=19.200000, rms=0.539 (0.210%), neg=0, invalid=96777
0406: dt=19.200000, rms=0.539 (0.125%), neg=0, invalid=96777
0407: dt=19.200000, rms=0.538 (0.154%), neg=0, invalid=96777
0408: dt=19.200000, rms=0.537 (0.173%), neg=0, invalid=96777
0409: dt=19.200000, rms=0.536 (0.109%), neg=0, invalid=96777
0410: dt=19.200000, rms=0.536 (0.116%), neg=0, invalid=96777
0411: dt=19.200000, rms=0.535 (0.116%), neg=0, invalid=96777
0412: dt=19.200000, rms=0.534 (0.118%), neg=0, invalid=96777
0413: dt=19.200000, rms=0.534 (0.107%), neg=0, invalid=96777
0414: dt=19.200000, rms=0.534 (0.028%), neg=0, invalid=96777
0415: dt=19.200000, rms=0.533 (0.109%), neg=0, invalid=96777
0416: dt=19.200000, rms=0.533 (0.086%), neg=0, invalid=96777
0417: dt=19.200000, rms=0.533 (-0.004%), neg=0, invalid=96777
0418: dt=2.800000, rms=0.533 (0.004%), neg=0, invalid=96777
0419: dt=2.800000, rms=0.533 (0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.533, neg=0, invalid=96777
0420: dt=32.000000, rms=0.531 (0.271%), neg=0, invalid=96777
0421: dt=19.200000, rms=0.530 (0.159%), neg=0, invalid=96777
0422: dt=6.400000, rms=0.530 (0.033%), neg=0, invalid=96777
0423: dt=6.400000, rms=0.530 (0.030%), neg=0, invalid=96777
0424: dt=6.400000, rms=0.530 (0.035%), neg=0, invalid=96777
0425: dt=6.400000, rms=0.530 (0.041%), neg=0, invalid=96777
0426: dt=6.400000, rms=0.529 (0.050%), neg=0, invalid=96777
0427: dt=6.400000, rms=0.529 (0.057%), neg=0, invalid=96777
0428: dt=6.400000, rms=0.529 (0.046%), neg=0, invalid=96777
0429: dt=6.400000, rms=0.529 (0.039%), neg=0, invalid=96777
0430: dt=6.400000, rms=0.528 (0.035%), neg=0, invalid=96777
0431: dt=6.400000, rms=0.528 (0.017%), neg=0, invalid=96777
0432: dt=6.400000, rms=0.528 (0.017%), neg=0, invalid=96777
0433: dt=6.400000, rms=0.528 (0.023%), neg=0, invalid=96777
0434: dt=6.400000, rms=0.528 (0.023%), neg=0, invalid=96777
0435: dt=6.400000, rms=0.528 (0.018%), neg=0, invalid=96777
0436: dt=44.800000, rms=0.528 (0.056%), neg=0, invalid=96777
0437: dt=11.200000, rms=0.527 (0.034%), neg=0, invalid=96777
0438: dt=11.200000, rms=0.527 (0.008%), neg=0, invalid=96777
0439: dt=11.200000, rms=0.527 (0.021%), neg=0, invalid=96777
0440: dt=11.200000, rms=0.527 (0.036%), neg=0, invalid=96777
0441: dt=11.200000, rms=0.527 (0.040%), neg=0, invalid=96777
0442: dt=11.200000, rms=0.527 (0.036%), neg=0, invalid=96777
0443: dt=11.200000, rms=0.526 (0.043%), neg=0, invalid=96777
0444: dt=11.200000, rms=0.526 (0.044%), neg=0, invalid=96777
0445: dt=11.200000, rms=0.526 (0.038%), neg=0, invalid=96777
0446: dt=11.200000, rms=0.526 (0.041%), neg=0, invalid=96777
0447: dt=11.200000, rms=0.526 (0.037%), neg=0, invalid=96777
0448: dt=11.200000, rms=0.525 (0.041%), neg=0, invalid=96777
0449: dt=11.200000, rms=0.525 (0.040%), neg=0, invalid=96777
0450: dt=11.200000, rms=0.525 (0.037%), neg=0, invalid=96777
0451: dt=11.200000, rms=0.525 (0.034%), neg=0, invalid=96777
0452: dt=11.200000, rms=0.525 (0.028%), neg=0, invalid=96777
0453: dt=11.200000, rms=0.524 (0.035%), neg=0, invalid=96777
0454: dt=11.200000, rms=0.524 (0.020%), neg=0, invalid=96777
0455: dt=11.200000, rms=0.524 (0.022%), neg=0, invalid=96777
0456: dt=11.200000, rms=0.524 (0.019%), neg=0, invalid=96777
0457: dt=44.800000, rms=0.524 (0.030%), neg=0, invalid=96777
0458: dt=0.000488, rms=0.524 (-0.006%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.545, neg=0, invalid=96777
0459: dt=0.000000, rms=0.545 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.545, neg=0, invalid=96777
0460: dt=0.000000, rms=0.545 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.586, neg=0, invalid=96777
0461: dt=0.448000, rms=0.584 (0.294%), neg=0, invalid=96777
0462: dt=0.520833, rms=0.583 (0.137%), neg=0, invalid=96777
0463: dt=0.080827, rms=0.583 (0.003%), neg=0, invalid=96777
0464: dt=0.080827, rms=0.583 (0.003%), neg=0, invalid=96777
0465: dt=0.080827, rms=0.583 (-0.006%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.583, neg=0, invalid=96777
0466: dt=0.458333, rms=0.583 (0.071%), neg=0, invalid=96777
0467: dt=0.112000, rms=0.583 (0.002%), neg=0, invalid=96777
0468: dt=0.112000, rms=0.583 (0.002%), neg=0, invalid=96777
0469: dt=0.112000, rms=0.583 (-0.011%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.533, neg=0, invalid=96777
0470: dt=0.112000, rms=0.528 (0.914%), neg=0, invalid=96777
0471: dt=0.112000, rms=0.524 (0.720%), neg=0, invalid=96777
0472: dt=0.007000, rms=0.524 (0.036%), neg=0, invalid=96777
0473: dt=0.007000, rms=0.524 (0.035%), neg=0, invalid=96777
0474: dt=0.007000, rms=0.524 (0.067%), neg=0, invalid=96777
0475: dt=0.007000, rms=0.523 (0.095%), neg=0, invalid=96777
0476: dt=0.007000, rms=0.522 (0.117%), neg=0, invalid=96777
0477: dt=0.007000, rms=0.522 (0.135%), neg=0, invalid=96777
0478: dt=0.007000, rms=0.521 (0.151%), neg=0, invalid=96777
0479: dt=0.007000, rms=0.520 (0.165%), neg=0, invalid=96777
0480: dt=0.007000, rms=0.519 (0.172%), neg=0, invalid=96777
0481: dt=0.007000, rms=0.518 (0.180%), neg=0, invalid=96777
0482: dt=0.007000, rms=0.517 (0.182%), neg=0, invalid=96777
0483: dt=0.007000, rms=0.516 (0.184%), neg=0, invalid=96777
0484: dt=0.007000, rms=0.515 (0.180%), neg=0, invalid=96777
0485: dt=0.007000, rms=0.515 (0.179%), neg=0, invalid=96777
0486: dt=0.007000, rms=0.514 (0.174%), neg=0, invalid=96777
0487: dt=0.007000, rms=0.513 (0.165%), neg=0, invalid=96777
0488: dt=0.007000, rms=0.512 (0.159%), neg=0, invalid=96777
0489: dt=0.007000, rms=0.511 (0.146%), neg=0, invalid=96777
0490: dt=0.007000, rms=0.510 (0.140%), neg=0, invalid=96777
0491: dt=0.007000, rms=0.510 (0.130%), neg=0, invalid=96777
0492: dt=0.007000, rms=0.509 (0.119%), neg=0, invalid=96777
0493: dt=0.007000, rms=0.509 (0.108%), neg=0, invalid=96777
0494: dt=0.007000, rms=0.508 (0.099%), neg=0, invalid=96777
0495: dt=0.007000, rms=0.508 (0.089%), neg=0, invalid=96777
0496: dt=0.007000, rms=0.507 (0.079%), neg=0, invalid=96777
0497: dt=0.007000, rms=0.507 (0.069%), neg=0, invalid=96777
0498: dt=0.007000, rms=0.507 (0.057%), neg=0, invalid=96777
0499: dt=0.007000, rms=0.506 (0.050%), neg=0, invalid=96777
0500: dt=0.007000, rms=0.506 (0.043%), neg=0, invalid=96777
0501: dt=0.007000, rms=0.506 (0.039%), neg=0, invalid=96777
0502: dt=0.007000, rms=0.506 (0.029%), neg=0, invalid=96777
0503: dt=0.007000, rms=0.506 (0.024%), neg=0, invalid=96777
0504: dt=0.007000, rms=0.506 (0.019%), neg=0, invalid=96777
0505: dt=0.000000, rms=0.506 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.506, neg=0, invalid=96777
0506: dt=0.112000, rms=0.504 (0.287%), neg=0, invalid=96777
0507: dt=0.112000, rms=0.503 (0.219%), neg=0, invalid=96777
0508: dt=0.028000, rms=0.503 (0.040%), neg=0, invalid=96777
0509: dt=0.028000, rms=0.503 (0.042%), neg=0, invalid=96777
0510: dt=0.028000, rms=0.502 (0.071%), neg=0, invalid=96777
0511: dt=0.028000, rms=0.502 (0.101%), neg=0, invalid=96777
0512: dt=0.028000, rms=0.501 (0.116%), neg=0, invalid=96777
0513: dt=0.028000, rms=0.501 (0.021%), neg=0, invalid=96777
0514: dt=0.028000, rms=0.501 (0.040%), neg=0, invalid=96777
0515: dt=0.028000, rms=0.501 (0.054%), neg=0, invalid=96777
0516: dt=0.028000, rms=0.500 (0.064%), neg=0, invalid=96777
0517: dt=0.028000, rms=0.500 (0.070%), neg=0, invalid=96777
0518: dt=0.028000, rms=0.500 (0.074%), neg=0, invalid=96777
0519: dt=0.028000, rms=0.499 (0.071%), neg=0, invalid=96777
0520: dt=0.028000, rms=0.499 (0.069%), neg=0, invalid=96777
0521: dt=0.028000, rms=0.499 (0.058%), neg=0, invalid=96777
0522: dt=0.028000, rms=0.498 (0.053%), neg=0, invalid=96777
0523: dt=0.028000, rms=0.498 (0.041%), neg=0, invalid=96777
0524: dt=0.028000, rms=0.498 (0.032%), neg=0, invalid=96777
0525: dt=0.028000, rms=0.498 (0.026%), neg=0, invalid=96777
0526: dt=0.028000, rms=0.498 (0.016%), neg=0, invalid=96777
0527: dt=0.028000, rms=0.498 (0.005%), neg=0, invalid=96777
0528: dt=0.000000, rms=0.498 (0.002%), neg=0, invalid=96777
0529: dt=0.050000, rms=0.498 (-0.007%), neg=0, invalid=96777
label assignment complete, 0 changed (0.00%)
*********************************************************************************************
*********************************************************************************************
*********************************************************************************************
********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
*********************************************************************************************
*********************************************************************************************
*********************************************************************************************
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.496, neg=0, invalid=96777
0530: dt=0.000000, rms=0.496 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.496, neg=0, invalid=96777
0531: dt=129.472000, rms=0.496 (0.034%), neg=0, invalid=96777
0532: dt=129.472000, rms=0.496 (0.018%), neg=0, invalid=96777
0533: dt=129.472000, rms=0.495 (0.015%), neg=0, invalid=96777
0534: dt=129.472000, rms=0.495 (0.014%), neg=0, invalid=96777
0535: dt=129.472000, rms=0.495 (0.032%), neg=0, invalid=96777
0536: dt=129.472000, rms=0.495 (0.032%), neg=0, invalid=96777
0537: dt=129.472000, rms=0.495 (-0.003%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.495, neg=0, invalid=96777
0538: dt=25.920000, rms=0.495 (0.045%), neg=0, invalid=96777
0539: dt=7.776000, rms=0.495 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.495, neg=0, invalid=96777
0540: dt=103.680000, rms=0.494 (0.232%), neg=0, invalid=96777
0541: dt=36.288000, rms=0.493 (0.157%), neg=0, invalid=96777
0542: dt=36.288000, rms=0.493 (0.022%), neg=0, invalid=96777
0543: dt=36.288000, rms=0.492 (0.112%), neg=0, invalid=96777
0544: dt=36.288000, rms=0.492 (0.128%), neg=0, invalid=96777
0545: dt=36.288000, rms=0.491 (0.114%), neg=0, invalid=96777
0546: dt=36.288000, rms=0.491 (0.037%), neg=0, invalid=96777
0547: dt=31.104000, rms=0.491 (0.076%), neg=0, invalid=96777
0548: dt=9.072000, rms=0.491 (0.002%), neg=0, invalid=96777
0549: dt=9.072000, rms=0.491 (0.003%), neg=0, invalid=96777
0550: dt=9.072000, rms=0.491 (0.002%), neg=0, invalid=96777
0551: dt=9.072000, rms=0.490 (0.013%), neg=0, invalid=96777
0552: dt=9.072000, rms=0.490 (0.017%), neg=0, invalid=96777
0553: dt=9.072000, rms=0.490 (0.017%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.490, neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0554: dt=32.000000, rms=0.488 (0.495%), neg=0, invalid=96777
iter 0, gcam->neg = 51
after 31 iterations, nbhd size=3, neg = 0
0555: dt=32.000000, rms=0.487 (0.282%), neg=0, invalid=96777
0556: dt=8.000000, rms=0.486 (0.111%), neg=0, invalid=96777
0557: dt=8.000000, rms=0.486 (0.081%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 13 iterations, nbhd size=2, neg = 0
0558: dt=8.000000, rms=0.485 (0.109%), neg=0, invalid=96777
0559: dt=8.000000, rms=0.484 (0.150%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0560: dt=8.000000, rms=0.484 (0.134%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0561: dt=8.000000, rms=0.483 (0.130%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0562: dt=8.000000, rms=0.483 (0.114%), neg=0, invalid=96777
0563: dt=8.000000, rms=0.482 (0.099%), neg=0, invalid=96777
0564: dt=11.200000, rms=0.482 (0.053%), neg=0, invalid=96777
0565: dt=11.200000, rms=0.482 (0.041%), neg=0, invalid=96777
0566: dt=11.200000, rms=0.481 (0.090%), neg=0, invalid=96777
0567: dt=11.200000, rms=0.481 (0.100%), neg=0, invalid=96777
0568: dt=11.200000, rms=0.480 (0.105%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0569: dt=11.200000, rms=0.480 (0.111%), neg=0, invalid=96777
0570: dt=11.200000, rms=0.479 (0.082%), neg=0, invalid=96777
iter 0, gcam->neg = 7
after 19 iterations, nbhd size=3, neg = 0
0571: dt=11.200000, rms=0.479 (0.081%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.479, neg=0, invalid=96777
iter 0, gcam->neg = 7
after 21 iterations, nbhd size=2, neg = 0
0572: dt=38.400000, rms=0.475 (0.740%), neg=0, invalid=96777
0573: dt=8.000000, rms=0.474 (0.222%), neg=0, invalid=96777
0574: dt=8.000000, rms=0.474 (0.136%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 5 iterations, nbhd size=1, neg = 0
0575: dt=8.000000, rms=0.473 (0.140%), neg=0, invalid=96777
0576: dt=8.000000, rms=0.472 (0.228%), neg=0, invalid=96777
0577: dt=8.000000, rms=0.471 (0.177%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0578: dt=8.000000, rms=0.470 (0.181%), neg=0, invalid=96777
0579: dt=8.000000, rms=0.470 (0.155%), neg=0, invalid=96777
0580: dt=8.000000, rms=0.469 (0.120%), neg=0, invalid=96777
0581: dt=8.000000, rms=0.468 (0.122%), neg=0, invalid=96777
0582: dt=8.000000, rms=0.468 (0.089%), neg=0, invalid=96777
0583: dt=9.600000, rms=0.468 (0.024%), neg=0, invalid=96777
0584: dt=9.600000, rms=0.468 (0.054%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0585: dt=9.600000, rms=0.467 (0.041%), neg=0, invalid=96777
0586: dt=9.600000, rms=0.467 (0.038%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.471, neg=0, invalid=96777
iter 0, gcam->neg = 18
after 17 iterations, nbhd size=1, neg = 0
0587: dt=2.333333, rms=0.471 (0.046%), neg=0, invalid=96777
0588: dt=1.008000, rms=0.471 (0.011%), neg=0, invalid=96777
0589: dt=1.008000, rms=0.471 (0.024%), neg=0, invalid=96777
0590: dt=1.008000, rms=0.470 (0.035%), neg=0, invalid=96777
iter 0, gcam->neg = 8
after 9 iterations, nbhd size=1, neg = 0
0591: dt=1.008000, rms=0.470 (0.022%), neg=0, invalid=96777
iter 0, gcam->neg = 7
after 7 iterations, nbhd size=1, neg = 0
0592: dt=1.008000, rms=0.470 (-0.018%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.470, neg=0, invalid=96777
iter 0, gcam->neg = 19
after 11 iterations, nbhd size=1, neg = 0
0593: dt=4.258065, rms=0.470 (0.149%), neg=0, invalid=96777
iter 0, gcam->neg = 44
after 16 iterations, nbhd size=1, neg = 0
0594: dt=7.111111, rms=0.468 (0.246%), neg=0, invalid=96777
0595: dt=0.015750, rms=0.468 (0.003%), neg=0, invalid=96777
0596: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777
0597: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777
0598: dt=0.015750, rms=0.468 (0.000%), neg=0, invalid=96777
0599: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777
0600: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777
0601: dt=0.015750, rms=0.468 (0.001%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.474, neg=0, invalid=96777
0602: dt=0.000000, rms=0.474 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.474, neg=0, invalid=96777
0603: dt=0.000000, rms=0.474 (0.000%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.465, neg=0, invalid=96777
iter 0, gcam->neg = 802
after 29 iterations, nbhd size=2, neg = 0
0604: dt=1.832792, rms=0.423 (8.972%), neg=0, invalid=96777
0605: dt=0.000109, rms=0.423 (-0.003%), neg=0, invalid=96777
0606: dt=0.000109, rms=0.423 (0.001%), neg=0, invalid=96777
0607: dt=0.000109, rms=0.423 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.423, neg=0, invalid=96777
0608: dt=0.000313, rms=0.423 (0.000%), neg=0, invalid=96777
0609: dt=0.000000, rms=0.423 (0.000%), neg=0, invalid=96777
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 ************************
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.408, neg=0, invalid=96777
0610: dt=0.000000, rms=0.409 (-0.320%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=96777
0611: dt=8.092000, rms=0.409 (0.001%), neg=0, invalid=96777
0612: dt=8.092000, rms=0.409 (0.000%), neg=0, invalid=96777
0613: dt=8.092000, rms=0.409 (-0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.409, neg=0, invalid=96777
0614: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.409, neg=0, invalid=96777
0615: dt=15.552000, rms=0.409 (0.012%), neg=0, invalid=96777
0616: dt=9.072000, rms=0.409 (0.002%), neg=0, invalid=96777
0617: dt=9.072000, rms=0.409 (0.000%), neg=0, invalid=96777
0618: dt=9.072000, rms=0.409 (-0.003%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.410, neg=0, invalid=96777
0619: dt=2.800000, rms=0.410 (0.010%), neg=0, invalid=96777
0620: dt=1.600000, rms=0.410 (0.001%), neg=0, invalid=96777
0621: dt=1.600000, rms=0.410 (0.002%), neg=0, invalid=96777
0622: dt=1.600000, rms=0.410 (-0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.410, neg=0, invalid=96777
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0623: dt=32.000000, rms=0.409 (0.182%), neg=0, invalid=96777
iter 0, gcam->neg = 16
after 16 iterations, nbhd size=2, neg = 0
0624: dt=25.600000, rms=0.409 (0.131%), neg=0, invalid=96777
iter 0, gcam->neg = 17
after 45 iterations, nbhd size=1, neg = 0
0625: dt=25.600000, rms=0.409 (-0.628%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.411, neg=0, invalid=96777
0626: dt=0.009000, rms=0.411 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 8
after 29 iterations, nbhd size=3, neg = 0
0627: dt=1.142857, rms=0.411 (0.016%), neg=0, invalid=96777
0628: dt=0.063000, rms=0.411 (0.001%), neg=0, invalid=96777
0629: dt=0.063000, rms=0.411 (0.003%), neg=0, invalid=96777
0630: dt=0.063000, rms=0.411 (0.007%), neg=0, invalid=96777
0631: dt=0.063000, rms=0.411 (0.010%), neg=0, invalid=96777
0632: dt=0.063000, rms=0.411 (0.013%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0633: dt=0.063000, rms=0.411 (0.015%), neg=0, invalid=96777
0634: dt=0.063000, rms=0.411 (0.013%), neg=0, invalid=96777
0635: dt=0.063000, rms=0.410 (0.014%), neg=0, invalid=96777
0636: dt=0.063000, rms=0.410 (0.016%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0637: dt=0.063000, rms=0.410 (0.017%), neg=0, invalid=96777
0638: dt=0.063000, rms=0.410 (0.018%), neg=0, invalid=96777
0639: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777
0640: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0641: dt=0.063000, rms=0.410 (0.026%), neg=0, invalid=96777
0642: dt=0.063000, rms=0.410 (0.019%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.410, neg=0, invalid=96777
iter 0, gcam->neg = 43
after 51 iterations, nbhd size=4, neg = 0
0643: dt=7.161905, rms=0.408 (0.428%), neg=0, invalid=96777
0644: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
0645: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
0646: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
0647: dt=0.003938, rms=0.408 (0.000%), neg=0, invalid=96777
0648: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0649: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0650: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0651: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0652: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0653: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0654: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0655: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0656: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0657: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0658: dt=0.003938, rms=0.408 (0.001%), neg=0, invalid=96777
0659: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0660: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0661: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0662: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0663: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0664: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0665: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0666: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0667: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0668: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0669: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0670: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0671: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0672: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0673: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0674: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0675: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0676: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0677: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0678: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0679: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0680: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0681: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0682: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0683: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0684: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
0685: dt=0.003938, rms=0.408 (0.002%), neg=0, invalid=96777
iter 0, gcam->neg = 132
after 56 iterations, nbhd size=4, neg = 0
0686: dt=13.824000, rms=0.406 (0.376%), neg=0, invalid=96777
0687: dt=0.000984, rms=0.406 (0.000%), neg=0, invalid=96777
0688: dt=0.000984, rms=0.406 (0.000%), neg=0, invalid=96777
0689: dt=0.000984, rms=0.406 (-0.000%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.412, neg=0, invalid=96777
0690: dt=0.000160, rms=0.412 (0.000%), neg=0, invalid=96777
0691: dt=0.000000, rms=0.412 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.412, neg=0, invalid=96777
0692: dt=0.000078, rms=0.412 (0.000%), neg=0, invalid=96777
0693: dt=0.000078, rms=0.412 (-0.000%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.403, neg=0, invalid=96777
iter 0, gcam->neg = 224
after 35 iterations, nbhd size=3, neg = 0
0694: dt=0.448000, rms=0.394 (2.045%), neg=0, invalid=96777
0695: dt=0.000015, rms=0.394 (0.001%), neg=0, invalid=96777
0696: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777
0697: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777
0698: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777
0699: dt=0.000015, rms=0.394 (0.000%), neg=0, invalid=96777
0700: dt=0.000750, rms=0.394 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 6
after 6 iterations, nbhd size=1, neg = 0
0701: dt=0.024000, rms=0.394 (0.010%), neg=0, invalid=96777
0702: dt=0.000004, rms=0.394 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.394, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0703: dt=0.000250, rms=0.394 (0.001%), neg=0, invalid=96777
0704: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0705: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0706: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0707: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0708: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0709: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0710: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0711: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0712: dt=0.000027, rms=0.394 (0.000%), neg=0, invalid=96777
0713: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0714: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0715: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0716: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0717: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0718: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0719: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0720: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0721: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0722: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0723: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0724: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0725: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0726: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0727: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0728: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0729: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0730: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0731: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0732: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0733: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0734: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0735: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0736: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0737: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0738: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0739: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0740: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0741: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0742: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0743: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0744: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0745: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0746: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
0747: dt=0.000027, rms=0.394 (0.001%), neg=0, invalid=96777
writing output transformation to transforms/talairach.m3z...
GCAMwrite
registration took 4 hours, 18 minutes and 0 seconds.
#--------------------------------------
#@# CA Reg Inv Thu Aug  8 16:31:57 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mri_ca_register -invert-and-save transforms/talairach.m3z 

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z 
Inverting GCAM
Saving inverse 
#--------------------------------------
#@# Remove Neck Thu Aug  8 16:33:31 CEST 2013

 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz 

erasing everything more than 25 mm from possible brain
reading atlas '/opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'...
reading input volume 'nu.mgz'...
reading transform 'transforms/talairach.m3z'...
removing structures at least 25 mm from brain...
11389683 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 1 minutes and 34 seconds.
#--------------------------------------
#@# SkullLTA Thu Aug  8 16:35:04 CEST 2013

 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta 



 ======= NUMBER OF OPENMP THREADS = 1 ======= 
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach_with_skull_2.log
reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
average std = 23.1   using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu_noneck.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7 
total sample mean = 92.0 (1443 zeros)
************************************************
spacing=8, using 3481 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=9.0
skull bounding box = (54, 13, 0) --> (212, 197, 196)
using (107, 74, 98) as brain centroid...
mean wm in atlas = 126, using box (88,51,74) --> (126, 96,122) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 107, scaling input intensities by 1.178
scaling channel 0 by 1.17757
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2)
 1.264   0.048  -0.071  -35.935;
-0.018   1.270   0.513  -54.525;
 0.125  -0.518   1.107   15.895;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.264   0.048  -0.071  -35.935;
-0.018   1.270   0.513  -54.525;
 0.125  -0.518   1.107   15.895;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
 1.239   0.047  -0.069  -30.915;
-0.022   1.310   0.483  -52.599;
 0.125  -0.478   1.123   12.280;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.239   0.047  -0.069  -30.915;
-0.022   1.285   0.474  -49.342;
 0.122  -0.469   1.102   14.038;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.236   0.047  -0.069  -30.548;
-0.021   1.283   0.484  -50.756;
 0.123  -0.480   1.098   14.970;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.236   0.047  -0.069  -30.548;
-0.021   1.283   0.484  -50.756;
 0.123  -0.480   1.098   14.970;
 0.000   0.000   0.000   1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3481 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.23617   0.04681  -0.06911  -30.54774;
-0.02084   1.28282   0.48392  -50.75591;
 0.12254  -0.47982   1.09813   14.96986;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.23617   0.04681  -0.06911  -30.54774;
-0.02084   1.28282   0.48392  -50.75591;
 0.12254  -0.47982   1.09813   14.96986;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.236   0.047  -0.069  -30.548;
-0.021   1.283   0.484  -50.756;
 0.123  -0.480   1.098   14.970;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
transform before final EM align:
 1.236   0.047  -0.069  -30.548;
-0.021   1.283   0.484  -50.756;
 0.123  -0.480   1.098   14.970;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 382743 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.23617   0.04681  -0.06911  -30.54774;
-0.02084   1.28282   0.48392  -50.75591;
 0.12254  -0.47982   1.09813   14.96986;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.23617   0.04681  -0.06911  -30.54774;
-0.02084   1.28282   0.48392  -50.75591;
 0.12254  -0.47982   1.09813   14.96986;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =    4.4  tol 0.000000
final transform:
 1.236   0.047  -0.069  -30.548;
-0.021   1.283   0.484  -50.756;
 0.123  -0.480   1.098   14.970;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull_2.lta...
registration took 31 minutes and 47 seconds.
#--------------------------------------
#@# SubCort Seg Thu Aug  8 17:06:52 CEST 2013

 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz 

sysname  Linux
hostname snake4
machine  x86_64

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri
mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz 

renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes...
reading classifier array from /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca...
reading input volume from norm.mgz...
average std[0] = 6.9
reading transform from transforms/talairach.m3z...
Atlas used for the 3D morph was /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15151 (27)
mri peak = 0.10814 ( 4)
Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (311 voxels, overlap=0.085)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (311 voxels, peak =  3), gca=10.8
gca peak = 0.14982 (20)
mri peak = 0.14647 ( 5)
Right_Lateral_Ventricle (43): linear fit = 0.19 x + 0.0 (179 voxels, overlap=0.007)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (179 voxels, peak =  4), gca=8.0
gca peak = 0.28003 (97)
mri peak = 0.12552 (83)
Right_Pallidum (52): linear fit = 0.82 x + 0.0 (321 voxels, overlap=0.039)
Right_Pallidum (52): linear fit = 0.82 x + 0.0 (321 voxels, peak = 80), gca=80.0
gca peak = 0.18160 (96)
mri peak = 0.12184 (78)
Left_Pallidum (13): linear fit = 0.79 x + 0.0 (271 voxels, overlap=0.047)
Left_Pallidum (13): linear fit = 0.79 x + 0.0 (271 voxels, peak = 75), gca=75.4
gca peak = 0.27536 (62)
mri peak = 0.10294 (53)
Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (530 voxels, overlap=0.031)
Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (530 voxels, peak = 52), gca=51.8
gca peak = 0.32745 (63)
mri peak = 0.09040 (58)
Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (600 voxels, overlap=0.060)
Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (600 voxels, peak = 53), gca=53.2
gca peak = 0.08597 (105)
mri peak = 0.06879 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31675 voxels, overlap=0.786)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31675 voxels, peak = 107), gca=106.6
gca peak = 0.09209 (106)
mri peak = 0.07904 (108)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (30610 voxels, overlap=0.709)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (30610 voxels, peak = 109), gca=108.6
gca peak = 0.07826 (63)
mri peak = 0.05015 (50)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (15235 voxels, overlap=0.375)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (15235 voxels, peak = 50), gca=50.1
gca peak = 0.08598 (64)
mri peak = 0.05696 (51)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14577 voxels, overlap=0.266)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (14577 voxels, peak = 53), gca=52.8
gca peak = 0.24164 (71)
mri peak = 0.12107 (58)
Right_Caudate (50): linear fit = 0.79 x + 0.0 (638 voxels, overlap=0.024)
Right_Caudate (50): linear fit = 0.79 x + 0.0 (638 voxels, peak = 56), gca=55.7
gca peak = 0.18227 (75)
mri peak = 0.10473 (58)
Left_Caudate (11): linear fit = 0.77 x + 0.0 (590 voxels, overlap=0.026)
Left_Caudate (11): linear fit = 0.77 x + 0.0 (590 voxels, peak = 58), gca=58.1
gca peak = 0.10629 (62)
mri peak = 0.06110 (59)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10502 voxels, overlap=0.995)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (10502 voxels, peak = 61), gca=61.1
gca peak = 0.11668 (59)
mri peak = 0.05820 (61)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (9892 voxels, overlap=0.999)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (9892 voxels, peak = 60), gca=60.5
gca peak = 0.17849 (88)
mri peak = 0.08017 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3946 voxels, overlap=0.991)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3946 voxels, peak = 88), gca=87.6
gca peak = 0.16819 (86)
mri peak = 0.06108 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (3732 voxels, overlap=0.997)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (3732 voxels, peak = 87), gca=87.3
gca peak = 0.41688 (64)
mri peak = 0.10381 (55)
Left_Amygdala (18): linear fit = 0.85 x + 0.0 (337 voxels, overlap=0.763)
Left_Amygdala (18): linear fit = 0.85 x + 0.0 (337 voxels, peak = 54), gca=54.1
gca peak = 0.42394 (62)
mri peak = 0.15749 (54)
Right_Amygdala (54): linear fit = 0.86 x + 0.0 (156 voxels, overlap=0.052)
Right_Amygdala (54): linear fit = 0.86 x + 0.0 (156 voxels, peak = 53), gca=53.0
gca peak = 0.10041 (96)
mri peak = 0.07050 (80)
Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (2851 voxels, overlap=0.291)
Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (2851 voxels, peak = 84), gca=84.0
gca peak = 0.13978 (88)
mri peak = 0.10651 (77)
Right_Thalamus_Proper (49): linear fit = 0.89 x + 0.0 (3096 voxels, overlap=0.419)
Right_Thalamus_Proper (49): linear fit = 0.89 x + 0.0 (3096 voxels, peak = 79), gca=78.8
gca peak = 0.08514 (81)
mri peak = 0.07602 (68)
Left_Putamen (12): linear fit = 0.81 x + 0.0 (1997 voxels, overlap=0.127)
Left_Putamen (12): linear fit = 0.81 x + 0.0 (1997 voxels, peak = 65), gca=65.2
gca peak = 0.09624 (82)
mri peak = 0.09486 (66)
Right_Putamen (51): linear fit = 0.79 x + 0.0 (1835 voxels, overlap=0.013)
Right_Putamen (51): linear fit = 0.79 x + 0.0 (1835 voxels, peak = 64), gca=64.4
gca peak = 0.07543 (88)
mri peak = 0.10827 (83)
Brain_Stem (16): linear fit = 0.96 x + 0.0 (7866 voxels, overlap=0.698)
Brain_Stem (16): linear fit = 0.96 x + 0.0 (7866 voxels, peak = 85), gca=84.9
gca peak = 0.12757 (95)
mri peak = 0.12170 (85)
Right_VentralDC (60): linear fit = 0.90 x + 0.0 (818 voxels, overlap=0.213)
Right_VentralDC (60): linear fit = 0.90 x + 0.0 (818 voxels, peak = 86), gca=86.0
gca peak = 0.17004 (92)
mri peak = 0.10560 (83)
Left_VentralDC (28): linear fit = 0.89 x + 0.0 (884 voxels, overlap=0.452)
Left_VentralDC (28): linear fit = 0.89 x + 0.0 (884 voxels, peak = 82), gca=82.3
gca peak = 0.21361 (36)
mri peak = 0.15680 (54)
gca peak = 0.26069 (23)
mri peak = 0.17261 ( 8)
Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (233 voxels, overlap=0.024)
Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (233 voxels, peak =  6), gca=6.1
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.31795 (35)
gca peak Third_Ventricle = 0.21361 (36)
gca peak Fourth_Ventricle = 0.26069 (23)
gca peak CSF = 0.14367 (38)
gca peak Left_Accumbens_area = 0.57033 (70)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.65201 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.31129 (32)
gca peak Right_Accumbens_area = 0.30219 (72)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.72939 (42)
gca peak WM_hypointensities = 0.14821 (82)
gca peak non_WM_hypointensities = 0.10354 (53)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 0.83 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.40 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.31600 (11)
mri peak = 0.10814 ( 4)
Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (311 voxels, overlap=0.465)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (311 voxels, peak =  3), gca=4.4
gca peak = 0.29325 ( 9)
mri peak = 0.14647 ( 5)
Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (179 voxels, overlap=0.716)
Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (179 voxels, peak =  4), gca=4.0
gca peak = 0.26612 (81)
mri peak = 0.12552 (83)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (321 voxels, overlap=0.995)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (321 voxels, peak = 81), gca=81.0
gca peak = 0.23030 (75)
mri peak = 0.12184 (78)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (271 voxels, overlap=1.006)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (271 voxels, peak = 75), gca=75.0
gca peak = 0.32075 (52)
mri peak = 0.10294 (53)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (530 voxels, overlap=1.005)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (530 voxels, peak = 52), gca=52.0
gca peak = 0.29771 (53)
mri peak = 0.09040 (58)
Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (600 voxels, overlap=1.004)
Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (600 voxels, peak = 54), gca=53.8
gca peak = 0.08541 (107)
mri peak = 0.06879 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31675 voxels, overlap=0.834)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31675 voxels, peak = 108), gca=107.5
gca peak = 0.08551 (108)
mri peak = 0.07904 (108)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30610 voxels, overlap=0.783)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (30610 voxels, peak = 108), gca=108.0
gca peak = 0.09720 (50)
mri peak = 0.05015 (50)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15235 voxels, overlap=0.993)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15235 voxels, peak = 50), gca=50.0
gca peak = 0.10545 (53)
mri peak = 0.05696 (51)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14577 voxels, overlap=0.985)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14577 voxels, peak = 52), gca=52.2
gca peak = 0.26700 (58)
mri peak = 0.12107 (58)
Right_Caudate (50): linear fit = 1.04 x + 0.0 (638 voxels, overlap=0.999)
Right_Caudate (50): linear fit = 1.04 x + 0.0 (638 voxels, peak = 61), gca=60.6
gca peak = 0.19395 (58)
mri peak = 0.10473 (58)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (590 voxels, overlap=0.986)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (590 voxels, peak = 58), gca=58.0
gca peak = 0.11171 (61)
mri peak = 0.06110 (59)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10502 voxels, overlap=0.991)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10502 voxels, peak = 63), gca=62.5
gca peak = 0.12569 (61)
mri peak = 0.05820 (61)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9892 voxels, overlap=0.992)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (9892 voxels, peak = 59), gca=58.9
gca peak = 0.18438 (87)
mri peak = 0.08017 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (3946 voxels, overlap=0.987)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (3946 voxels, peak = 88), gca=88.3
gca peak = 0.16063 (88)
mri peak = 0.06108 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3732 voxels, overlap=1.000)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3732 voxels, peak = 88), gca=87.6
gca peak = 0.57967 (54)
mri peak = 0.10381 (55)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (337 voxels, overlap=1.023)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (337 voxels, peak = 54), gca=54.0
gca peak = 0.49427 (53)
mri peak = 0.15749 (54)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (156 voxels, overlap=1.014)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (156 voxels, peak = 53), gca=53.0
gca peak = 0.10699 (84)
mri peak = 0.07050 (80)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2851 voxels, overlap=0.969)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2851 voxels, peak = 84), gca=83.6
gca peak = 0.10983 (79)
mri peak = 0.10651 (77)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3096 voxels, overlap=0.894)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3096 voxels, peak = 79), gca=78.6
gca peak = 0.10378 (65)
mri peak = 0.07602 (68)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (1997 voxels, overlap=0.991)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (1997 voxels, peak = 67), gca=66.6
gca peak = 0.12788 (60)
mri peak = 0.09486 (66)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (1835 voxels, overlap=0.990)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (1835 voxels, peak = 62), gca=61.5
gca peak = 0.08675 (85)
mri peak = 0.10827 (83)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (7866 voxels, overlap=0.662)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (7866 voxels, peak = 87), gca=87.1
gca peak = 0.12656 (86)
mri peak = 0.12170 (85)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (818 voxels, overlap=0.780)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (818 voxels, peak = 86), gca=86.0
gca peak = 0.15972 (83)
mri peak = 0.10560 (83)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (884 voxels, overlap=0.856)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (884 voxels, peak = 84), gca=84.2
gca peak = 0.35640 (14)
mri peak = 0.15680 (54)
gca peak = 0.33827 ( 9)
mri peak = 0.17261 ( 8)
Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (233 voxels, overlap=0.798)
Fourth_Ventricle (15): linear fit = 0.68 x + 0.0 (233 voxels, peak =  6), gca=6.1
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.27462 (30)
gca peak Third_Ventricle = 0.35640 (14)
gca peak CSF = 0.30128 (18)
gca peak Left_Accumbens_area = 0.58351 (54)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.43797 (61)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.30433 (27)
gca peak Right_Accumbens_area = 0.41720 (58)
gca peak Right_vessel = 0.57787 (60)
gca peak Right_choroid_plexus = 0.10381 (48)
gca peak Fifth_Ventricle = 0.45329 (19)
gca peak WM_hypointensities = 0.17688 (83)
gca peak non_WM_hypointensities = 0.11865 (54)
gca peak Optic_Chiasm = 0.34833 (76)
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 0.51 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
11423 gm and wm labels changed (%12 to gray, %88 to white out of all changed labels)
289 hippocampal voxels changed.
2 amygdala voxels changed.
pass 1: 88309 changed. image ll: -2.193, PF=1.000
pass 2: 15767 changed. image ll: -2.190, PF=1.000
pass 3: 5631 changed.
pass 4: 2444 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
auto-labeling took 20 minutes and 45 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/cc_up.lta sub005 

will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/cc_up.lta
reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.auto_noCCseg.mgz
reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/norm.mgz
37418 voxels in left wm, 96637 in right wm, xrange [119, 135]
searching rotation angles z=[-11  3], y=[-11  3]

searching scale 1 Z rot -10.7  
searching scale 1 Z rot -10.4  
searching scale 1 Z rot -10.2  
searching scale 1 Z rot -9.9  
searching scale 1 Z rot -9.7  
searching scale 1 Z rot -9.4  
searching scale 1 Z rot -9.2  
searching scale 1 Z rot -8.9  
searching scale 1 Z rot -8.7  
searching scale 1 Z rot -8.4  
searching scale 1 Z rot -8.2  
searching scale 1 Z rot -7.9  
searching scale 1 Z rot -7.7  
searching scale 1 Z rot -7.4  
searching scale 1 Z rot -7.2  
searching scale 1 Z rot -6.9  
searching scale 1 Z rot -6.7  
searching scale 1 Z rot -6.4  
searching scale 1 Z rot -6.2  
searching scale 1 Z rot -5.9  
searching scale 1 Z rot -5.7  
searching scale 1 Z rot -5.4  
searching scale 1 Z rot -5.2  
searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  global minimum found at slice 129.0, rotations (-4.50, -3.17)
final transformation (x=129.0, yr=-4.495, zr=-3.173):
 0.995   0.055  -0.078   2.066;
-0.055   0.998   0.004   50.852;
 0.078  -0.000   0.997   27.169;
 0.000   0.000   0.000   1.000;
updating x range to be [126, 130] in xformed coordinates
best xformed slice 128
cc center is found at 128 143 135
eigenvectors:
-0.001  -0.003   1.000;
-0.190  -0.982  -0.003;
 0.982  -0.190   0.001;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.auto.mgz...
corpus callosum matter segmentation took 1.7 minutes
#--------------------------------------
#@# Merge ASeg Thu Aug  8 17:29:22 CEST 2013

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Thu Aug  8 17:29:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz 

using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
2381 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 111
white matter peak found at 109
gm peak at 56 (56), valley at 20 (20)
csf peak at 28, setting threshold to 46
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 56 (56), valley at 19 (19)
csf peak at 28, setting threshold to 46
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 4 minutes and 18 seconds.
#--------------------------------------------
#@# Mask BFS Thu Aug  8 17:33:42 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1476227 voxels in mask (pct=  8.80)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Thu Aug  8 17:33:44 CEST 2013

 mri_segment brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (107.0): 107.1 +- 4.9 [80.0 --> 125.0]
GM (67.0) : 66.0 +- 9.4 [30.0 --> 96.0]
setting bottom of white matter range to 75.4
setting top of gray matter range to 84.7
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
8711 sparsely connected voxels removed...
thickening thin strands....
20 segments, 6051 filled
785 bright non-wm voxels segmented.
4744 diagonally connected voxels added...
white matter segmentation took 1.8 minutes
writing output to wm.seg.mgz...

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

preserving editing changes in input volume...
auto filling took 0.62 minutes
reading wm segmentation from wm.seg.mgz...
92 voxels added to wm to prevent paths from MTL structures to cortex
791 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 38026 voxels turned on, 36556 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  17 found -  17 modified     |    TOTAL:  17
pass   2 (xy+):   0 found -  17 modified     |    TOTAL:  17
pass   1 (xy-):  22 found -  22 modified     |    TOTAL:  39
pass   2 (xy-):   0 found -  22 modified     |    TOTAL:  39
pass   1 (yz+):  34 found -  34 modified     |    TOTAL:  73
pass   2 (yz+):   0 found -  34 modified     |    TOTAL:  73
pass   1 (yz-):  30 found -  30 modified     |    TOTAL: 103
pass   2 (yz-):   0 found -  30 modified     |    TOTAL: 103
pass   1 (xz+):  20 found -  20 modified     |    TOTAL: 123
pass   2 (xz+):   0 found -  20 modified     |    TOTAL: 123
pass   1 (xz-):  23 found -  23 modified     |    TOTAL: 146
pass   2 (xz-):   0 found -  23 modified     |    TOTAL: 146
Iteration Number : 1
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  10
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  10
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  22
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  22
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  34
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  34
pass   1 (+++):  11 found -  11 modified     |    TOTAL:  45
pass   2 (+++):   0 found -  11 modified     |    TOTAL:  45
Iteration Number : 1
pass   1 (++): 290 found - 290 modified     |    TOTAL: 290
pass   2 (++):   0 found - 290 modified     |    TOTAL: 290
pass   1 (+-): 235 found - 235 modified     |    TOTAL: 525
pass   2 (+-):   1 found - 236 modified     |    TOTAL: 526
pass   3 (+-):   0 found - 236 modified     |    TOTAL: 526
pass   1 (--): 257 found - 257 modified     |    TOTAL: 783
pass   2 (--):   0 found - 257 modified     |    TOTAL: 783
pass   1 (-+): 240 found - 240 modified     |    TOTAL: 1023
pass   2 (-+):   0 found - 240 modified     |    TOTAL: 1023
Iteration Number : 2
pass   1 (xy+):   5 found -   5 modified     |    TOTAL:   5
pass   2 (xy+):   0 found -   5 modified     |    TOTAL:   5
pass   1 (xy-):   7 found -   7 modified     |    TOTAL:  12
pass   2 (xy-):   0 found -   7 modified     |    TOTAL:  12
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:  15
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:  15
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  19
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  19
pass   1 (xz+):   5 found -   5 modified     |    TOTAL:  24
pass   2 (xz+):   0 found -   5 modified     |    TOTAL:  24
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  26
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  26
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 (+++):   0 found -   0 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   1
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 = 1248 (out of 502039: 0.248586)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Thu Aug  8 17:36:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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
 1.099   0.042  -0.061  -14.845;
-0.028   1.149   0.325  -20.792;
 0.099  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 1.099   0.042  -0.061  -14.845;
-0.028   1.149   0.325  -20.792;
 0.099  -0.272   0.946   13.810;
 0.000   0.000   0.000   1.000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2587 (min = 350, max = 1400), aspect = 1.43 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 116, 146), TAL = (2.0, 18.0, 12.0)
talairach voxel to voxel transform
 0.904  -0.017   0.065   12.161;
 0.045   0.804  -0.273   21.157;
-0.081   0.233   0.972  -9.785;
 0.000   0.000   0.000   1.000;
segmentation indicates cc at (126,  116,  146) --> (2.0, 18.0, 12.0)
done.
writing output to filled.mgz...
filling took 0.9 minutes
talairach cc position changed to (2.00, 18.00, 12.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 18.00, 12.00) SRC: (117.19, 79.40, 150.28)
search lh wm seed point around talairach space (-16.00, 18.00, 12.00), SRC: (149.73, 81.03, 147.36)
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 Thu Aug  8 17:37:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   5
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   3 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 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 11 (out of 243070: 0.004525)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 30: 275 vertices, 334 faces
slice 40: 5225 vertices, 5463 faces
slice 50: 14011 vertices, 14356 faces
slice 60: 25378 vertices, 25806 faces
slice 70: 37928 vertices, 38377 faces
slice 80: 49484 vertices, 49874 faces
slice 90: 60012 vertices, 60374 faces
slice 100: 71070 vertices, 71447 faces
slice 110: 81719 vertices, 82133 faces
slice 120: 92216 vertices, 92635 faces
slice 130: 102284 vertices, 102683 faces
slice 140: 112784 vertices, 113151 faces
slice 150: 121893 vertices, 122235 faces
slice 160: 129983 vertices, 130269 faces
slice 170: 135798 vertices, 136026 faces
slice 180: 140298 vertices, 140506 faces
slice 190: 143125 vertices, 143245 faces
slice 200: 143522 vertices, 143568 faces
slice 210: 143522 vertices, 143568 faces
slice 220: 143522 vertices, 143568 faces
slice 230: 143522 vertices, 143568 faces
slice 240: 143522 vertices, 143568 faces
slice 250: 143522 vertices, 143568 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   143522 voxel in cpt #1: X=-46 [v=143522,e=430704,f=287136] located at (-27.371929, -26.230808, 38.191643)
For the whole surface: X=-46 [v=143522,e=430704,f=287136]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Thu Aug  8 17:37:15 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 lh Thu Aug  8 17:37:20 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
avg radius = 47.8 mm, total surface area = 74380 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.6 minutes
Not saving sulc

step 000: RMS=0.104 (target=0.015)   
step 005: RMS=0.076 (target=0.015)   
step 010: RMS=0.056 (target=0.015)   
step 015: RMS=0.047 (target=0.015)   
step 020: RMS=0.040 (target=0.015)   
step 025: RMS=0.036 (target=0.015)   
step 030: RMS=0.032 (target=0.015)   
step 035: RMS=0.029 (target=0.015)   
step 040: RMS=0.028 (target=0.015)   
step 045: RMS=0.026 (target=0.015)   
step 050: RMS=0.025 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.025 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Thu Aug  8 17:37:54 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 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 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.96 +- 0.59 (0.00-->7.70) (max @ vno 59673 --> 60711)
face area 0.02 +- 0.03 (-0.22-->0.80)
scaling brain by 0.302...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.621, avgs=0
005/300: dt: 0.9000, rms radial error=176.366, avgs=0
010/300: dt: 0.9000, rms radial error=175.818, avgs=0
015/300: dt: 0.9000, rms radial error=175.096, avgs=0
020/300: dt: 0.9000, rms radial error=174.271, avgs=0
025/300: dt: 0.9000, rms radial error=173.388, avgs=0
030/300: dt: 0.9000, rms radial error=172.468, avgs=0
035/300: dt: 0.9000, rms radial error=171.533, avgs=0
040/300: dt: 0.9000, rms radial error=170.590, avgs=0
045/300: dt: 0.9000, rms radial error=169.645, avgs=0
050/300: dt: 0.9000, rms radial error=168.701, avgs=0
055/300: dt: 0.9000, rms radial error=167.760, avgs=0
060/300: dt: 0.9000, rms radial error=166.822, avgs=0
065/300: dt: 0.9000, rms radial error=165.889, avgs=0
070/300: dt: 0.9000, rms radial error=164.960, avgs=0
075/300: dt: 0.9000, rms radial error=164.035, avgs=0
080/300: dt: 0.9000, rms radial error=163.116, avgs=0
085/300: dt: 0.9000, rms radial error=162.202, avgs=0
090/300: dt: 0.9000, rms radial error=161.292, avgs=0
095/300: dt: 0.9000, rms radial error=160.387, avgs=0
100/300: dt: 0.9000, rms radial error=159.487, avgs=0
105/300: dt: 0.9000, rms radial error=158.592, avgs=0
110/300: dt: 0.9000, rms radial error=157.702, avgs=0
115/300: dt: 0.9000, rms radial error=156.816, avgs=0
120/300: dt: 0.9000, rms radial error=155.935, avgs=0
125/300: dt: 0.9000, rms radial error=155.059, avgs=0
130/300: dt: 0.9000, rms radial error=154.187, avgs=0
135/300: dt: 0.9000, rms radial error=153.320, avgs=0
140/300: dt: 0.9000, rms radial error=152.458, avgs=0
145/300: dt: 0.9000, rms radial error=151.600, avgs=0
150/300: dt: 0.9000, rms radial error=150.747, avgs=0
155/300: dt: 0.9000, rms radial error=149.898, avgs=0
160/300: dt: 0.9000, rms radial error=149.055, avgs=0
165/300: dt: 0.9000, rms radial error=148.216, avgs=0
170/300: dt: 0.9000, rms radial error=147.382, avgs=0
175/300: dt: 0.9000, rms radial error=146.552, avgs=0
180/300: dt: 0.9000, rms radial error=145.727, avgs=0
185/300: dt: 0.9000, rms radial error=144.906, avgs=0
190/300: dt: 0.9000, rms radial error=144.090, avgs=0
195/300: dt: 0.9000, rms radial error=143.279, avgs=0
200/300: dt: 0.9000, rms radial error=142.471, avgs=0
205/300: dt: 0.9000, rms radial error=141.669, avgs=0
210/300: dt: 0.9000, rms radial error=140.870, avgs=0
215/300: dt: 0.9000, rms radial error=140.077, avgs=0
220/300: dt: 0.9000, rms radial error=139.287, avgs=0
225/300: dt: 0.9000, rms radial error=138.502, avgs=0
230/300: dt: 0.9000, rms radial error=137.721, avgs=0
235/300: dt: 0.9000, rms radial error=136.945, avgs=0
240/300: dt: 0.9000, rms radial error=136.172, avgs=0
245/300: dt: 0.9000, rms radial error=135.405, avgs=0
250/300: dt: 0.9000, rms radial error=134.641, avgs=0
255/300: dt: 0.9000, rms radial error=133.882, avgs=0
260/300: dt: 0.9000, rms radial error=133.127, avgs=0
265/300: dt: 0.9000, rms radial error=132.376, avgs=0
270/300: dt: 0.9000, rms radial error=131.629, avgs=0
275/300: dt: 0.9000, rms radial error=130.886, avgs=0
280/300: dt: 0.9000, rms radial error=130.148, avgs=0
285/300: dt: 0.9000, rms radial error=129.414, avgs=0
290/300: dt: 0.9000, rms radial error=128.683, avgs=0
295/300: dt: 0.9000, rms radial error=127.957, avgs=0
300/300: dt: 0.9000, rms radial error=127.235, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17016.37
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
epoch 2 (K=40.0), pass 1, starting sse = 2959.58
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
epoch 3 (K=160.0), pass 1, starting sse = 342.52
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00504
epoch 4 (K=640.0), pass 1, starting sse = 26.16
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.12/13 = 0.00932
final writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology lh Thu Aug  8 17:42:53 CEST 2013

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


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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub005 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 1.48 2011/03/02 00:04:32 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
before topology correction, eno=-46 (nv=143522, nf=287136, ne=430704, g=24)
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 13 iterations
marking ambiguous vertices...
3404 ambiguous faces found in tessellation
segmenting defects...
32 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 5 into 4
31 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8018  (-4.9009)
      -vertex     loglikelihood: -6.6801  (-3.3400)
      -normal dot loglikelihood: -3.6316  (-3.6316)
      -quad curv  loglikelihood: -6.5082  (-3.2541)
      Total Loglikelihood : -26.6216

CORRECTING DEFECT 0 (vertices=36, convex hull=80)
After retessellation of defect 0, euler #=-28 (141428,423391,281935) : difference with theory (-28) = 0 

CORRECTING DEFECT 1 (vertices=33, convex hull=67)
After retessellation of defect 1, euler #=-27 (141442,423458,281989) : difference with theory (-27) = 0 

CORRECTING DEFECT 2 (vertices=26, convex hull=40)
After retessellation of defect 2, euler #=-26 (141444,423480,282010) : difference with theory (-26) = 0 

CORRECTING DEFECT 3 (vertices=7, convex hull=30)
After retessellation of defect 3, euler #=-25 (141447,423499,282027) : difference with theory (-25) = 0 

CORRECTING DEFECT 4 (vertices=213, convex hull=130)
After retessellation of defect 4, euler #=-23 (141496,423706,282187) : difference with theory (-24) = -1 

CORRECTING DEFECT 5 (vertices=54, convex hull=64)
After retessellation of defect 5, euler #=-22 (141520,423802,282260) : difference with theory (-23) = -1 

CORRECTING DEFECT 6 (vertices=43, convex hull=89)
After retessellation of defect 6, euler #=-21 (141536,423888,282331) : difference with theory (-22) = -1 

CORRECTING DEFECT 7 (vertices=44, convex hull=76)
After retessellation of defect 7, euler #=-20 (141565,424007,282422) : difference with theory (-21) = -1 

CORRECTING DEFECT 8 (vertices=26, convex hull=62)
After retessellation of defect 8, euler #=-19 (141582,424082,282481) : difference with theory (-20) = -1 

CORRECTING DEFECT 9 (vertices=24, convex hull=68)
After retessellation of defect 9, euler #=-18 (141596,424151,282537) : difference with theory (-19) = -1 

CORRECTING DEFECT 10 (vertices=358, convex hull=225)
After retessellation of defect 10, euler #=-17 (141611,424305,282677) : difference with theory (-18) = -1 

CORRECTING DEFECT 11 (vertices=28, convex hull=57)
After retessellation of defect 11, euler #=-16 (141631,424387,282740) : difference with theory (-17) = -1 

CORRECTING DEFECT 12 (vertices=11, convex hull=25)
After retessellation of defect 12, euler #=-15 (141634,424403,282754) : difference with theory (-16) = -1 

CORRECTING DEFECT 13 (vertices=11, convex hull=30)
After retessellation of defect 13, euler #=-14 (141637,424422,282771) : difference with theory (-15) = -1 

CORRECTING DEFECT 14 (vertices=49, convex hull=21)
After retessellation of defect 14, euler #=-13 (141638,424431,282780) : difference with theory (-14) = -1 

CORRECTING DEFECT 15 (vertices=170, convex hull=93)
After retessellation of defect 15, euler #=-13 (141666,424567,282888) : difference with theory (-13) = 0 

CORRECTING DEFECT 16 (vertices=23, convex hull=18)
After retessellation of defect 16, euler #=-12 (141672,424590,282906) : difference with theory (-12) = 0 

CORRECTING DEFECT 17 (vertices=197, convex hull=176)
After retessellation of defect 17, euler #=-11 (141715,424800,283074) : difference with theory (-11) = 0 

CORRECTING DEFECT 18 (vertices=72, convex hull=82)
After retessellation of defect 18, euler #=-10 (141744,424925,283171) : difference with theory (-10) = 0 

CORRECTING DEFECT 19 (vertices=5, convex hull=19)
After retessellation of defect 19, euler #=-9 (141744,424931,283178) : difference with theory (-9) = 0 

CORRECTING DEFECT 20 (vertices=57, convex hull=81)
After retessellation of defect 20, euler #=-8 (141770,425043,283265) : difference with theory (-8) = 0 

CORRECTING DEFECT 21 (vertices=8, convex hull=9)
After retessellation of defect 21, euler #=-7 (141770,425045,283268) : difference with theory (-7) = 0 

CORRECTING DEFECT 22 (vertices=25, convex hull=63)
After retessellation of defect 22, euler #=-6 (141787,425123,283330) : difference with theory (-6) = 0 

CORRECTING DEFECT 23 (vertices=240, convex hull=50)
After retessellation of defect 23, euler #=-5 (141798,425178,283375) : difference with theory (-5) = 0 

CORRECTING DEFECT 24 (vertices=88, convex hull=55)
After retessellation of defect 24, euler #=-4 (141813,425246,283429) : difference with theory (-4) = 0 

CORRECTING DEFECT 25 (vertices=83, convex hull=104)
After retessellation of defect 25, euler #=-3 (141858,425428,283567) : difference with theory (-3) = 0 

CORRECTING DEFECT 26 (vertices=89, convex hull=105)
After retessellation of defect 26, euler #=-2 (141884,425552,283666) : difference with theory (-2) = 0 

CORRECTING DEFECT 27 (vertices=10, convex hull=34)
After retessellation of defect 27, euler #=-1 (141886,425569,283682) : difference with theory (-1) = 0 

CORRECTING DEFECT 28 (vertices=32, convex hull=70)
After retessellation of defect 28, euler #=0 (141900,425638,283738) : difference with theory (0) = 0 

CORRECTING DEFECT 29 (vertices=29, convex hull=68)
After retessellation of defect 29, euler #=1 (141909,425693,283785) : difference with theory (1) = 0 

CORRECTING DEFECT 30 (vertices=19, convex hull=68)
After retessellation of defect 30, euler #=2 (141918,425748,283832) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.23 (0.06-->9.14) (max @ vno 60346 --> 65969)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.23 (0.06-->9.14) (max @ vno 60346 --> 65969)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
93 mutations (33.5%), 185 crossovers (66.5%), 223 vertices were eliminated
building final representation...
1604 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=141918, nf=283832, ne=425748, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 26.5 minutes
0 defective edges
removing intersecting faces
000: 220 intersecting
001: 15 intersecting

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 141918 - 425748 + 283832 = 2 --> 0 holes
      F =2V-4:          283832 = 283836-4 (0)
      2E=3F:            851496 = 851496 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

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

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

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make White Surf lh Thu Aug  8 18:09:28 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub005 lh 

only generating white matter surface
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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
16905 bright wm thresholded.
908 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig...
computing class statistics...
border white:    254363 voxels (1.52%)
border gray      296177 voxels (1.77%)
WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0]
GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70)
setting MAX_BORDER_WHITE to 114.3 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.6 (was 40)
setting MAX_GRAY to 93.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.01-->3.88) (max @ vno 67884 --> 71912)
face area 0.28 +- 0.12 (0.00-->6.13)
mean absolute distance = 0.64 +- 0.75
4354 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104,    GM=59
mean inside = 92.3, mean outside = 67.9
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=72.7, 45 (45) missing vertices, mean dist 0.3 [0.5 (%33.5)->0.7 (%66.5))]
%74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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 +- 0.27 (0.04-->5.98) (max @ vno 60346 --> 65969)
face area 0.28 +- 0.13 (0.00-->4.83)
mean absolute distance = 0.29 +- 0.45
2871 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7465551.0, rms=13.21
001: dt: 0.5000, sse=7823105.0, rms=9.481 (0.000%)
002: dt: 0.5000, sse=8288571.5, rms=7.465 (0.000%)
003: dt: 0.5000, sse=8446310.0, rms=6.251 (0.000%)
004: dt: 0.5000, sse=8744839.0, rms=5.521 (0.000%)
005: dt: 0.5000, sse=8775113.0, rms=5.122 (0.000%)
006: dt: 0.5000, sse=8937678.0, rms=4.871 (0.000%)
007: dt: 0.5000, sse=8850499.0, rms=4.747 (0.000%)
008: dt: 0.5000, sse=8937956.0, rms=4.631 (0.000%)
rms = 4.59, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=8824802.0, rms=4.586 (0.000%)
010: dt: 0.2500, sse=5836391.5, rms=3.250 (0.000%)
011: dt: 0.2500, sse=5373295.5, rms=2.813 (0.000%)
012: dt: 0.2500, sse=5091939.5, rms=2.713 (0.000%)
013: dt: 0.2500, sse=5008144.0, rms=2.627 (0.000%)
rms = 2.60, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=4908885.0, rms=2.600 (0.000%)
015: dt: 0.1250, sse=4619963.5, rms=2.301 (0.000%)
rms = 2.26, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=4568109.0, rms=2.259 (0.000%)
positioning took 2.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=76.9, 33 (3) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))]
%83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.06-->6.25) (max @ vno 60346 --> 65969)
face area 0.35 +- 0.17 (0.00-->6.29)
mean absolute distance = 0.21 +- 0.30
3014 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5456520.0, rms=5.76
017: dt: 0.5000, sse=5856689.5, rms=4.107 (0.000%)
rms = 4.62, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=5323868.5, rms=2.954 (0.000%)
019: dt: 0.2500, sse=5138993.5, rms=2.467 (0.000%)
020: dt: 0.2500, sse=5071286.5, rms=2.113 (0.000%)
rms = 2.09, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=5062744.5, rms=2.086 (0.000%)
022: dt: 0.1250, sse=4871787.0, rms=1.829 (0.000%)
rms = 1.79, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=4819964.5, rms=1.785 (0.000%)
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 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=80.0, 24 (1) missing vertices, mean dist -0.1 [0.2 (%74.6)->0.2 (%25.4))]
%89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.12-->6.37) (max @ vno 60346 --> 65969)
face area 0.34 +- 0.17 (0.00-->6.20)
mean absolute distance = 0.16 +- 0.25
2371 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5157340.0, rms=4.08
rms = 4.12, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=4968705.0, rms=2.871 (0.000%)
025: dt: 0.2500, sse=4855665.0, rms=1.873 (0.000%)
026: dt: 0.2500, sse=4894005.0, rms=1.737 (0.000%)
027: dt: 0.2500, sse=4925580.5, rms=1.673 (0.000%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
028: dt: 0.1250, sse=4866839.0, rms=1.601 (0.000%)
029: dt: 0.1250, sse=4781871.5, rms=1.520 (0.000%)
rms = 1.52, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=4781871.5, rms=1.520 (0.002%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=81.0, 36 (1) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=4805187.0, rms=1.86
rms = 2.87, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=4889560.5, rms=1.247 (0.000%)
032: dt: 0.2500, sse=5074887.5, rms=1.124 (0.000%)
rms = 1.13, time step reduction 2 of 3 to 0.125...
rms = 1.11, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=5078172.0, rms=1.111 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
9 non-cortical segments detected
only using segment with 1837 vertices
erasing segment 1 (vno[0] = 86517)
erasing segment 2 (vno[0] = 93790)
erasing segment 3 (vno[0] = 100688)
erasing segment 4 (vno[0] = 102748)
erasing segment 5 (vno[0] = 107796)
erasing segment 6 (vno[0] = 107856)
erasing segment 7 (vno[0] = 108814)
erasing segment 8 (vno[0] = 109084)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area
vertex spacing 0.90 +- 0.26 (0.06-->6.37) (max @ vno 60346 --> 65969)
face area 0.34 +- 0.16 (0.00-->6.17)
refinement took 6.9 minutes
#--------------------------------------------
#@# Smooth2 lh Thu Aug  8 18:16:24 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
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...
#--------------------------------------------
#@# Inflation2 lh Thu Aug  8 18:16:28 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated 

avg radius = 48.1 mm, total surface area = 86492 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.121 (target=0.015)   
step 005: RMS=0.082 (target=0.015)   
step 010: RMS=0.060 (target=0.015)   
step 015: RMS=0.049 (target=0.015)   
step 020: RMS=0.040 (target=0.015)   
step 025: RMS=0.034 (target=0.015)   
step 030: RMS=0.028 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.018 (target=0.015)   
step 050: RMS=0.016 (target=0.015)   
step 055: RMS=0.015 (target=0.015)   
inflation complete.
inflation took 0.5 minutes

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

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
156 vertices thresholded to be in k1 ~ [-0.22 1.31], k2 ~ [-0.11 0.05]
total integrated curvature = 0.539*4pi (6.769) --> 0 handles
ICI = 1.6, FI = 11.3, variation=188.525
116 vertices thresholded to be in [-0.04 0.01]
writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
106 vertices thresholded to be in [-0.14 0.28]
done.
writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023
done.

#-----------------------------------------
#@# Curvature Stats lh Thu Aug  8 18:18:49 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub005 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       [ sub005/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                      [ 252 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.208057
WARN:    S explicit min:                          0.000000	vertex = 345
#--------------------------------------------
#@# Sphere lh Thu Aug  8 18:18:54 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
scaling brain by 0.279...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=snake, 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 %21.03
pass 1: epoch 2 of 3 starting distance error %20.99
unfolding complete - removing small folds...
starting distance error %20.92
removing remaining folds...
final distance error %20.94
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.93 hours
#--------------------------------------------
#@# Surf Reg lh Thu Aug  8 19:14:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 

using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading surface from ../surf/lh.sphere...
reading template parameterization from /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
MRISregister() -------
max_passes = 4 
min_degrees = 0.500000 
max_degrees = 64.000000 
nangles = 8 
tol=5.0e-01, sigma=0.0, host=snake, 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=snake, 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 = 0.565
curvature mean = 0.044, std = 0.936
curvature mean = 0.024, std = 0.846
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 346648.8, tmin=1.1476
  d=32.00 min @ (8.00, 0.00, -8.00) sse = 268100.4, tmin=2.2979
  d=16.00 min @ (0.00, 4.00, 0.00) sse = 239922.3, tmin=3.4634
  d=4.00 min @ (-1.00, -1.00, 0.00) sse = 237072.4, tmin=5.8038
  d=2.00 min @ (0.00, 0.50, -0.50) sse = 236492.4, tmin=6.9803
  d=1.00 min @ (0.00, -0.25, 0.00) sse = 236457.6, tmin=8.1529
  d=0.50 min @ (-0.12, 0.00, 0.12) sse = 236426.1, tmin=9.3353
tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.34 min
curvature mean = 0.008, std = 0.945
curvature mean = 0.012, std = 0.931
curvature mean = 0.005, std = 0.957
curvature mean = 0.006, std = 0.967
curvature mean = 0.003, std = 0.958
curvature mean = 0.002, std = 0.984
2 Reading smoothwm
curvature mean = -0.023, std = 0.319
curvature mean = 0.003, std = 0.067
curvature mean = 0.075, std = 0.300
curvature mean = 0.003, std = 0.079
curvature mean = 0.035, std = 0.481
curvature mean = 0.004, std = 0.084
curvature mean = 0.018, std = 0.625
curvature mean = 0.004, std = 0.087
curvature mean = 0.007, std = 0.740
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white lh Thu Aug  8 19:42:54 CEST 2013

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

reading surface from ../surf/lh.white...
writing curvature file ../surf/lh.jacobian_white
#--------------------------------------------
#@# AvgCurv lh Thu Aug  8 19:42:56 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.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 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
writing curvature file to ../surf/lh.avg_curv...
#-----------------------------------------
#@# Cortical Parc lh Thu Aug  8 19:42:58 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
reading color table from GCSA file....
average std = 1.0   using min determinant for regularization = 0.011
0 singular and 384 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1217 labels changed using aseg
relabeling using gibbs priors...
000:   3352 changed, 141918 examined...
001:    780 changed, 14134 examined...
002:    182 changed, 4320 examined...
003:     74 changed, 1125 examined...
004:     25 changed, 423 examined...
005:     12 changed, 157 examined...
006:      2 changed, 74 examined...
007:      3 changed, 14 examined...
008:      3 changed, 14 examined...
009:      0 changed, 17 examined...
217 labels changed using aseg
000: 129 total segments, 79 labels (294 vertices) changed
001: 51 total segments, 3 labels (8 vertices) changed
002: 48 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 53 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1496 vertices marked for relabeling...
1496 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 1 minutes and 3 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Thu Aug  8 19:44:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub005 lh 

-white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
16905 bright wm thresholded.
908 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig...
computing class statistics...
border white:    254363 voxels (1.52%)
border gray      296177 voxels (1.77%)
WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0]
GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70)
setting MAX_BORDER_WHITE to 114.3 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.6 (was 40)
setting MAX_GRAY to 93.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104,    GM=59
mean inside = 92.3, mean outside = 67.9
smoothing surface for 5 iterations...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.01-->3.88) (max @ vno 67884 --> 71912)
face area 0.28 +- 0.12 (0.00-->6.13)
mean absolute distance = 0.64 +- 0.75
4354 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 0.00% unknown
deleting segment 4 with 7 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 12 points - only 0.00% unknown
deleting segment 8 with 11 points - only 0.00% unknown
mean border=72.7, 45 (45) missing vertices, mean dist 0.3 [0.5 (%33.5)->0.7 (%66.5))]
%74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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 +- 0.27 (0.04-->5.98) (max @ vno 60346 --> 65969)
face area 0.28 +- 0.13 (0.00-->4.83)
mean absolute distance = 0.29 +- 0.45
2898 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7467556.5, rms=13.21
001: dt: 0.5000, sse=7823144.0, rms=9.481 (0.000%)
002: dt: 0.5000, sse=8288121.5, rms=7.465 (0.000%)
003: dt: 0.5000, sse=8444273.0, rms=6.250 (0.000%)
004: dt: 0.5000, sse=8744771.0, rms=5.521 (0.000%)
005: dt: 0.5000, sse=8774059.0, rms=5.121 (0.000%)
006: dt: 0.5000, sse=8938711.0, rms=4.871 (0.000%)
007: dt: 0.5000, sse=8848783.0, rms=4.747 (0.000%)
008: dt: 0.5000, sse=8938806.0, rms=4.631 (0.000%)
rms = 4.59, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=8824362.0, rms=4.586 (0.000%)
010: dt: 0.2500, sse=5834917.0, rms=3.249 (0.000%)
011: dt: 0.2500, sse=5370926.5, rms=2.813 (0.000%)
012: dt: 0.2500, sse=5090155.0, rms=2.713 (0.000%)
013: dt: 0.2500, sse=5006923.0, rms=2.627 (0.000%)
rms = 2.60, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=4908233.0, rms=2.600 (0.000%)
015: dt: 0.1250, sse=4618744.5, rms=2.301 (0.000%)
rms = 2.26, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=4566825.0, rms=2.259 (0.000%)
positioning took 2.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 12 with 5 points - only 0.00% unknown
deleting segment 16 with 10 points - only 0.00% unknown
deleting segment 17 with 26 points - only 0.00% unknown
deleting segment 18 with 13 points - only 0.00% unknown
mean border=76.9, 33 (3) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))]
%83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.06-->6.25) (max @ vno 60346 --> 65969)
face area 0.35 +- 0.17 (0.00-->6.29)
mean absolute distance = 0.21 +- 0.31
3043 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5461817.5, rms=5.76
017: dt: 0.5000, sse=5862041.5, rms=4.109 (0.000%)
rms = 4.62, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=5328916.0, rms=2.957 (0.000%)
019: dt: 0.2500, sse=5143362.5, rms=2.471 (0.000%)
020: dt: 0.2500, sse=5076333.5, rms=2.117 (0.000%)
rms = 2.09, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=5067423.0, rms=2.090 (0.000%)
022: dt: 0.1250, sse=4876173.5, rms=1.833 (0.000%)
rms = 1.79, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=4825049.0, rms=1.789 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
deleting segment 6 with 12 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 9 points - only 0.00% unknown
deleting segment 11 with 10 points - only 0.00% unknown
deleting segment 12 with 10 points - only 0.00% unknown
deleting segment 13 with 23 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
deleting segment 15 with 13 points - only 0.00% unknown
mean border=80.0, 26 (1) missing vertices, mean dist -0.1 [0.2 (%74.6)->0.2 (%25.4))]
%89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.12-->6.37) (max @ vno 60346 --> 65969)
face area 0.34 +- 0.17 (0.00-->6.20)
mean absolute distance = 0.16 +- 0.25
2374 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5162456.5, rms=4.07
rms = 4.12, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=4973562.0, rms=2.871 (0.000%)
025: dt: 0.2500, sse=4860126.5, rms=1.874 (0.000%)
026: dt: 0.2500, sse=4898094.5, rms=1.739 (0.000%)
027: dt: 0.2500, sse=4930149.0, rms=1.674 (0.000%)
rms = 1.74, time step reduction 2 of 3 to 0.125...
028: dt: 0.1250, sse=4871542.5, rms=1.603 (0.000%)
029: dt: 0.1250, sse=4786188.0, rms=1.522 (0.000%)
rms = 1.52, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=4786188.0, rms=1.522 (0.002%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 12 points - only 0.00% unknown
deleting segment 6 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 10 points - only 0.00% unknown
deleting segment 10 with 26 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 13 points - only 0.00% unknown
mean border=81.0, 37 (1) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4809803.0, rms=1.86
rms = 2.87, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=4895558.5, rms=1.248 (0.000%)
032: dt: 0.2500, sse=5083564.5, rms=1.125 (0.000%)
rms = 1.13, time step reduction 2 of 3 to 0.125...
rms = 1.11, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=5086603.5, rms=1.112 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=48.8, 50 (50) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.4 (%100.0))]
%14 local maxima, %53 large gradients and %29 min vals, 2134 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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=30289990.0, rms=31.59
001: dt: 0.5000, sse=21800954.0, rms=26.170 (0.000%)
002: dt: 0.5000, sse=15971152.0, rms=21.701 (0.000%)
003: dt: 0.5000, sse=12148614.0, rms=18.115 (0.000%)
004: dt: 0.5000, sse=9780426.0, rms=15.278 (0.000%)
005: dt: 0.5000, sse=8437585.0, rms=13.078 (0.000%)
006: dt: 0.5000, sse=7662182.0, rms=11.387 (0.000%)
007: dt: 0.5000, sse=7225883.0, rms=9.970 (0.000%)
008: dt: 0.5000, sse=6913676.0, rms=8.697 (0.000%)
009: dt: 0.5000, sse=6786730.5, rms=7.576 (0.000%)
010: dt: 0.5000, sse=6749302.0, rms=6.605 (0.000%)
011: dt: 0.5000, sse=6830642.0, rms=5.824 (0.000%)
012: dt: 0.5000, sse=6971648.0, rms=5.217 (0.000%)
013: dt: 0.5000, sse=7091683.0, rms=4.818 (0.000%)
014: dt: 0.5000, sse=7275634.5, rms=4.533 (0.000%)
015: dt: 0.5000, sse=7341044.0, rms=4.376 (0.000%)
016: dt: 0.5000, sse=7434937.0, rms=4.253 (0.000%)
017: dt: 0.5000, sse=7446205.5, rms=4.195 (0.000%)
018: dt: 0.5000, sse=7537203.0, rms=4.118 (0.000%)
rms = 4.08, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=7507748.0, rms=4.084 (0.000%)
020: dt: 0.2500, sse=5595185.5, rms=3.491 (0.000%)
021: dt: 0.2500, sse=5435547.5, rms=3.331 (0.000%)
rms = 3.31, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=5313698.0, rms=3.315 (0.000%)
023: dt: 0.1250, sse=5111725.5, rms=3.205 (0.000%)
rms = 3.19, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=5080553.5, rms=3.191 (0.000%)
positioning took 3.0 minutes
mean border=46.7, 968 (6) missing vertices, mean dist 0.2 [0.2 (%49.6)->0.7 (%50.4))]
%31 local maxima, %41 large gradients and %24 min vals, 755 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, 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=5729900.0, rms=4.94
025: dt: 0.5000, sse=6068042.5, rms=4.384 (0.000%)
026: dt: 0.5000, sse=7701572.0, rms=4.262 (0.000%)
rms = 4.25, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=7383714.0, rms=4.246 (0.000%)
028: dt: 0.2500, sse=6186324.5, rms=3.485 (0.000%)
029: dt: 0.2500, sse=6044504.0, rms=3.247 (0.000%)
rms = 3.22, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=5939641.0, rms=3.225 (0.000%)
031: dt: 0.1250, sse=5726174.5, rms=3.064 (0.000%)
rms = 3.04, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=5701814.5, rms=3.035 (0.000%)
positioning took 1.0 minutes
mean border=44.5, 1143 (6) missing vertices, mean dist 0.1 [0.2 (%38.5)->0.4 (%61.5))]
%50 local maxima, %21 large gradients and %24 min vals, 972 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, 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=5982376.5, rms=4.27
033: dt: 0.5000, sse=6237107.0, rms=4.116 (0.000%)
rms = 4.08, time step reduction 1 of 3 to 0.250...
034: dt: 0.5000, sse=8157539.0, rms=4.081 (0.000%)
035: dt: 0.2500, sse=6246182.0, rms=3.293 (0.000%)
036: dt: 0.2500, sse=6389504.5, rms=3.050 (0.000%)
rms = 3.06, time step reduction 2 of 3 to 0.125...
037: dt: 0.1250, sse=6265465.5, rms=2.968 (0.000%)
038: dt: 0.1250, sse=6056920.0, rms=2.853 (0.000%)
rms = 2.83, time step reduction 3 of 3 to 0.062...
039: dt: 0.1250, sse=6003770.5, rms=2.835 (0.000%)
positioning took 1.0 minutes
mean border=43.4, 2406 (4) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.3 (%55.4))]
%54 local maxima, %17 large gradients and %24 min vals, 744 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=6071459.0, rms=3.22
rms = 3.84, time step reduction 1 of 3 to 0.250...
040: dt: 0.2500, sse=5918450.0, rms=2.969 (0.000%)
041: dt: 0.2500, sse=6100094.5, rms=2.889 (0.000%)
rms = 2.87, time step reduction 2 of 3 to 0.125...
042: dt: 0.2500, sse=6193060.5, rms=2.868 (0.000%)
043: dt: 0.1250, sse=6082456.0, rms=2.754 (0.000%)
rms = 2.73, time step reduction 3 of 3 to 0.062...
044: dt: 0.1250, sse=6088207.0, rms=2.734 (0.000%)
positioning took 0.7 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area.pial
vertex spacing 1.03 +- 0.44 (0.06-->9.25) (max @ vno 100866 --> 99891)
face area 0.42 +- 0.32 (0.00-->11.30)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 141918 vertices processed
25000 of 141918 vertices processed
50000 of 141918 vertices processed
75000 of 141918 vertices processed
100000 of 141918 vertices processed
125000 of 141918 vertices processed
0 of 141918 vertices processed
25000 of 141918 vertices processed
50000 of 141918 vertices processed
75000 of 141918 vertices processed
100000 of 141918 vertices processed
125000 of 141918 vertices processed
thickness calculation complete, 398:1170 truncations.
26237 vertices at 0 distance
88713 vertices at 1 distance
94532 vertices at 2 distance
43911 vertices at 3 distance
13606 vertices at 4 distance
3907 vertices at 5 distance
1120 vertices at 6 distance
387 vertices at 7 distance
191 vertices at 8 distance
98 vertices at 9 distance
53 vertices at 10 distance
43 vertices at 11 distance
26 vertices at 12 distance
28 vertices at 13 distance
16 vertices at 14 distance
19 vertices at 15 distance
27 vertices at 16 distance
17 vertices at 17 distance
6 vertices at 18 distance
9 vertices at 19 distance
14 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.thickness
positioning took 13.8 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 19:57:51 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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_calc -o lh.volume lh.area.mid mul lh.thickness 

Saving result to 'lh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#-----------------------------------------
#@# WM/GM Contrast lh Thu Aug  8 19:57:51 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 pctsurfcon --s sub005 --lh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts/pctsurfcon.log
Thu Aug  8 19:57:51 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3.0
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh --regheader sub005 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 109466
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh
Dim: 141918 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh --projfrac 0.3 --regheader sub005 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 126137
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh
Dim: 141918 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.32269/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh --annot sub005 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/stats/lh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh --annot sub005 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
Constructing seg from annotation

Reading annotation
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Seg base 1000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.w-g.pct.mgh
Vertex Area is 0.670531 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   1000                            unknown       0       0.000
  1   1001                           bankssts    1722    1207.068
  2   1002            caudalanteriorcingulate     877     616.236
  3   1003                caudalmiddlefrontal    3619    2446.539
  4   1004                     corpuscallosum       0       0.000
  5   1005                             cuneus    2565    1689.801
  6   1006                         entorhinal     606     428.386
  7   1007                           fusiform    4512    3134.628
  8   1008                   inferiorparietal    6034    3977.454
  9   1009                   inferiortemporal    5113    3484.146
 10   1010                   isthmuscingulate    1632    1065.528
 11   1011                   lateraloccipital    9016    5810.531
 12   1012               lateralorbitofrontal    4111    2725.845
 13   1013                            lingual    5608    3867.486
 14   1014                medialorbitofrontal    2772    1890.563
 15   1015                     middletemporal    4814    3256.627
 16   1016                    parahippocampal     926     622.722
 17   1017                        paracentral    1973    1270.574
 18   1018                    parsopercularis    2922    1995.094
 19   1019                      parsorbitalis    1048     686.831
 20   1020                   parstriangularis    2076    1369.012
 21   1021                      pericalcarine    2558    1771.464
 22   1022                        postcentral    7081    4667.076
 23   1023                 posteriorcingulate    1867    1243.578
 24   1024                         precentral    6904    4575.087
 25   1025                          precuneus    5653    3799.979
 26   1026           rostralanteriorcingulate    1532    1033.005
 27   1027               rostralmiddlefrontal    8995    6119.219
 28   1028                    superiorfrontal   11617    7997.352
 29   1029                   superiorparietal    8754    5766.701
 30   1030                   superiortemporal    6406    4413.473
 31   1031                      supramarginal    5764    3893.233
 32   1032                        frontalpole     418     251.037
 33   1033                       temporalpole     837     553.961
 34   1034                 transversetemporal     822     507.131
 35   1035                             insula    3345    2193.028

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats lh Thu Aug  8 19:58:04 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub005 lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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

 1722   1207   2999  2.567 0.457     0.135     0.038       20     2.6  bankssts
  877    616   1558  2.320 0.599     0.145     0.045       16     1.5  caudalanteriorcingulate
 3619   2447   6845  2.489 0.417     0.140     0.042       51     6.3  caudalmiddlefrontal
 2565   1690   4212  2.219 0.475     0.166     0.064       57     7.2  cuneus
  606    428   2268  3.682 0.648     0.171     0.072       11     1.9  entorhinal
 4512   3135   9751  2.761 0.589     0.161     0.060       88    10.9  fusiform
 6034   3977  11629  2.586 0.463     0.147     0.059      122    12.9  inferiorparietal
 5113   3484  11423  2.753 0.658     0.160     0.089      143    15.3  inferiortemporal
 1632   1066   3029  2.570 0.730     0.165     0.074       38     4.5  isthmuscingulate
 9016   5811  14639  2.251 0.483     0.160     0.071      215    24.2  lateraloccipital
 4111   2726   8158  2.581 0.671     0.158     0.070       97    10.8  lateralorbitofrontal
 5608   3867   9904  2.311 0.556     0.175     0.077      134    17.1  lingual
 2772   1891   5268  2.243 0.856     0.190     0.115      142    10.7  medialorbitofrontal
 4814   3257  11042  2.672 0.611     0.156     0.070      117    12.8  middletemporal
  926    623   2362  3.298 0.667     0.155     0.062       20     2.2  parahippocampal
 1973   1271   3634  2.482 0.539     0.128     0.041       26     3.2  paracentral
 2922   1995   6104  2.625 0.434     0.151     0.056       54     6.6  parsopercularis
 1048    687   2215  2.421 0.659     0.171     0.076       29     2.8  parsorbitalis
 2076   1369   3814  2.470 0.558     0.148     0.056       38     4.5  parstriangularis
 2558   1771   3523  2.023 0.528     0.164     0.076       45     7.3  pericalcarine
 7081   4667  12024  2.211 0.588     0.146     0.053      132    14.9  postcentral
 1867   1244   3475  2.633 0.551     0.169     0.124      149     5.1  posteriorcingulate
 6904   4575  13529  2.642 0.519     0.128     0.056      105    16.4  precentral
 5653   3800  10487  2.603 0.500     0.153     0.062      113    13.2  precuneus
 1532   1033   3300  2.736 0.720     0.153     0.061       33     3.9  rostralanteriorcingulate
 8995   6119  16203  2.242 0.560     0.179     0.095      275    32.4  rostralmiddlefrontal
11617   7997  23675  2.528 0.561     0.148     0.053      215    24.3  superiorfrontal
 8754   5767  14762  2.282 0.417     0.139     0.064      296    28.4  superiorparietal
 6406   4413  14656  2.846 0.591     0.150     0.051      126    13.8  superiortemporal
 5764   3893  11519  2.656 0.490     0.152     0.064      113    14.9  supramarginal
  418    251    782  2.194 0.751     0.219     0.132       26     2.2  frontalpole
  837    554   2851  3.583 0.651     0.154     0.072       15     2.6  temporalpole
  822    507   1644  2.808 0.362     0.145     0.049       13     1.6  transversetemporal
 3345   2193   7111  3.161 0.837     0.124     0.068       55     7.9  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Thu Aug  8 19:58:23 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs...
reading color table from GCSA file....
average std = 3.9 0.2   using min determinant for regularization = 0.000
0 singular and 1066 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
52 labels changed using aseg
relabeling using gibbs priors...
000:   9826 changed, 141918 examined...
001:   2460 changed, 37405 examined...
002:    781 changed, 12468 examined...
003:    300 changed, 4185 examined...
004:    116 changed, 1682 examined...
005:     71 changed, 654 examined...
006:     42 changed, 404 examined...
007:     21 changed, 221 examined...
008:     19 changed, 124 examined...
009:     14 changed, 92 examined...
010:      5 changed, 61 examined...
011:      0 changed, 25 examined...
14 labels changed using aseg
000: 310 total segments, 227 labels (2923 vertices) changed
001: 105 total segments, 22 labels (72 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 154 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
849 vertices marked for relabeling...
849 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 1 minutes and 12 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Thu Aug  8 19:59:34 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_anatomical_stats -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 sub005 lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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

 1378    920   2400  2.108 0.663     0.191     0.113       51     5.6  G_and_S_frontomargin
 2137   1388   4192  2.534 0.497     0.172     0.075       48     5.4  G_and_S_occipital_inf
 1433    892   2756  2.463 0.533     0.143     0.113       38     6.4  G_and_S_paracentral
 1687   1137   3728  2.800 0.498     0.158     0.057       34     4.1  G_and_S_subcentral
  855    564   1523  2.088 0.539     0.203     0.151       37     4.2  G_and_S_transv_frontopol
 2884   1986   5490  2.523 0.718     0.150     0.053       53     6.2  G_and_S_cingul-Ant
 1436   1023   2855  2.592 0.537     0.137     0.060       35     3.0  G_and_S_cingul-Mid-Ant
 1437    979   2702  2.627 0.433     0.134     0.045       20     2.4  G_and_S_cingul-Mid-Post
  555    371   1371  2.977 0.492     0.198     0.098       20     2.4  G_cingul-Post-dorsal
  419    269    860  2.553 0.872     0.173     0.087       12     1.2  G_cingul-Post-ventral
 2319   1544   3782  2.101 0.476     0.179     0.077       60     7.8  G_cuneus
 1839   1236   4307  2.751 0.443     0.163     0.065       43     4.6  G_front_inf-Opercular
  308    188    818  2.873 0.439     0.169     0.063        8     0.8  G_front_inf-Orbital
 1298    865   3033  2.748 0.476     0.179     0.087       38     4.4  G_front_inf-Triangul
 4376   2983   9909  2.551 0.482     0.185     0.093      148    16.4  G_front_middle
 7586   5135  17357  2.653 0.542     0.158     0.062      165    18.4  G_front_sup
  411    247   1034  3.697 0.833     0.128     0.069        7     1.1  G_Ins_lg_and_S_cent_ins
  828    506   2535  3.749 0.786     0.155     0.139       31     3.8  G_insular_short
 2469   1549   5012  2.536 0.418     0.169     0.073       82     7.4  G_occipital_middle
 2099   1345   3730  2.273 0.505     0.156     0.146      193    17.5  G_occipital_sup
 1349    941   3454  2.830 0.453     0.187     0.076       39     4.3  G_oc-temp_lat-fusifor
 3839   2584   7020  2.335 0.577     0.194     0.094      113    14.3  G_oc-temp_med-Lingual
 1312    897   3979  3.324 0.692     0.165     0.067       27     3.5  G_oc-temp_med-Parahip
 2634   1745   6352  2.661 0.726     0.185     0.099       93     9.7  G_orbital
 2305   1493   5492  2.809 0.400     0.165     0.077       71     6.6  G_pariet_inf-Angular
 2786   1914   6816  2.834 0.494     0.168     0.076       73     8.7  G_pariet_inf-Supramar
 2945   1960   5603  2.359 0.396     0.152     0.054       64     6.3  G_parietal_sup
 2788   1803   5312  2.286 0.517     0.158     0.062       70     6.5  G_postcentral
 2489   1608   6267  2.854 0.473     0.136     0.055       45     5.8  G_precentral
 2128   1440   5062  2.863 0.443     0.178     0.079       62     5.9  G_precuneus
  971    642   2029  2.161 0.743     0.225     0.136       84     4.3  G_rectus
  386    280    996  3.136 0.819     0.243     0.230       31     2.8  G_subcallosal
  735    447   1700  2.922 0.329     0.159     0.055       14     1.6  G_temp_sup-G_T_transv
 2548   1741   7321  3.120 0.549     0.182     0.076       81     7.6  G_temp_sup-Lateral
  809    613   2338  3.316 0.753     0.145     0.048       11     1.7  G_temp_sup-Plan_polar
 1099    752   2287  2.648 0.476     0.123     0.046       15     1.8  G_temp_sup-Plan_tempo
 2622   1759   6914  2.844 0.720     0.181     0.122      105    10.3  G_temporal_inf
 3152   2141   8157  2.712 0.602     0.168     0.078       90     8.9  G_temporal_middle
  334    216    424  2.220 0.372     0.102     0.028        2     0.3  Lat_Fis-ant-Horizont
  313    216    569  2.707 0.398     0.136     0.039        3     0.6  Lat_Fis-ant-Vertical
 1254    838   1702  2.478 0.385     0.130     0.039       13     2.1  Lat_Fis-post
 2689   1680   3876  2.019 0.502     0.168     0.094       82     9.5  Pole_occipital
 2203   1485   7022  3.451 0.652     0.174     0.087       58     7.3  Pole_temporal
 3185   2225   4539  2.107 0.553     0.147     0.063       49     7.5  S_calcarine
 3244   2207   4057  1.992 0.570     0.120     0.032       25     4.5  S_central
 1047    695   1580  2.329 0.491     0.158     0.064       22     2.4  S_cingul-Marginalis
  517    342    915  2.774 0.424     0.099     0.024        2     0.6  S_circular_insula_ant
 1382    936   2162  2.717 0.609     0.098     0.022        7     1.3  S_circular_insula_inf
 1891   1288   2962  2.584 0.481     0.113     0.035       14     2.6  S_circular_insula_sup
 1249    895   2023  2.493 0.408     0.110     0.022        9     1.2  S_collat_transv_ant
  641    434    732  2.152 0.335     0.154     0.049        9     1.3  S_collat_transv_post
 2379   1609   3381  2.168 0.452     0.139     0.041       32     4.1  S_front_inf
 1677   1160   2496  2.029 0.499     0.158     0.078       34     5.0  S_front_middle
 3655   2520   5939  2.264 0.444     0.140     0.040       55     6.0  S_front_sup
  283    196    376  2.214 0.280     0.120     0.024        2     0.4  S_interm_prim-Jensen
 2513   1694   3835  2.315 0.343     0.135     0.040       33     3.9  S_intrapariet_and_P_trans
 1281    890   1710  2.027 0.401     0.140     0.039       14     2.1  S_oc_middle_and_Lunatus
 1579   1040   2518  2.320 0.388     0.145     0.048       24     3.1  S_oc_sup_and_transversal
 1113    759   1706  2.322 0.394     0.128     0.040       12     1.6  S_occipital_ant
  815    566   1243  2.458 0.445     0.143     0.051       11     1.5  S_oc-temp_lat
 2022   1442   3743  2.711 0.603     0.141     0.044       29     3.5  S_oc-temp_med_and_Lingual
  349    244    476  1.709 0.481     0.160     0.054        7     0.7  S_orbital_lateral
  869    577   1213  2.181 0.985     0.114     0.031        7     1.0  S_orbital_med-olfact
 1647   1094   2575  2.338 0.505     0.148     0.058       25     3.4  S_orbital-H_Shaped
 2922   1941   4366  2.454 0.442     0.127     0.036       30     4.4  S_parieto_occipital
 1242    762   1435  2.260 0.699     0.150     0.130      119     2.8  S_pericallosal
 3378   2213   4710  2.252 0.418     0.122     0.038       33     5.3  S_postcentral
 1443    960   2116  2.453 0.379     0.110     0.025       11     1.6  S_precentral-inf-part
 1417    987   2064  2.378 0.371     0.114     0.033       13     2.1  S_precentral-sup-part
  727    499   1459  2.366 0.805     0.193     0.111       25     3.0  S_suborbital
  908    626   1673  2.536 0.422     0.148     0.061       14     2.4  S_subparietal
 1618   1090   2551  2.494 0.570     0.140     0.044       20     3.1  S_temporal_inf
 5634   3826   9162  2.498 0.446     0.129     0.046       71    10.2  S_temporal_sup
  428    292    591  2.311 0.348     0.129     0.038        4     0.7  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Thu Aug  8 19:59:53 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3.0/average/lh.DKTatlas40.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.007
0 singular and 293 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
885 labels changed using aseg
relabeling using gibbs priors...
000:   2945 changed, 141918 examined...
001:    688 changed, 12520 examined...
002:    204 changed, 3815 examined...
003:     64 changed, 1156 examined...
004:     29 changed, 370 examined...
005:     19 changed, 181 examined...
006:      6 changed, 103 examined...
007:      5 changed, 33 examined...
008:      6 changed, 29 examined...
009:      4 changed, 32 examined...
010:      2 changed, 24 examined...
011:      2 changed, 13 examined...
012:      0 changed, 9 examined...
120 labels changed using aseg
000: 76 total segments, 43 labels (294 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 50 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
548 vertices marked for relabeling...
548 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas40.annot...
classification took 1 minutes and 3 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Thu Aug  8 20:00:57 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub005 lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas40.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

 1671   1153   3163  2.490 0.601     0.142     0.052       38     2.9  caudalanteriorcingulate
 3626   2449   6864  2.490 0.417     0.139     0.042       51     6.3  caudalmiddlefrontal
 3762   2482   6201  2.243 0.484     0.158     0.060       76     9.5  cuneus
  573    410   2117  3.651 0.657     0.175     0.072       11     1.7  entorhinal
 3815   2663   7446  2.660 0.490     0.157     0.055       70     8.5  fusiform
 5685   3744  10981  2.586 0.459     0.147     0.059      117    12.1  inferiorparietal
 5444   3708  13060  2.824 0.711     0.162     0.090      152    16.7  inferiortemporal
 1575   1036   2928  2.568 0.738     0.167     0.075       37     4.5  isthmuscingulate
 9358   6044  15353  2.247 0.493     0.159     0.071      223    24.8  lateraloccipital
 4491   2954   8915  2.535 0.742     0.168     0.086      129    13.8  lateralorbitofrontal
 5567   3840   9821  2.313 0.551     0.175     0.077      132    16.9  lingual
 2370   1617   4625  2.223 0.858     0.199     0.125      137    10.1  medialorbitofrontal
 6389   4331  13618  2.615 0.587     0.151     0.062      136    15.6  middletemporal
  950    640   2411  3.280 0.675     0.156     0.061       21     2.3  parahippocampal
 2314   1496   4189  2.477 0.514     0.126     0.041       29     3.8  paracentral
 2616   1773   5364  2.620 0.442     0.151     0.058       51     6.0  parsopercularis
 1199    780   2457  2.532 0.517     0.141     0.050       21     2.4  parsorbitalis
 2606   1746   4857  2.452 0.549     0.150     0.055       47     5.9  parstriangularis
 2555   1773   3550  2.032 0.526     0.161     0.073       44     7.0  pericalcarine
 7867   5196  13271  2.227 0.579     0.147     0.053      144    16.6  postcentral
 1950   1311   3572  2.629 0.520     0.165     0.111      139     5.0  posteriorcingulate
 6928   4596  13547  2.643 0.516     0.127     0.055      104    16.4  precentral
 5405   3636  10347  2.613 0.499     0.154     0.063      110    13.0  precuneus
 1926   1309   4152  2.719 0.746     0.156     0.062       42     4.8  rostralanteriorcingulate
 5870   3989  10343  2.256 0.562     0.176     0.088      170    20.5  rostralmiddlefrontal
13343   9154  26756  2.445 0.580     0.157     0.066      300    33.3  superiorfrontal
 6797   4449  11473  2.299 0.410     0.140     0.069      268    24.9  superiorparietal
 8836   6083  20519  2.901 0.635     0.150     0.054      166    19.6  superiortemporal
 5438   3668  10765  2.660 0.490     0.151     0.064      107    14.1  supramarginal
  775    478   1556  2.808 0.357     0.144     0.049       12     1.4  transversetemporal
 2798   1822   6173  3.228 0.806     0.120     0.069       46     6.8  insula
#--------------------------------------------
#@# Tessellate rh Thu Aug  8 20:01:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

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


Iteration Number : 1
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   4
pass   1 (yz-):   6 found -   6 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   6 modified     |    TOTAL:  10
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:  10
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  11
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  11
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   3 found -   3 modified     |    TOTAL:   3
pass   2 (--):   0 found -   3 modified     |    TOTAL:   3
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 15 (out of 240260: 0.006243)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 40: 1452 vertices, 1594 faces
slice 50: 7719 vertices, 8000 faces
slice 60: 16737 vertices, 17128 faces
slice 70: 28710 vertices, 29125 faces
slice 80: 40003 vertices, 40388 faces
slice 90: 51408 vertices, 51787 faces
slice 100: 62316 vertices, 62685 faces
slice 110: 72926 vertices, 73310 faces
slice 120: 83757 vertices, 84160 faces
slice 130: 94781 vertices, 95175 faces
slice 140: 106061 vertices, 106508 faces
slice 150: 117008 vertices, 117377 faces
slice 160: 126598 vertices, 126940 faces
slice 170: 133174 vertices, 133404 faces
slice 180: 138488 vertices, 138680 faces
slice 190: 142387 vertices, 142536 faces
slice 200: 143688 vertices, 143714 faces
slice 210: 143688 vertices, 143714 faces
slice 220: 143688 vertices, 143714 faces
slice 230: 143688 vertices, 143714 faces
slice 240: 143688 vertices, 143714 faces
slice 250: 143688 vertices, 143714 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   143688 voxel in cpt #1: X=-26 [v=143688,e=431142,f=287428] located at (24.793489, -19.142183, 42.190880)
For the whole surface: X=-26 [v=143688,e=431142,f=287428]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 rh Thu Aug  8 20:01:23 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 rh Thu Aug  8 20:01:28 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
avg radius = 46.7 mm, total surface area = 74244 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.7 minutes
Not saving sulc

step 000: RMS=0.103 (target=0.015)   
step 005: RMS=0.075 (target=0.015)   
step 010: RMS=0.054 (target=0.015)   
step 015: RMS=0.045 (target=0.015)   
step 020: RMS=0.039 (target=0.015)   
step 025: RMS=0.034 (target=0.015)   
step 030: RMS=0.030 (target=0.015)   
step 035: RMS=0.028 (target=0.015)   
step 040: RMS=0.026 (target=0.015)   
step 045: RMS=0.024 (target=0.015)   
step 050: RMS=0.023 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Thu Aug  8 20:02:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 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 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.97 +- 0.58 (0.00-->6.28) (max @ vno 59778 --> 60967)
face area 0.02 +- 0.03 (-0.07-->0.60)
scaling brain by 0.306...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.619, avgs=0
005/300: dt: 0.9000, rms radial error=176.360, avgs=0
010/300: dt: 0.9000, rms radial error=175.805, avgs=0
015/300: dt: 0.9000, rms radial error=175.076, avgs=0
020/300: dt: 0.9000, rms radial error=174.245, avgs=0
025/300: dt: 0.9000, rms radial error=173.354, avgs=0
030/300: dt: 0.9000, rms radial error=172.432, avgs=0
035/300: dt: 0.9000, rms radial error=171.492, avgs=0
040/300: dt: 0.9000, rms radial error=170.546, avgs=0
045/300: dt: 0.9000, rms radial error=169.603, avgs=0
050/300: dt: 0.9000, rms radial error=168.661, avgs=0
055/300: dt: 0.9000, rms radial error=167.721, avgs=0
060/300: dt: 0.9000, rms radial error=166.784, avgs=0
065/300: dt: 0.9000, rms radial error=165.852, avgs=0
070/300: dt: 0.9000, rms radial error=164.924, avgs=0
075/300: dt: 0.9000, rms radial error=164.000, avgs=0
080/300: dt: 0.9000, rms radial error=163.082, avgs=0
085/300: dt: 0.9000, rms radial error=162.168, avgs=0
090/300: dt: 0.9000, rms radial error=161.259, avgs=0
095/300: dt: 0.9000, rms radial error=160.355, avgs=0
100/300: dt: 0.9000, rms radial error=159.456, avgs=0
105/300: dt: 0.9000, rms radial error=158.562, avgs=0
110/300: dt: 0.9000, rms radial error=157.673, avgs=0
115/300: dt: 0.9000, rms radial error=156.788, avgs=0
120/300: dt: 0.9000, rms radial error=155.909, avgs=0
125/300: dt: 0.9000, rms radial error=155.034, avgs=0
130/300: dt: 0.9000, rms radial error=154.163, avgs=0
135/300: dt: 0.9000, rms radial error=153.298, avgs=0
140/300: dt: 0.9000, rms radial error=152.437, avgs=0
145/300: dt: 0.9000, rms radial error=151.581, avgs=0
150/300: dt: 0.9000, rms radial error=150.730, avgs=0
155/300: dt: 0.9000, rms radial error=149.883, avgs=0
160/300: dt: 0.9000, rms radial error=149.040, avgs=0
165/300: dt: 0.9000, rms radial error=148.203, avgs=0
170/300: dt: 0.9000, rms radial error=147.370, avgs=0
175/300: dt: 0.9000, rms radial error=146.541, avgs=0
180/300: dt: 0.9000, rms radial error=145.717, avgs=0
185/300: dt: 0.9000, rms radial error=144.898, avgs=0
190/300: dt: 0.9000, rms radial error=144.083, avgs=0
195/300: dt: 0.9000, rms radial error=143.273, avgs=0
200/300: dt: 0.9000, rms radial error=142.467, avgs=0
205/300: dt: 0.9000, rms radial error=141.665, avgs=0
210/300: dt: 0.9000, rms radial error=140.868, avgs=0
215/300: dt: 0.9000, rms radial error=140.075, avgs=0
220/300: dt: 0.9000, rms radial error=139.286, avgs=0
225/300: dt: 0.9000, rms radial error=138.502, avgs=0
230/300: dt: 0.9000, rms radial error=137.722, avgs=0
235/300: dt: 0.9000, rms radial error=136.947, avgs=0
240/300: dt: 0.9000, rms radial error=136.175, avgs=0
245/300: dt: 0.9000, rms radial error=135.409, avgs=0
250/300: dt: 0.9000, rms radial error=134.646, avgs=0
255/300: dt: 0.9000, rms radial error=133.888, avgs=0
260/300: dt: 0.9000, rms radial error=133.133, avgs=0
265/300: dt: 0.9000, rms radial error=132.384, avgs=0
270/300: dt: 0.9000, rms radial error=131.638, avgs=0
275/300: dt: 0.9000, rms radial error=130.897, avgs=0
280/300: dt: 0.9000, rms radial error=130.159, avgs=0
285/300: dt: 0.9000, rms radial error=129.426, avgs=0
290/300: dt: 0.9000, rms radial error=128.697, avgs=0
295/300: dt: 0.9000, rms radial error=127.972, avgs=0
300/300: dt: 0.9000, rms radial error=127.251, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 16961.32
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
epoch 2 (K=40.0), pass 1, starting sse = 2903.24
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 3 (K=160.0), pass 1, starting sse = 313.09
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/11 = 0.00783
epoch 4 (K=640.0), pass 1, starting sse = 17.73
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/13 = 0.00827
final writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology rh Thu Aug  8 20:06:51 CEST 2013

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


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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub005 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 1.48 2011/03/02 00:04:32 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
before topology correction, eno=-26 (nv=143688, nf=287428, ne=431142, g=14)
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...
2055 ambiguous faces found in tessellation
segmenting defects...
27 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
27 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8290  (-4.9145)
      -vertex     loglikelihood: -6.6454  (-3.3227)
      -normal dot loglikelihood: -3.5952  (-3.5952)
      -quad curv  loglikelihood: -6.5467  (-3.2734)
      Total Loglikelihood : -26.6163

CORRECTING DEFECT 0 (vertices=19, convex hull=60)
After retessellation of defect 0, euler #=-24 (142408,426667,284235) : difference with theory (-24) = 0 

CORRECTING DEFECT 1 (vertices=33, convex hull=49)
After retessellation of defect 1, euler #=-23 (142413,426700,284264) : difference with theory (-23) = 0 

CORRECTING DEFECT 2 (vertices=85, convex hull=62)
After retessellation of defect 2, euler #=-22 (142430,426773,284321) : difference with theory (-22) = 0 

CORRECTING DEFECT 3 (vertices=91, convex hull=93)
After retessellation of defect 3, euler #=-21 (142440,426843,284382) : difference with theory (-21) = 0 

CORRECTING DEFECT 4 (vertices=25, convex hull=67)
After retessellation of defect 4, euler #=-20 (142450,426900,284430) : difference with theory (-20) = 0 

CORRECTING DEFECT 5 (vertices=18, convex hull=25)
After retessellation of defect 5, euler #=-19 (142453,426917,284445) : difference with theory (-19) = 0 

CORRECTING DEFECT 6 (vertices=35, convex hull=59)
After retessellation of defect 6, euler #=-18 (142462,426970,284490) : difference with theory (-18) = 0 

CORRECTING DEFECT 7 (vertices=48, convex hull=67)
After retessellation of defect 7, euler #=-17 (142491,427087,284579) : difference with theory (-17) = 0 

CORRECTING DEFECT 8 (vertices=15, convex hull=32)
After retessellation of defect 8, euler #=-16 (142496,427112,284600) : difference with theory (-16) = 0 

CORRECTING DEFECT 9 (vertices=136, convex hull=30)
After retessellation of defect 9, euler #=-15 (142504,427145,284626) : difference with theory (-15) = 0 

CORRECTING DEFECT 10 (vertices=6, convex hull=13)
After retessellation of defect 10, euler #=-14 (142504,427148,284630) : difference with theory (-14) = 0 

CORRECTING DEFECT 11 (vertices=88, convex hull=27)
After retessellation of defect 11, euler #=-13 (142512,427179,284654) : difference with theory (-13) = 0 

CORRECTING DEFECT 12 (vertices=18, convex hull=23)
After retessellation of defect 12, euler #=-12 (142515,427195,284668) : difference with theory (-12) = 0 

CORRECTING DEFECT 13 (vertices=39, convex hull=56)
After retessellation of defect 13, euler #=-11 (142535,427275,284729) : difference with theory (-11) = 0 

CORRECTING DEFECT 14 (vertices=56, convex hull=53)
After retessellation of defect 14, euler #=-10 (142553,427353,284790) : difference with theory (-10) = 0 

CORRECTING DEFECT 15 (vertices=10, convex hull=14)
After retessellation of defect 15, euler #=-9 (142555,427364,284800) : difference with theory (-9) = 0 

CORRECTING DEFECT 16 (vertices=84, convex hull=79)
After retessellation of defect 16, euler #=-8 (142574,427456,284874) : difference with theory (-8) = 0 

CORRECTING DEFECT 17 (vertices=32, convex hull=61)
After retessellation of defect 17, euler #=-7 (142594,427544,284943) : difference with theory (-7) = 0 

CORRECTING DEFECT 18 (vertices=20, convex hull=50)
After retessellation of defect 18, euler #=-6 (142606,427599,284987) : difference with theory (-6) = 0 

CORRECTING DEFECT 19 (vertices=128, convex hull=53)
After retessellation of defect 19, euler #=-5 (142614,427645,285026) : difference with theory (-5) = 0 

CORRECTING DEFECT 20 (vertices=45, convex hull=90)
After retessellation of defect 20, euler #=-4 (142639,427755,285112) : difference with theory (-4) = 0 

CORRECTING DEFECT 21 (vertices=69, convex hull=84)
After retessellation of defect 21, euler #=-3 (142657,427841,285181) : difference with theory (-3) = 0 

CORRECTING DEFECT 22 (vertices=47, convex hull=66)
After retessellation of defect 22, euler #=-2 (142685,427954,285267) : difference with theory (-2) = 0 

CORRECTING DEFECT 23 (vertices=86, convex hull=95)
After retessellation of defect 23, euler #=-1 (142711,428075,285363) : difference with theory (-1) = 0 

CORRECTING DEFECT 24 (vertices=11, convex hull=19)
After retessellation of defect 24, euler #=0 (142712,428082,285370) : difference with theory (0) = 0 

CORRECTING DEFECT 25 (vertices=24, convex hull=53)
After retessellation of defect 25, euler #=1 (142722,428134,285413) : difference with theory (1) = 0 

CORRECTING DEFECT 26 (vertices=23, convex hull=66)
After retessellation of defect 26, euler #=2 (142731,428187,285458) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.08-->9.58) (max @ vno 16176 --> 26838)
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 (0.08-->9.58) (max @ vno 16176 --> 26838)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
103 mutations (36.1%), 182 crossovers (63.9%), 53 vertices were eliminated
building final representation...
957 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=142731, nf=285458, ne=428187, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 16.0 minutes
0 defective edges
removing intersecting faces
000: 77 intersecting

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 142731 - 428187 + 285458 = 2 --> 0 holes
      F =2V-4:          285458 = 285462-4 (0)
      2E=3F:            856374 = 856374 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 16 intersecting
001: 6 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Thu Aug  8 20:22:58 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub005 rh 

only generating white matter surface
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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
17487 bright wm thresholded.
908 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig...
computing class statistics...
border white:    254363 voxels (1.52%)
border gray      296177 voxels (1.77%)
WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0]
GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70)
setting MAX_BORDER_WHITE to 115.3 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 31.3 (was 40)
setting MAX_GRAY to 94.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.01-->3.89) (max @ vno 16176 --> 26838)
face area 0.27 +- 0.12 (0.00-->1.52)
mean absolute distance = 0.64 +- 0.71
5092 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=57
mean inside = 92.4, mean outside = 67.6
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=71.6, 17 (17) missing vertices, mean dist 0.4 [0.4 (%30.8)->0.7 (%69.2))]
%78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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 +- 0.27 (0.08-->3.85) (max @ vno 100129 --> 101238)
face area 0.27 +- 0.13 (0.00-->1.99)
mean absolute distance = 0.29 +- 0.43
3359 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7953829.5, rms=13.82
001: dt: 0.5000, sse=8023892.0, rms=9.975 (0.000%)
002: dt: 0.5000, sse=8355369.0, rms=7.823 (0.000%)
003: dt: 0.5000, sse=8480620.0, rms=6.470 (0.000%)
004: dt: 0.5000, sse=8764958.0, rms=5.656 (0.000%)
005: dt: 0.5000, sse=8813126.0, rms=5.178 (0.000%)
006: dt: 0.5000, sse=8973657.0, rms=4.904 (0.000%)
007: dt: 0.5000, sse=8960889.0, rms=4.754 (0.000%)
008: dt: 0.5000, sse=9043888.0, rms=4.639 (0.000%)
009: dt: 0.5000, sse=8924771.0, rms=4.582 (0.000%)
010: dt: 0.5000, sse=8987706.0, rms=4.514 (0.000%)
rms = 4.49, time step reduction 1 of 3 to 0.250...
011: dt: 0.5000, sse=8876608.0, rms=4.495 (0.000%)
012: dt: 0.2500, sse=5798995.0, rms=3.158 (0.000%)
013: dt: 0.2500, sse=5317273.0, rms=2.702 (0.000%)
014: dt: 0.2500, sse=5017348.5, rms=2.594 (0.000%)
015: dt: 0.2500, sse=4933934.5, rms=2.504 (0.000%)
rms = 2.47, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=4830886.0, rms=2.471 (0.000%)
017: dt: 0.1250, sse=4575423.5, rms=2.219 (0.000%)
rms = 2.18, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=4526973.0, rms=2.184 (0.000%)
positioning took 2.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=76.1, 30 (0) missing vertices, mean dist -0.2 [0.3 (%78.7)->0.2 (%21.3))]
%86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.03-->3.41) (max @ vno 16176 --> 26838)
face area 0.35 +- 0.17 (0.00-->2.12)
mean absolute distance = 0.21 +- 0.29
2676 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5551025.0, rms=6.07
019: dt: 0.5000, sse=5772346.5, rms=4.079 (0.000%)
rms = 4.63, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=5267387.5, rms=2.914 (0.000%)
021: dt: 0.2500, sse=5100009.5, rms=2.430 (0.000%)
022: dt: 0.2500, sse=5021002.0, rms=2.053 (0.000%)
rms = 2.02, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=5002119.0, rms=2.023 (0.000%)
024: dt: 0.1250, sse=4814917.5, rms=1.773 (0.000%)
rms = 1.74, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=4759359.5, rms=1.740 (0.000%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=79.4, 26 (0) missing vertices, mean dist -0.1 [0.2 (%76.4)->0.2 (%23.6))]
%92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.05-->3.40) (max @ vno 16176 --> 26838)
face area 0.34 +- 0.16 (0.00-->1.90)
mean absolute distance = 0.16 +- 0.23
2959 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5157159.5, rms=4.29
026: dt: 0.5000, sse=5526874.5, rms=4.197 (0.000%)
rms = 4.46, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=5029497.0, rms=2.643 (0.000%)
028: dt: 0.2500, sse=4918106.5, rms=2.197 (0.000%)
029: dt: 0.2500, sse=4975793.0, rms=1.864 (0.000%)
rms = 1.92, time step reduction 2 of 3 to 0.125...
030: dt: 0.1250, sse=4901236.0, rms=1.721 (0.000%)
031: dt: 0.1250, sse=4798075.0, rms=1.525 (0.000%)
rms = 1.51, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=4759845.5, rms=1.507 (0.000%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=80.5, 27 (0) missing vertices, mean dist -0.0 [0.2 (%58.4)->0.2 (%41.6))]
%93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=4783962.0, rms=1.86
rms = 2.90, time step reduction 1 of 3 to 0.250...
033: dt: 0.2500, sse=4886889.0, rms=1.227 (0.000%)
034: dt: 0.2500, sse=5051746.0, rms=1.116 (0.000%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
035: dt: 0.2500, sse=5147129.5, rms=1.115 (0.000%)
rms = 1.09, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=5181376.0, rms=1.094 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
generating cortex label...
10 non-cortical segments detected
only using segment with 1811 vertices
erasing segment 1 (vno[0] = 64919)
erasing segment 2 (vno[0] = 65987)
erasing segment 3 (vno[0] = 87960)
erasing segment 4 (vno[0] = 90268)
erasing segment 5 (vno[0] = 95842)
erasing segment 6 (vno[0] = 101342)
erasing segment 7 (vno[0] = 101668)
erasing segment 8 (vno[0] = 107056)
erasing segment 9 (vno[0] = 113300)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area
vertex spacing 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838)
face area 0.34 +- 0.16 (0.00-->1.92)
refinement took 7.0 minutes
#--------------------------------------------
#@# Smooth2 rh Thu Aug  8 20:30:00 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
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...
#--------------------------------------------
#@# Inflation2 rh Thu Aug  8 20:30:05 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated 

avg radius = 46.9 mm, total surface area = 86834 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.120 (target=0.015)   
step 005: RMS=0.082 (target=0.015)   
step 010: RMS=0.058 (target=0.015)   
step 015: RMS=0.048 (target=0.015)   
step 020: RMS=0.039 (target=0.015)   
step 025: RMS=0.033 (target=0.015)   
step 030: RMS=0.027 (target=0.015)   
step 035: RMS=0.022 (target=0.015)   
step 040: RMS=0.019 (target=0.015)   
step 045: RMS=0.018 (target=0.015)   
step 050: RMS=0.016 (target=0.015)   
step 055: RMS=0.015 (target=0.015)   
inflation complete.
inflation took 0.6 minutes

 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated 

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
151 vertices thresholded to be in k1 ~ [-0.20 1.09], k2 ~ [-0.08 0.07]
total integrated curvature = 0.660*4pi (8.297) --> 0 handles
ICI = 1.7, FI = 10.8, variation=182.011
123 vertices thresholded to be in [-0.03 0.01]
writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
118 vertices thresholded to be in [-0.11 0.24]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.023
done.

#-----------------------------------------
#@# Curvature Stats rh Thu Aug  8 20:32:31 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub005 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       [ sub005/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                      [ 270 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.130205
WARN:    S explicit min:                          0.000000	vertex = 162
#--------------------------------------------
#@# Sphere rh Thu Aug  8 20:32:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
scaling brain by 0.282...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=snake, 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 %21.20
pass 1: epoch 2 of 3 starting distance error %21.15
unfolding complete - removing small folds...
starting distance error %21.07
removing remaining folds...
final distance error %21.09
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.12 hours
#--------------------------------------------
#@# Surf Reg rh Thu Aug  8 21:40:02 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_register -curv ../surf/rh.sphere /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 

using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading surface from ../surf/rh.sphere...
reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
MRISregister() -------
max_passes = 4 
min_degrees = 0.500000 
max_degrees = 64.000000 
nangles = 8 
tol=5.0e-01, sigma=0.0, host=snake, 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=snake, 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 = 0.576
curvature mean = 0.032, std = 0.936
curvature mean = 0.024, std = 0.848
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 379358.7, tmin=1.1240
  d=32.00 min @ (0.00, -8.00, 0.00) sse = 276429.3, tmin=2.2516
  d=16.00 min @ (-4.00, 0.00, 0.00) sse = 261174.7, tmin=3.3972
  d=8.00 min @ (2.00, 0.00, 0.00) sse = 259918.8, tmin=4.5631
  d=4.00 min @ (-1.00, 0.00, 0.00) sse = 258530.6, tmin=5.7408
  d=2.00 min @ (0.00, -0.50, -0.50) sse = 257876.9, tmin=6.9290
  d=1.00 min @ (0.00, 0.00, 0.25) sse = 257809.8, tmin=8.1105
  d=0.50 min @ (0.00, 0.00, -0.12) sse = 257800.2, tmin=9.2995
tol=1.0e+00, sigma=0.5, host=snake, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.30 min
curvature mean = 0.003, std = 0.940
curvature mean = 0.012, std = 0.934
curvature mean = -0.003, std = 0.946
curvature mean = 0.006, std = 0.969
curvature mean = -0.004, std = 0.946
curvature mean = 0.001, std = 0.987
2 Reading smoothwm
curvature mean = -0.026, std = 0.339
curvature mean = 0.005, std = 0.070
curvature mean = 0.066, std = 0.291
curvature mean = 0.006, std = 0.083
curvature mean = 0.033, std = 0.463
curvature mean = 0.006, std = 0.089
curvature mean = 0.018, std = 0.596
curvature mean = 0.007, std = 0.090
curvature mean = 0.006, std = 0.707
MRISregister() return, current seed 0
writing registered surface to ../surf/rh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white rh Thu Aug  8 22:09:57 CEST 2013

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

reading surface from ../surf/rh.white...
writing curvature file ../surf/rh.jacobian_white
#--------------------------------------------
#@# AvgCurv rh Thu Aug  8 22:09:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.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 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
writing curvature file to ../surf/rh.avg_curv...
#-----------------------------------------
#@# Cortical Parc rh Thu Aug  8 22:10:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
reading color table from GCSA file....
average std = 0.7   using min determinant for regularization = 0.006
0 singular and 311 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1263 labels changed using aseg
relabeling using gibbs priors...
000:   3060 changed, 142731 examined...
001:    693 changed, 13043 examined...
002:    182 changed, 3884 examined...
003:     63 changed, 1039 examined...
004:     33 changed, 395 examined...
005:     15 changed, 211 examined...
006:      7 changed, 82 examined...
007:      3 changed, 46 examined...
008:      3 changed, 17 examined...
009:      2 changed, 16 examined...
010:      1 changed, 12 examined...
011:      0 changed, 10 examined...
179 labels changed using aseg
000: 106 total segments, 69 labels (430 vertices) changed
001: 41 total segments, 4 labels (9 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 34 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1537 vertices marked for relabeling...
1537 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 1 minutes and 4 seconds.
#--------------------------------------------
#@# Make Pial Surf rh Thu Aug  8 22:11:05 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub005 rh 

-white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
17487 bright wm thresholded.
908 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig...
computing class statistics...
border white:    254363 voxels (1.52%)
border gray      296177 voxels (1.77%)
WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0]
GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70)
setting MAX_BORDER_WHITE to 115.3 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 31.3 (was 40)
setting MAX_GRAY to 94.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=57
mean inside = 92.4, mean outside = 67.6
smoothing surface for 5 iterations...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.01-->3.89) (max @ vno 16176 --> 26838)
face area 0.27 +- 0.12 (0.00-->1.52)
mean absolute distance = 0.64 +- 0.71
4497 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 21 points - only 0.00% unknown
deleting segment 3 with 407 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 15 points - only 0.00% unknown
deleting segment 6 with 35 points - only 0.00% unknown
deleting segment 8 with 131 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 11 with 3 points - only 0.00% unknown
mean border=71.5, 17 (17) missing vertices, mean dist 0.4 [0.4 (%30.8)->0.7 (%69.2))]
%78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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 +- 0.27 (0.08-->3.85) (max @ vno 100129 --> 101238)
face area 0.27 +- 0.13 (0.00-->1.99)
mean absolute distance = 0.29 +- 0.43
2898 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7974956.0, rms=13.81
001: dt: 0.5000, sse=8051567.5, rms=9.964 (0.000%)
002: dt: 0.5000, sse=8390382.0, rms=7.816 (0.000%)
003: dt: 0.5000, sse=8513470.0, rms=6.464 (0.000%)
004: dt: 0.5000, sse=8805081.0, rms=5.650 (0.000%)
005: dt: 0.5000, sse=8847354.0, rms=5.173 (0.000%)
006: dt: 0.5000, sse=9017397.0, rms=4.899 (0.000%)
007: dt: 0.5000, sse=8997915.0, rms=4.750 (0.000%)
008: dt: 0.5000, sse=9087754.0, rms=4.635 (0.000%)
009: dt: 0.5000, sse=8963565.0, rms=4.578 (0.000%)
010: dt: 0.5000, sse=9031501.0, rms=4.510 (0.000%)
rms = 4.49, time step reduction 1 of 3 to 0.250...
011: dt: 0.5000, sse=8915012.0, rms=4.491 (0.000%)
012: dt: 0.2500, sse=5827361.5, rms=3.157 (0.000%)
013: dt: 0.2500, sse=5342220.0, rms=2.702 (0.000%)
014: dt: 0.2500, sse=5041012.5, rms=2.594 (0.000%)
015: dt: 0.2500, sse=4959373.0, rms=2.504 (0.000%)
rms = 2.47, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=4856800.0, rms=2.472 (0.000%)
017: dt: 0.1250, sse=4602698.0, rms=2.221 (0.000%)
rms = 2.19, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=4552583.0, rms=2.186 (0.000%)
positioning took 2.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 24 points - only 0.00% unknown
deleting segment 2 with 337 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 14 points - only 0.00% unknown
deleting segment 5 with 21 points - only 0.00% unknown
deleting segment 6 with 82 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
mean border=76.1, 36 (0) missing vertices, mean dist -0.2 [0.3 (%78.7)->0.2 (%21.3))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.26 (0.03-->3.41) (max @ vno 16176 --> 26838)
face area 0.35 +- 0.16 (0.00-->2.12)
mean absolute distance = 0.21 +- 0.29
2731 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5578387.0, rms=6.06
019: dt: 0.5000, sse=5803824.0, rms=4.075 (0.000%)
rms = 4.63, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=5297082.0, rms=2.913 (0.000%)
021: dt: 0.2500, sse=5130555.0, rms=2.431 (0.000%)
022: dt: 0.2500, sse=5050317.0, rms=2.056 (0.000%)
rms = 2.03, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=5033606.5, rms=2.025 (0.000%)
024: dt: 0.1250, sse=4846455.0, rms=1.777 (0.000%)
rms = 1.74, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=4789915.5, rms=1.745 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 26 points - only 0.00% unknown
deleting segment 1 with 347 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 14 points - only 0.00% unknown
deleting segment 4 with 35 points - only 0.00% unknown
deleting segment 5 with 96 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
mean border=79.4, 36 (0) missing vertices, mean dist -0.1 [0.2 (%76.3)->0.2 (%23.7))]
%92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.05-->3.40) (max @ vno 16176 --> 26838)
face area 0.34 +- 0.16 (0.00-->1.90)
mean absolute distance = 0.16 +- 0.24
3015 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5188923.0, rms=4.29
026: dt: 0.5000, sse=5556812.0, rms=4.194 (0.000%)
rms = 4.45, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=5059351.0, rms=2.643 (0.000%)
028: dt: 0.2500, sse=4949751.0, rms=2.198 (0.000%)
029: dt: 0.2500, sse=5007317.0, rms=1.866 (0.000%)
rms = 1.93, time step reduction 2 of 3 to 0.125...
030: dt: 0.1250, sse=4932588.0, rms=1.724 (0.000%)
031: dt: 0.1250, sse=4830113.5, rms=1.528 (0.000%)
rms = 1.51, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=4792010.5, rms=1.511 (0.000%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 27 points - only 0.00% unknown
deleting segment 1 with 357 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 14 points - only 0.00% unknown
deleting segment 4 with 38 points - only 0.00% unknown
deleting segment 5 with 97 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
mean border=80.4, 44 (0) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))]
%94 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4816013.0, rms=1.86
rms = 2.89, time step reduction 1 of 3 to 0.250...
033: dt: 0.2500, sse=4921099.0, rms=1.229 (0.000%)
034: dt: 0.2500, sse=5086477.0, rms=1.120 (0.000%)
rms = 1.12, time step reduction 2 of 3 to 0.125...
035: dt: 0.2500, sse=5182359.5, rms=1.118 (0.000%)
rms = 1.10, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=5216694.0, rms=1.098 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
smoothing surface for 5 iterations...
mean border=47.0, 17 (17) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.5 (%100.0))]
%13 local maxima, %49 large gradients and %34 min vals, 1981 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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=32687258.0, rms=32.87
001: dt: 0.5000, sse=23541896.0, rms=27.294 (0.000%)
002: dt: 0.5000, sse=17181850.0, rms=22.662 (0.000%)
003: dt: 0.5000, sse=12882107.0, rms=18.921 (0.000%)
004: dt: 0.5000, sse=10166871.0, rms=15.962 (0.000%)
005: dt: 0.5000, sse=8560958.0, rms=13.686 (0.000%)
006: dt: 0.5000, sse=7721739.0, rms=11.966 (0.000%)
007: dt: 0.5000, sse=7264538.5, rms=10.538 (0.000%)
008: dt: 0.5000, sse=6987229.0, rms=9.271 (0.000%)
009: dt: 0.5000, sse=6821755.0, rms=8.116 (0.000%)
010: dt: 0.5000, sse=6813513.0, rms=7.128 (0.000%)
011: dt: 0.5000, sse=6887935.5, rms=6.267 (0.000%)
012: dt: 0.5000, sse=7026273.0, rms=5.592 (0.000%)
013: dt: 0.5000, sse=7175993.5, rms=5.107 (0.000%)
014: dt: 0.5000, sse=7383276.0, rms=4.783 (0.000%)
015: dt: 0.5000, sse=7477753.5, rms=4.552 (0.000%)
016: dt: 0.5000, sse=7615588.5, rms=4.414 (0.000%)
017: dt: 0.5000, sse=7696858.0, rms=4.308 (0.000%)
018: dt: 0.5000, sse=7721887.0, rms=4.250 (0.000%)
019: dt: 0.5000, sse=7753909.5, rms=4.193 (0.000%)
rms = 4.16, time step reduction 1 of 3 to 0.250...
020: dt: 0.5000, sse=7737565.0, rms=4.163 (0.000%)
021: dt: 0.2500, sse=5664220.0, rms=3.557 (0.000%)
022: dt: 0.2500, sse=5510557.0, rms=3.383 (0.000%)
rms = 3.37, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=5390627.0, rms=3.371 (0.000%)
024: dt: 0.1250, sse=5130935.0, rms=3.255 (0.000%)
rms = 3.24, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=5100158.5, rms=3.240 (0.000%)
positioning took 3.2 minutes
mean border=45.2, 1262 (1) missing vertices, mean dist 0.1 [0.2 (%51.6)->0.6 (%48.4))]
%27 local maxima, %40 large gradients and %29 min vals, 627 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, 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=5669908.5, rms=4.67
026: dt: 0.5000, sse=6032153.5, rms=4.185 (0.000%)
rms = 4.18, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=7871497.5, rms=4.175 (0.000%)
028: dt: 0.2500, sse=5947648.0, rms=3.437 (0.000%)
029: dt: 0.2500, sse=6007609.0, rms=3.230 (0.000%)
rms = 3.21, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=5869163.0, rms=3.211 (0.000%)
031: dt: 0.1250, sse=5675499.5, rms=3.045 (0.000%)
rms = 3.02, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=5653774.5, rms=3.019 (0.000%)
positioning took 0.9 minutes
mean border=43.2, 1446 (0) missing vertices, mean dist 0.1 [0.2 (%40.2)->0.4 (%59.8))]
%46 local maxima, %20 large gradients and %29 min vals, 845 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, 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=5880118.5, rms=4.05
rms = 4.11, time step reduction 1 of 3 to 0.250...
033: dt: 0.2500, sse=5654855.5, rms=3.538 (0.000%)
034: dt: 0.2500, sse=5666655.5, rms=3.227 (0.000%)
035: dt: 0.2500, sse=5916288.0, rms=3.131 (0.000%)
rms = 3.11, time step reduction 2 of 3 to 0.125...
036: dt: 0.2500, sse=6017766.0, rms=3.107 (0.000%)
037: dt: 0.1250, sse=5807498.5, rms=2.969 (0.000%)
rms = 2.94, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=5821897.5, rms=2.941 (0.000%)
positioning took 0.9 minutes
mean border=42.2, 3039 (0) missing vertices, mean dist 0.0 [0.2 (%46.3)->0.3 (%53.7))]
%49 local maxima, %17 large gradients and %28 min vals, 714 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=5880054.5, rms=3.27
rms = 3.94, time step reduction 1 of 3 to 0.250...
039: dt: 0.2500, sse=5762743.0, rms=3.028 (0.000%)
040: dt: 0.2500, sse=6033981.0, rms=2.963 (0.000%)
rms = 2.94, time step reduction 2 of 3 to 0.125...
041: dt: 0.2500, sse=6114455.5, rms=2.939 (0.000%)
042: dt: 0.1250, sse=5996697.0, rms=2.822 (0.000%)
rms = 2.80, time step reduction 3 of 3 to 0.062...
043: dt: 0.1250, sse=6027581.5, rms=2.799 (0.000%)
positioning took 0.8 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area.pial
vertex spacing 1.02 +- 0.44 (0.08-->10.36) (max @ vno 100313 --> 100290)
face area 0.41 +- 0.31 (0.00-->8.44)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 142731 vertices processed
25000 of 142731 vertices processed
50000 of 142731 vertices processed
75000 of 142731 vertices processed
100000 of 142731 vertices processed
125000 of 142731 vertices processed
0 of 142731 vertices processed
25000 of 142731 vertices processed
50000 of 142731 vertices processed
75000 of 142731 vertices processed
100000 of 142731 vertices processed
125000 of 142731 vertices processed
thickness calculation complete, 509:894 truncations.
26532 vertices at 0 distance
86068 vertices at 1 distance
94051 vertices at 2 distance
45703 vertices at 3 distance
15020 vertices at 4 distance
4402 vertices at 5 distance
1461 vertices at 6 distance
497 vertices at 7 distance
208 vertices at 8 distance
99 vertices at 9 distance
69 vertices at 10 distance
54 vertices at 11 distance
42 vertices at 12 distance
31 vertices at 13 distance
41 vertices at 14 distance
27 vertices at 15 distance
22 vertices at 16 distance
30 vertices at 17 distance
15 vertices at 18 distance
26 vertices at 19 distance
30 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.thickness
positioning took 14.0 minutes
#--------------------------------------------
#@# Surf Volume rh Thu Aug  8 22:25:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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_calc -o rh.volume rh.area.mid mul rh.thickness 

Saving result to 'rh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#-----------------------------------------
#@# WM/GM Contrast rh Thu Aug  8 22:25:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 pctsurfcon --s sub005 --rh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts/pctsurfcon.log
Thu Aug  8 22:25:08 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3.0
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh --regheader sub005 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 109659
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh
Dim: 142731 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh --projfrac 0.3 --regheader sub005 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 = 126459
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh
Dim: 142731 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/tmp.pctsurfcon.3128/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh --annot sub005 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/stats/rh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh --annot sub005 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
Constructing seg from annotation

Reading annotation
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Seg base 2000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.w-g.pct.mgh
Vertex Area is 0.668906 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   2000                            unknown       0       0.000
  1   2001                           bankssts    1466    1011.292
  2   2002            caudalanteriorcingulate    1392     963.256
  3   2003                caudalmiddlefrontal    2933    1968.508
  4   2004                     corpuscallosum       0       0.000
  5   2005                             cuneus    2742    1828.445
  6   2006                         entorhinal     409     296.847
  7   2007                           fusiform    4234    2918.080
  8   2008                   inferiorparietal    7531    5073.565
  9   2009                   inferiortemporal    4962    3371.515
 10   2010                   isthmuscingulate    1391     913.005
 11   2011                   lateraloccipital    8721    5637.396
 12   2012               lateralorbitofrontal    3882    2586.580
 13   2013                            lingual    5061    3518.732
 14   2014                medialorbitofrontal    2758    1879.153
 15   2015                     middletemporal    5832    3893.341
 16   2016                    parahippocampal    1017     695.444
 17   2017                        paracentral    2053    1357.055
 18   2018                    parsopercularis    2225    1508.707
 19   2019                      parsorbitalis    1283     864.903
 20   2020                   parstriangularis    2251    1520.839
 21   2021                      pericalcarine    2693    1885.410
 22   2022                        postcentral    7051    4680.771
 23   2023                 posteriorcingulate    2072    1355.862
 24   2024                         precentral    7509    4989.827
 25   2025                          precuneus    6367    4323.134
 26   2026           rostralanteriorcingulate    1172     801.977
 27   2027               rostralmiddlefrontal    9311    6297.768
 28   2028                    superiorfrontal   11943    8113.219
 29   2029                   superiorparietal    8560    5645.194
 30   2030                   superiortemporal    6303    4164.996
 31   2031                      supramarginal    5440    3636.528
 32   2032                        frontalpole     440     298.384
 33   2033                       temporalpole     609     439.274
 34   2034                 transversetemporal     586     359.799
 35   2035                             insula    3048    1982.912

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats rh Thu Aug  8 22:25:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub005 rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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

 1466   1011   2843  2.862 0.444     0.123     0.031       12     2.0  bankssts
 1392    963   2920  2.794 0.861     0.162     0.047       32     2.6  caudalanteriorcingulate
 2933   1969   5442  2.524 0.420     0.135     0.045       41     4.9  caudalmiddlefrontal
 2742   1828   4417  2.135 0.463     0.186     0.068       63     8.2  cuneus
  409    297   1418  3.459 0.640     0.181     0.065        8     1.1  entorhinal
 4234   2918   8870  2.747 0.626     0.162     0.066       93    10.4  fusiform
 7531   5074  14195  2.456 0.488     0.152     0.059      161    17.2  inferiorparietal
 4962   3372  10567  2.743 0.649     0.166     0.081      127    15.5  inferiortemporal
 1391    913   2984  2.722 0.737     0.168     0.073       33     3.7  isthmuscingulate
 8721   5637  14933  2.342 0.487     0.159     0.063      184    21.4  lateraloccipital
 3882   2587   7910  2.706 0.679     0.153     0.072       75    11.5  lateralorbitofrontal
 5061   3519   8685  2.272 0.570     0.179     0.076      121    15.5  lingual
 2758   1879   5533  2.555 0.737     0.170     0.094       87    10.8  medialorbitofrontal
 5832   3893  14311  3.017 0.593     0.155     0.061      126    14.2  middletemporal
 1017    695   2693  3.388 0.725     0.164     0.082       19     2.7  parahippocampal
 2053   1357   3598  2.404 0.521     0.128     0.040       25     3.7  paracentral
 2225   1509   4406  2.626 0.412     0.151     0.054       41     5.0  parsopercularis
 1283    865   2929  2.632 0.624     0.169     0.074       35     3.7  parsorbitalis
 2251   1521   4403  2.572 0.544     0.151     0.076       48     5.0  parstriangularis
 2693   1885   3347  1.868 0.385     0.154     0.060       41     6.6  pericalcarine
 7051   4681  12337  2.291 0.666     0.146     0.052      123    15.2  postcentral
 2072   1356   3583  2.553 0.782     0.152     0.053       37     4.3  posteriorcingulate
 7509   4990  14781  2.617 0.529     0.131     0.040      100    12.6  precentral
 6367   4323  11532  2.516 0.534     0.160     0.104      181    16.1  precuneus
 1172    802   2983  3.140 0.563     0.186     0.074       36     3.3  rostralanteriorcingulate
 9311   6298  18017  2.411 0.516     0.174     0.083      262    27.8  rostralmiddlefrontal
11943   8113  24982  2.643 0.527     0.148     0.049      204    24.7  superiorfrontal
 8560   5645  13489  2.166 0.385     0.134     0.046      150    15.9  superiorparietal
 6303   4165  14776  3.025 0.565     0.131     0.044       83    10.8  superiortemporal
 5440   3637  10297  2.539 0.506     0.147     0.050      101    11.1  supramarginal
  440    298   1089  2.682 0.473     0.235     0.149       24     2.0  frontalpole
  609    439   2191  3.708 0.776     0.194     0.112       18     2.7  temporalpole
  586    360   1196  2.869 0.399     0.140     0.043        8     1.1  transversetemporal
 3048   1983   6248  3.030 0.721     0.146     0.132      122     9.1  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Thu Aug  8 22:25:40 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs...
reading color table from GCSA file....
average std = 1.9 0.2   using min determinant for regularization = 0.000
0 singular and 851 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1 labels changed using aseg
relabeling using gibbs priors...
000:  10303 changed, 142731 examined...
001:   2418 changed, 39284 examined...
002:    725 changed, 12393 examined...
003:    309 changed, 4022 examined...
004:    137 changed, 1713 examined...
005:     71 changed, 771 examined...
006:     32 changed, 398 examined...
007:     14 changed, 171 examined...
008:      6 changed, 73 examined...
009:      1 changed, 33 examined...
010:      0 changed, 7 examined...
1 labels changed using aseg
000: 280 total segments, 198 labels (2806 vertices) changed
001: 91 total segments, 10 labels (85 vertices) changed
002: 81 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 170 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1015 vertices marked for relabeling...
1015 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 1 minutes and 12 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Thu Aug  8 22:26:52 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_anatomical_stats -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 sub005 rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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

 1108    756   2276  2.516 0.659     0.190     0.096       35     3.8  G_and_S_frontomargin
 1549   1024   3239  2.627 0.567     0.172     0.063       32     4.0  G_and_S_occipital_inf
 1222    811   2579  2.497 0.536     0.144     0.052       22     2.7  G_and_S_paracentral
 1584   1077   3694  2.983 0.569     0.178     0.068       40     4.2  G_and_S_subcentral
 1041    722   2191  2.400 0.478     0.209     0.114       45     4.3  G_and_S_transv_frontopol
 3083   2124   6447  2.783 0.627     0.150     0.051       60     6.4  G_and_S_cingul-Ant
 1743   1230   3628  2.861 0.606     0.143     0.044       28     3.0  G_and_S_cingul-Mid-Ant
 1618   1066   3101  2.762 0.553     0.140     0.045       23     2.9  G_and_S_cingul-Mid-Post
  583    391   1516  3.170 0.616     0.182     0.075       13     1.8  G_cingul-Post-dorsal
  308    216    907  3.088 0.494     0.180     0.083        8     0.9  G_cingul-Post-ventral
 2424   1653   3889  2.027 0.462     0.186     0.068       58     7.1  G_cuneus
 1253    880   3286  2.796 0.384     0.175     0.068       37     3.5  G_front_inf-Opercular
  453    281   1074  2.807 0.388     0.157     0.067       13     1.2  G_front_inf-Orbital
 1146    767   2911  2.875 0.525     0.182     0.120       40     3.4  G_front_inf-Triangul
 4282   2878   9989  2.613 0.466     0.186     0.096      135    13.7  G_front_middle
 7812   5249  17851  2.690 0.535     0.162     0.062      167    19.9  G_front_sup
  390    231    858  3.242 0.844     0.142     0.131       27     1.8  G_Ins_lg_and_S_cent_ins
  492    334   1657  3.445 0.769     0.205     0.130       20     2.2  G_insular_short
 2484   1587   5560  2.651 0.431     0.181     0.079       73     7.6  G_occipital_middle
 2166   1376   3595  2.218 0.372     0.138     0.048       42     4.2  G_occipital_sup
 1465    977   3183  2.673 0.588     0.179     0.086       42     4.3  G_oc-temp_lat-fusifor
 3441   2387   6426  2.338 0.597     0.202     0.096      104    12.9  G_oc-temp_med-Lingual
 1347    922   3927  3.392 0.615     0.198     0.225       87     5.2  G_oc-temp_med-Parahip
 2825   1869   6987  2.844 0.761     0.173     0.090       81     9.6  G_orbital
 2767   1853   6243  2.630 0.483     0.175     0.084       89     8.5  G_pariet_inf-Angular
 2999   1989   6905  2.695 0.507     0.159     0.058       74     7.4  G_pariet_inf-Supramar
 2514   1656   4383  2.177 0.417     0.137     0.055       56     5.2  G_parietal_sup
 2687   1736   5477  2.442 0.541     0.162     0.062       63     7.2  G_postcentral
 2735   1754   6735  2.862 0.465     0.139     0.046       45     5.4  G_precentral
 2549   1693   5430  2.552 0.442     0.184     0.185      129     8.6  G_precuneus
  685    458   1499  2.414 0.604     0.208     0.129       36     3.5  G_rectus
  374    237    946  3.492 0.658     0.086     0.032        2     0.4  G_subcallosal
  524    318   1175  3.038 0.408     0.143     0.045        8     1.0  G_temp_sup-G_T_transv
 2216   1451   6790  3.273 0.525     0.156     0.066       48     5.3  G_temp_sup-Lateral
  803    540   2236  3.614 0.548     0.148     0.056       11     1.6  G_temp_sup-Plan_polar
  653    444   1390  2.803 0.463     0.123     0.035        9     0.9  G_temp_sup-Plan_tempo
 2620   1772   6373  2.819 0.664     0.190     0.112       98    10.8  G_temporal_inf
 3481   2316  10197  3.233 0.555     0.178     0.077      104    10.9  G_temporal_middle
  433    291    554  2.153 0.328     0.103     0.024        2     0.5  Lat_Fis-ant-Horizont
  158    113    278  2.516 0.396     0.111     0.027        1     0.1  Lat_Fis-ant-Vertical
 1337    878   1965  2.681 0.452     0.139     0.046       14     2.6  Lat_Fis-post
 3497   2251   5303  2.118 0.487     0.172     0.074       90    10.2  Pole_occipital
 1904   1290   5707  3.275 0.754     0.177     0.094       48     7.0  Pole_temporal
 3123   2185   4083  1.994 0.518     0.153     0.060       51     7.8  S_calcarine
 3113   2117   3790  1.947 0.568     0.117     0.033       25     4.4  S_central
 1331    897   2062  2.218 0.436     0.130     0.044       17     2.4  S_cingul-Marginalis
  431    296    765  2.350 0.543     0.102     0.027        2     0.5  S_circular_insula_ant
 1472    972   2444  2.834 0.576     0.104     0.027        9     1.8  S_circular_insula_inf
 1536   1030   2456  2.611 0.424     0.110     0.031       11     2.1  S_circular_insula_sup
  961    688   1533  2.438 0.422     0.120     0.030        9     1.3  S_collat_transv_ant
  799    548   1074  2.381 0.488     0.160     0.056       12     1.7  S_collat_transv_post
 2330   1591   3634  2.315 0.407     0.159     0.056       46     5.5  S_front_inf
 2032   1370   3355  2.210 0.451     0.139     0.054       46     4.2  S_front_middle
 2901   1990   4381  2.289 0.397     0.122     0.033       27     4.1  S_front_sup
  422    273    513  2.178 0.362     0.128     0.034        4     0.6  S_interm_prim-Jensen
 3092   2104   4297  2.096 0.341     0.125     0.035       36     4.8  S_intrapariet_and_P_trans
 1401    949   1795  2.019 0.388     0.136     0.041       14     2.3  S_oc_middle_and_Lunatus
 1895   1251   2820  2.315 0.386     0.123     0.032       20     2.5  S_oc_sup_and_transversal
  885    598   1491  2.553 0.382     0.132     0.038       11     1.4  S_occipital_ant
  797    561   1483  2.375 0.461     0.145     0.044       13     1.3  S_oc-temp_lat
 1772   1259   3190  2.769 0.570     0.127     0.034       15     2.6  S_oc-temp_med_and_Lingual
  450    314    821  2.505 0.712     0.184     0.077       10     1.5  S_orbital_lateral
  753    542   1293  2.471 0.675     0.113     0.030        6     0.8  S_orbital_med-olfact
 1514   1011   2576  2.517 0.533     0.159     0.075       27     5.2  S_orbital-H_Shaped
 3033   2023   4590  2.512 0.573     0.141     0.048       39     5.8  S_parieto_occipital
 1733   1106   2170  2.203 0.868     0.150     0.051       33     3.1  S_pericallosal
 2790   1867   3906  2.182 0.423     0.124     0.039       30     4.4  S_postcentral
 2078   1365   3190  2.500 0.359     0.133     0.044       25     3.6  S_precentral-inf-part
 1550   1044   2302  2.351 0.395     0.110     0.024       10     1.7  S_precentral-sup-part
  546    387   1188  2.761 0.685     0.199     0.128       19     3.4  S_suborbital
 1409    949   2539  2.483 0.419     0.152     0.054       27     3.1  S_subparietal
 1527   1037   2351  2.573 0.517     0.127     0.032       13     2.2  S_temporal_inf
 6414   4323  10724  2.609 0.502     0.120     0.032       56     8.4  S_temporal_sup
  402    288    735  2.728 0.391     0.101     0.017        2     0.3  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Thu Aug  8 22:27:12 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub005 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3.0/average/rh.DKTatlas40.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.008
0 singular and 237 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
868 labels changed using aseg
relabeling using gibbs priors...
000:   2762 changed, 142731 examined...
001:    620 changed, 11882 examined...
002:    150 changed, 3350 examined...
003:     56 changed, 873 examined...
004:     29 changed, 336 examined...
005:     21 changed, 188 examined...
006:     11 changed, 112 examined...
007:      6 changed, 56 examined...
008:      2 changed, 28 examined...
009:      2 changed, 12 examined...
010:      3 changed, 14 examined...
011:      1 changed, 10 examined...
012:      2 changed, 8 examined...
013:      4 changed, 9 examined...
014:      2 changed, 17 examined...
015:      4 changed, 16 examined...
016:      5 changed, 22 examined...
017:      3 changed, 25 examined...
018:      2 changed, 17 examined...
019:      2 changed, 10 examined...
020:      4 changed, 15 examined...
021:      4 changed, 20 examined...
022:      6 changed, 19 examined...
023:      2 changed, 24 examined...
024:      0 changed, 14 examined...
123 labels changed using aseg
000: 60 total segments, 27 labels (142 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 38 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
882 vertices marked for relabeling...
882 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 1 minutes and 3 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Thu Aug  8 22:28:15 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub005 rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas40.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

 1481   1023   3113  2.785 0.879     0.164     0.048       34     2.8  caudalanteriorcingulate
 3008   2012   5518  2.522 0.418     0.136     0.045       42     5.0  caudalmiddlefrontal
 3414   2266   5375  2.168 0.474     0.179     0.062       75     9.3  cuneus
  476    348   1547  3.386 0.667     0.177     0.063        9     1.3  entorhinal
 3620   2523   7105  2.663 0.563     0.158     0.062       77     8.1  fusiform
 7071   4757  13141  2.429 0.488     0.150     0.058      149    15.8  inferiorparietal
 5470   3706  12225  2.807 0.682     0.168     0.083      141    17.7  inferiortemporal
 1456    951   3021  2.667 0.747     0.159     0.067       30     3.5  isthmuscingulate
 9060   5834  15587  2.343 0.492     0.160     0.063      195    22.6  lateraloccipital
 4314   2878   9192  2.727 0.706     0.163     0.079       98    13.4  lateralorbitofrontal
 5028   3488   8609  2.273 0.571     0.177     0.075      119    15.2  lingual
 2228   1510   4623  2.599 0.779     0.170     0.093       72     9.0  medialorbitofrontal
 6930   4654  16399  2.990 0.569     0.151     0.057      137    15.9  middletemporal
 1013    692   2666  3.367 0.724     0.164     0.082       19     2.7  parahippocampal
 2206   1456   3926  2.411 0.514     0.128     0.042       28     4.0  paracentral
 2296   1547   4447  2.602 0.406     0.151     0.056       43     5.2  parsopercularis
 1376    923   2876  2.597 0.564     0.150     0.059       28     3.2  parsorbitalis
 2428   1648   4962  2.613 0.550     0.168     0.086       68     6.8  parstriangularis
 2731   1925   3440  1.870 0.384     0.157     0.064       43     7.1  pericalcarine
 7512   5021  13182  2.294 0.654     0.146     0.053      138    16.2  postcentral
 2084   1363   3682  2.633 0.759     0.154     0.054       38     4.4  posteriorcingulate
 7216   4802  14396  2.640 0.530     0.132     0.040       97    12.1  precentral
 6437   4368  11732  2.493 0.534     0.158     0.103      185    16.3  precuneus
 1289    882   3250  3.113 0.561     0.183     0.071       37     3.5  rostralanteriorcingulate
 6222   4217  11979  2.401 0.498     0.171     0.082      169    18.0  rostralmiddlefrontal
15115  10273  30789  2.575 0.537     0.153     0.058      297    35.1  superiorfrontal
 7177   4734  11399  2.172 0.390     0.134     0.045      120    13.3  superiorparietal
 8069   5373  19040  3.048 0.613     0.139     0.071      164    16.1  superiortemporal
 5127   3422   9698  2.542 0.504     0.148     0.050       95    10.4  supramarginal
  567    346   1170  2.872 0.397     0.139     0.043        8     1.1  transversetemporal
 2826   1840   5815  2.961 0.706     0.134     0.068       64     7.2  insula
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR Thu Aug  8 22:28:33 CEST 2013

 bbregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta --init-fsl --T2 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.log
Thu Aug  8 22:28:33 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3.0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998148, -0.0400878, -0.0457496)
j_ras = (-0.0459461, 0.989757, 0.135168)
k_ras = (-0.0398624, -0.13702, 0.989766)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii...
fslregister --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fslregister.log

Thu Aug  8 22:28:38 CEST 2013
--s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
snake4
Linux snake4 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 4.19095e-09, 3.72529e-09)
j_ras = (7.45058e-09, 1.49012e-08, -1)
k_ras = (-6.0536e-09, 1, -1.49012e-08)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998148, -0.0400878, -0.0457496)
j_ras = (-0.0459461, 0.989757, 0.135168)
k_ras = (-0.0398624, -0.13702, 0.989766)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311072
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/reg0.3412.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat0 --s sub005 --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/reg0.3412.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 0.998   0.040   0.046   0.000;
-0.040  -0.137   0.990   0.000;
 0.046  -0.990  -0.135  -0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.998   0.040   0.046   0.000;
-0.040  -0.137   0.990   0.000;
 0.046  -0.990  -0.135  -0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub005
RegMat ---------------------------
 0.998   0.040   0.046   0.000;
-0.040  -0.137   0.990   0.000;
 0.046  -0.990  -0.135  -0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311072, ref det = -1
Thu Aug  8 22:28:45 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat0
Thu Aug  8 22:33:07 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub005 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.998   0.047   0.039   21.016;
 0.045  -0.142  -0.989   269.550;
-0.041   0.989  -0.144   23.522;
 0.000   0.000   0.000   1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI 
fsl2TkReg: mov det = -0.311072, ref det = -1
---- Input registration matrix (computed) --------
 0.998   0.041   0.045  -0.245;
-0.039  -0.144   0.989   1.084;
 0.047  -0.989  -0.142  -0.427;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.998   0.041   0.045  -0.245;
-0.039  -0.144   0.989   1.084;
 0.047  -0.989  -0.142  -0.427;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub005
RegMat ---------------------------
 0.998   0.041   0.045  -0.245;
-0.039  -0.144   0.989   1.084;
 0.047  -0.989  -0.142  -0.427;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 22:28:38 CEST 2013 
Ended   at Thu Aug  8 22:39:14 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.init.dat
subject sub005
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1376880629
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.998   0.041   0.045  -0.245;
-0.039  -0.144   0.989   1.084;
 0.047  -0.989  -0.142  -0.427;
 0.000   0.000   0.000   1.000;

Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Projecting RH Surfs
Computing relative cost
 0  -25.0 -25.0 -25.0   1.023099
 1  -25.0 -25.0  25.0   0.979907
 2  -25.0  25.0 -25.0   1.030559
 3  -25.0  25.0  25.0   0.988352
 4   25.0 -25.0 -25.0   1.019131
 5   25.0 -25.0  25.0   1.007005
 6   25.0  25.0 -25.0   0.997025
 7   25.0  25.0  25.0   0.996223
REL:  8  0.289642    8.041302  1.005163 rel = 0.288155 
Initial costs ----------------
Number of surface hits 2708
WM  Intensity    62.0586 +/-   9.7971
Ctx Intensity    75.0981 +/-  11.8063
Pct Contrast     18.8287 +/-  18.3670
Cost   0.2896
RelCost   0.2882

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9907   0.9907  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9867   0.9867  0.0
     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9472   0.9472  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8797   0.8797  0.0
    21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.8635   0.8635  0.0
    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.8061   0.8061  0.0
   102  -4.0000   0.0000  -4.0000   4.0000   0.0000  -4.0000      0.7972   0.7972  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.6820   0.6820  0.0
   346   0.0000   0.0000  -4.0000   4.0000   0.0000   0.0000      0.6487   0.6487  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.2896   0.2896  0.0
Brute Force --------------------------
Min cost was 0.289642
Number of iterations   729
Search time 2.071000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
   6  0.382  0.000  0.000  0.000  0.000  0.000   0.2875510287
   7  0.222  0.000  0.000  0.000  0.000  0.000   0.2849389020
   9  0.242  0.000  0.000  0.000  0.000  0.000   0.2847667733
  10  0.295  0.000  0.000  0.000  0.000  0.000   0.2843241020
  13  0.302  0.000  0.000  0.000  0.000  0.000   0.2842948424
  15  0.304  0.000  0.000  0.000  0.000  0.000   0.2842915679
  16  0.305  0.000  0.000  0.000  0.000  0.000   0.2842905660
  20  0.305 -1.618  0.000  0.000  0.000  0.000   0.2495972257
  21  0.305 -0.949  0.000  0.000  0.000  0.000   0.2002943882
  26  0.305 -0.927  0.000  0.000  0.000  0.000   0.2002444441
  27  0.305 -0.926  0.000  0.000  0.000  0.000   0.2002406533
  28  0.305 -0.907  0.000  0.000  0.000  0.000   0.2001984559
  30  0.305 -0.911  0.000  0.000  0.000  0.000   0.2001899098
  32  0.305 -0.912  0.000  0.000  0.000  0.000   0.2001892511
  33  0.305 -0.913  0.000  0.000  0.000  0.000   0.2001891441
  36  0.305 -0.913  1.000  0.000  0.000  0.000   0.1381889852
  40  0.305 -0.913  0.618  0.000  0.000  0.000   0.1324581935
  41  0.305 -0.913  0.723  0.000  0.000  0.000   0.1297224871
  52  0.305 -0.913  0.723  0.186  0.000  0.000   0.1236983204
  55  0.305 -0.913  0.723  0.205  0.000  0.000   0.1236259223
  56  0.305 -0.913  0.723  0.201  0.000  0.000   0.1236165933
  58  0.305 -0.913  0.723  0.202  0.000  0.000   0.1236164808
  66  0.305 -0.913  0.723  0.202 -0.055  0.000   0.1236023184
  67  0.305 -0.913  0.723  0.202 -0.028  0.000   0.1233162785
  69  0.305 -0.913  0.723  0.202 -0.031  0.000   0.1233137649
  71  0.305 -0.913  0.723  0.202 -0.030  0.000   0.1233131600
  78  0.305 -0.913  0.723  0.202 -0.030  0.014   0.1232478044
  80  0.305 -0.913  0.723  0.202 -0.030  0.013   0.1232431079
  82  0.305 -0.913  0.723  0.202 -0.030  0.011   0.1232418379
  91  0.131 -0.913  0.723  0.202 -0.030  0.011   0.1215356273
  92  0.169 -0.913  0.723  0.202 -0.030  0.011   0.1212382536
  93  0.180 -0.913  0.723  0.202 -0.030  0.011   0.1209722775
  95  0.201 -0.913  0.723  0.202 -0.030  0.011   0.1207660962
  96  0.202 -0.913  0.723  0.202 -0.030  0.011   0.1207640196
  98  0.203 -0.913  0.723  0.202 -0.030  0.011   0.1207634108
 104  0.203 -0.531  0.723  0.202 -0.030  0.011   0.1199165303
 105  0.203 -0.712  0.723  0.202 -0.030  0.011   0.1172291128
 106  0.203 -0.709  0.723  0.202 -0.030  0.011   0.1171359149
 107  0.203 -0.648  0.723  0.202 -0.030  0.011   0.1149859175
 109  0.203 -0.646  0.723  0.202 -0.030  0.011   0.1149601028
 110  0.203 -0.638  0.723  0.202 -0.030  0.011   0.1149341249
 112  0.203 -0.641  0.723  0.202 -0.030  0.011   0.1149093135
 114  0.203 -0.640  0.723  0.202 -0.030  0.011   0.1149081895
 122  0.203 -0.640  0.618  0.202 -0.030  0.011   0.1137925047
 123  0.203 -0.640  0.637  0.202 -0.030  0.011   0.1133155955
 124  0.203 -0.640  0.658  0.202 -0.030  0.011   0.1131624220
 126  0.203 -0.640  0.659  0.202 -0.030  0.011   0.1131607241
 138  0.203 -0.640  0.659  0.239 -0.030  0.011   0.1117690752
 139  0.203 -0.640  0.659  0.249 -0.030  0.011   0.1116990746
 148  0.203 -0.640  0.659  0.249  0.002  0.011   0.1110058374
 150  0.203 -0.640  0.659  0.249  0.009  0.011   0.1109928885
 152  0.203 -0.640  0.659  0.249  0.012  0.011   0.1109923277
 155  0.203 -0.640  0.659  0.249  0.011  0.011   0.1109918560
 165  0.203 -0.640  0.659  0.249  0.011  0.023   0.1108774772
 166  0.203 -0.640  0.659  0.249  0.011  0.025   0.1108740055
 176  0.185 -0.640  0.659  0.249  0.011  0.025   0.1104775027
 178  0.148 -0.640  0.659  0.249  0.011  0.025   0.1101365746
 179  0.147 -0.640  0.659  0.249  0.011  0.025   0.1101230889
 181  0.141 -0.640  0.659  0.249  0.011  0.025   0.1101047797
 182  0.142 -0.640  0.659  0.249  0.011  0.025   0.1101038582
 193  0.142 -0.637  0.659  0.249  0.011  0.025   0.1100936795
 194  0.142 -0.636  0.659  0.249  0.011  0.025   0.1100920155
 203  0.142 -0.636  0.624  0.249  0.011  0.025   0.1099191270
 204  0.142 -0.636  0.626  0.249  0.011  0.025   0.1099004090
 205  0.142 -0.636  0.635  0.249  0.011  0.025   0.1098696713
 206  0.142 -0.636  0.634  0.249  0.011  0.025   0.1098682124
 207  0.142 -0.636  0.633  0.249  0.011  0.025   0.1098679143
 218  0.142 -0.636  0.633  0.275  0.011  0.025   0.1095496118
 219  0.142 -0.636  0.633  0.272  0.011  0.025   0.1095292521
 220  0.142 -0.636  0.633  0.269  0.011  0.025   0.1095254362
 222  0.142 -0.636  0.633  0.268  0.011  0.025   0.1095240561
 225  0.142 -0.636  0.633  0.267  0.011  0.025   0.1095237670
 236  0.142 -0.636  0.633  0.267  0.008  0.025   0.1095152913
 246  0.142 -0.636  0.633  0.267  0.008  0.016   0.1094430861
 248  0.142 -0.636  0.633  0.267  0.008  0.013   0.1094347720
 251  0.081 -0.631  0.608  0.285  0.005  0.001   0.1092368770
 258  0.070 -0.630  0.604  0.289  0.004 -0.001   0.1091834610
 259  0.064 -0.630  0.601  0.290  0.004 -0.002   0.1091705622
 261  0.063 -0.630  0.601  0.291  0.004 -0.002   0.1091695847
 262  0.063 -0.630  0.601  0.291  0.004 -0.002   0.1091694202
 276  0.063 -0.630  0.601  0.291  0.004 -0.018   0.1090683424
 278  0.063 -0.630  0.601  0.291  0.004 -0.016   0.1090664895
 287  0.063 -0.697  0.601  0.291  0.004 -0.016   0.1088188134
 288  0.063 -0.675  0.601  0.291  0.004 -0.016   0.1087908274
 289  0.063 -0.680  0.601  0.291  0.004 -0.016   0.1087791364
 290  0.063 -0.683  0.601  0.291  0.004 -0.016   0.1087740261
 292  0.063 -0.685  0.601  0.291  0.004 -0.016   0.1087714766
 300  0.063 -0.685  0.527  0.291  0.004 -0.016   0.1086968602
 301  0.063 -0.685  0.561  0.291  0.004 -0.016   0.1084013625
 304  0.063 -0.685  0.559  0.291  0.004 -0.016   0.1083982760
 312  0.063 -0.685  0.559  0.374  0.004 -0.016   0.1074879688
 313  0.063 -0.685  0.559  0.359  0.004 -0.016   0.1073068643
 314  0.063 -0.685  0.559  0.348  0.004 -0.016   0.1072600868
 316  0.063 -0.685  0.559  0.350  0.004 -0.016   0.1072584777
 319  0.063 -0.685  0.559  0.349  0.004 -0.016   0.1072583324
 329  0.063 -0.685  0.559  0.349 -0.007 -0.016   0.1072306562
 330  0.063 -0.685  0.559  0.349 -0.005 -0.016   0.1072226564
 331  0.063 -0.685  0.559  0.349 -0.003 -0.016   0.1072206461
 338  0.040 -0.683  0.549  0.356 -0.004 -0.020   0.1069850578
 340  0.037 -0.683  0.548  0.357 -0.005 -0.021   0.1069819009
 344  0.037 -0.683  0.548  0.357 -0.005 -0.021   0.1069818886
 345  0.037 -0.683  0.548  0.357 -0.005 -0.021   0.1069818819
 346  0.037 -0.683  0.548  0.357 -0.005 -0.021   0.1069814242
 357  0.037 -0.683  0.548  0.357 -0.005 -0.033   0.1069710359
 358  0.037 -0.683  0.548  0.357 -0.005 -0.029   0.1069617699
 359  0.037 -0.683  0.548  0.357 -0.005 -0.028   0.1069584656
 360  0.037 -0.683  0.548  0.357 -0.005 -0.025   0.1069570477
 362  0.037 -0.683  0.548  0.357 -0.005 -0.026   0.1069561095
 369  0.037 -0.684  0.548  0.357 -0.005 -0.026   0.1069349676
 372  0.037 -0.704  0.548  0.357 -0.005 -0.026   0.1066906814
 374  0.037 -0.706  0.548  0.357 -0.005 -0.026   0.1066889689
 383  0.037 -0.706  0.521  0.357 -0.005 -0.026   0.1063755448
 385  0.037 -0.706  0.520  0.357 -0.005 -0.026   0.1063749633
 395  0.037 -0.706  0.520  0.366 -0.005 -0.026   0.1063218328
 396  0.037 -0.706  0.520  0.365 -0.005 -0.026   0.1063215903
 407  0.037 -0.706  0.520  0.365  0.001 -0.026   0.1062978189
 408  0.037 -0.706  0.520  0.365  0.003 -0.026   0.1062949581
 435  0.037 -0.706  0.520  0.365  0.003 -0.030   0.1062665141
 436  0.037 -0.706  0.520  0.365  0.003 -0.037   0.1062642181
 438  0.037 -0.706  0.520  0.365  0.003 -0.034   0.1062610066
 449  0.037 -0.702  0.520  0.365  0.003 -0.034   0.1062574819
 450  0.037 -0.703  0.520  0.365  0.003 -0.034   0.1062574307
 451  0.037 -0.704  0.520  0.365  0.003 -0.034   0.1062573129
 459  0.037 -0.704  0.514  0.365  0.003 -0.034   0.1062290992
 461  0.037 -0.704  0.512  0.365  0.003 -0.034   0.1062276281
 463  0.037 -0.704  0.513  0.365  0.003 -0.034   0.1062273500
 472  0.037 -0.704  0.513  0.368  0.003 -0.034   0.1062175192
 484  0.037 -0.704  0.513  0.368  0.004 -0.034   0.1062170679
 492  0.036 -0.704  0.513  0.368  0.004 -0.034   0.1062162706
 493  0.035 -0.704  0.512  0.368  0.004 -0.034   0.1062161029
 494  0.036 -0.704  0.512  0.368  0.004 -0.034   0.1062159616
 495  0.036 -0.704  0.513  0.368  0.004 -0.034   0.1062158085
 497  0.036 -0.704  0.513  0.368  0.004 -0.034   0.1062158018
 509  0.036 -0.704  0.513  0.368  0.004 -0.033   0.1062156146
 519  0.036 -0.699  0.513  0.368  0.004 -0.033   0.1062084337
 520  0.036 -0.700  0.513  0.368  0.004 -0.033   0.1062080971
 529  0.036 -0.700  0.511  0.368  0.004 -0.033   0.1062052817
 531  0.036 -0.700  0.510  0.368  0.004 -0.033   0.1062044378
 541  0.036 -0.700  0.510  0.371  0.004 -0.033   0.1061932443
 553  0.036 -0.700  0.510  0.371  0.005 -0.033   0.1061928190
 568  0.036 -0.696  0.507  0.374  0.006 -0.032   0.1061794847
 571  0.036 -0.691  0.502  0.378  0.008 -0.030   0.1061737460
 572  0.036 -0.692  0.503  0.378  0.008 -0.031   0.1061729740
 590  0.036 -0.692  0.503  0.378  0.008 -0.029   0.1061704114
 601  0.036 -0.694  0.503  0.378  0.008 -0.029   0.1061696215
 611  0.036 -0.694  0.502  0.378  0.008 -0.029   0.1061683423
 620  0.037 -0.694  0.502  0.377  0.008 -0.029   0.1061682512
 621  0.036 -0.694  0.502  0.377  0.008 -0.029   0.1061681329
 634  0.036 -0.694  0.502  0.377  0.006 -0.029   0.1061662794
 637  0.036 -0.690  0.499  0.380  0.008 -0.028   0.1061635550
 642  0.036 -0.689  0.499  0.381  0.008 -0.028   0.1061633157
 643  0.036 -0.689  0.498  0.381  0.008 -0.028   0.1061632022
 649  0.036 -0.689  0.498  0.381  0.008 -0.028   0.1061630480
 651  0.036 -0.689  0.498  0.381  0.008 -0.028   0.1061627578
Powell done niters = 7
Computing relative cost
 0  -25.0 -25.0 -25.0   1.019498
 1  -25.0 -25.0  25.0   0.985191
 2  -25.0  25.0 -25.0   1.045901
 3  -25.0  25.0  25.0   0.969446
 4   25.0 -25.0 -25.0   1.019311
 5   25.0 -25.0  25.0   1.015777
 6   25.0  25.0 -25.0   1.017980
 7   25.0  25.0  25.0   0.995817
REL:  8  0.106163    8.068922  1.008615 rel = 0.105256 
Number of iterations     7
Min cost was 0.106163
Number of FunctionCalls   653
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 1.758000 sec
Parameters at optimum (transmm)  0.03647 -0.68907  0.49831
Parameters at optimum (rotdeg)  0.38096  0.00784 -0.02772 
Final costs ----------------
Number of surface hits 2708
WM  Intensity    61.6351 +/-   8.8930
Ctx Intensity    74.6180 +/-   8.4127
Pct Contrast     19.3022 +/-  12.5299
Cost   0.1062
RelCost   0.2882
Reg at min cost was 
 0.998   0.040   0.046  -0.208;
-0.040  -0.138   0.990   0.397;
 0.046  -0.990  -0.136   0.078;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat, type = 14 
Original Reg 
 0.998   0.041   0.045  -0.245;
-0.039  -0.144   0.989   1.084;
 0.047  -0.989  -0.142  -0.427;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000   0.000  -0.000  -0.037;
 0.001  -0.007  -0.001   0.686;
 0.000   0.001  -0.007  -0.506;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 1.154599
Computing change in rh position
Surface RMS Diff (mm) 1.150041 1.538647
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/tmp.bbregister.3373/bbr.pass1.dat
subject sub005
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1375996544
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.998   0.040   0.046  -0.208;
-0.040  -0.138   0.990   0.397;
 0.046  -0.990  -0.136   0.078;
 0.000   0.000   0.000   1.000;

Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Projecting RH Surfs
Computing relative cost
 0  -25.0 -25.0 -25.0   1.005462
 1  -25.0 -25.0  25.0   0.992291
 2  -25.0  25.0 -25.0   0.996881
 3  -25.0  25.0  25.0   1.003206
 4   25.0 -25.0 -25.0   1.011859
 5   25.0 -25.0  25.0   1.013799
 6   25.0  25.0 -25.0   1.010146
 7   25.0  25.0  25.0   1.017436
REL:  8  0.128535    8.051080  1.006385 rel = 0.127719 
Initial costs ----------------
Number of surface hits 269746
WM  Intensity    61.6292 +/-   8.6363
Ctx Intensity    74.3609 +/-   8.5585
Pct Contrast     18.9094 +/-  12.8492
Cost   0.1285
RelCost   0.1277

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.1173   0.1173  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.1115   0.1115  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.1090   0.1090  0.0
    30  -0.1000  -0.1000   0.0000  -0.1000   0.0000  -0.1000      0.1083   0.1083  0.0
    39  -0.1000  -0.1000   0.0000   0.0000   0.0000  -0.1000      0.1074   0.1074  0.0
   174  -0.1000   0.1000  -0.1000   0.0000   0.0000  -0.1000      0.1074   0.1074  0.0
   177  -0.1000   0.1000  -0.1000   0.0000   0.1000  -0.1000      0.1069   0.1069  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.1062   0.1062  0.0
Brute Force --------------------------
Min cost was 0.106163
Number of iterations   729
Search time 1.975000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
   7  0.095  0.000  0.000  0.000  0.000  0.000   0.1276986789
   8  0.086  0.000  0.000  0.000  0.000  0.000   0.1276851776
  17  0.086 -0.033  0.000  0.000  0.000  0.000   0.1276021483
  18  0.086 -0.026  0.000  0.000  0.000  0.000   0.1275904397
  19  0.086 -0.024  0.000  0.000  0.000  0.000   0.1275888059
  20  0.086 -0.023  0.000  0.000  0.000  0.000   0.1275887083
  29  0.086 -0.023 -0.025  0.000  0.000  0.000   0.1275488480
  31  0.086 -0.023 -0.018  0.000  0.000  0.000   0.1275401496
  40  0.086 -0.023 -0.018  0.057  0.000  0.000   0.1273557294
  41  0.086 -0.023 -0.018  0.037  0.000  0.000   0.1272652095
  42  0.086 -0.023 -0.018  0.036  0.000  0.000   0.1272638958
  43  0.086 -0.023 -0.018  0.032  0.000  0.000   0.1272637054
  45  0.086 -0.023 -0.018  0.034  0.000  0.000   0.1272628172
  53  0.086 -0.023 -0.018  0.034  0.073  0.000   0.1262796992
  54  0.086 -0.023 -0.018  0.034  0.082  0.000   0.1262495215
  55  0.086 -0.023 -0.018  0.034  0.091  0.000   0.1262414946
  56  0.086 -0.023 -0.018  0.034  0.090  0.000   0.1262411198
  64  0.086 -0.023 -0.018  0.034  0.090 -0.061   0.1259444663
  65  0.086 -0.023 -0.018  0.034  0.090 -0.047   0.1259245357
  66  0.086 -0.023 -0.018  0.034  0.090 -0.049   0.1259242525
  75  0.028 -0.023 -0.018  0.034  0.090 -0.049   0.1253291140
  76  0.011 -0.023 -0.018  0.034  0.090 -0.049   0.1253221404
  77  0.018 -0.023 -0.018  0.034  0.090 -0.049   0.1253176300
  86  0.018 -0.020 -0.018  0.034  0.090 -0.049   0.1253106241
  87  0.018 -0.012 -0.018  0.034  0.090 -0.049   0.1253004838
  89  0.018 -0.013 -0.018  0.034  0.090 -0.049   0.1253004170
  98  0.018 -0.013 -0.029  0.034  0.090 -0.049   0.1252166108
  99  0.018 -0.013 -0.060  0.034  0.090 -0.049   0.1251544413
 101  0.018 -0.013 -0.052  0.034  0.090 -0.049   0.1251455374
 111  0.018 -0.013 -0.052  0.055  0.090 -0.049   0.1250470272
 113  0.018 -0.013 -0.052  0.054  0.090 -0.049   0.1250469694
 123  0.018 -0.013 -0.052  0.054  0.104 -0.049   0.1250054866
 134  0.018 -0.013 -0.052  0.054  0.105 -0.101   0.1247433447
 135  0.018 -0.013 -0.052  0.054  0.105 -0.092   0.1247348076
 136  0.018 -0.013 -0.052  0.054  0.105 -0.093   0.1247346904
 138 -0.051 -0.002 -0.085  0.073  0.121 -0.138   0.1241889945
 145 -0.064 -0.000 -0.092  0.077  0.124 -0.147   0.1241772385
 146 -0.063 -0.001 -0.091  0.077  0.124 -0.146   0.1241769550
 147 -0.062 -0.001 -0.091  0.076  0.123 -0.146   0.1241769070
 148 -0.062 -0.001 -0.091  0.077  0.123 -0.146   0.1241768290
 150 -0.062 -0.001 -0.091  0.077  0.123 -0.146   0.1241768221
 159 -0.062 -0.001 -0.091  0.077  0.124 -0.142   0.1241742429
 161 -0.062 -0.001 -0.091  0.077  0.124 -0.140   0.1241741537
 163 -0.062 -0.001 -0.091  0.077  0.124 -0.141   0.1241740603
 170 -0.062 -0.008 -0.091  0.077  0.124 -0.141   0.1241513131
 171 -0.062 -0.018 -0.091  0.077  0.124 -0.141   0.1241390012
 172 -0.062 -0.017 -0.091  0.077  0.124 -0.141   0.1241385887
 181 -0.062 -0.017 -0.100  0.077  0.124 -0.141   0.1241307105
 191 -0.062 -0.017 -0.100  0.078  0.124 -0.141   0.1241300920
 192 -0.062 -0.017 -0.100  0.079  0.124 -0.141   0.1241300738
 202 -0.062 -0.017 -0.100  0.079  0.121 -0.141   0.1241295335
 229 -0.062 -0.017 -0.100  0.079  0.121 -0.144   0.1241288897
 240 -0.062 -0.016 -0.100  0.079  0.121 -0.144   0.1241288124
 249 -0.062 -0.016 -0.101  0.079  0.121 -0.144   0.1241284920
 268 -0.062 -0.016 -0.101  0.079  0.122 -0.144   0.1241283505
 283 -0.061 -0.016 -0.101  0.078  0.122 -0.143   0.1241282091
 284 -0.061 -0.016 -0.101  0.078  0.122 -0.143   0.1241281650
Powell done niters = 4
Computing relative cost
 0  -25.0 -25.0 -25.0   1.005757
 1  -25.0 -25.0  25.0   0.993111
 2  -25.0  25.0 -25.0   0.997448
 3  -25.0  25.0  25.0   1.004378
 4   25.0 -25.0 -25.0   1.012542
 5   25.0 -25.0  25.0   1.014481
 6   25.0  25.0 -25.0   1.010670
 7   25.0  25.0  25.0   1.015250
REL:  8  0.124128    8.053638  1.006705 rel = 0.123301 
Number of iterations     4
Min cost was 0.124128
Number of FunctionCalls   347
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 37.643000 sec
Parameters at optimum (transmm) -0.06133 -0.01618 -0.10078
Parameters at optimum (rotdeg)  0.07825  0.12163 -0.14307 
Final costs ----------------
Number of surface hits 269746
WM  Intensity    61.6231 +/-   8.6135
Ctx Intensity    74.3282 +/-   8.5477
Pct Contrast     18.8727 +/-  12.8167
Cost   0.1241
RelCost   0.1277
Reg at min cost was 
 0.998   0.038   0.048  -0.268;
-0.042  -0.136   0.990   0.382;
 0.044  -0.990  -0.134  -0.021;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.998   0.040   0.046  -0.208;
-0.040  -0.138   0.990   0.397;
 0.046  -0.990  -0.136   0.078;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000   0.002  -0.002   0.060;
 0.003  -0.001  -0.000   0.016;
 0.002   0.000  -0.001   0.100;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.148487
Computing change in rh position
Surface RMS Diff (mm) 0.171396 0.321705
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
 0.998   0.038   0.048  -0.268;
-0.042  -0.136   0.990   0.382;
 0.044  -0.990  -0.134  -0.021;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 0.998   0.038   0.048  -0.268;
-0.042  -0.136   0.990   0.382;
 0.044  -0.990  -0.134  -0.021;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub005
RegMat ---------------------------
 0.998   0.038   0.048  -0.268;
-0.042  -0.136   0.990   0.382;
 0.044  -0.990  -0.134  -0.021;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000   0.002  -0.002   0.180;
-0.002   1.000   0.001   0.052;
 0.002  -0.001   1.000  -0.349;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.699   0.029   0.028   20.940;
 0.034  -0.090  -0.660   267.665;
-0.027   0.660  -0.091   22.410;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 22:28:33 CEST 2013 
Ended   at Thu Aug  8 22:40:43 CEST 2013
BBR-Run-Time-Sec 730
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.dat --surf
 

 mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz 

mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998148, -0.0400878, -0.0457496)
j_ras = (-0.0459461, 0.989757, 0.135168)
k_ras = (-0.0398624, -0.13702, 0.989766)
INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
reading extra input line subject sub005
reading extra input line fscale 0.150000
reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/orig.mgz...
INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/transforms/T2raw.lta...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
 1.000   0.002  -0.002   0.180;
-0.002   1.000   0.001   0.052;
 0.002  -0.001   1.000  -0.349;
 0.000   0.000   0.000   1.000;
---------------------------------
Applying LTAtransformInterp (resample_type 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz...

 mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz 

using segmentation for initial intensity normalization
using Gaussian smoothing of bias field, sigma=4.000
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz...
computing distance transform
computing distance transform
computing nonmaximum suppression
8547 non wm control points removed
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
smoothing bias field
writing normalized volume to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/T2.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub005 lh 

-white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
refining pial surfaces placement using T2 volume ../mri/T2
using white starting white location...
using woT2.pial starting pial locations...
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
16905 bright wm thresholded.
908 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig...
computing class statistics...
border white:    254363 voxels (1.52%)
border gray      296177 voxels (1.77%)
WM (91.0): 92.4 +- 10.3 [70.0 --> 110.0]
GM (74.0) : 72.6 +- 12.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.3 (was 70)
setting MAX_BORDER_WHITE to 114.3 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.6 (was 40)
setting MAX_GRAY to 93.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.9 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104,    GM=59
mean inside = 92.3, mean outside = 67.9
smoothing surface for 5 iterations...
reading initial white vertex positions from white...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.26 (0.02-->6.37) (max @ vno 60346 --> 65969)
face area 0.34 +- 0.16 (0.00-->6.14)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 7 with 7 points - only 0.00% unknown
deleting segment 8 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
deleting segment 15 with 11 points - only 0.00% unknown
tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.25 (0.07-->6.37) (max @ vno 60346 --> 65969)
face area 0.34 +- 0.16 (0.00-->6.14)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5050607.0, rms=0.00
rms = 2.57, time step reduction 1 of 3 to 0.250...
rms = 0.65, time step reduction 2 of 3 to 0.125...
rms = 0.08, time step reduction 3 of 3 to 0.062...
001: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 7 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 11 points - only 0.00% unknown
tol=1.0e-04, sigma=1.0, host=snake, 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 (0.07-->6.37) (max @ vno 60346 --> 65969)
face area 0.34 +- 0.16 (0.00-->6.14)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5050607.0, rms=0.00
rms = 2.58, time step reduction 1 of 3 to 0.250...
rms = 0.66, time step reduction 2 of 3 to 0.125...
rms = 0.08, time step reduction 3 of 3 to 0.062...
002: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 7 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 11 points - only 0.00% unknown
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.07-->6.37) (max @ vno 60346 --> 65969)
face area 0.34 +- 0.16 (0.00-->6.14)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5050607.0, rms=0.00
rms = 2.57, time step reduction 1 of 3 to 0.250...
rms = 0.65, time step reduction 2 of 3 to 0.125...
rms = 0.08, time step reduction 3 of 3 to 0.062...
003: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 5 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 7 points - only 0.00% unknown
deleting segment 5 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 11 points - only 0.00% unknown
tol=1.0e-04, sigma=0.2, host=snake, 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
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5050607.0, rms=0.00
rms = 2.58, time step reduction 1 of 3 to 0.250...
rms = 0.66, time step reduction 2 of 3 to 0.125...
rms = 0.08, time step reduction 3 of 3 to 0.062...
004: dt: 0.1250, sse=5050607.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from woT2.pial...
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [93.00 201.00], gm=147.00+-18.00, and vertices in regions > 138.0
39902 surface locations found to contain inconsistent values (4917 in, 34985 out)
tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=600642.1, rms=0.23
001: dt: 0.5000, sse=558236.2, rms=0.225 (0.000%)
002: dt: 0.5000, sse=533914.7, rms=0.213 (0.000%)
003: dt: 0.5000, sse=515651.6, rms=0.204 (0.000%)
004: dt: 0.5000, sse=502599.2, rms=0.196 (0.000%)
005: dt: 0.5000, sse=492409.3, rms=0.188 (0.000%)
006: dt: 0.5000, sse=483755.8, rms=0.182 (0.000%)
007: dt: 0.5000, sse=476508.9, rms=0.177 (0.000%)
008: dt: 0.5000, sse=470561.8, rms=0.173 (0.000%)
009: dt: 0.5000, sse=466122.2, rms=0.169 (0.000%)
010: dt: 0.5000, sse=461843.5, rms=0.166 (0.000%)
011: dt: 0.5000, sse=458462.7, rms=0.163 (0.000%)
012: dt: 0.5000, sse=454836.3, rms=0.161 (0.000%)
013: dt: 0.5000, sse=451619.2, rms=0.159 (0.000%)
014: dt: 0.5000, sse=448957.2, rms=0.157 (0.000%)
015: dt: 0.5000, sse=446102.2, rms=0.156 (0.000%)
016: dt: 0.5000, sse=443480.9, rms=0.155 (0.000%)
017: dt: 0.5000, sse=441197.8, rms=0.154 (0.000%)
018: dt: 0.5000, sse=439113.6, rms=0.153 (0.000%)
019: dt: 0.5000, sse=437142.9, rms=0.152 (0.000%)
020: dt: 0.5000, sse=435140.2, rms=0.152 (0.000%)
021: dt: 0.5000, sse=433160.8, rms=0.152 (0.000%)
022: dt: 0.5000, sse=431352.5, rms=0.151 (0.000%)
023: dt: 0.5000, sse=429420.1, rms=0.151 (0.000%)
024: dt: 0.5000, sse=427848.3, rms=0.151 (0.000%)
025: dt: 0.5000, sse=426204.8, rms=0.152 (0.000%)
026: dt: 0.5000, sse=424777.1, rms=0.152 (0.000%)
027: dt: 0.5000, sse=423328.6, rms=0.152 (0.000%)
028: dt: 0.5000, sse=421760.3, rms=0.152 (0.000%)
029: dt: 0.5000, sse=420302.5, rms=0.153 (0.000%)
030: dt: 0.5000, sse=418962.1, rms=0.153 (0.000%)
positioning took 3.9 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [95.00 203.00], gm=149.00+-18.00, and vertices in regions > 140.0
33374 surface locations found to contain inconsistent values (2355 in, 31019 out)
tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=43511.0, rms=0.13
031: dt: 0.5000, sse=43237.3, rms=0.124 (0.000%)
032: dt: 0.5000, sse=44110.6, rms=0.114 (0.000%)
033: dt: 0.5000, sse=45179.7, rms=0.106 (0.000%)
034: dt: 0.5000, sse=46053.3, rms=0.101 (0.000%)
035: dt: 0.5000, sse=46756.7, rms=0.096 (0.000%)
036: dt: 0.5000, sse=47483.6, rms=0.091 (0.000%)
037: dt: 0.5000, sse=48150.4, rms=0.087 (0.000%)
038: dt: 0.5000, sse=48806.6, rms=0.083 (0.000%)
039: dt: 0.5000, sse=49470.3, rms=0.079 (0.000%)
040: dt: 0.5000, sse=50079.9, rms=0.076 (0.000%)
041: dt: 0.5000, sse=50691.2, rms=0.072 (0.000%)
042: dt: 0.5000, sse=51227.9, rms=0.070 (0.000%)
043: dt: 0.5000, sse=51750.8, rms=0.067 (0.000%)
044: dt: 0.5000, sse=52241.1, rms=0.064 (0.000%)
045: dt: 0.5000, sse=52685.6, rms=0.062 (0.000%)
046: dt: 0.5000, sse=53108.8, rms=0.060 (0.000%)
047: dt: 0.5000, sse=53478.3, rms=0.058 (0.000%)
048: dt: 0.5000, sse=53860.7, rms=0.056 (0.000%)
049: dt: 0.5000, sse=54227.8, rms=0.055 (0.000%)
050: dt: 0.5000, sse=54557.1, rms=0.053 (0.000%)
051: dt: 0.5000, sse=54863.1, rms=0.051 (0.000%)
052: dt: 0.5000, sse=55143.0, rms=0.050 (0.000%)
053: dt: 0.5000, sse=55400.5, rms=0.049 (0.000%)
054: dt: 0.5000, sse=55647.8, rms=0.048 (0.000%)
055: dt: 0.5000, sse=55892.6, rms=0.047 (0.000%)
056: dt: 0.5000, sse=56113.1, rms=0.045 (0.000%)
057: dt: 0.5000, sse=56309.4, rms=0.044 (0.000%)
058: dt: 0.5000, sse=56514.7, rms=0.044 (0.000%)
059: dt: 0.5000, sse=56702.4, rms=0.043 (0.000%)
060: dt: 0.5000, sse=56866.8, rms=0.042 (0.000%)
positioning took 3.8 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [86.70 207.30], gm=147.00+-20.10, and vertices in regions > 136.9
31361 surface locations found to contain inconsistent values (145 in, 31216 out)
tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=6152.8, rms=0.06
061: dt: 0.5000, sse=6117.8, rms=0.056 (0.000%)
062: dt: 0.5000, sse=6198.5, rms=0.049 (0.000%)
063: dt: 0.5000, sse=6289.8, rms=0.045 (0.000%)
064: dt: 0.5000, sse=6363.1, rms=0.042 (0.000%)
065: dt: 0.5000, sse=6414.4, rms=0.040 (0.000%)
066: dt: 0.5000, sse=6444.6, rms=0.038 (0.000%)
067: dt: 0.5000, sse=6463.7, rms=0.037 (0.000%)
068: dt: 0.5000, sse=6477.9, rms=0.035 (0.000%)
069: dt: 0.5000, sse=6494.1, rms=0.034 (0.000%)
070: dt: 0.5000, sse=6508.1, rms=0.033 (0.000%)
071: dt: 0.5000, sse=6521.8, rms=0.032 (0.000%)
072: dt: 0.5000, sse=6535.8, rms=0.031 (0.000%)
073: dt: 0.5000, sse=6546.9, rms=0.030 (0.000%)
074: dt: 0.5000, sse=6556.2, rms=0.030 (0.000%)
075: dt: 0.5000, sse=6563.5, rms=0.029 (0.000%)
076: dt: 0.5000, sse=6570.3, rms=0.028 (0.000%)
077: dt: 0.5000, sse=6577.6, rms=0.028 (0.000%)
078: dt: 0.5000, sse=6583.6, rms=0.027 (0.000%)
079: dt: 0.5000, sse=6590.4, rms=0.027 (0.000%)
080: dt: 0.5000, sse=6594.0, rms=0.026 (0.000%)
081: dt: 0.5000, sse=6597.6, rms=0.026 (0.000%)
082: dt: 0.5000, sse=6603.0, rms=0.026 (0.000%)
083: dt: 0.5000, sse=6605.6, rms=0.025 (0.000%)
084: dt: 0.5000, sse=6609.8, rms=0.025 (0.000%)
085: dt: 0.5000, sse=6612.6, rms=0.025 (0.000%)
086: dt: 0.5000, sse=6617.1, rms=0.025 (0.000%)
087: dt: 0.5000, sse=6619.4, rms=0.025 (0.000%)
088: dt: 0.5000, sse=6621.2, rms=0.024 (0.000%)
089: dt: 0.5000, sse=6622.7, rms=0.024 (0.000%)
090: dt: 0.5000, sse=6622.9, rms=0.024 (0.000%)
positioning took 3.8 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [94.50 205.50], gm=150.00+-18.50, and vertices in regions > 140.7
30232 surface locations found to contain inconsistent values (315 in, 29917 out)
tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000
mom=0.00, dt=0.50
writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=788.6, rms=0.03
091: dt: 0.5000, sse=787.5, rms=0.031 (0.000%)
092: dt: 0.5000, sse=777.6, rms=0.030 (0.000%)
093: dt: 0.5000, sse=770.0, rms=0.029 (0.000%)
094: dt: 0.5000, sse=763.9, rms=0.028 (0.000%)
095: dt: 0.5000, sse=758.1, rms=0.027 (0.000%)
096: dt: 0.5000, sse=754.1, rms=0.026 (0.000%)
097: dt: 0.5000, sse=751.2, rms=0.026 (0.000%)
098: dt: 0.5000, sse=748.6, rms=0.026 (0.000%)
099: dt: 0.5000, sse=746.1, rms=0.025 (0.000%)
100: dt: 0.5000, sse=743.8, rms=0.025 (0.000%)
101: dt: 0.5000, sse=741.2, rms=0.025 (0.000%)
102: dt: 0.5000, sse=739.0, rms=0.024 (0.000%)
103: dt: 0.5000, sse=736.9, rms=0.024 (0.000%)
104: dt: 0.5000, sse=735.0, rms=0.023 (0.000%)
105: dt: 0.5000, sse=733.7, rms=0.023 (0.000%)
106: dt: 0.5000, sse=732.3, rms=0.023 (0.000%)
107: dt: 0.5000, sse=730.8, rms=0.023 (0.000%)
108: dt: 0.5000, sse=729.8, rms=0.023 (0.000%)
109: dt: 0.5000, sse=728.8, rms=0.022 (0.000%)
110: dt: 0.5000, sse=727.3, rms=0.022 (0.000%)
111: dt: 0.5000, sse=726.6, rms=0.022 (0.000%)
112: dt: 0.5000, sse=725.8, rms=0.022 (0.000%)
113: dt: 0.5000, sse=725.5, rms=0.022 (0.000%)
114: dt: 0.5000, sse=724.7, rms=0.022 (0.000%)
115: dt: 0.5000, sse=724.0, rms=0.022 (0.000%)
116: dt: 0.5000, sse=723.7, rms=0.021 (0.000%)
117: dt: 0.5000, sse=723.5, rms=0.021 (0.000%)
118: dt: 0.5000, sse=723.0, rms=0.021 (0.000%)
119: dt: 0.5000, sse=722.6, rms=0.021 (0.000%)
120: dt: 0.5000, sse=722.6, rms=0.021 (0.000%)
positioning took 3.8 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.area.pial
vertex spacing 1.03 +- 0.45 (0.07-->9.27) (max @ vno 100866 --> 99891)
face area 0.42 +- 0.33 (0.00-->7.39)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 141918 vertices processed
25000 of 141918 vertices processed
50000 of 141918 vertices processed
75000 of 141918 vertices processed
100000 of 141918 vertices processed
125000 of 141918 vertices processed
0 of 141918 vertices processed
25000 of 141918 vertices processed
50000 of 141918 vertices processed
75000 of 141918 vertices processed
100000 of 141918 vertices processed
125000 of 141918 vertices processed
thickness calculation complete, 408:1172 truncations.
26003 vertices at 0 distance
88664 vertices at 1 distance
93876 vertices at 2 distance
44360 vertices at 3 distance
13906 vertices at 4 distance
3987 vertices at 5 distance
1213 vertices at 6 distance
454 vertices at 7 distance
208 vertices at 8 distance
105 vertices at 9 distance
62 vertices at 10 distance
50 vertices at 11 distance
21 vertices at 12 distance
28 vertices at 13 distance
13 vertices at 14 distance
16 vertices at 15 distance
13 vertices at 16 distance
14 vertices at 17 distance
8 vertices at 18 distance
6 vertices at 19 distance
9 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.thickness
positioning took 18.7 minutes
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub005 rh 

-white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
refining pial surfaces placement using T2 volume ../mri/T2
using white starting white location...
using woT2.pial starting pial locations...
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
17487 bright wm thresholded.
908 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig...
computing class statistics...
border white:    254363 voxels (1.52%)
border gray      296177 voxels (1.77%)
WM (91.0): 92.5 +- 10.3 [70.0 --> 110.0]
GM (74.0) : 72.5 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 44.2 (was 70)
setting MAX_BORDER_WHITE to 115.3 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 31.3 (was 40)
setting MAX_GRAY to 94.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=57
mean inside = 92.4, mean outside = 67.6
smoothing surface for 5 iterations...
reading initial white vertex positions from white...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.25 (0.01-->3.85) (max @ vno 100129 --> 101238)
face area 0.33 +- 0.16 (0.00-->1.91)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 3 with 417 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 15 points - only 0.00% unknown
deleting segment 6 with 35 points - only 0.00% unknown
deleting segment 8 with 123 points - only 0.00% unknown
removing 2 vertex label from ripped group
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 11 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 13 with 1 points - only 0.00% unknown
tol=1.0e-04, sigma=2.0, host=snake, 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 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838)
face area 0.33 +- 0.16 (0.00-->1.91)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5162962.0, rms=0.00
rms = 1.14, time step reduction 1 of 3 to 0.250...
rms = 0.29, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
001: dt: 0.1250, sse=5162962.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 1 with 417 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 15 points - only 0.00% unknown
deleting segment 4 with 35 points - only 0.00% unknown
deleting segment 5 with 123 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
tol=1.0e-04, sigma=1.0, host=snake, 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-->3.45) (max @ vno 16176 --> 26838)
face area 0.33 +- 0.16 (0.00-->1.91)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5162962.0, rms=0.00
rms = 1.14, time step reduction 1 of 3 to 0.250...
rms = 0.29, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
002: dt: 0.1250, sse=5162962.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 1 with 417 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 15 points - only 0.00% unknown
deleting segment 4 with 35 points - only 0.00% unknown
deleting segment 5 with 123 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.04-->3.45) (max @ vno 16176 --> 26838)
face area 0.33 +- 0.16 (0.00-->1.91)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5162962.0, rms=0.00
rms = 1.14, time step reduction 1 of 3 to 0.250...
rms = 0.29, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
003: dt: 0.1250, sse=5162962.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 1 with 417 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 15 points - only 0.00% unknown
deleting segment 4 with 35 points - only 0.00% unknown
deleting segment 5 with 123 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
tol=1.0e-04, sigma=0.2, host=snake, 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
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5162962.0, rms=0.00
rms = 1.14, time step reduction 1 of 3 to 0.250...
rms = 0.29, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
004: dt: 0.1250, sse=5162962.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from woT2.pial...
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [109.60 186.40], gm=148.00+-12.80, and vertices in regions > 141.6
47738 surface locations found to contain inconsistent values (14669 in, 33069 out)
tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=595744.5, rms=0.30
001: dt: 0.5000, sse=553502.8, rms=0.293 (0.000%)
002: dt: 0.5000, sse=526265.1, rms=0.278 (0.000%)
003: dt: 0.5000, sse=507833.2, rms=0.267 (0.000%)
004: dt: 0.5000, sse=493413.0, rms=0.256 (0.000%)
005: dt: 0.5000, sse=482884.1, rms=0.247 (0.000%)
006: dt: 0.5000, sse=475175.9, rms=0.238 (0.000%)
007: dt: 0.5000, sse=468719.2, rms=0.231 (0.000%)
008: dt: 0.5000, sse=464184.7, rms=0.224 (0.000%)
009: dt: 0.5000, sse=460380.4, rms=0.218 (0.000%)
010: dt: 0.5000, sse=456370.3, rms=0.213 (0.000%)
011: dt: 0.5000, sse=452858.3, rms=0.208 (0.000%)
012: dt: 0.5000, sse=449262.8, rms=0.204 (0.000%)
013: dt: 0.5000, sse=447372.7, rms=0.200 (0.000%)
014: dt: 0.5000, sse=445664.4, rms=0.196 (0.000%)
015: dt: 0.5000, sse=442769.7, rms=0.193 (0.000%)
016: dt: 0.5000, sse=440411.4, rms=0.190 (0.000%)
017: dt: 0.5000, sse=438380.6, rms=0.188 (0.000%)
018: dt: 0.5000, sse=436463.2, rms=0.186 (0.000%)
019: dt: 0.5000, sse=434983.2, rms=0.184 (0.000%)
020: dt: 0.5000, sse=433417.6, rms=0.182 (0.000%)
021: dt: 0.5000, sse=431715.5, rms=0.181 (0.000%)
022: dt: 0.5000, sse=430139.5, rms=0.180 (0.000%)
023: dt: 0.5000, sse=428766.2, rms=0.179 (0.000%)
024: dt: 0.5000, sse=427525.1, rms=0.178 (0.000%)
025: dt: 0.5000, sse=426358.1, rms=0.177 (0.000%)
026: dt: 0.5000, sse=425162.5, rms=0.176 (0.000%)
027: dt: 0.5000, sse=423851.8, rms=0.175 (0.000%)
028: dt: 0.5000, sse=422741.6, rms=0.175 (0.000%)
029: dt: 0.5000, sse=421578.2, rms=0.175 (0.000%)
030: dt: 0.5000, sse=420429.8, rms=0.174 (0.000%)
positioning took 4.0 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [92.50 203.50], gm=148.00+-18.50, and vertices in regions > 138.7
33313 surface locations found to contain inconsistent values (596 in, 32717 out)
tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=44169.9, rms=0.15
031: dt: 0.5000, sse=43709.6, rms=0.140 (0.000%)
032: dt: 0.5000, sse=43635.3, rms=0.126 (0.000%)
033: dt: 0.5000, sse=44064.6, rms=0.116 (0.000%)
034: dt: 0.5000, sse=44681.9, rms=0.109 (0.000%)
035: dt: 0.5000, sse=45409.6, rms=0.102 (0.000%)
036: dt: 0.5000, sse=46091.4, rms=0.096 (0.000%)
037: dt: 0.5000, sse=46703.8, rms=0.092 (0.000%)
038: dt: 0.5000, sse=47346.7, rms=0.087 (0.000%)
039: dt: 0.5000, sse=48021.3, rms=0.083 (0.000%)
040: dt: 0.5000, sse=48703.4, rms=0.080 (0.000%)
041: dt: 0.5000, sse=49356.8, rms=0.076 (0.000%)
042: dt: 0.5000, sse=49973.1, rms=0.073 (0.000%)
043: dt: 0.5000, sse=50597.7, rms=0.070 (0.000%)
044: dt: 0.5000, sse=51164.7, rms=0.068 (0.000%)
045: dt: 0.5000, sse=51701.1, rms=0.065 (0.000%)
046: dt: 0.5000, sse=52197.3, rms=0.063 (0.000%)
047: dt: 0.5000, sse=52662.8, rms=0.061 (0.000%)
048: dt: 0.5000, sse=53139.7, rms=0.059 (0.000%)
049: dt: 0.5000, sse=53547.9, rms=0.057 (0.000%)
050: dt: 0.5000, sse=53955.6, rms=0.056 (0.000%)
051: dt: 0.5000, sse=54322.5, rms=0.054 (0.000%)
052: dt: 0.5000, sse=54684.1, rms=0.053 (0.000%)
053: dt: 0.5000, sse=55005.9, rms=0.052 (0.000%)
054: dt: 0.5000, sse=55301.5, rms=0.050 (0.000%)
055: dt: 0.5000, sse=55574.7, rms=0.049 (0.000%)
056: dt: 0.5000, sse=55856.3, rms=0.048 (0.000%)
057: dt: 0.5000, sse=56084.7, rms=0.047 (0.000%)
058: dt: 0.5000, sse=56310.9, rms=0.046 (0.000%)
059: dt: 0.5000, sse=56538.4, rms=0.045 (0.000%)
060: dt: 0.5000, sse=56739.1, rms=0.045 (0.000%)
positioning took 3.9 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [91.00 205.00], gm=148.00+-19.00, and vertices in regions > 138.5
32297 surface locations found to contain inconsistent values (167 in, 32130 out)
tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=6056.2, rms=0.05
061: dt: 0.5000, sse=6037.1, rms=0.052 (0.000%)
062: dt: 0.5000, sse=6115.4, rms=0.046 (0.000%)
063: dt: 0.5000, sse=6191.6, rms=0.042 (0.000%)
064: dt: 0.5000, sse=6254.1, rms=0.040 (0.000%)
065: dt: 0.5000, sse=6296.4, rms=0.038 (0.000%)
066: dt: 0.5000, sse=6318.2, rms=0.037 (0.000%)
067: dt: 0.5000, sse=6332.2, rms=0.035 (0.000%)
068: dt: 0.5000, sse=6344.6, rms=0.034 (0.000%)
069: dt: 0.5000, sse=6354.9, rms=0.033 (0.000%)
070: dt: 0.5000, sse=6366.8, rms=0.033 (0.000%)
071: dt: 0.5000, sse=6376.0, rms=0.032 (0.000%)
072: dt: 0.5000, sse=6388.8, rms=0.031 (0.000%)
073: dt: 0.5000, sse=6396.9, rms=0.030 (0.000%)
074: dt: 0.5000, sse=6404.4, rms=0.030 (0.000%)
075: dt: 0.5000, sse=6411.4, rms=0.029 (0.000%)
076: dt: 0.5000, sse=6418.0, rms=0.029 (0.000%)
077: dt: 0.5000, sse=6423.0, rms=0.028 (0.000%)
078: dt: 0.5000, sse=6428.2, rms=0.028 (0.000%)
079: dt: 0.5000, sse=6431.9, rms=0.028 (0.000%)
080: dt: 0.5000, sse=6435.7, rms=0.027 (0.000%)
081: dt: 0.5000, sse=6438.2, rms=0.027 (0.000%)
082: dt: 0.5000, sse=6443.0, rms=0.027 (0.000%)
083: dt: 0.5000, sse=6445.1, rms=0.026 (0.000%)
084: dt: 0.5000, sse=6448.3, rms=0.026 (0.000%)
085: dt: 0.5000, sse=6451.8, rms=0.026 (0.000%)
086: dt: 0.5000, sse=6454.8, rms=0.026 (0.000%)
087: dt: 0.5000, sse=6456.1, rms=0.026 (0.000%)
088: dt: 0.5000, sse=6458.5, rms=0.026 (0.000%)
089: dt: 0.5000, sse=6458.8, rms=0.026 (0.000%)
090: dt: 0.5000, sse=6460.6, rms=0.025 (0.000%)
positioning took 3.8 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [90.10 205.90], gm=148.00+-19.30, and vertices in regions > 138.3
32407 surface locations found to contain inconsistent values (38 in, 32369 out)
tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000
mom=0.00, dt=0.50
writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=790.5, rms=0.03
091: dt: 0.5000, sse=783.6, rms=0.033 (0.000%)
092: dt: 0.5000, sse=761.9, rms=0.029 (0.000%)
093: dt: 0.5000, sse=755.3, rms=0.028 (0.000%)
094: dt: 0.5000, sse=752.2, rms=0.027 (0.000%)
095: dt: 0.5000, sse=749.1, rms=0.026 (0.000%)
096: dt: 0.5000, sse=746.9, rms=0.026 (0.000%)
097: dt: 0.5000, sse=745.1, rms=0.026 (0.000%)
098: dt: 0.5000, sse=743.6, rms=0.026 (0.000%)
099: dt: 0.5000, sse=741.8, rms=0.025 (0.000%)
100: dt: 0.5000, sse=740.3, rms=0.025 (0.000%)
101: dt: 0.5000, sse=739.0, rms=0.025 (0.000%)
102: dt: 0.5000, sse=737.9, rms=0.025 (0.000%)
103: dt: 0.5000, sse=736.8, rms=0.024 (0.000%)
104: dt: 0.5000, sse=735.8, rms=0.024 (0.000%)
105: dt: 0.5000, sse=735.2, rms=0.024 (0.000%)
106: dt: 0.5000, sse=734.3, rms=0.024 (0.000%)
107: dt: 0.5000, sse=733.7, rms=0.024 (0.000%)
108: dt: 0.5000, sse=733.1, rms=0.024 (0.000%)
109: dt: 0.5000, sse=732.4, rms=0.024 (0.000%)
110: dt: 0.5000, sse=732.1, rms=0.024 (0.000%)
111: dt: 0.5000, sse=731.6, rms=0.024 (0.000%)
112: dt: 0.5000, sse=731.3, rms=0.023 (0.000%)
113: dt: 0.5000, sse=731.4, rms=0.023 (0.000%)
114: dt: 0.5000, sse=731.1, rms=0.023 (0.000%)
115: dt: 0.5000, sse=730.8, rms=0.023 (0.000%)
116: dt: 0.5000, sse=730.6, rms=0.023 (0.000%)
117: dt: 0.5000, sse=730.5, rms=0.023 (0.000%)
118: dt: 0.5000, sse=730.4, rms=0.023 (0.000%)
119: dt: 0.5000, sse=730.3, rms=0.023 (0.000%)
120: dt: 0.5000, sse=730.0, rms=0.023 (0.000%)
positioning took 3.8 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.area.pial
vertex spacing 1.03 +- 0.45 (0.06-->9.77) (max @ vno 101427 --> 100291)
face area 0.41 +- 0.32 (0.00-->8.28)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 142731 vertices processed
25000 of 142731 vertices processed
50000 of 142731 vertices processed
75000 of 142731 vertices processed
100000 of 142731 vertices processed
125000 of 142731 vertices processed
0 of 142731 vertices processed
25000 of 142731 vertices processed
50000 of 142731 vertices processed
75000 of 142731 vertices processed
100000 of 142731 vertices processed
125000 of 142731 vertices processed
thickness calculation complete, 479:847 truncations.
26619 vertices at 0 distance
86850 vertices at 1 distance
93570 vertices at 2 distance
45217 vertices at 3 distance
14907 vertices at 4 distance
4679 vertices at 5 distance
1443 vertices at 6 distance
510 vertices at 7 distance
201 vertices at 8 distance
105 vertices at 9 distance
67 vertices at 10 distance
46 vertices at 11 distance
39 vertices at 12 distance
35 vertices at 13 distance
32 vertices at 14 distance
22 vertices at 15 distance
23 vertices at 16 distance
28 vertices at 17 distance
14 vertices at 18 distance
27 vertices at 19 distance
32 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.thickness
positioning took 19.2 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 23:20:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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_calc -o lh.volume lh.area.mid mul lh.thickness 

Saving result to 'lh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#--------------------------------------------
#@# Surf Volume rh Thu Aug  8 23:20:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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_calc -o rh.volume rh.area.mid mul rh.thickness 

Saving result to 'rh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#--------------------------------------------
#@# Cortical ribbon mask Thu Aug  8 23:20:14 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub005 

SUBJECTS_DIR is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
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 = 11
writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/ribbon.mgz
 writing ribbon files
#--------------------------------------------
#@# ASeg Stats Thu Aug  8 23:37:33 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005

 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 /opt/freesurfer/5.3.0/ASegStatsLUT.txt --subject sub005 


$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 /opt/freesurfer/5.3.0/ASegStatsLUT.txt --subject sub005 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1108117 mm^3    (det: 1.758032 )
Computing euler number
orig.nofix lheno =  -46, rheno = -26
orig.nofix lhholes =   24, rhholes = 14
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 265530.343 264563.000  diff=  967.3  pctdiff= 0.364
rhCtxGM: 265717.542 264874.000  diff=  843.5  pctdiff= 0.317
lhCtxWM: 210790.046 210779.500  diff=   10.5  pctdiff= 0.005
rhCtxWM: 210686.930 210543.500  diff=  143.4  pctdiff= 0.068
SubCortGMVol  62575.000
SupraTentVol  1025743.861 (1023088.000) diff=2655.861 pctdiff=0.259
SupraTentVolNotVent  1016210.861 (1013555.000) diff=2655.861 pctdiff=0.261
BrainSegVol  1150498.000 (1149006.000) diff=1492.000 pctdiff=0.130
BrainSegVolNotVent  1139009.000 (1140759.861) diff=-1750.861 pctdiff=-0.154
BrainSegVolNotVent  1139009.000
CerebellumVol 125240.000
VentChorVol    9533.000
3rd4th5thCSF   1956.000
CSFVol   477.000, OptChiasmVol   201.000
MaskVol 1526731.000
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
  3     4             Left-Lateral-Ventricle    3278    3277.959
  4     5                  Left-Inf-Lat-Vent     580     579.936
  5     7       Left-Cerebellum-White-Matter   12975   12975.378
  6     8             Left-Cerebellum-Cortex   49757   49756.992
  7    10               Left-Thalamus-Proper    7832    7832.081
  8    11                       Left-Caudate    3508    3508.107
  9    12                       Left-Putamen    6400    6400.005
 10    13                      Left-Pallidum    1978    1978.220
 11    14                      3rd-Ventricle     341     341.234
 12    15                      4th-Ventricle    1298    1297.907
 13    16                         Brain-Stem   20989   20988.875
 14    17                   Left-Hippocampus    3854    3853.685
 15    18                      Left-Amygdala    1671    1670.966
 16    24                                CSF     491     491.288
 17    26                Left-Accumbens-area     577     577.471
 18    28                     Left-VentralDC    4012    4012.331
 19    30                        Left-vessel     127     127.376
 20    31                Left-choroid-plexus    1356    1356.293
 23    43            Right-Lateral-Ventricle    2569    2569.490
 24    44                 Right-Inf-Lat-Vent     409     409.412
 25    46      Right-Cerebellum-White-Matter   14142   14142.228
 26    47            Right-Cerebellum-Cortex   50562   50562.211
 27    49              Right-Thalamus-Proper    7753    7752.948
 28    50                      Right-Caudate    3833    3832.621
 29    51                      Right-Putamen    6146    6145.553
 30    52                     Right-Pallidum    2178    2178.489
 31    53                  Right-Hippocampus    4059    4058.912
 32    54                     Right-Amygdala    1391    1391.412
 33    58               Right-Accumbens-area     632     631.959
 34    60                    Right-VentralDC    4180    4180.111
 35    62                       Right-vessel      65      65.004
 36    63               Right-choroid-plexus    1217    1216.556
 37    72                      5th-Ventricle       0       0.000
 38    77                 WM-hypointensities    1410    1410.145
 39    78            Left-WM-hypointensities       0       0.000
 40    79           Right-WM-hypointensities       0       0.000
 41    80             non-WM-hypointensities       9       9.365
 42    81        Left-non-WM-hypointensities       0       0.000
 43    82       Right-non-WM-hypointensities       0       0.000
 44    85                       Optic-Chiasm     220     220.139
 45   251                       CC_Posterior     700     700.031
 46   252                   CC_Mid_Posterior     332     332.204
 47   253                         CC_Central     354     353.958
 48   254                    CC_Mid_Anterior     393     392.745
 49   255                        CC_Anterior     742     742.297

Reporting on  45 segmentations
mri_segstats done
#-----------------------------------------
#@# AParc-to-ASeg Thu Aug  8 23:40:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005

 mri_aparc2aseg --s sub005 --volmask 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub005
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-------------------------

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 = 527907
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005

 mri_aparc2aseg --s sub005 --volmask --a2009s 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub005
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)

Reading rh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-------------------------

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 = 527907
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Thu Aug  8 23:45:15 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005

 mri_aparc2aseg --s sub005 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub005
outvol mri/wmparc.mgz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 5.000000
RipUnknown 1
CtxSeg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/ribbon.mgz
Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 7419 vertices from left hemi
Ripped 7484 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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aseg.mgz
Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/aparc+aseg.mgz
ASeg Vox2RAS: -----------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-------------------------

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 = 948174
Used brute-force search on 3 voxels
Fixing Parahip LH WM
  Found 11 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1.000000
     3 k 4.000000
     4 k 6.000000
     5 k 1.000000
     6 k 1.000000
     7 k 3.000000
     8 k 2.000000
     9 k 1266.000000
     10 k 5.000000
Fixing Parahip RH WM
  Found 1 clusters
     0 k 1504.000000
Writing output aseg to mri/wmparc.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005

 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 sub005 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv 


$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 sub005 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1108117 mm^3    (det: 1.758032 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 265530.343 264563.000  diff=  967.3  pctdiff= 0.364
rhCtxGM: 265717.542 264874.000  diff=  843.5  pctdiff= 0.317
lhCtxWM: 210790.046 210779.500  diff=   10.5  pctdiff= 0.005
rhCtxWM: 210686.930 210543.500  diff=  143.4  pctdiff= 0.068
SubCortGMVol  62575.000
SupraTentVol  1025743.861 (1023088.000) diff=2655.861 pctdiff=0.259
SupraTentVolNotVent  1016210.861 (1013555.000) diff=2655.861 pctdiff=0.261
BrainSegVol  1150498.000 (1149006.000) diff=1492.000 pctdiff=0.130
BrainSegVolNotVent  1139009.000 (1140759.861) diff=-1750.861 pctdiff=-0.154
BrainSegVolNotVent  1139009.000
CerebellumVol 125240.000
VentChorVol    9533.000
3rd4th5thCSF   1956.000
CSFVol   477.000, OptChiasmVol   201.000
MaskVol 1526731.000
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
  0   3000                      wm-lh-unknown       0       0.000
  1   3001                     wm-lh-bankssts    3450    3450.128
  2   3002      wm-lh-caudalanteriorcingulate    3079    3079.494
  3   3003          wm-lh-caudalmiddlefrontal    5858    5858.020
  4   3004               wm-lh-corpuscallosum       0       0.000
  5   3005                       wm-lh-cuneus    2317    2316.710
  6   3006                   wm-lh-entorhinal     737     737.111
  7   3007                     wm-lh-fusiform    6795    6795.264
  8   3008             wm-lh-inferiorparietal    8042    8041.741
  9   3009             wm-lh-inferiortemporal    5693    5693.238
 10   3010             wm-lh-isthmuscingulate    3544    3544.322
 11   3011             wm-lh-lateraloccipital    9210    9210.244
 12   3012         wm-lh-lateralorbitofrontal    6234    6234.106
 13   3013                      wm-lh-lingual    5646    5646.042
 14   3014          wm-lh-medialorbitofrontal    2965    2965.262
 15   3015               wm-lh-middletemporal    4819    4819.383
 16   3016              wm-lh-parahippocampal    1324    1324.135
 17   3017                  wm-lh-paracentral    2937    2937.116
 18   3018              wm-lh-parsopercularis    3904    3903.856
 19   3019                wm-lh-parsorbitalis     887     887.268
 20   3020             wm-lh-parstriangularis    3079    3079.248
 21   3021                wm-lh-pericalcarine    3652    3652.237
 22   3022                  wm-lh-postcentral    7938    7937.846
 23   3023           wm-lh-posteriorcingulate    4597    4596.842
 24   3024                   wm-lh-precentral   11645   11645.031
 25   3025                    wm-lh-precuneus    8653    8652.616
 26   3026     wm-lh-rostralanteriorcingulate    3059    3058.752
 27   3027         wm-lh-rostralmiddlefrontal   12814   12814.424
 28   3028              wm-lh-superiorfrontal   17570   17569.916
 29   3029             wm-lh-superiorparietal    9900    9900.281
 30   3030             wm-lh-superiortemporal    8486    8486.334
 31   3031                wm-lh-supramarginal    8145    8145.244
 32   3032                  wm-lh-frontalpole     244     244.129
 33   3033                 wm-lh-temporalpole     612     612.238
 34   3034           wm-lh-transversetemporal     894     894.139
 35   3035                       wm-lh-insula    8582    8582.195
 36   3100                      wm-lh-Unknown       0       0.000
 37   3101              wm-lh-Corpus_callosum       0       0.000
 38   3102  wm-lh-G_and_S_Insula_ONLY_AVERAGE       0       0.000
 39   3103          wm-lh-G_cingulate-Isthmus       0       0.000
 40   3104        wm-lh-G_cingulate-Main_part       0       0.000
 41   3105                     wm-lh-G_cuneus       0       0.000
 42   3106  wm-lh-G_frontal_inf-Opercular_part       0       0.000
 43   3107   wm-lh-G_frontal_inf-Orbital_part       0       0.000
 44   3108  wm-lh-G_frontal_inf-Triangular_part       0       0.000
 45   3109             wm-lh-G_frontal_middle       0       0.000
 46   3110           wm-lh-G_frontal_superior       0       0.000
 47   3111             wm-lh-G_frontomarginal       0       0.000
 48   3112               wm-lh-G_insular_long       0       0.000
 49   3113              wm-lh-G_insular_short       0       0.000
 50   3114   wm-lh-G_and_S_occipital_inferior       0       0.000
 51   3115           wm-lh-G_occipital_middle       0       0.000
 52   3116         wm-lh-G_occipital_superior       0       0.000
 53   3117  wm-lh-G_occipit-temp_lat-Or_fusiform       0       0.000
 54   3118  wm-lh-G_occipit-temp_med-Lingual_part       0       0.000
 55   3119  wm-lh-G_occipit-temp_med-Parahippocampal_part       0       0.000
 56   3120                    wm-lh-G_orbital       0       0.000
 57   3121                wm-lh-G_paracentral       0       0.000
 58   3122  wm-lh-G_parietal_inferior-Angular_part       0       0.000
 59   3123  wm-lh-G_parietal_inferior-Supramarginal_part       0       0.000
 60   3124          wm-lh-G_parietal_superior       0       0.000
 61   3125                wm-lh-G_postcentral       0       0.000
 62   3126                 wm-lh-G_precentral       0       0.000
 63   3127                  wm-lh-G_precuneus       0       0.000
 64   3128                     wm-lh-G_rectus       0       0.000
 65   3129                wm-lh-G_subcallosal       0       0.000
 66   3130                 wm-lh-G_subcentral       0       0.000
 67   3131          wm-lh-G_temporal_inferior       0       0.000
 68   3132            wm-lh-G_temporal_middle       0       0.000
 69   3133  wm-lh-G_temp_sup-G_temp_transv_and_interm_S       0       0.000
 70   3134    wm-lh-G_temp_sup-Lateral_aspect       0       0.000
 71   3135     wm-lh-G_temp_sup-Planum_polare       0       0.000
 72   3136  wm-lh-G_temp_sup-Planum_tempolare       0       0.000
 73   3137  wm-lh-G_and_S_transverse_frontopolar       0       0.000
 74   3138  wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal       0       0.000
 75   3139  wm-lh-Lat_Fissure-ant_sgt-ramus_vertical       0       0.000
 76   3140         wm-lh-Lat_Fissure-post_sgt       0       0.000
 77   3141                  wm-lh-Medial_wall       0       0.000
 78   3142               wm-lh-Pole_occipital       0       0.000
 79   3143                wm-lh-Pole_temporal       0       0.000
 80   3144                  wm-lh-S_calcarine       0       0.000
 81   3145                    wm-lh-S_central       0       0.000
 82   3146             wm-lh-S_central_insula       0       0.000
 83   3147  wm-lh-S_cingulate-Main_part_and_Intracingulate       0       0.000
 84   3148  wm-lh-S_cingulate-Marginalis_part       0       0.000
 85   3149   wm-lh-S_circular_insula_anterior       0       0.000
 86   3150   wm-lh-S_circular_insula_inferior       0       0.000
 87   3151   wm-lh-S_circular_insula_superior       0       0.000
 88   3152  wm-lh-S_collateral_transverse_ant       0       0.000
 89   3153  wm-lh-S_collateral_transverse_post       0       0.000
 90   3154           wm-lh-S_frontal_inferior       0       0.000
 91   3155             wm-lh-S_frontal_middle       0       0.000
 92   3156           wm-lh-S_frontal_superior       0       0.000
 93   3157             wm-lh-S_frontomarginal       0       0.000
 94   3158  wm-lh-S_intermedius_primus-Jensen       0       0.000
 95   3159  wm-lh-S_intraparietal-and_Parietal_transverse       0       0.000
 96   3160         wm-lh-S_occipital_anterior       0       0.000
 97   3161  wm-lh-S_occipital_middle_and_Lunatus       0       0.000
 98   3162  wm-lh-S_occipital_superior_and_transversalis       0       0.000
 99   3163  wm-lh-S_occipito-temporal_lateral       0       0.000
100   3164  wm-lh-S_occipito-temporal_medial_and_S_Lingual       0       0.000
101   3165          wm-lh-S_orbital-H_shapped       0       0.000
102   3166            wm-lh-S_orbital_lateral       0       0.000
103   3167  wm-lh-S_orbital_medial-Or_olfactory       0       0.000
104   3168                wm-lh-S_paracentral       0       0.000
105   3169          wm-lh-S_parieto_occipital       0       0.000
106   3170               wm-lh-S_pericallosal       0       0.000
107   3171                wm-lh-S_postcentral       0       0.000
108   3172   wm-lh-S_precentral-Inferior-part       0       0.000
109   3173   wm-lh-S_precentral-Superior-part       0       0.000
110   3174             wm-lh-S_subcentral_ant       0       0.000
111   3175            wm-lh-S_subcentral_post       0       0.000
112   3176                 wm-lh-S_suborbital       0       0.000
113   3177                wm-lh-S_subparietal       0       0.000
114   3178             wm-lh-S_supracingulate       0       0.000
115   3179          wm-lh-S_temporal_inferior       0       0.000
116   3180          wm-lh-S_temporal_superior       0       0.000
117   3181        wm-lh-S_temporal_transverse       0       0.000
118   4000                      wm-rh-unknown       0       0.000
119   4001                     wm-rh-bankssts    3220    3219.576
120   4002      wm-rh-caudalanteriorcingulate    3311    3310.707
121   4003          wm-rh-caudalmiddlefrontal    4912    4912.257
122   4004               wm-rh-corpuscallosum       0       0.000
123   4005                       wm-rh-cuneus    2049    2048.841
124   4006                   wm-rh-entorhinal     470     469.973
125   4007                     wm-rh-fusiform    5955    5954.564
126   4008             wm-rh-inferiorparietal    9604    9604.001
127   4009             wm-rh-inferiortemporal    5882    5882.254
128   4010             wm-rh-isthmuscingulate    2583    2582.677
129   4011             wm-rh-lateraloccipital    9286    9286.469
130   4012         wm-rh-lateralorbitofrontal    6155    6154.931
131   4013                      wm-rh-lingual    5510    5509.599
132   4014          wm-rh-medialorbitofrontal    3455    3455.048
133   4015               wm-rh-middletemporal    6159    6158.569
134   4016              wm-rh-parahippocampal    1559    1558.510
135   4017                  wm-rh-paracentral    3884    3884.006
136   4018              wm-rh-parsopercularis    3478    3478.004
137   4019                wm-rh-parsorbitalis    1207    1207.092
138   4020             wm-rh-parstriangularis    3691    3690.768
139   4021                wm-rh-pericalcarine    3452    3452.041
140   4022                  wm-rh-postcentral    7737    7737.457
141   4023           wm-rh-posteriorcingulate    5053    5053.350
142   4024                   wm-rh-precentral   12575   12574.738
143   4025                    wm-rh-precuneus    9707    9706.634
144   4026     wm-rh-rostralanteriorcingulate    2264    2264.011
145   4027         wm-rh-rostralmiddlefrontal   12224   12223.950
146   4028              wm-rh-superiorfrontal   17833   17832.582
147   4029             wm-rh-superiorparietal    9683    9682.954
148   4030             wm-rh-superiortemporal    7574    7574.444
149   4031                wm-rh-supramarginal    7712    7712.035
150   4032                  wm-rh-frontalpole     276     275.609
151   4033                 wm-rh-temporalpole     623     622.763
152   4034           wm-rh-transversetemporal     632     632.412
153   4035                       wm-rh-insula    7648    7648.365
154   4100                      wm-rh-Unknown       0       0.000
155   4101              wm-rh-Corpus_callosum       0       0.000
156   4102  wm-rh-G_and_S_Insula_ONLY_AVERAGE       0       0.000
157   4103          wm-rh-G_cingulate-Isthmus       0       0.000
158   4104        wm-rh-G_cingulate-Main_part       0       0.000
159   4105                     wm-rh-G_cuneus       0       0.000
160   4106  wm-rh-G_frontal_inf-Opercular_part       0       0.000
161   4107   wm-rh-G_frontal_inf-Orbital_part       0       0.000
162   4108  wm-rh-G_frontal_inf-Triangular_part       0       0.000
163   4109             wm-rh-G_frontal_middle       0       0.000
164   4110           wm-rh-G_frontal_superior       0       0.000
165   4111             wm-rh-G_frontomarginal       0       0.000
166   4112               wm-rh-G_insular_long       0       0.000
167   4113              wm-rh-G_insular_short       0       0.000
168   4114   wm-rh-G_and_S_occipital_inferior       0       0.000
169   4115           wm-rh-G_occipital_middle       0       0.000
170   4116         wm-rh-G_occipital_superior       0       0.000
171   4117  wm-rh-G_occipit-temp_lat-Or_fusiform       0       0.000
172   4118  wm-rh-G_occipit-temp_med-Lingual_part       0       0.000
173   4119  wm-rh-G_occipit-temp_med-Parahippocampal_part       0       0.000
174   4120                    wm-rh-G_orbital       0       0.000
175   4121                wm-rh-G_paracentral       0       0.000
176   4122  wm-rh-G_parietal_inferior-Angular_part       0       0.000
177   4123  wm-rh-G_parietal_inferior-Supramarginal_part       0       0.000
178   4124          wm-rh-G_parietal_superior       0       0.000
179   4125                wm-rh-G_postcentral       0       0.000
180   4126                 wm-rh-G_precentral       0       0.000
181   4127                  wm-rh-G_precuneus       0       0.000
182   4128                     wm-rh-G_rectus       0       0.000
183   4129                wm-rh-G_subcallosal       0       0.000
184   4130                 wm-rh-G_subcentral       0       0.000
185   4131          wm-rh-G_temporal_inferior       0       0.000
186   4132            wm-rh-G_temporal_middle       0       0.000
187   4133  wm-rh-G_temp_sup-G_temp_transv_and_interm_S       0       0.000
188   4134    wm-rh-G_temp_sup-Lateral_aspect       0       0.000
189   4135     wm-rh-G_temp_sup-Planum_polare       0       0.000
190   4136  wm-rh-G_temp_sup-Planum_tempolare       0       0.000
191   4137  wm-rh-G_and_S_transverse_frontopolar       0       0.000
192   4138  wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal       0       0.000
193   4139  wm-rh-Lat_Fissure-ant_sgt-ramus_vertical       0       0.000
194   4140         wm-rh-Lat_Fissure-post_sgt       0       0.000
195   4141                  wm-rh-Medial_wall       0       0.000
196   4142               wm-rh-Pole_occipital       0       0.000
197   4143                wm-rh-Pole_temporal       0       0.000
198   4144                  wm-rh-S_calcarine       0       0.000
199   4145                    wm-rh-S_central       0       0.000
200   4146             wm-rh-S_central_insula       0       0.000
201   4147  wm-rh-S_cingulate-Main_part_and_Intracingulate       0       0.000
202   4148  wm-rh-S_cingulate-Marginalis_part       0       0.000
203   4149   wm-rh-S_circular_insula_anterior       0       0.000
204   4150   wm-rh-S_circular_insula_inferior       0       0.000
205   4151   wm-rh-S_circular_insula_superior       0       0.000
206   4152  wm-rh-S_collateral_transverse_ant       0       0.000
207   4153  wm-rh-S_collateral_transverse_post       0       0.000
208   4154           wm-rh-S_frontal_inferior       0       0.000
209   4155             wm-rh-S_frontal_middle       0       0.000
210   4156           wm-rh-S_frontal_superior       0       0.000
211   4157             wm-rh-S_frontomarginal       0       0.000
212   4158  wm-rh-S_intermedius_primus-Jensen       0       0.000
213   4159  wm-rh-S_intraparietal-and_Parietal_transverse       0       0.000
214   4160         wm-rh-S_occipital_anterior       0       0.000
215   4161  wm-rh-S_occipital_middle_and_Lunatus       0       0.000
216   4162  wm-rh-S_occipital_superior_and_transversalis       0       0.000
217   4163  wm-rh-S_occipito-temporal_lateral       0       0.000
218   4164  wm-rh-S_occipito-temporal_medial_and_S_Lingual       0       0.000
219   4165          wm-rh-S_orbital-H_shapped       0       0.000
220   4166            wm-rh-S_orbital_lateral       0       0.000
221   4167  wm-rh-S_orbital_medial-Or_olfactory       0       0.000
222   4168                wm-rh-S_paracentral       0       0.000
223   4169          wm-rh-S_parieto_occipital       0       0.000
224   4170               wm-rh-S_pericallosal       0       0.000
225   4171                wm-rh-S_postcentral       0       0.000
226   4172   wm-rh-S_precentral-Inferior-part       0       0.000
227   4173   wm-rh-S_precentral-Superior-part       0       0.000
228   4174             wm-rh-S_subcentral_ant       0       0.000
229   4175            wm-rh-S_subcentral_post       0       0.000
230   4176                 wm-rh-S_suborbital       0       0.000
231   4177                wm-rh-S_subparietal       0       0.000
232   4178             wm-rh-S_supracingulate       0       0.000
233   4179          wm-rh-S_temporal_inferior       0       0.000
234   4180          wm-rh-S_temporal_superior       0       0.000
235   4181        wm-rh-S_temporal_transverse       0       0.000
236   5001        Left-UnsegmentedWhiteMatter   24132   24131.932
237   5002       Right-UnsegmentedWhiteMatter   24033   24033.498
238   13100                      wm_lh_Unknown       0       0.000
239   13101         wm_lh_G_and_S_frontomargin       0       0.000
240   13102        wm_lh_G_and_S_occipital_inf       0       0.000
241   13103          wm_lh_G_and_S_paracentral       0       0.000
242   13104           wm_lh_G_and_S_subcentral       0       0.000
243   13105     wm_lh_G_and_S_transv_frontopol       0       0.000
244   13106           wm_lh_G_and_S_cingul-Ant       0       0.000
245   13107       wm_lh_G_and_S_cingul-Mid-Ant       0       0.000
246   13108      wm_lh_G_and_S_cingul-Mid-Post       0       0.000
247   13109         wm_lh_G_cingul-Post-dorsal       0       0.000
248   13110        wm_lh_G_cingul-Post-ventral       0       0.000
249   13111                     wm_lh_G_cuneus       0       0.000
250   13112        wm_lh_G_front_inf-Opercular       0       0.000
251   13113          wm_lh_G_front_inf-Orbital       0       0.000
252   13114         wm_lh_G_front_inf-Triangul       0       0.000
253   13115               wm_lh_G_front_middle       0       0.000
254   13116                  wm_lh_G_front_sup       0       0.000
255   13117      wm_lh_G_Ins_lg_and_S_cent_ins       0       0.000
256   13118              wm_lh_G_insular_short       0       0.000
257   13119           wm_lh_G_occipital_middle       0       0.000
258   13120              wm_lh_G_occipital_sup       0       0.000
259   13121        wm_lh_G_oc-temp_lat-fusifor       0       0.000
260   13122        wm_lh_G_oc-temp_med-Lingual       0       0.000
261   13123        wm_lh_G_oc-temp_med-Parahip       0       0.000
262   13124                    wm_lh_G_orbital       0       0.000
263   13125         wm_lh_G_pariet_inf-Angular       0       0.000
264   13126        wm_lh_G_pariet_inf-Supramar       0       0.000
265   13127               wm_lh_G_parietal_sup       0       0.000
266   13128                wm_lh_G_postcentral       0       0.000
267   13129                 wm_lh_G_precentral       0       0.000
268   13130                  wm_lh_G_precuneus       0       0.000
269   13131                     wm_lh_G_rectus       0       0.000
270   13132                wm_lh_G_subcallosal       0       0.000
271   13133        wm_lh_G_temp_sup-G_T_transv       0       0.000
272   13134           wm_lh_G_temp_sup-Lateral       0       0.000
273   13135        wm_lh_G_temp_sup-Plan_polar       0       0.000
274   13136        wm_lh_G_temp_sup-Plan_tempo       0       0.000
275   13137               wm_lh_G_temporal_inf       0       0.000
276   13138            wm_lh_G_temporal_middle       0       0.000
277   13139         wm_lh_Lat_Fis-ant-Horizont       0       0.000
278   13140         wm_lh_Lat_Fis-ant-Vertical       0       0.000
279   13141                 wm_lh_Lat_Fis-post       0       0.000
280   13142                  wm_lh_Medial_wall       0       0.000
281   13143               wm_lh_Pole_occipital       0       0.000
282   13144                wm_lh_Pole_temporal       0       0.000
283   13145                  wm_lh_S_calcarine       0       0.000
284   13146                    wm_lh_S_central       0       0.000
285   13147          wm_lh_S_cingul-Marginalis       0       0.000
286   13148        wm_lh_S_circular_insula_ant       0       0.000
287   13149        wm_lh_S_circular_insula_inf       0       0.000
288   13150        wm_lh_S_circular_insula_sup       0       0.000
289   13151          wm_lh_S_collat_transv_ant       0       0.000
290   13152         wm_lh_S_collat_transv_post       0       0.000
291   13153                  wm_lh_S_front_inf       0       0.000
292   13154               wm_lh_S_front_middle       0       0.000
293   13155                  wm_lh_S_front_sup       0       0.000
294   13156         wm_lh_S_interm_prim-Jensen       0       0.000
295   13157    wm_lh_S_intrapariet_and_P_trans       0       0.000
296   13158      wm_lh_S_oc_middle_and_Lunatus       0       0.000
297   13159     wm_lh_S_oc_sup_and_transversal       0       0.000
298   13160              wm_lh_S_occipital_ant       0       0.000
299   13161                wm_lh_S_oc-temp_lat       0       0.000
300   13162    wm_lh_S_oc-temp_med_and_Lingual       0       0.000
301   13163            wm_lh_S_orbital_lateral       0       0.000
302   13164         wm_lh_S_orbital_med-olfact       0       0.000
303   13165           wm_lh_S_orbital-H_Shaped       0       0.000
304   13166          wm_lh_S_parieto_occipital       0       0.000
305   13167               wm_lh_S_pericallosal       0       0.000
306   13168                wm_lh_S_postcentral       0       0.000
307   13169        wm_lh_S_precentral-inf-part       0       0.000
308   13170        wm_lh_S_precentral-sup-part       0       0.000
309   13171                 wm_lh_S_suborbital       0       0.000
310   13172                wm_lh_S_subparietal       0       0.000
311   13173               wm_lh_S_temporal_inf       0       0.000
312   13174               wm_lh_S_temporal_sup       0       0.000
313   13175        wm_lh_S_temporal_transverse       0       0.000
314   14100                      wm_rh_Unknown       0       0.000
315   14101         wm_rh_G_and_S_frontomargin       0       0.000
316   14102        wm_rh_G_and_S_occipital_inf       0       0.000
317   14103          wm_rh_G_and_S_paracentral       0       0.000
318   14104           wm_rh_G_and_S_subcentral       0       0.000
319   14105     wm_rh_G_and_S_transv_frontopol       0       0.000
320   14106           wm_rh_G_and_S_cingul-Ant       0       0.000
321   14107       wm_rh_G_and_S_cingul-Mid-Ant       0       0.000
322   14108      wm_rh_G_and_S_cingul-Mid-Post       0       0.000
323   14109         wm_rh_G_cingul-Post-dorsal       0       0.000
324   14110        wm_rh_G_cingul-Post-ventral       0       0.000
325   14111                     wm_rh_G_cuneus       0       0.000
326   14112        wm_rh_G_front_inf-Opercular       0       0.000
327   14113          wm_rh_G_front_inf-Orbital       0       0.000
328   14114         wm_rh_G_front_inf-Triangul       0       0.000
329   14115               wm_rh_G_front_middle       0       0.000
330   14116                  wm_rh_G_front_sup       0       0.000
331   14117      wm_rh_G_Ins_lg_and_S_cent_ins       0       0.000
332   14118              wm_rh_G_insular_short       0       0.000
333   14119           wm_rh_G_occipital_middle       0       0.000
334   14120              wm_rh_G_occipital_sup       0       0.000
335   14121        wm_rh_G_oc-temp_lat-fusifor       0       0.000
336   14122        wm_rh_G_oc-temp_med-Lingual       0       0.000
337   14123        wm_rh_G_oc-temp_med-Parahip       0       0.000
338   14124                    wm_rh_G_orbital       0       0.000
339   14125         wm_rh_G_pariet_inf-Angular       0       0.000
340   14126        wm_rh_G_pariet_inf-Supramar       0       0.000
341   14127               wm_rh_G_parietal_sup       0       0.000
342   14128                wm_rh_G_postcentral       0       0.000
343   14129                 wm_rh_G_precentral       0       0.000
344   14130                  wm_rh_G_precuneus       0       0.000
345   14131                     wm_rh_G_rectus       0       0.000
346   14132                wm_rh_G_subcallosal       0       0.000
347   14133        wm_rh_G_temp_sup-G_T_transv       0       0.000
348   14134           wm_rh_G_temp_sup-Lateral       0       0.000
349   14135        wm_rh_G_temp_sup-Plan_polar       0       0.000
350   14136        wm_rh_G_temp_sup-Plan_tempo       0       0.000
351   14137               wm_rh_G_temporal_inf       0       0.000
352   14138            wm_rh_G_temporal_middle       0       0.000
353   14139         wm_rh_Lat_Fis-ant-Horizont       0       0.000
354   14140         wm_rh_Lat_Fis-ant-Vertical       0       0.000
355   14141                 wm_rh_Lat_Fis-post       0       0.000
356   14142                  wm_rh_Medial_wall       0       0.000
357   14143               wm_rh_Pole_occipital       0       0.000
358   14144                wm_rh_Pole_temporal       0       0.000
359   14145                  wm_rh_S_calcarine       0       0.000
360   14146                    wm_rh_S_central       0       0.000
361   14147          wm_rh_S_cingul-Marginalis       0       0.000
362   14148        wm_rh_S_circular_insula_ant       0       0.000
363   14149        wm_rh_S_circular_insula_inf       0       0.000
364   14150        wm_rh_S_circular_insula_sup       0       0.000
365   14151          wm_rh_S_collat_transv_ant       0       0.000
366   14152         wm_rh_S_collat_transv_post       0       0.000
367   14153                  wm_rh_S_front_inf       0       0.000
368   14154               wm_rh_S_front_middle       0       0.000
369   14155                  wm_rh_S_front_sup       0       0.000
370   14156         wm_rh_S_interm_prim-Jensen       0       0.000
371   14157    wm_rh_S_intrapariet_and_P_trans       0       0.000
372   14158      wm_rh_S_oc_middle_and_Lunatus       0       0.000
373   14159     wm_rh_S_oc_sup_and_transversal       0       0.000
374   14160              wm_rh_S_occipital_ant       0       0.000
375   14161                wm_rh_S_oc-temp_lat       0       0.000
376   14162    wm_rh_S_oc-temp_med_and_Lingual       0       0.000
377   14163            wm_rh_S_orbital_lateral       0       0.000
378   14164         wm_rh_S_orbital_med-olfact       0       0.000
379   14165           wm_rh_S_orbital-H_Shaped       0       0.000
380   14166          wm_rh_S_parieto_occipital       0       0.000
381   14167               wm_rh_S_pericallosal       0       0.000
382   14168                wm_rh_S_postcentral       0       0.000
383   14169        wm_rh_S_precentral-inf-part       0       0.000
384   14170        wm_rh_S_precentral-sup-part       0       0.000
385   14171                 wm_rh_S_suborbital       0       0.000
386   14172                wm_rh_S_subparietal       0       0.000
387   14173               wm_rh_S_temporal_inf       0       0.000
388   14174               wm_rh_S_temporal_sup       0       0.000
389   14175        wm_rh_S_temporal_transverse       0       0.000

Reporting on  70 segmentations
mri_segstats done
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label
#--------------------------------------------
#@# BA Labels lh Thu Aug  8 23:56:39 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub005 --trglabel ./lh.BA1.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA1.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 365
Checking for and removing duplicates
Writing label file ./lh.BA1.label 4494
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub005 --trglabel ./lh.BA2.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA2.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 907
Checking for and removing duplicates
Writing label file ./lh.BA2.label 8816
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub005 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA3a.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4077 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 198
Checking for and removing duplicates
Writing label file ./lh.BA3a.label 4275
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub005 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA3b.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5983 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 428
Checking for and removing duplicates
Writing label file ./lh.BA3b.label 6411
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub005 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA4a.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5784 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 261
Checking for and removing duplicates
Writing label file ./lh.BA4a.label 6045
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub005 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA4p.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4070 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 239
Checking for and removing duplicates
Writing label file ./lh.BA4p.label 4309
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub005 --trglabel ./lh.BA6.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA6.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 13589 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 1562
Checking for and removing duplicates
Writing label file ./lh.BA6.label 15151
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub005 --trglabel ./lh.BA44.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA44.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4181 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 621
Checking for and removing duplicates
Writing label file ./lh.BA44.label 4802
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub005 --trglabel ./lh.BA45.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA45.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 994
Checking for and removing duplicates
Writing label file ./lh.BA45.label 4416
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub005 --trglabel ./lh.V1.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.V1.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 2066
Checking for and removing duplicates
Writing label file ./lh.V1.label 6707
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub005 --trglabel ./lh.V2.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.V2.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 4214
Checking for and removing duplicates
Writing label file ./lh.V2.label 12328
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub005 --trglabel ./lh.MT.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.MT.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 844
Checking for and removing duplicates
Writing label file ./lh.MT.label 2862
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub005 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.perirhinal.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1199 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 171
Checking for and removing duplicates
Writing label file ./lh.perirhinal.label 1370
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub005 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA1.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1014 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 53
Checking for and removing duplicates
Writing label file ./lh.BA1.thresh.label 1067
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub005 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA2.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2092 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 421
Checking for and removing duplicates
Writing label file ./lh.BA2.thresh.label 2513
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub005 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA3a.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1504 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 35
Checking for and removing duplicates
Writing label file ./lh.BA3a.thresh.label 1539
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub005 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA3b.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1996 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 160
Checking for and removing duplicates
Writing label file ./lh.BA3b.thresh.label 2156
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub005 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA4a.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2319 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 108
Checking for and removing duplicates
Writing label file ./lh.BA4a.thresh.label 2427
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub005 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA4p.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1549 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 119
Checking for and removing duplicates
Writing label file ./lh.BA4p.thresh.label 1668
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub005 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA6.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 7035 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 682
Checking for and removing duplicates
Writing label file ./lh.BA6.thresh.label 7717
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub005 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA44.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1912 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 285
Checking for and removing duplicates
Writing label file ./lh.BA44.thresh.label 2197
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub005 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.BA45.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1151 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 531
Checking for and removing duplicates
Writing label file ./lh.BA45.thresh.label 1682
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub005 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.V1.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3405 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 1544
Checking for and removing duplicates
Writing label file ./lh.V1.thresh.label 4949
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub005 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.V2.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3334 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 1787
Checking for and removing duplicates
Writing label file ./lh.V2.thresh.label 5121
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub005 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./lh.MT.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 513 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 141918
Number of reverse mapping hits = 248
Checking for and removing duplicates
Writing label file ./lh.MT.thresh.label 761
mri_label2label: Done


 mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose 

Reading ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt
Number of ctab entries 14

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label
cmdline mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule

subject sub005
hemi    lh
SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA
nlables 13
LabelThresh 0 0.000000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig
 1 1530880 BA1
 2 16749699 BA2
 3 16711680 BA3a
 4 3368703 BA3b
 5 1376196 BA4a
 6 13382655 BA4p
 7 10036737 BA6
 8 2490521 BA44
 9 39283 BA45
10 3993 V1
11 8508928 V2
12 10027163 MT
13 16422433 perirhinal
Mapping unhit to unknown
Found 95912 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.BA.annot

 mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 

Reading ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt
Number of ctab entries 14

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label
cmdline mris_label2annot --s sub005 --hemi lh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule

subject sub005
hemi    lh
SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA.thresh
nlables 12
LabelThresh 0 0.000000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.orig
 1 1530880 BA1
 2 16749699 BA2
 3 16711680 BA3a
 4 3368703 BA3b
 5 1376196 BA4a
 6 13382655 BA4p
 7 10036737 BA6
 8 2490521 BA44
 9 39283 BA45
10 3993 V1
11 8508928 V2
12 10027163 MT
Mapping unhit to unknown
Found 115470 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/lh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub005 lh white 

computing statistics for each annotation in ./lh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3.0/average/colortable_BA.txt)
Saving annotation colortable ./BA.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

 1026    622   2411  2.723 0.400     0.177     0.069       27     2.7  BA1
 4750   3166   8222  2.418 0.459     0.134     0.044       64     8.5  BA2
  981    660   1032  2.009 0.416     0.131     0.073       10     1.6  BA3a
 2545   1704   4262  2.134 0.609     0.142     0.056       55     5.5  BA3b
 1426    887   3348  2.907 0.563     0.122     0.057       23     3.4  BA4a
 1346    911   2520  2.663 0.446     0.118     0.074       23     5.7  BA4p
10036   6823  23603  2.795 0.545     0.135     0.043      150    18.1  BA6
 2472   1671   5347  2.737 0.459     0.148     0.050       44     4.8  BA44
 3412   2305   6933  2.529 0.607     0.155     0.063       69     8.4  BA45
 4350   3000   6105  1.972 0.520     0.166     0.079       87    12.6  V1
 9950   6520  15611  2.236 0.515     0.173     0.084      254    31.5  V2
 2611   1725   4760  2.450 0.433     0.156     0.064       59     6.7  MT
 1101    746   3309  3.365 0.725     0.175     0.102       29     4.1  perirhinal

 mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub005 lh white 

computing statistics for each annotation in ./lh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3.0/average/colortable_BA.txt)
Saving annotation colortable ./BA.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

  630    380   1469  2.704 0.443     0.183     0.077       17     1.7  BA1
 2031   1338   3733  2.372 0.437     0.144     0.055       35     4.4  BA2
  815    554    815  1.971 0.412     0.139     0.040        7     1.3  BA3a
 1591   1079   2219  1.844 0.441     0.121     0.033       16     2.3  BA3b
 1353    861   3359  2.992 0.504     0.119     0.057       21     3.3  BA4a
 1134    759   1989  2.619 0.429     0.110     0.030        8     1.4  BA4p
 5447   3689  12997  2.825 0.542     0.137     0.043       78     9.9  BA6
 1718   1154   3620  2.670 0.455     0.142     0.044       27     3.1  BA44
 1585   1060   3854  2.844 0.441     0.182     0.085       45     5.4  BA45
 4634   3169   6415  1.960 0.513     0.166     0.079       92    13.8  V1
 4772   3149   7474  2.177 0.540     0.187     0.100      143    17.3  V2
  738    500   1210  2.380 0.431     0.136     0.041        8     1.2  MT
#--------------------------------------------
#@# BA Labels rh Fri Aug  9 00:01:11 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub005 --trglabel ./rh.BA1.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA1.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 464
Checking for and removing duplicates
Writing label file ./rh.BA1.label 4426
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub005 --trglabel ./rh.BA2.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA2.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 750
Checking for and removing duplicates
Writing label file ./rh.BA2.label 7437
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub005 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA3a.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3980 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 223
Checking for and removing duplicates
Writing label file ./rh.BA3a.label 4203
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub005 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA3b.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4522 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 370
Checking for and removing duplicates
Writing label file ./rh.BA3b.label 4892
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub005 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA4a.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5747 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 244
Checking for and removing duplicates
Writing label file ./rh.BA4a.label 5991
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub005 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA4p.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4473 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 184
Checking for and removing duplicates
Writing label file ./rh.BA4p.label 4657
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub005 --trglabel ./rh.BA6.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA6.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 12256 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 1182
Checking for and removing duplicates
Writing label file ./rh.BA6.label 13438
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub005 --trglabel ./rh.BA44.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA44.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6912 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 1300
Checking for and removing duplicates
Writing label file ./rh.BA44.label 8212
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub005 --trglabel ./rh.BA45.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA45.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5355 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 1267
Checking for and removing duplicates
Writing label file ./rh.BA45.label 6622
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub005 --trglabel ./rh.V1.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.V1.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 2180
Checking for and removing duplicates
Writing label file ./rh.V1.label 6907
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub005 --trglabel ./rh.V2.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.V2.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 4090
Checking for and removing duplicates
Writing label file ./rh.V2.label 12106
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub005 --trglabel ./rh.MT.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.MT.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 678
Checking for and removing duplicates
Writing label file ./rh.MT.label 2610
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub005 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.perirhinal.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 752 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 67
Checking for and removing duplicates
Writing label file ./rh.perirhinal.label 819
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub005 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA1.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 876 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./rh.BA1.thresh.label 961
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub005 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA2.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2688 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 400
Checking for and removing duplicates
Writing label file ./rh.BA2.thresh.label 3088
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub005 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA3a.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1698 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 51
Checking for and removing duplicates
Writing label file ./rh.BA3a.thresh.label 1749
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub005 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA3b.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2183 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 253
Checking for and removing duplicates
Writing label file ./rh.BA3b.thresh.label 2436
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub005 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA4a.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1388 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 52
Checking for and removing duplicates
Writing label file ./rh.BA4a.thresh.label 1440
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub005 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA4p.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1489 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 84
Checking for and removing duplicates
Writing label file ./rh.BA4p.thresh.label 1573
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub005 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA6.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6959 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 634
Checking for and removing duplicates
Writing label file ./rh.BA6.thresh.label 7593
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub005 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA44.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1012 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 294
Checking for and removing duplicates
Writing label file ./rh.BA44.thresh.label 1306
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub005 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.BA45.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1178 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 210
Checking for and removing duplicates
Writing label file ./rh.BA45.thresh.label 1388
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub005 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.V1.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3232 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 1478
Checking for and removing duplicates
Writing label file ./rh.V1.thresh.label 4710
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub005 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.V2.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3437 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 1846
Checking for and removing duplicates
Writing label file ./rh.V2.thresh.label 5283
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub005 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label
srcsubject = fsaverage
trgsubject = sub005
trglabel = ./rh.MT.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    /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 268 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/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 142731
Number of reverse mapping hits = 104
Checking for and removing duplicates
Writing label file ./rh.MT.thresh.label 372
mri_label2label: Done


 mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose 

Reading ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt
Number of ctab entries 14

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label
cmdline mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule

subject sub005
hemi    rh
SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA
nlables 13
LabelThresh 0 0.000000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig
 1 1530880 BA1
 2 16749699 BA2
 3 16711680 BA3a
 4 3368703 BA3b
 5 1376196 BA4a
 6 13382655 BA4p
 7 10036737 BA6
 8 2490521 BA44
 9 39283 BA45
10 3993 V1
11 8508928 V2
12 10027163 MT
13 16422433 perirhinal
Mapping unhit to unknown
Found 97144 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.BA.annot

 mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 

Reading ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt
Number of ctab entries 14

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label
cmdline mris_label2annot --s sub005 --hemi rh --ctab /opt/freesurfer/5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule

subject sub005
hemi    rh
SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA.thresh
nlables 12
LabelThresh 0 0.000000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.orig
 1 1530880 BA1
 2 16749699 BA2
 3 16711680 BA3a
 4 3368703 BA3b
 5 1376196 BA4a
 6 13382655 BA4p
 7 10036737 BA6
 8 2490521 BA44
 9 39283 BA45
10 3993 V1
11 8508928 V2
12 10027163 MT
Mapping unhit to unknown
Found 117875 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label/rh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub005 rh white 

computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3.0/average/colortable_BA.txt)
Saving annotation colortable ./BA.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

  975    595   2203  2.639 0.530     0.171     0.065       25     2.4  BA1
 3840   2574   6869  2.407 0.495     0.136     0.047       59     7.9  BA2
 1071    723   1151  1.991 0.455     0.139     0.040       11     2.0  BA3a
 2158   1451   3589  2.086 0.615     0.137     0.043       32     3.8  BA3b
 1379    886   3306  2.871 0.451     0.115     0.035       12     2.1  BA4a
 1210    820   2193  2.588 0.464     0.111     0.033       10     1.6  BA4p
 8459   5637  20058  2.858 0.530     0.138     0.045      124    16.2  BA6
 4455   3008   8970  2.721 0.412     0.147     0.049       78     9.3  BA44
 4707   3204  10460  2.699 0.493     0.171     0.081      127    13.1  BA45
 4620   3252   6567  1.959 0.449     0.171     0.075      105    13.7  V1
 9723   6398  14910  2.208 0.498     0.173     0.075      268    27.2  V2
 2416   1636   4124  2.457 0.483     0.137     0.043       34     4.3  MT
  574    404   1552  3.250 0.612     0.181     0.076       11     1.9  perirhinal

 mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub005 rh white 

computing statistics for each annotation in ./rh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3.0/average/colortable_BA.txt)
Saving annotation colortable ./BA.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

  657    378   1476  2.700 0.521     0.167     0.062       17     1.6  BA1
 2341   1576   4341  2.410 0.509     0.137     0.045       36     4.0  BA2
  896    602    889  1.983 0.436     0.140     0.040        8     1.5  BA3a
 1801   1240   2555  1.856 0.456     0.123     0.035       19     2.8  BA3b
  787    493   1834  2.889 0.432     0.120     0.039        9     1.3  BA4a
 1029    701   1835  2.580 0.468     0.110     0.032        8     1.4  BA4p
 5314   3504  12341  2.823 0.558     0.133     0.043       74     9.7  BA6
 1147    777   2509  2.793 0.368     0.152     0.056       23     2.7  BA44
 1152    784   3010  2.942 0.412     0.186     0.119       42     3.4  BA45
 4420   3110   6220  1.954 0.446     0.166     0.073       96    12.7  V1
 4971   3333   7490  2.104 0.529     0.188     0.093      178    15.6  V2
  341    227    697  2.638 0.407     0.158     0.064        8     0.9  MT
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label lh Fri Aug  9 00:05:43 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub005 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

painting output onto subject sub005.
processing subject lh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.sphere.reg...
eroding label 1 times before writing
thresholding label stat at 0.400 before writing
only 1 subject - copying statistics...
writing label with 1036 points to lh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub005 lh white 

limiting computations to label ./lh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/lh.white...
INFO: assuming MGZ format for volumes.

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

  348    238   1115  3.022 0.738     0.148     0.061        6     1.1  ./lh.entorhinal_exvivo.label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label rh Fri Aug  9 00:05:58 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub005 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 

painting output onto subject sub005.
processing subject rh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.sphere.reg...
eroding label 1 times before writing
thresholding label stat at 0.400 before writing
only 1 subject - copying statistics...
writing label with 680 points to rh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub005 rh white 

limiting computations to label ./rh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub005/surf/rh.white...
INFO: assuming MGZ format for volumes.

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

  186    126    548  2.946 0.441     0.175     0.047        4     0.4  ./rh.entorhinal_exvivo.label

#------------------------------------------

Started at Thu Aug 8 10:53:42 CEST 2013 
Ended   at Fri Aug 9 00:06:13 CEST 2013
#@#%# recon-all-run-time-hours 13.209
recon-all -s sub005 finished without error at Fri Aug  9 00:06:14 CEST 2013