cortical-surfaces-freesurfer/sub-13/scripts/recon-all.log

Thu Aug  8 10:53:42 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013
/opt/freesurfer/5.3.0/bin/recon-all
-i /home/data/exppsy/forrest_gump/openfmri.org/sub013/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub013/anatomy/other/t2w001.nii.gz -T2pial -subjid sub013 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subjid sub013
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/sub013

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub013/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/001.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub013/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/anatomy/highres001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996032, 0.0582575, 0.0672728)
j_ras = (0.0588709, 0.99824, 0.00717099)
k_ras = (0.0667366, -0.011103, 0.997709)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Thu Aug  8 10:54:03 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub013/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub013/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/anatomy/other/t2w001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996032, 0.0582575, 0.0672728)
j_ras = (0.0588709, 0.99824, 0.00717099)
k_ras = (0.0667366, -0.011103, 0.997709)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Thu Aug  8 10:54:16 CEST 2013
Found 1 runs
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/rawavg.mgz 

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig.mgz --conform --cw256 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996032, 0.0582575, 0.0672728)
j_ras = (0.0588709, 0.99824, 0.00717099)
k_ras = (0.0667366, -0.011103, 0.997709)
Original Data has (0.69989, 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/sub013/mri/orig.mgz...

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Aug  8 10:54:55 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 10:57:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7219, pval=0.4932 >= threshold=0.0050)

 awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/talairach_avi.log 


 tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/talairach_avi.log 

TalAviQA: 0.96707
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Thu Aug  8 10:57:24 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/sub013/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 10:57:25 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.18951
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18951/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18951/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, -5.12227e-09, -7.45058e-09)
j_ras = (-7.45058e-09, -9.31323e-10, -1)
k_ras = (-5.99539e-09, 1, -9.31323e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.18951/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Thu Aug  8 10:57:29 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.18951/nu0.mnc ./tmp.mri_nu_correct.mni.18951/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18951/0/
[fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/] [2013-08-08 10:57:29] 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.18951/0/ ./tmp.mri_nu_correct.mni.18951/nu0.mnc ./tmp.mri_nu_correct.mni.18951/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 24 
CV of field change: 0.000997041
[fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/] [2013-08-08 10:57:51] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.18951/nu0.mnc ./tmp.mri_nu_correct.mni.18951/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Thu Aug  8 10:57:58 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.18951/nu1.mnc ./tmp.mri_nu_correct.mni.18951/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.18951/1/
[fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/] [2013-08-08 10:57:58] 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.18951/1/ ./tmp.mri_nu_correct.mni.18951/nu1.mnc ./tmp.mri_nu_correct.mni.18951/nu2.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 23 
CV of field change: 0.000997273
[fkaule@snake4:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/] [2013-08-08 10:58:20] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.18951/nu1.mnc ./tmp.mri_nu_correct.mni.18951/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.18951/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18951/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/sub013/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.18951/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18951/ones.mgz 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule

input      ./tmp.mri_nu_correct.mni.18951/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.18951/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.18951/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18951/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18951/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.18951/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18951/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18951/input.mean.dat 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.18951/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.18951/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18951/ones.mgz --i ./tmp.mri_nu_correct.mni.18951/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18951/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18951/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.18951/ones.mgz --i ./tmp.mri_nu_correct.mni.18951/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18951/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18951/output.mean.dat 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.18951/ones.mgz
Loading ./tmp.mri_nu_correct.mni.18951/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.18951/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.18951/nu2.mnc ./tmp.mri_nu_correct.mni.18951/nu2.mnc mul .94657458363940703989
Saving result to './tmp.mri_nu_correct.mni.18951/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.18951/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.18951/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.18951/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -5.12227e-09, -7.45058e-09)
j_ras = (-7.45058e-09, -9.31323e-10, -1)
k_ras = (-5.99539e-09, 1, -9.31323e-10)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping (10, 201) to ( 3, 110)
 
 
Thu Aug  8 10:59:09 CEST 2013
mri_nu_correct.mni done

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Aug  8 10:59:10 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri

 mri_normalize -g 1 nu.mgz T1.mgz 

using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
 1.173  -0.063  -0.054   5.056;
 0.086   1.208   0.219  -35.495;
 0.061  -0.342   1.314  -11.004;
 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 = 16
Starting OpenSpline(): npoints = 16
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 54 (54), valley at 43 (43)
csf peak at 10, setting threshold to 39
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 57 (57), valley at 39 (39)
csf peak at 10, setting threshold to 41
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 44 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Aug  8 11:01:55 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = (57, 28, 28) --> (197, 255, 197)
using (104, 104, 113) as brain centroid...
mean wm in atlas = 126, using box (87,76,92) --> (121, 132,133) to find MRI wm
before smoothing, mri peak at 109
after smoothing, mri peak at 109, scaling input intensities by 1.156
scaling channel 0 by 1.15596
initial log_p = -4.9
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.700170 @ (-9.091, 9.091, -9.091)
max log p =    -4.611142 @ (13.636, 4.545, -4.545)
max log p =    -4.553312 @ (-2.273, 2.273, 2.273)
max log p =    -4.531579 @ (-1.136, -1.136, -1.136)
max log p =    -4.495128 @ (0.568, -0.568, 1.705)
max log p =    -4.495128 @ (0.000, 0.000, 0.000)
Found translation: (1.7, 14.2, -10.8): log p = -4.495
****************************************
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)
 1.150   0.000   0.000  -16.904;
 0.000   1.226   0.161  -21.274;
 0.000  -0.150   1.140  -11.124;
 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)
 1.150   0.000   0.000  -16.904;
 0.000   1.410   0.186  -42.631;
 0.000  -0.150   1.140  -11.124;
 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)
 1.150   0.000   0.000  -16.904;
 0.000   1.410   0.186  -42.631;
 0.000  -0.150   1.140  -11.124;
 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)
 1.083  -0.058   0.063  -11.793;
 0.038   1.325   0.213  -42.018;
-0.072  -0.188   1.089   9.557;
 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)
 1.083  -0.058   0.063  -11.793;
 0.035   1.293   0.243  -41.972;
-0.075  -0.236   1.101   13.238;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.083  -0.058   0.063  -11.793;
 0.035   1.293   0.243  -41.972;
-0.075  -0.236   1.101   13.238;
 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=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.080  -0.083   0.077  -10.981;
 0.053   1.292   0.235  -42.783;
-0.093  -0.224   1.104   13.574;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-3.9)
 1.080  -0.083   0.077  -10.981;
 0.053   1.292   0.235  -42.783;
-0.093  -0.224   1.104   13.574;
 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
 1.07976  -0.08311   0.07690  -10.98143;
 0.05300   1.29232   0.23521  -42.78325;
-0.09256  -0.22418   1.10352   13.57435;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.07976  -0.08311   0.07690  -10.98143;
 0.05300   1.29232   0.23521  -42.78325;
-0.09256  -0.22418   1.10352   13.57435;
 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: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.080  -0.083   0.077  -10.981;
 0.053   1.292   0.235  -42.783;
-0.093  -0.224   1.104   13.574;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.9)
transform before final EM align:
 1.080  -0.083   0.077  -10.981;
 0.053   1.292   0.235  -42.783;
-0.093  -0.224   1.104   13.574;
 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
 1.07976  -0.08311   0.07690  -10.98143;
 0.05300   1.29232   0.23521  -42.78325;
-0.09256  -0.22418   1.10352   13.57435;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.07976  -0.08311   0.07690  -10.98143;
 0.05300   1.29232   0.23521  -42.78325;
-0.09256  -0.22418   1.10352   13.57435;
 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: 012: -log(p) =    4.4  tol 0.000000
final transform:
 1.080  -0.083   0.077  -10.981;
 0.053   1.292   0.235  -42.783;
-0.093  -0.224   1.104   13.574;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 38 minutes and 17 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=125 y=91 z=118 r=85
      first estimation of the main basin volume: 2659744 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        15 found in the rest of the brain 
      global maximum in x=149, y=86, z=83, 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=19118441908 voxels, voxel volume =1.000 
                     = 19118441908 mmm3 = 19118442.496 cm3
done.
PostAnalyze...Basin Prior
 91 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=126,y=98, z=114, r=9455 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 45278
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = -1037840793
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 1084047588
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = -1071531287
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=7 , nb = 1071802688
    OTHER      CSF_MIN=0, CSF_intensity=8, CSF_MAX=26 , nb = 1075967062
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    7,      10,        29,   57
  after  analyzing :    7,      22,        29,   30
   RIGHT_CER   
  before analyzing :    14,      14,        16,   60
  after  analyzing :    14,      21,        25,   30
   LEFT_CER    
  before analyzing :    12,      14,        25,   59
  after  analyzing :    12,      21,        25,   30
  RIGHT_BRAIN  
  before analyzing :    7,      10,        28,   56
  after  analyzing :    7,      22,        28,   30
  LEFT_BRAIN   
  before analyzing :    7,      10,        28,   57
  after  analyzing :    7,      22,        28,   30
     OTHER     
  before analyzing :    26,      52,        77,   94
  after  analyzing :    26,      68,        77,   74
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...64 iterations

*********************VALIDATION*********************
curvature mean = -0.014, std = 0.012
curvature mean = 66.930, std = 7.643

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 1.72, sigma = 2.89
      after  rotation: sse = 1.72, sigma = 2.89
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  1.75, its var is  2.36   
      before Erosion-Dilatation  0.00% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...44 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1486014 voxels, voxel volume = 1.000 mm3
           = 1486014 mmm3 = 1486.014 cm3


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

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Thu Aug  8 11:40:39 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = (61, 44, 42) --> (192, 160, 200)
using (105, 83, 121) as brain centroid...
mean wm in atlas = 107, using box (89,69,102) --> (121, 97,140) to find MRI wm
before smoothing, mri peak at 109
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
initial log_p = -4.4
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.135993 @ (-9.091, 27.273, -9.091)
max log p =    -3.951991 @ (4.545, -4.545, -4.545)
max log p =    -3.949564 @ (2.273, -6.818, -2.273)
max log p =    -3.906960 @ (-1.136, 1.136, 3.409)
max log p =    -3.894625 @ (0.568, -0.568, -0.568)
max log p =    -3.894625 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, 16.5, -13.1): log p = -3.895
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.9 (thresh=-3.9)
 1.150   0.000   0.000  -22.288;
 0.000   1.226   0.140  -15.741;
 0.000  -0.161   1.066  -4.338;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
 1.055  -0.039   0.125  -20.932;
 0.000   1.194   0.278  -28.904;
-0.150  -0.317   1.029   41.911;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
 1.145  -0.019  -0.015  -19.126;
 0.020   1.225   0.141  -19.362;
-0.009  -0.150   0.984   4.640;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
 1.145  -0.019  -0.015  -19.126;
 0.020   1.225   0.141  -19.362;
-0.009  -0.150   0.984   4.640;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.5 (thresh=-3.5)
 1.098  -0.072   0.039  -10.347;
 0.052   1.203   0.240  -34.668;
-0.091  -0.282   1.020   27.791;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
 1.098  -0.072   0.039  -10.347;
 0.052   1.203   0.240  -34.668;
-0.091  -0.282   1.020   27.791;
 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=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.283   1.024   27.518;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.2)
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.284   1.027   27.244;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.284   1.027   27.244;
 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
 1.09529  -0.07186   0.03923  -10.02505;
 0.05187   1.19994   0.23930  -34.30827;
-0.09135  -0.28353   1.02716   27.24434;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2772
Quasinewton: input matrix
 1.09529  -0.07186   0.03923  -10.02505;
 0.05187   1.19994   0.23930  -34.30827;
-0.09135  -0.28353   1.02716   27.24434;
 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:
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.284   1.027   27.244;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.2 (old=-4.4)
transform before final EM align:
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.284   1.027   27.244;
 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
 1.09529  -0.07186   0.03923  -10.02505;
 0.05187   1.19994   0.23930  -34.30827;
-0.09135  -0.28353   1.02716   27.24434;
 0.00000   0.00000   0.00000   1.00000;
nsamples 312841
Quasinewton: input matrix
 1.09529  -0.07186   0.03923  -10.02505;
 0.05187   1.19994   0.23930  -34.30827;
-0.09135  -0.28353   1.02716   27.24434;
 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: 013: -log(p) =    3.8  tol 0.000000
final transform:
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.284   1.027   27.244;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 33 minutes and 47 seconds.
#--------------------------------------
#@# CA Normalize Thu Aug  8 12:14:27 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = (61, 44, 42) --> (192, 160, 200)
using (105, 83, 121) as brain centroid...
mean wm in atlas = 107, using box (89,69,102) --> (121, 97,140) to find MRI wm
before smoothing, mri peak at 109
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
using 244171 sample points...
INFO: compute sample coordinates transform
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.284   1.027   27.244;
 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 (126, 45, 44) --> (188, 137, 199)
Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 135.0
0 of 148 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 47, 41) --> (127, 139, 199)
Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 135.0
0 of 87 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 117, 72) --> (176, 152, 122)
Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 135.0
2 of 11 (18.2%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (88, 117, 67) --> (130, 154, 121)
Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 135.0
0 of 10 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (113, 108, 103) --> (143, 165, 131)
Brain_Stem: limiting intensities to 94.0 --> 135.0
8 of 9 (88.9%) samples deleted
using 265 total control points for intensity normalization...
bias field = 1.001 +- 0.049
0 of 255 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (126, 45, 44) --> (188, 137, 199)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 127.0
0 of 194 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 47, 41) --> (127, 139, 199)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 127.0
0 of 140 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 117, 72) --> (176, 152, 122)
Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 127.0
0 of 58 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (88, 117, 67) --> (130, 154, 121)
Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 127.0
0 of 45 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (113, 108, 103) --> (143, 165, 131)
Brain_Stem: limiting intensities to 72.0 --> 127.0
0 of 60 (0.0%) samples deleted
using 497 total control points for intensity normalization...
bias field = 0.999 +- 0.049
0 of 497 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (126, 45, 44) --> (188, 137, 199)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 124.0
0 of 274 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 47, 41) --> (127, 139, 199)
Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 124.0
0 of 188 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 117, 72) --> (176, 152, 122)
Left_Cerebellum_White_Matter: limiting intensities to 78.0 --> 124.0
0 of 61 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (88, 117, 67) --> (130, 154, 121)
Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 124.0
2 of 40 (5.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (113, 108, 103) --> (143, 165, 131)
Brain_Stem: limiting intensities to 71.0 --> 124.0
0 of 111 (0.0%) samples deleted
using 674 total control points for intensity normalization...
bias field = 1.019 +- 0.045
1 of 672 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 12:16:30 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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) = 1.43 (predicted orig area = 5.6)
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=0.887, neg=0, invalid=96777
0001: dt=129.472000, rms=0.793 (10.598%), neg=0, invalid=96777
0002: dt=221.952000, rms=0.769 (3.046%), neg=0, invalid=96777
0003: dt=295.936000, rms=0.756 (1.666%), neg=0, invalid=96777
0004: dt=110.976000, rms=0.749 (0.940%), neg=0, invalid=96777
0005: dt=129.472000, rms=0.744 (0.626%), neg=0, invalid=96777
0006: dt=129.472000, rms=0.741 (0.382%), neg=0, invalid=96777
0007: dt=295.936000, rms=0.736 (0.699%), neg=0, invalid=96777
0008: dt=55.488000, rms=0.734 (0.337%), neg=0, invalid=96777
0009: dt=295.936000, rms=0.731 (0.330%), neg=0, invalid=96777
0010: dt=110.976000, rms=0.727 (0.530%), neg=0, invalid=96777
0011: dt=55.488000, rms=0.727 (0.056%), neg=0, invalid=96777
0012: dt=55.488000, rms=0.726 (0.076%), neg=0, invalid=96777
0013: dt=55.488000, rms=0.725 (0.159%), neg=0, invalid=96777
0014: dt=55.488000, rms=0.724 (0.228%), neg=0, invalid=96777
0015: dt=55.488000, rms=0.722 (0.269%), neg=0, invalid=96777
0016: dt=55.488000, rms=0.720 (0.291%), neg=0, invalid=96777
0017: dt=55.488000, rms=0.717 (0.290%), neg=0, invalid=96777
0018: dt=55.488000, rms=0.715 (0.282%), neg=0, invalid=96777
0019: dt=55.488000, rms=0.713 (0.273%), neg=0, invalid=96777
0020: dt=55.488000, rms=0.711 (0.281%), neg=0, invalid=96777
0021: dt=55.488000, rms=0.710 (0.273%), neg=0, invalid=96777
0022: dt=55.488000, rms=0.708 (0.260%), neg=0, invalid=96777
0023: dt=55.488000, rms=0.706 (0.233%), neg=0, invalid=96777
0024: dt=55.488000, rms=0.705 (0.201%), neg=0, invalid=96777
0025: dt=55.488000, rms=0.703 (0.179%), neg=0, invalid=96777
0026: dt=55.488000, rms=0.702 (0.175%), neg=0, invalid=96777
0027: dt=55.488000, rms=0.701 (0.183%), neg=0, invalid=96777
0028: dt=55.488000, rms=0.700 (0.169%), neg=0, invalid=96777
0029: dt=55.488000, rms=0.699 (0.143%), neg=0, invalid=96777
0030: dt=55.488000, rms=0.698 (0.133%), neg=0, invalid=96777
0031: dt=55.488000, rms=0.697 (0.131%), neg=0, invalid=96777
0032: dt=55.488000, rms=0.696 (0.128%), neg=0, invalid=96777
0033: dt=55.488000, rms=0.695 (0.130%), neg=0, invalid=96777
0034: dt=55.488000, rms=0.694 (0.116%), neg=0, invalid=96777
0035: dt=55.488000, rms=0.693 (0.112%), neg=0, invalid=96777
0036: dt=517.888000, rms=0.693 (0.074%), neg=0, invalid=96777
0037: dt=517.888000, rms=0.693 (-0.645%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.693, neg=0, invalid=96777
0038: dt=129.472000, rms=0.692 (0.148%), neg=0, invalid=96777
0039: dt=129.472000, rms=0.692 (0.036%), neg=0, invalid=96777
0040: dt=129.472000, rms=0.691 (0.095%), neg=0, invalid=96777
0041: dt=129.472000, rms=0.691 (0.064%), neg=0, invalid=96777
0042: dt=129.472000, rms=0.691 (-0.002%), neg=0, invalid=96777
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.696, neg=0, invalid=96777
0043: dt=145.152000, rms=0.680 (2.211%), neg=0, invalid=96777
0044: dt=103.680000, rms=0.673 (1.143%), neg=0, invalid=96777
0045: dt=36.288000, rms=0.667 (0.837%), neg=0, invalid=96777
0046: dt=82.944000, rms=0.665 (0.269%), neg=0, invalid=96777
0047: dt=36.288000, rms=0.661 (0.687%), neg=0, invalid=96777
0048: dt=20.736000, rms=0.660 (0.058%), neg=0, invalid=96777
0049: dt=20.736000, rms=0.659 (0.153%), neg=0, invalid=96777
0050: dt=20.736000, rms=0.657 (0.262%), neg=0, invalid=96777
0051: dt=20.736000, rms=0.655 (0.346%), neg=0, invalid=96777
0052: dt=20.736000, rms=0.652 (0.415%), neg=0, invalid=96777
0053: dt=20.736000, rms=0.649 (0.473%), neg=0, invalid=96777
0054: dt=20.736000, rms=0.646 (0.496%), neg=0, invalid=96777
0055: dt=20.736000, rms=0.643 (0.498%), neg=0, invalid=96777
0056: dt=20.736000, rms=0.640 (0.471%), neg=0, invalid=96777
0057: dt=20.736000, rms=0.637 (0.441%), neg=0, invalid=96777
0058: dt=20.736000, rms=0.635 (0.402%), neg=0, invalid=96777
0059: dt=20.736000, rms=0.632 (0.397%), neg=0, invalid=96777
0060: dt=20.736000, rms=0.630 (0.384%), neg=0, invalid=96777
0061: dt=20.736000, rms=0.627 (0.350%), neg=0, invalid=96777
0062: dt=20.736000, rms=0.625 (0.322%), neg=0, invalid=96777
0063: dt=20.736000, rms=0.624 (0.290%), neg=0, invalid=96777
0064: dt=20.736000, rms=0.622 (0.272%), neg=0, invalid=96777
0065: dt=20.736000, rms=0.620 (0.235%), neg=0, invalid=96777
0066: dt=20.736000, rms=0.619 (0.199%), neg=0, invalid=96777
0067: dt=20.736000, rms=0.618 (0.162%), neg=0, invalid=96777
0068: dt=20.736000, rms=0.617 (0.146%), neg=0, invalid=96777
0069: dt=20.736000, rms=0.616 (0.142%), neg=0, invalid=96777
0070: dt=20.736000, rms=0.615 (0.138%), neg=0, invalid=96777
0071: dt=20.736000, rms=0.615 (0.125%), neg=0, invalid=96777
0072: dt=20.736000, rms=0.614 (0.108%), neg=0, invalid=96777
0073: dt=20.736000, rms=0.614 (0.087%), neg=0, invalid=96777
0074: dt=145.152000, rms=0.613 (0.061%), neg=0, invalid=96777
0075: dt=145.152000, rms=0.613 (-0.344%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.613, neg=0, invalid=96777
0076: dt=36.288000, rms=0.613 (0.055%), neg=0, invalid=96777
0077: dt=36.288000, rms=0.612 (0.063%), neg=0, invalid=96777
0078: dt=9.072000, rms=0.612 (0.000%), neg=0, invalid=96777
0079: dt=9.072000, rms=0.612 (-0.001%), neg=0, invalid=96777
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.638, neg=0, invalid=96777
0080: dt=5.333333, rms=0.638 (0.050%), neg=0, invalid=96777
0081: dt=0.700000, rms=0.638 (0.001%), neg=0, invalid=96777
0082: dt=0.700000, rms=0.638 (0.001%), neg=0, invalid=96777
0083: dt=0.700000, rms=0.638 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.638, neg=0, invalid=96777
0084: dt=0.000000, rms=0.638 (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=0.708, neg=0, invalid=96777
0085: dt=5.060773, rms=0.690 (2.555%), neg=0, invalid=96777
0086: dt=2.304000, rms=0.689 (0.087%), neg=0, invalid=96777
0087: dt=2.304000, rms=0.689 (-0.010%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.689, neg=0, invalid=96777
0088: dt=0.000000, rms=0.689 (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=0.763, neg=0, invalid=96777
0089: dt=1.189130, rms=0.758 (0.648%), neg=0, invalid=96777
0090: dt=1.280000, rms=0.752 (0.679%), neg=0, invalid=96777
0091: dt=1.162602, rms=0.751 (0.168%), neg=0, invalid=96777
0092: dt=0.581301, rms=0.751 (0.083%), neg=0, invalid=96777
0093: dt=0.581301, rms=0.750 (0.058%), neg=0, invalid=96777
0094: dt=0.581301, rms=0.750 (0.047%), neg=0, invalid=96777
0095: dt=0.384000, rms=0.750 (0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.750, neg=0, invalid=96777
0096: dt=1.536000, rms=0.748 (0.203%), neg=0, invalid=96777
0097: dt=0.000000, rms=0.748 (-0.000%), 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=0.698, neg=0, invalid=96777
0098: dt=0.028000, rms=0.696 (0.235%), neg=0, invalid=96777
0099: dt=0.028000, rms=0.695 (0.184%), neg=0, invalid=96777
0100: dt=0.028000, rms=0.694 (0.148%), neg=0, invalid=96777
0101: dt=0.028000, rms=0.692 (0.250%), neg=0, invalid=96777
0102: dt=0.028000, rms=0.690 (0.296%), neg=0, invalid=96777
0103: dt=0.028000, rms=0.688 (0.291%), neg=0, invalid=96777
0104: dt=0.028000, rms=0.686 (0.248%), neg=0, invalid=96777
0105: dt=0.028000, rms=0.686 (-0.028%), neg=0, invalid=96777
0106: dt=0.000000, rms=0.686 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.686, neg=0, invalid=96777
0107: dt=0.028000, rms=0.686 (0.059%), neg=0, invalid=96777
0108: dt=0.028000, rms=0.686 (0.041%), neg=0, invalid=96777
0109: dt=0.028000, rms=0.685 (0.029%), neg=0, invalid=96777
0110: dt=0.028000, rms=0.685 (0.022%), neg=0, invalid=96777
0111: dt=0.028000, rms=0.685 (0.038%), neg=0, invalid=96777
0112: dt=0.028000, rms=0.685 (0.042%), neg=0, invalid=96777
0113: dt=0.028000, rms=0.684 (0.041%), neg=0, invalid=96777
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.11725 (24)
mri peak = 0.10164 (10)
Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (908 voxels, overlap=0.005)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (908 voxels, peak =  8), gca=9.6
gca peak = 0.14022 (22)
mri peak = 0.12066 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (456 voxels, overlap=0.006)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (456 voxels, peak =  7), gca=8.8
gca peak = 0.24234 (100)
mri peak = 0.07466 (89)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (296 voxels, overlap=0.044)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (296 voxels, peak = 88), gca=87.5
gca peak = 0.19192 (97)
mri peak = 0.10976 (75)
Left_Pallidum (13): linear fit = 0.77 x + 0.0 (271 voxels, overlap=0.048)
Left_Pallidum (13): linear fit = 0.77 x + 0.0 (271 voxels, peak = 75), gca=75.2
gca peak = 0.24007 (63)
mri peak = 0.08177 (63)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (468 voxels, overlap=0.972)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (468 voxels, peak = 62), gca=62.1
gca peak = 0.29892 (64)
mri peak = 0.08339 (61)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (554 voxels, overlap=0.824)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (554 voxels, peak = 59), gca=59.2
gca peak = 0.12541 (104)
mri peak = 0.09318 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (51356 voxels, overlap=0.634)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (51356 voxels, peak = 109), gca=108.7
gca peak = 0.13686 (104)
mri peak = 0.09721 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (51310 voxels, overlap=0.651)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (51310 voxels, peak = 109), gca=108.7
gca peak = 0.11691 (63)
mri peak = 0.05646 (54)
Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (11609 voxels, overlap=0.379)
Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (11609 voxels, peak = 53), gca=53.2
gca peak = 0.13270 (63)
mri peak = 0.05727 (56)
Right_Cerebral_Cortex (42): linear fit = 0.85 x + 0.0 (12018 voxels, overlap=0.270)
Right_Cerebral_Cortex (42): linear fit = 0.85 x + 0.0 (12018 voxels, peak = 53), gca=53.2
gca peak = 0.15182 (70)
mri peak = 0.08533 (65)
Right_Caudate (50): linear fit = 0.90 x + 0.0 (264 voxels, overlap=0.473)
Right_Caudate (50): linear fit = 0.90 x + 0.0 (264 voxels, peak = 63), gca=63.3
gca peak = 0.14251 (76)
mri peak = 0.06885 (75)
Left_Caudate (11): linear fit = 0.89 x + 0.0 (602 voxels, overlap=0.522)
Left_Caudate (11): linear fit = 0.89 x + 0.0 (602 voxels, peak = 68), gca=68.0
gca peak = 0.12116 (60)
mri peak = 0.03382 (63)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7239 voxels, overlap=0.748)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7239 voxels, peak = 62), gca=61.5
gca peak = 0.12723 (61)
mri peak = 0.03300 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (8849 voxels, overlap=0.804)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (8849 voxels, peak = 63), gca=62.5
gca peak = 0.22684 (88)
mri peak = 0.05940 (92)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (4670 voxels, overlap=0.749)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (4670 voxels, peak = 95), gca=95.5
gca peak = 0.21067 (87)
mri peak = 0.07087 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4028 voxels, overlap=0.869)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4028 voxels, peak = 91), gca=90.9
gca peak = 0.25455 (62)
mri peak = 0.07631 (55)
Left_Amygdala (18): linear fit = 0.83 x + 0.0 (192 voxels, overlap=0.622)
Left_Amygdala (18): linear fit = 0.83 x + 0.0 (192 voxels, peak = 52), gca=51.8
gca peak = 0.39668 (62)
mri peak = 0.11243 (56)
Right_Amygdala (54): linear fit = 0.88 x + 0.0 (188 voxels, overlap=0.776)
Right_Amygdala (54): linear fit = 0.88 x + 0.0 (188 voxels, peak = 55), gca=54.9
gca peak = 0.10129 (93)
mri peak = 0.05092 (93)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4410 voxels, overlap=0.980)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4410 voxels, peak = 93), gca=93.5
gca peak = 0.12071 (89)
mri peak = 0.06936 (85)
Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3341 voxels, overlap=0.933)
Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3341 voxels, peak = 85), gca=85.0
gca peak = 0.13716 (82)
mri peak = 0.05414 (80)
Left_Putamen (12): linear fit = 0.93 x + 0.0 (1662 voxels, overlap=0.752)
Left_Putamen (12): linear fit = 0.93 x + 0.0 (1662 voxels, peak = 76), gca=75.8
gca peak = 0.15214 (84)
mri peak = 0.07032 (74)
Right_Putamen (51): linear fit = 0.90 x + 0.0 (1648 voxels, overlap=0.332)
Right_Putamen (51): linear fit = 0.90 x + 0.0 (1648 voxels, peak = 76), gca=76.0
gca peak = 0.08983 (85)
mri peak = 0.08741 (86)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (7553 voxels, overlap=0.777)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (7553 voxels, peak = 87), gca=87.1
gca peak = 0.11809 (92)
mri peak = 0.07586 (83)
Right_VentralDC (60): linear fit = 0.94 x + 0.0 (500 voxels, overlap=0.781)
Right_VentralDC (60): linear fit = 0.94 x + 0.0 (500 voxels, peak = 86), gca=86.0
gca peak = 0.12914 (94)
mri peak = 0.06733 (85)
Left_VentralDC (28): linear fit = 0.94 x + 0.0 (570 voxels, overlap=0.793)
Left_VentralDC (28): linear fit = 0.94 x + 0.0 (570 voxels, peak = 89), gca=88.8
gca peak = 0.21100 (36)
mri peak = 1.00000 (54)
gca peak = 0.13542 (27)
mri peak = 0.17913 (10)
Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (409 voxels, overlap=0.031)
Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (409 voxels, peak =  9), gca=8.5
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.21802 (40)
gca peak Third_Ventricle = 0.21100 (36)
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 0.89 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.40 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=0.726, neg=0, invalid=96777
0114: dt=129.472000, rms=0.720 (0.849%), neg=0, invalid=96777
0115: dt=110.976000, rms=0.717 (0.421%), neg=0, invalid=96777
0116: dt=73.984000, rms=0.715 (0.248%), neg=0, invalid=96777
0117: dt=129.472000, rms=0.713 (0.317%), neg=0, invalid=96777
0118: dt=110.976000, rms=0.711 (0.162%), neg=0, invalid=96777
0119: dt=110.976000, rms=0.710 (0.208%), neg=0, invalid=96777
0120: dt=73.984000, rms=0.709 (0.107%), neg=0, invalid=96777
0121: dt=129.472000, rms=0.708 (0.176%), neg=0, invalid=96777
0122: dt=92.480000, rms=0.707 (0.091%), neg=0, invalid=96777
0123: dt=129.472000, rms=0.706 (0.137%), neg=0, invalid=96777
0124: dt=73.984000, rms=0.706 (0.076%), neg=0, invalid=96777
0125: dt=295.936000, rms=0.704 (0.188%), neg=0, invalid=96777
0126: dt=55.488000, rms=0.704 (0.101%), neg=0, invalid=96777
0127: dt=1183.744000, rms=0.700 (0.461%), neg=0, invalid=96777
0128: dt=32.368000, rms=0.699 (0.180%), neg=0, invalid=96777
0129: dt=73.984000, rms=0.699 (0.052%), neg=0, invalid=96777
0130: dt=129.472000, rms=0.698 (0.056%), neg=0, invalid=96777
0131: dt=110.976000, rms=0.698 (0.031%), neg=0, invalid=96777
0132: dt=110.976000, rms=0.698 (0.044%), neg=0, invalid=96777
0133: dt=110.976000, rms=0.697 (0.076%), neg=0, invalid=96777
0134: dt=110.976000, rms=0.697 (0.081%), neg=0, invalid=96777
0135: dt=110.976000, rms=0.696 (0.131%), neg=0, invalid=96777
0136: dt=110.976000, rms=0.695 (0.108%), neg=0, invalid=96777
0137: dt=110.976000, rms=0.694 (0.130%), neg=0, invalid=96777
0138: dt=110.976000, rms=0.693 (0.115%), neg=0, invalid=96777
0139: dt=110.976000, rms=0.693 (0.125%), neg=0, invalid=96777
0140: dt=110.976000, rms=0.692 (0.107%), neg=0, invalid=96777
0141: dt=110.976000, rms=0.691 (0.113%), neg=0, invalid=96777
0142: dt=110.976000, rms=0.690 (0.104%), neg=0, invalid=96777
0143: dt=110.976000, rms=0.690 (0.100%), neg=0, invalid=96777
0144: dt=110.976000, rms=0.689 (0.092%), neg=0, invalid=96777
0145: dt=110.976000, rms=0.688 (0.082%), neg=0, invalid=96777
0146: dt=110.976000, rms=0.688 (0.089%), neg=0, invalid=96777
0147: dt=110.976000, rms=0.687 (0.080%), neg=0, invalid=96777
0148: dt=110.976000, rms=0.687 (0.078%), neg=0, invalid=96777
0149: dt=110.976000, rms=0.686 (0.075%), neg=0, invalid=96777
0150: dt=110.976000, rms=0.686 (0.074%), neg=0, invalid=96777
0151: dt=110.976000, rms=0.685 (0.077%), neg=0, invalid=96777
0152: dt=110.976000, rms=0.685 (0.070%), neg=0, invalid=96777
0153: dt=110.976000, rms=0.684 (0.062%), neg=0, invalid=96777
0154: dt=110.976000, rms=0.684 (0.059%), neg=0, invalid=96777
0155: dt=110.976000, rms=0.684 (0.059%), neg=0, invalid=96777
0156: dt=110.976000, rms=0.683 (0.065%), neg=0, invalid=96777
0157: dt=110.976000, rms=0.683 (0.066%), neg=0, invalid=96777
0158: dt=110.976000, rms=0.682 (0.057%), neg=0, invalid=96777
0159: dt=110.976000, rms=0.682 (0.057%), neg=0, invalid=96777
0160: dt=110.976000, rms=0.681 (0.061%), neg=0, invalid=96777
0161: dt=110.976000, rms=0.681 (0.052%), neg=0, invalid=96777
0162: dt=110.976000, rms=0.681 (0.052%), neg=0, invalid=96777
0163: dt=110.976000, rms=0.680 (0.049%), neg=0, invalid=96777
0164: dt=110.976000, rms=0.680 (0.049%), neg=0, invalid=96777
0165: dt=110.976000, rms=0.680 (0.049%), neg=0, invalid=96777
0166: dt=110.976000, rms=0.679 (0.042%), neg=0, invalid=96777
0167: dt=110.976000, rms=0.679 (0.041%), neg=0, invalid=96777
0168: dt=110.976000, rms=0.679 (0.040%), neg=0, invalid=96777
0169: dt=110.976000, rms=0.679 (0.040%), neg=0, invalid=96777
0170: dt=110.976000, rms=0.678 (0.037%), neg=0, invalid=96777
0171: dt=110.976000, rms=0.678 (0.036%), neg=0, invalid=96777
0172: dt=110.976000, rms=0.678 (0.027%), neg=0, invalid=96777
0173: dt=110.976000, rms=0.678 (0.042%), neg=0, invalid=96777
0174: dt=110.976000, rms=0.677 (0.036%), neg=0, invalid=96777
0175: dt=110.976000, rms=0.677 (0.038%), neg=0, invalid=96777
0176: dt=110.976000, rms=0.677 (0.027%), neg=0, invalid=96777
0177: dt=110.976000, rms=0.677 (0.031%), neg=0, invalid=96777
0178: dt=110.976000, rms=0.677 (0.027%), neg=0, invalid=96777
0179: dt=110.976000, rms=0.676 (0.031%), neg=0, invalid=96777
0180: dt=110.976000, rms=0.676 (0.025%), neg=0, invalid=96777
0181: dt=110.976000, rms=0.676 (0.029%), neg=0, invalid=96777
0182: dt=110.976000, rms=0.676 (0.031%), neg=0, invalid=96777
0183: dt=110.976000, rms=0.676 (0.037%), neg=0, invalid=96777
0184: dt=110.976000, rms=0.675 (0.021%), neg=0, invalid=96777
0185: dt=110.976000, rms=0.675 (0.024%), neg=0, invalid=96777
0186: dt=110.976000, rms=0.675 (0.022%), neg=0, invalid=96777
0187: dt=73.984000, rms=0.675 (0.008%), neg=0, invalid=96777
0188: dt=73.984000, rms=0.675 (0.004%), neg=0, invalid=96777
0189: dt=73.984000, rms=0.675 (0.002%), neg=0, invalid=96777
0190: dt=73.984000, rms=0.675 (0.005%), neg=0, invalid=96777
0191: dt=73.984000, rms=0.675 (0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.675, neg=0, invalid=96777
0192: dt=129.472000, rms=0.675 (0.047%), neg=0, invalid=96777
0193: dt=443.904000, rms=0.674 (0.153%), neg=0, invalid=96777
0194: dt=73.984000, rms=0.673 (0.020%), neg=0, invalid=96777
0195: dt=73.984000, rms=0.673 (0.011%), neg=0, invalid=96777
0196: dt=73.984000, rms=0.673 (0.009%), neg=0, invalid=96777
0197: dt=73.984000, rms=0.673 (0.018%), neg=0, invalid=96777
0198: dt=73.984000, rms=0.673 (0.028%), neg=0, invalid=96777
0199: dt=73.984000, rms=0.673 (0.032%), neg=0, invalid=96777
0200: dt=73.984000, rms=0.673 (0.030%), neg=0, invalid=96777
0201: dt=73.984000, rms=0.672 (0.023%), neg=0, invalid=96777
0202: dt=73.984000, rms=0.672 (0.014%), neg=0, invalid=96777
0203: dt=129.472000, rms=0.672 (0.003%), neg=0, invalid=96777
0204: dt=129.472000, rms=0.672 (0.008%), neg=0, invalid=96777
0205: dt=129.472000, rms=0.672 (0.009%), neg=0, invalid=96777
0206: dt=129.472000, rms=0.672 (0.008%), neg=0, invalid=96777
0207: dt=129.472000, rms=0.672 (0.014%), neg=0, invalid=96777
0208: dt=129.472000, rms=0.672 (0.018%), neg=0, invalid=96777
0209: dt=129.472000, rms=0.672 (0.022%), neg=0, invalid=96777
0210: dt=129.472000, rms=0.672 (0.027%), neg=0, invalid=96777
0211: dt=129.472000, rms=0.671 (0.024%), neg=0, invalid=96777
0212: dt=129.472000, rms=0.671 (0.023%), neg=0, invalid=96777
0213: dt=517.888000, rms=0.671 (0.010%), neg=0, invalid=96777
0214: dt=517.888000, rms=0.671 (-0.478%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.672, neg=0, invalid=96777
0215: dt=124.416000, rms=0.667 (0.771%), neg=0, invalid=96777
0216: dt=31.104000, rms=0.664 (0.399%), neg=0, invalid=96777
0217: dt=82.944000, rms=0.661 (0.547%), neg=0, invalid=96777
0218: dt=20.736000, rms=0.659 (0.305%), neg=0, invalid=96777
0219: dt=497.664000, rms=0.648 (1.676%), neg=0, invalid=96777
0220: dt=22.343708, rms=0.642 (0.861%), neg=0, invalid=96777
0221: dt=36.288000, rms=0.641 (0.243%), neg=0, invalid=96777
0222: dt=145.152000, rms=0.639 (0.290%), neg=0, invalid=96777
0223: dt=31.104000, rms=0.637 (0.291%), neg=0, invalid=96777
0224: dt=20.736000, rms=0.637 (0.053%), neg=0, invalid=96777
0225: dt=414.720000, rms=0.630 (1.034%), neg=0, invalid=96777
0226: dt=20.736000, rms=0.629 (0.072%), neg=0, invalid=96777
0227: dt=331.776000, rms=0.627 (0.375%), neg=0, invalid=96777
0228: dt=31.104000, rms=0.626 (0.172%), neg=0, invalid=96777
0229: dt=36.288000, rms=0.625 (0.178%), neg=0, invalid=96777
0230: dt=25.920000, rms=0.625 (0.034%), neg=0, invalid=96777
0231: dt=25.920000, rms=0.624 (0.059%), neg=0, invalid=96777
0232: dt=25.920000, rms=0.624 (0.090%), neg=0, invalid=96777
0233: dt=25.920000, rms=0.623 (0.119%), neg=0, invalid=96777
0234: dt=25.920000, rms=0.622 (0.137%), neg=0, invalid=96777
0235: dt=25.920000, rms=0.621 (0.159%), neg=0, invalid=96777
0236: dt=25.920000, rms=0.620 (0.179%), neg=0, invalid=96777
0237: dt=25.920000, rms=0.619 (0.194%), neg=0, invalid=96777
0238: dt=25.920000, rms=0.618 (0.208%), neg=0, invalid=96777
0239: dt=25.920000, rms=0.616 (0.206%), neg=0, invalid=96777
0240: dt=25.920000, rms=0.615 (0.210%), neg=0, invalid=96777
0241: dt=25.920000, rms=0.614 (0.217%), neg=0, invalid=96777
0242: dt=25.920000, rms=0.612 (0.207%), neg=0, invalid=96777
0243: dt=25.920000, rms=0.611 (0.193%), neg=0, invalid=96777
0244: dt=25.920000, rms=0.610 (0.184%), neg=0, invalid=96777
0245: dt=25.920000, rms=0.610 (0.037%), neg=0, invalid=96777
0246: dt=25.920000, rms=0.610 (0.045%), neg=0, invalid=96777
0247: dt=25.920000, rms=0.609 (0.053%), neg=0, invalid=96777
0248: dt=25.920000, rms=0.609 (0.065%), neg=0, invalid=96777
0249: dt=25.920000, rms=0.608 (0.081%), neg=0, invalid=96777
0250: dt=25.920000, rms=0.608 (0.090%), neg=0, invalid=96777
0251: dt=25.920000, rms=0.607 (0.106%), neg=0, invalid=96777
0252: dt=25.920000, rms=0.606 (0.120%), neg=0, invalid=96777
0253: dt=25.920000, rms=0.606 (0.116%), neg=0, invalid=96777
0254: dt=25.920000, rms=0.605 (0.117%), neg=0, invalid=96777
0255: dt=25.920000, rms=0.604 (0.118%), neg=0, invalid=96777
0256: dt=25.920000, rms=0.604 (0.110%), neg=0, invalid=96777
0257: dt=25.920000, rms=0.603 (0.124%), neg=0, invalid=96777
0258: dt=25.920000, rms=0.602 (0.116%), neg=0, invalid=96777
0259: dt=25.920000, rms=0.602 (0.119%), neg=0, invalid=96777
0260: dt=25.920000, rms=0.601 (0.123%), neg=0, invalid=96777
0261: dt=25.920000, rms=0.600 (0.118%), neg=0, invalid=96777
0262: dt=25.920000, rms=0.599 (0.115%), neg=0, invalid=96777
0263: dt=25.920000, rms=0.599 (0.110%), neg=0, invalid=96777
0264: dt=25.920000, rms=0.598 (0.099%), neg=0, invalid=96777
0265: dt=25.920000, rms=0.598 (0.103%), neg=0, invalid=96777
0266: dt=25.920000, rms=0.597 (0.103%), neg=0, invalid=96777
0267: dt=25.920000, rms=0.596 (0.100%), neg=0, invalid=96777
0268: dt=25.920000, rms=0.596 (0.095%), neg=0, invalid=96777
0269: dt=25.920000, rms=0.595 (0.090%), neg=0, invalid=96777
0270: dt=25.920000, rms=0.595 (0.082%), neg=0, invalid=96777
0271: dt=25.920000, rms=0.594 (0.070%), neg=0, invalid=96777
0272: dt=25.920000, rms=0.594 (0.073%), neg=0, invalid=96777
0273: dt=25.920000, rms=0.593 (0.078%), neg=0, invalid=96777
0274: dt=25.920000, rms=0.593 (0.076%), neg=0, invalid=96777
0275: dt=25.920000, rms=0.593 (0.072%), neg=0, invalid=96777
0276: dt=25.920000, rms=0.592 (0.074%), neg=0, invalid=96777
0277: dt=25.920000, rms=0.592 (0.076%), neg=0, invalid=96777
0278: dt=25.920000, rms=0.591 (0.075%), neg=0, invalid=96777
0279: dt=25.920000, rms=0.591 (0.060%), neg=0, invalid=96777
0280: dt=25.920000, rms=0.591 (0.057%), neg=0, invalid=96777
0281: dt=25.920000, rms=0.590 (0.065%), neg=0, invalid=96777
0282: dt=25.920000, rms=0.590 (0.068%), neg=0, invalid=96777
0283: dt=25.920000, rms=0.589 (0.068%), neg=0, invalid=96777
0284: dt=25.920000, rms=0.589 (0.052%), neg=0, invalid=96777
0285: dt=25.920000, rms=0.589 (0.052%), neg=0, invalid=96777
0286: dt=25.920000, rms=0.588 (0.056%), neg=0, invalid=96777
0287: dt=25.920000, rms=0.588 (0.065%), neg=0, invalid=96777
0288: dt=25.920000, rms=0.588 (0.064%), neg=0, invalid=96777
0289: dt=25.920000, rms=0.587 (0.059%), neg=0, invalid=96777
0290: dt=25.920000, rms=0.587 (0.053%), neg=0, invalid=96777
0291: dt=25.920000, rms=0.587 (0.054%), neg=0, invalid=96777
0292: dt=25.920000, rms=0.586 (0.053%), neg=0, invalid=96777
0293: dt=25.920000, rms=0.586 (0.052%), neg=0, invalid=96777
0294: dt=25.920000, rms=0.586 (0.041%), neg=0, invalid=96777
0295: dt=25.920000, rms=0.586 (0.038%), neg=0, invalid=96777
0296: dt=25.920000, rms=0.585 (0.046%), neg=0, invalid=96777
0297: dt=25.920000, rms=0.585 (0.046%), neg=0, invalid=96777
0298: dt=25.920000, rms=0.585 (0.042%), neg=0, invalid=96777
0299: dt=25.920000, rms=0.585 (0.034%), neg=0, invalid=96777
0300: dt=25.920000, rms=0.584 (0.036%), neg=0, invalid=96777
0301: dt=25.920000, rms=0.584 (0.048%), neg=0, invalid=96777
0302: dt=25.920000, rms=0.584 (0.045%), neg=0, invalid=96777
0303: dt=25.920000, rms=0.584 (0.040%), neg=0, invalid=96777
0304: dt=25.920000, rms=0.583 (0.036%), neg=0, invalid=96777
0305: dt=25.920000, rms=0.583 (0.037%), neg=0, invalid=96777
0306: dt=25.920000, rms=0.583 (0.038%), neg=0, invalid=96777
0307: dt=25.920000, rms=0.583 (0.041%), neg=0, invalid=96777
0308: dt=25.920000, rms=0.583 (0.032%), neg=0, invalid=96777
0309: dt=25.920000, rms=0.582 (0.033%), neg=0, invalid=96777
0310: dt=25.920000, rms=0.582 (0.032%), neg=0, invalid=96777
0311: dt=25.920000, rms=0.582 (0.035%), neg=0, invalid=96777
0312: dt=25.920000, rms=0.582 (0.031%), neg=0, invalid=96777
0313: dt=25.920000, rms=0.582 (0.028%), neg=0, invalid=96777
0314: dt=25.920000, rms=0.581 (0.029%), neg=0, invalid=96777
0315: dt=25.920000, rms=0.581 (0.040%), neg=0, invalid=96777
0316: dt=25.920000, rms=0.581 (0.036%), neg=0, invalid=96777
0317: dt=25.920000, rms=0.581 (0.028%), neg=0, invalid=96777
0318: dt=25.920000, rms=0.581 (0.029%), neg=0, invalid=96777
0319: dt=25.920000, rms=0.580 (0.029%), neg=0, invalid=96777
0320: dt=25.920000, rms=0.580 (0.033%), neg=0, invalid=96777
0321: dt=25.920000, rms=0.580 (0.030%), neg=0, invalid=96777
0322: dt=25.920000, rms=0.580 (0.026%), neg=0, invalid=96777
0323: dt=25.920000, rms=0.580 (0.022%), neg=0, invalid=96777
0324: dt=25.920000, rms=0.580 (0.029%), neg=0, invalid=96777
0325: dt=25.920000, rms=0.580 (0.024%), neg=0, invalid=96777
0326: dt=25.920000, rms=0.579 (0.019%), neg=0, invalid=96777
0327: dt=25.920000, rms=0.579 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.579, neg=0, invalid=96777
0328: dt=82.944000, rms=0.578 (0.218%), neg=0, invalid=96777
0329: dt=62.208000, rms=0.577 (0.175%), neg=0, invalid=96777
0330: dt=20.736000, rms=0.577 (0.020%), neg=0, invalid=96777
0331: dt=20.736000, rms=0.577 (0.014%), neg=0, invalid=96777
0332: dt=20.736000, rms=0.577 (0.030%), neg=0, invalid=96777
0333: dt=20.736000, rms=0.577 (0.052%), neg=0, invalid=96777
0334: dt=20.736000, rms=0.576 (0.062%), neg=0, invalid=96777
0335: dt=20.736000, rms=0.576 (0.053%), neg=0, invalid=96777
0336: dt=20.736000, rms=0.576 (0.054%), neg=0, invalid=96777
0337: dt=20.736000, rms=0.575 (0.046%), neg=0, invalid=96777
0338: dt=20.736000, rms=0.575 (0.046%), neg=0, invalid=96777
0339: dt=20.736000, rms=0.575 (0.043%), neg=0, invalid=96777
0340: dt=20.736000, rms=0.575 (0.036%), neg=0, invalid=96777
0341: dt=20.736000, rms=0.574 (0.046%), neg=0, invalid=96777
0342: dt=20.736000, rms=0.574 (0.051%), neg=0, invalid=96777
0343: dt=20.736000, rms=0.574 (0.052%), neg=0, invalid=96777
0344: dt=20.736000, rms=0.573 (0.047%), neg=0, invalid=96777
0345: dt=20.736000, rms=0.573 (0.042%), neg=0, invalid=96777
0346: dt=20.736000, rms=0.573 (0.041%), neg=0, invalid=96777
0347: dt=20.736000, rms=0.573 (0.043%), neg=0, invalid=96777
0348: dt=20.736000, rms=0.572 (0.049%), neg=0, invalid=96777
0349: dt=20.736000, rms=0.572 (0.039%), neg=0, invalid=96777
0350: dt=20.736000, rms=0.572 (0.038%), neg=0, invalid=96777
0351: dt=20.736000, rms=0.572 (0.035%), neg=0, invalid=96777
0352: dt=20.736000, rms=0.572 (0.030%), neg=0, invalid=96777
0353: dt=20.736000, rms=0.571 (0.040%), neg=0, invalid=96777
0354: dt=20.736000, rms=0.571 (0.045%), neg=0, invalid=96777
0355: dt=20.736000, rms=0.571 (0.045%), neg=0, invalid=96777
0356: dt=20.736000, rms=0.571 (0.033%), neg=0, invalid=96777
0357: dt=20.736000, rms=0.570 (0.035%), neg=0, invalid=96777
0358: dt=20.736000, rms=0.570 (0.027%), neg=0, invalid=96777
0359: dt=20.736000, rms=0.570 (0.025%), neg=0, invalid=96777
0360: dt=20.736000, rms=0.570 (0.029%), neg=0, invalid=96777
0361: dt=20.736000, rms=0.570 (0.033%), neg=0, invalid=96777
0362: dt=20.736000, rms=0.570 (0.036%), neg=0, invalid=96777
0363: dt=20.736000, rms=0.569 (0.030%), neg=0, invalid=96777
0364: dt=20.736000, rms=0.569 (0.029%), neg=0, invalid=96777
0365: dt=20.736000, rms=0.569 (0.029%), neg=0, invalid=96777
0366: dt=20.736000, rms=0.569 (0.011%), neg=0, invalid=96777
0367: dt=20.736000, rms=0.569 (0.016%), neg=0, invalid=96777
0368: dt=20.736000, rms=0.569 (0.021%), neg=0, invalid=96777
0369: dt=20.736000, rms=0.569 (0.030%), neg=0, invalid=96777
0370: dt=20.736000, rms=0.569 (0.024%), neg=0, invalid=96777
0371: dt=20.736000, rms=0.568 (0.020%), neg=0, invalid=96777
0372: dt=82.944000, rms=0.568 (0.020%), neg=0, invalid=96777
0373: dt=82.944000, rms=0.568 (-0.168%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.577, neg=0, invalid=96777
0374: dt=11.200000, rms=0.576 (0.233%), neg=0, invalid=96777
0375: dt=38.400000, rms=0.573 (0.421%), neg=0, invalid=96777
0376: dt=9.600000, rms=0.573 (0.125%), neg=0, invalid=96777
0377: dt=38.400000, rms=0.570 (0.413%), neg=0, invalid=96777
0378: dt=6.226506, rms=0.569 (0.285%), neg=0, invalid=96777
0379: dt=44.800000, rms=0.565 (0.650%), neg=0, invalid=96777
0380: dt=11.200000, rms=0.564 (0.124%), neg=0, invalid=96777
0381: dt=44.800000, rms=0.562 (0.353%), neg=0, invalid=96777
0382: dt=2.800000, rms=0.562 (0.113%), neg=0, invalid=96777
0383: dt=8.000000, rms=0.561 (0.135%), neg=0, invalid=96777
0384: dt=76.800000, rms=0.559 (0.411%), neg=0, invalid=96777
0385: dt=7.888889, rms=0.557 (0.260%), neg=0, invalid=96777
0386: dt=9.416667, rms=0.556 (0.188%), neg=0, invalid=96777
0387: dt=11.200000, rms=0.555 (0.130%), neg=0, invalid=96777
0388: dt=128.000000, rms=0.552 (0.534%), neg=0, invalid=96777
0389: dt=7.191011, rms=0.551 (0.316%), neg=0, invalid=96777
0390: dt=11.200000, rms=0.549 (0.213%), neg=0, invalid=96777
0391: dt=11.200000, rms=0.549 (0.074%), neg=0, invalid=96777
0392: dt=44.800000, rms=0.548 (0.154%), neg=0, invalid=96777
0393: dt=6.400000, rms=0.548 (0.098%), neg=0, invalid=96777
0394: dt=102.400000, rms=0.546 (0.270%), neg=0, invalid=96777
0395: dt=7.766990, rms=0.545 (0.208%), neg=0, invalid=96777
0396: dt=11.200000, rms=0.544 (0.125%), neg=0, invalid=96777
0397: dt=25.600000, rms=0.544 (0.064%), neg=0, invalid=96777
0398: dt=9.600000, rms=0.544 (0.075%), neg=0, invalid=96777
0399: dt=9.600000, rms=0.544 (0.024%), neg=0, invalid=96777
0400: dt=9.600000, rms=0.543 (0.060%), neg=0, invalid=96777
0401: dt=9.600000, rms=0.543 (0.061%), neg=0, invalid=96777
0402: dt=9.600000, rms=0.542 (0.087%), neg=0, invalid=96777
0403: dt=9.600000, rms=0.542 (0.108%), neg=0, invalid=96777
0404: dt=9.600000, rms=0.541 (0.150%), neg=0, invalid=96777
0405: dt=9.600000, rms=0.540 (0.147%), neg=0, invalid=96777
0406: dt=9.600000, rms=0.539 (0.155%), neg=0, invalid=96777
0407: dt=9.600000, rms=0.539 (0.156%), neg=0, invalid=96777
0408: dt=9.600000, rms=0.538 (0.172%), neg=0, invalid=96777
0409: dt=9.600000, rms=0.537 (0.184%), neg=0, invalid=96777
0410: dt=9.600000, rms=0.536 (0.187%), neg=0, invalid=96777
0411: dt=9.600000, rms=0.535 (0.165%), neg=0, invalid=96777
0412: dt=9.600000, rms=0.534 (0.159%), neg=0, invalid=96777
0413: dt=9.600000, rms=0.533 (0.170%), neg=0, invalid=96777
0414: dt=9.600000, rms=0.532 (0.166%), neg=0, invalid=96777
0415: dt=9.600000, rms=0.531 (0.152%), neg=0, invalid=96777
0416: dt=9.600000, rms=0.530 (0.148%), neg=0, invalid=96777
0417: dt=9.600000, rms=0.530 (0.144%), neg=0, invalid=96777
0418: dt=9.600000, rms=0.529 (0.142%), neg=0, invalid=96777
0419: dt=9.600000, rms=0.528 (0.121%), neg=0, invalid=96777
0420: dt=9.600000, rms=0.528 (0.123%), neg=0, invalid=96777
0421: dt=9.600000, rms=0.527 (0.106%), neg=0, invalid=96777
0422: dt=9.600000, rms=0.527 (0.103%), neg=0, invalid=96777
0423: dt=9.600000, rms=0.526 (0.110%), neg=0, invalid=96777
0424: dt=9.600000, rms=0.525 (0.100%), neg=0, invalid=96777
0425: dt=9.600000, rms=0.525 (0.087%), neg=0, invalid=96777
0426: dt=9.600000, rms=0.525 (0.077%), neg=0, invalid=96777
0427: dt=9.600000, rms=0.524 (0.074%), neg=0, invalid=96777
0428: dt=9.600000, rms=0.524 (0.066%), neg=0, invalid=96777
0429: dt=9.600000, rms=0.524 (0.059%), neg=0, invalid=96777
0430: dt=9.600000, rms=0.523 (0.059%), neg=0, invalid=96777
0431: dt=9.600000, rms=0.523 (0.065%), neg=0, invalid=96777
0432: dt=9.600000, rms=0.523 (0.062%), neg=0, invalid=96777
0433: dt=9.600000, rms=0.522 (0.056%), neg=0, invalid=96777
0434: dt=9.600000, rms=0.522 (0.054%), neg=0, invalid=96777
0435: dt=9.600000, rms=0.522 (0.049%), neg=0, invalid=96777
0436: dt=9.600000, rms=0.522 (0.039%), neg=0, invalid=96777
0437: dt=9.600000, rms=0.521 (0.039%), neg=0, invalid=96777
0438: dt=9.600000, rms=0.521 (0.042%), neg=0, invalid=96777
0439: dt=9.600000, rms=0.521 (0.047%), neg=0, invalid=96777
0440: dt=9.600000, rms=0.521 (0.047%), neg=0, invalid=96777
0441: dt=9.600000, rms=0.520 (0.051%), neg=0, invalid=96777
0442: dt=9.600000, rms=0.520 (0.047%), neg=0, invalid=96777
0443: dt=9.600000, rms=0.520 (0.037%), neg=0, invalid=96777
0444: dt=9.600000, rms=0.520 (0.036%), neg=0, invalid=96777
0445: dt=9.600000, rms=0.520 (0.040%), neg=0, invalid=96777
0446: dt=9.600000, rms=0.519 (0.037%), neg=0, invalid=96777
0447: dt=9.600000, rms=0.519 (0.035%), neg=0, invalid=96777
0448: dt=9.600000, rms=0.519 (0.030%), neg=0, invalid=96777
0449: dt=9.600000, rms=0.519 (0.031%), neg=0, invalid=96777
0450: dt=9.600000, rms=0.519 (0.031%), neg=0, invalid=96777
0451: dt=9.600000, rms=0.519 (0.029%), neg=0, invalid=96777
0452: dt=9.600000, rms=0.518 (0.023%), neg=0, invalid=96777
0453: dt=9.600000, rms=0.518 (0.033%), neg=0, invalid=96777
0454: dt=9.600000, rms=0.518 (0.026%), neg=0, invalid=96777
0455: dt=9.600000, rms=0.518 (0.031%), neg=0, invalid=96777
0456: dt=9.600000, rms=0.518 (0.025%), neg=0, invalid=96777
0457: dt=9.600000, rms=0.518 (0.027%), neg=0, invalid=96777
0458: dt=9.600000, rms=0.518 (0.025%), neg=0, invalid=96777
0459: dt=9.600000, rms=0.517 (0.021%), neg=0, invalid=96777
0460: dt=9.600000, rms=0.517 (0.027%), neg=0, invalid=96777
0461: dt=9.600000, rms=0.517 (0.023%), neg=0, invalid=96777
0462: dt=9.600000, rms=0.517 (0.021%), neg=0, invalid=96777
0463: dt=44.800000, rms=0.517 (0.013%), neg=0, invalid=96777
0464: dt=44.800000, rms=0.517 (-0.152%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.517, neg=0, invalid=96777
0465: dt=25.600000, rms=0.516 (0.255%), neg=0, invalid=96777
0466: dt=6.400000, rms=0.515 (0.064%), neg=0, invalid=96777
0467: dt=38.400000, rms=0.515 (0.132%), neg=0, invalid=96777
0468: dt=6.400000, rms=0.514 (0.044%), neg=0, invalid=96777
0469: dt=6.400000, rms=0.514 (0.022%), neg=0, invalid=96777
0470: dt=6.400000, rms=0.514 (0.023%), neg=0, invalid=96777
0471: dt=6.400000, rms=0.514 (0.025%), neg=0, invalid=96777
0472: dt=6.400000, rms=0.514 (0.033%), neg=0, invalid=96777
0473: dt=6.400000, rms=0.514 (0.034%), neg=0, invalid=96777
0474: dt=6.400000, rms=0.514 (0.028%), neg=0, invalid=96777
0475: dt=6.400000, rms=0.513 (0.029%), neg=0, invalid=96777
0476: dt=6.400000, rms=0.513 (0.017%), neg=0, invalid=96777
0477: dt=6.400000, rms=0.513 (0.014%), neg=0, invalid=96777
0478: dt=9.600000, rms=0.513 (0.005%), neg=0, invalid=96777
0479: dt=9.600000, rms=0.513 (0.012%), neg=0, invalid=96777
0480: dt=9.600000, rms=0.513 (0.015%), neg=0, invalid=96777
0481: dt=9.600000, rms=0.513 (0.012%), neg=0, invalid=96777
0482: dt=9.600000, rms=0.513 (0.014%), neg=0, invalid=96777
0483: dt=9.600000, rms=0.513 (0.025%), neg=0, invalid=96777
0484: dt=9.600000, rms=0.513 (0.023%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.535, neg=0, invalid=96777
0485: dt=0.000000, rms=0.535 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.535, neg=0, invalid=96777
0486: dt=0.000000, rms=0.535 (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=0.580, neg=0, invalid=96777
0487: dt=1.085052, rms=0.577 (0.624%), neg=0, invalid=96777
0488: dt=0.192000, rms=0.577 (0.012%), neg=0, invalid=96777
0489: dt=0.192000, rms=0.577 (-0.006%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.577, neg=0, invalid=96777
0490: dt=0.500000, rms=0.576 (0.098%), neg=0, invalid=96777
0491: dt=0.256000, rms=0.576 (0.014%), neg=0, invalid=96777
0492: dt=0.256000, rms=0.576 (-0.009%), 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=0.525, neg=0, invalid=96777
0493: dt=0.028000, rms=0.524 (0.243%), neg=0, invalid=96777
0494: dt=0.112000, rms=0.519 (0.917%), neg=0, invalid=96777
0495: dt=0.028000, rms=0.518 (0.179%), neg=0, invalid=96777
0496: dt=0.028000, rms=0.517 (0.173%), neg=0, invalid=96777
0497: dt=0.024000, rms=0.517 (0.140%), neg=0, invalid=96777
0498: dt=0.000438, rms=0.517 (0.003%), neg=0, invalid=96777
0499: dt=0.000438, rms=0.517 (0.002%), neg=0, invalid=96777
0500: dt=0.000438, rms=0.517 (0.005%), neg=0, invalid=96777
0501: dt=0.000438, rms=0.516 (0.007%), neg=0, invalid=96777
0502: dt=0.000438, rms=0.516 (0.009%), neg=0, invalid=96777
0503: dt=0.000438, rms=0.516 (0.010%), neg=0, invalid=96777
0504: dt=0.000438, rms=0.516 (0.011%), neg=0, invalid=96777
0505: dt=0.000438, rms=0.516 (0.013%), neg=0, invalid=96777
0506: dt=0.000438, rms=0.516 (0.014%), neg=0, invalid=96777
0507: dt=0.000438, rms=0.516 (0.015%), neg=0, invalid=96777
0508: dt=0.000438, rms=0.516 (0.016%), neg=0, invalid=96777
0509: dt=0.000438, rms=0.516 (0.016%), neg=0, invalid=96777
0510: dt=0.000438, rms=0.516 (0.017%), neg=0, invalid=96777
0511: dt=0.000438, rms=0.516 (0.018%), neg=0, invalid=96777
0512: dt=0.000438, rms=0.516 (0.018%), neg=0, invalid=96777
0513: dt=0.000438, rms=0.516 (0.019%), neg=0, invalid=96777
0514: dt=0.000438, rms=0.515 (0.019%), neg=0, invalid=96777
0515: dt=0.000438, rms=0.515 (0.020%), neg=0, invalid=96777
0516: dt=0.000438, rms=0.515 (0.020%), neg=0, invalid=96777
0517: dt=0.000438, rms=0.515 (0.020%), neg=0, invalid=96777
0518: dt=0.000438, rms=0.515 (0.020%), neg=0, invalid=96777
0519: dt=0.000438, rms=0.515 (0.021%), neg=0, invalid=96777
0520: dt=0.000438, rms=0.515 (0.021%), neg=0, invalid=96777
0521: dt=0.000438, rms=0.515 (0.021%), neg=0, invalid=96777
0522: dt=0.000438, rms=0.515 (0.021%), neg=0, invalid=96777
0523: dt=0.000438, rms=0.515 (0.021%), neg=0, invalid=96777
0524: dt=0.028000, rms=0.514 (0.137%), neg=0, invalid=96777
0525: dt=0.028000, rms=0.513 (0.131%), neg=0, invalid=96777
0526: dt=0.000438, rms=0.513 (0.003%), neg=0, invalid=96777
0527: dt=0.000438, rms=0.513 (0.002%), neg=0, invalid=96777
0528: dt=0.000438, rms=0.513 (0.003%), neg=0, invalid=96777
0529: dt=0.000438, rms=0.513 (0.006%), neg=0, invalid=96777
0530: dt=0.000438, rms=0.513 (0.006%), neg=0, invalid=96777
0531: dt=0.000438, rms=0.513 (0.008%), neg=0, invalid=96777
0532: dt=0.000438, rms=0.513 (0.009%), neg=0, invalid=96777
0533: dt=0.000438, rms=0.513 (0.011%), neg=0, invalid=96777
0534: dt=0.000438, rms=0.513 (0.011%), neg=0, invalid=96777
0535: dt=0.000438, rms=0.513 (0.012%), neg=0, invalid=96777
0536: dt=0.000438, rms=0.513 (0.012%), neg=0, invalid=96777
0537: dt=0.096000, rms=0.511 (0.412%), neg=0, invalid=96777
0538: dt=0.080000, rms=0.509 (0.288%), neg=0, invalid=96777
0539: dt=0.007000, rms=0.509 (0.022%), neg=0, invalid=96777
0540: dt=0.007000, rms=0.509 (0.023%), neg=0, invalid=96777
0541: dt=0.007000, rms=0.509 (0.041%), neg=0, invalid=96777
0542: dt=0.007000, rms=0.508 (0.058%), neg=0, invalid=96777
0543: dt=0.003500, rms=0.508 (0.010%), neg=0, invalid=96777
0544: dt=0.003500, rms=0.508 (0.020%), neg=0, invalid=96777
0545: dt=0.003500, rms=0.508 (0.010%), neg=0, invalid=96777
0546: dt=0.112000, rms=0.507 (0.318%), neg=0, invalid=96777
0547: dt=0.112000, rms=0.505 (0.265%), neg=0, invalid=96777
0548: dt=0.028000, rms=0.505 (0.054%), neg=0, invalid=96777
0549: dt=0.028000, rms=0.505 (0.053%), neg=0, invalid=96777
0550: dt=0.028000, rms=0.504 (0.054%), neg=0, invalid=96777
0551: dt=0.005000, rms=0.504 (0.008%), neg=0, invalid=96777
0552: dt=0.005000, rms=0.504 (0.009%), neg=0, invalid=96777
0553: dt=0.005000, rms=0.504 (0.006%), neg=0, invalid=96777
0554: dt=0.005000, rms=0.504 (0.019%), neg=0, invalid=96777
0555: dt=0.005000, rms=0.504 (0.026%), neg=0, invalid=96777
0556: dt=0.005000, rms=0.504 (0.028%), neg=0, invalid=96777
0557: dt=0.005000, rms=0.504 (0.032%), neg=0, invalid=96777
0558: dt=0.005000, rms=0.504 (0.041%), neg=0, invalid=96777
0559: dt=0.005000, rms=0.503 (0.041%), neg=0, invalid=96777
0560: dt=0.005000, rms=0.503 (0.047%), neg=0, invalid=96777
0561: dt=0.005000, rms=0.503 (0.010%), neg=0, invalid=96777
0562: dt=0.005000, rms=0.503 (0.010%), neg=0, invalid=96777
0563: dt=0.005000, rms=0.503 (0.020%), neg=0, invalid=96777
0564: dt=0.005000, rms=0.503 (0.024%), neg=0, invalid=96777
0565: dt=0.005000, rms=0.503 (0.027%), neg=0, invalid=96777
0566: dt=0.005000, rms=0.503 (0.033%), neg=0, invalid=96777
0567: dt=0.005000, rms=0.502 (0.036%), neg=0, invalid=96777
0568: dt=0.005000, rms=0.502 (0.039%), neg=0, invalid=96777
0569: dt=0.005000, rms=0.502 (0.039%), neg=0, invalid=96777
0570: dt=0.005000, rms=0.502 (0.041%), neg=0, invalid=96777
0571: dt=0.005000, rms=0.502 (0.046%), neg=0, invalid=96777
0572: dt=0.005000, rms=0.501 (0.040%), neg=0, invalid=96777
0573: dt=0.005000, rms=0.501 (0.048%), neg=0, invalid=96777
0574: dt=0.005000, rms=0.501 (0.044%), neg=0, invalid=96777
0575: dt=0.005000, rms=0.501 (0.047%), neg=0, invalid=96777
0576: dt=0.005000, rms=0.500 (0.044%), neg=0, invalid=96777
0577: dt=0.005000, rms=0.500 (0.041%), neg=0, invalid=96777
0578: dt=0.005000, rms=0.500 (0.044%), neg=0, invalid=96777
0579: dt=0.005000, rms=0.500 (0.039%), neg=0, invalid=96777
0580: dt=0.005000, rms=0.500 (0.044%), neg=0, invalid=96777
0581: dt=0.005000, rms=0.499 (0.041%), neg=0, invalid=96777
0582: dt=0.005000, rms=0.499 (0.041%), neg=0, invalid=96777
0583: dt=0.005000, rms=0.499 (0.037%), neg=0, invalid=96777
0584: dt=0.000625, rms=0.499 (-0.001%), neg=0, invalid=96777
0585: dt=0.000438, rms=0.499 (0.000%), neg=0, invalid=96777
0586: dt=0.028000, rms=0.499 (0.013%), neg=0, invalid=96777
0587: dt=0.000438, rms=0.499 (0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.499, neg=0, invalid=96777
0588: dt=0.028000, rms=0.498 (0.092%), neg=0, invalid=96777
0589: dt=0.080000, rms=0.497 (0.243%), neg=0, invalid=96777
0590: dt=0.001750, rms=0.497 (0.008%), neg=0, invalid=96777
0591: dt=0.001750, rms=0.497 (0.005%), neg=0, invalid=96777
0592: dt=0.001750, rms=0.497 (0.009%), neg=0, invalid=96777
0593: dt=0.001750, rms=0.497 (0.012%), neg=0, invalid=96777
0594: dt=0.001750, rms=0.497 (0.015%), neg=0, invalid=96777
0595: dt=0.001750, rms=0.497 (0.018%), neg=0, invalid=96777
0596: dt=0.001750, rms=0.497 (0.022%), neg=0, invalid=96777
0597: dt=0.001750, rms=0.497 (0.023%), neg=0, invalid=96777
0598: dt=0.001750, rms=0.497 (0.023%), neg=0, invalid=96777
0599: dt=0.001750, rms=0.496 (0.025%), neg=0, invalid=96777
0600: dt=0.001750, rms=0.496 (0.029%), neg=0, invalid=96777
0601: dt=0.001750, rms=0.496 (0.029%), neg=0, invalid=96777
0602: dt=0.001750, rms=0.496 (0.027%), neg=0, invalid=96777
0603: dt=0.001750, rms=0.496 (0.031%), neg=0, invalid=96777
0604: dt=0.001750, rms=0.496 (0.030%), neg=0, invalid=96777
0605: dt=0.001750, rms=0.496 (0.031%), neg=0, invalid=96777
0606: dt=0.001750, rms=0.495 (0.032%), neg=0, invalid=96777
0607: dt=0.001750, rms=0.495 (0.033%), neg=0, invalid=96777
0608: dt=0.001750, rms=0.495 (0.032%), neg=0, invalid=96777
0609: dt=0.001750, rms=0.495 (0.030%), neg=0, invalid=96777
0610: dt=0.001750, rms=0.495 (0.033%), neg=0, invalid=96777
0611: dt=0.001750, rms=0.495 (0.031%), neg=0, invalid=96777
0612: dt=0.001750, rms=0.494 (0.031%), neg=0, invalid=96777
0613: dt=0.001750, rms=0.494 (0.031%), neg=0, invalid=96777
0614: dt=0.001750, rms=0.494 (0.029%), neg=0, invalid=96777
0615: dt=0.001750, rms=0.494 (0.030%), neg=0, invalid=96777
0616: dt=0.001750, rms=0.494 (0.029%), neg=0, invalid=96777
0617: dt=0.001750, rms=0.494 (0.028%), neg=0, invalid=96777
0618: dt=0.001750, rms=0.494 (0.028%), neg=0, invalid=96777
0619: dt=0.001750, rms=0.493 (0.028%), neg=0, invalid=96777
0620: dt=0.001750, rms=0.493 (0.024%), neg=0, invalid=96777
0621: dt=0.001750, rms=0.493 (0.021%), neg=0, invalid=96777
0622: dt=0.112000, rms=0.493 (0.118%), neg=0, invalid=96777
0623: dt=0.028000, rms=0.493 (0.028%), neg=0, invalid=96777
0624: dt=0.028000, rms=0.492 (0.021%), neg=0, invalid=96777
0625: dt=0.003500, rms=0.492 (0.002%), neg=0, invalid=96777
0626: dt=0.003500, rms=0.492 (0.003%), neg=0, invalid=96777
0627: dt=0.003500, rms=0.492 (0.004%), neg=0, invalid=96777
0628: dt=0.003500, rms=0.492 (0.007%), neg=0, invalid=96777
0629: dt=0.003500, rms=0.492 (0.009%), neg=0, invalid=96777
0630: dt=0.003500, rms=0.492 (0.015%), neg=0, invalid=96777
0631: dt=0.003500, rms=0.492 (0.012%), neg=0, invalid=96777
0632: dt=0.028000, rms=0.492 (0.016%), neg=0, invalid=96777
0633: dt=0.112000, rms=0.492 (0.079%), neg=0, invalid=96777
0634: dt=0.000438, rms=0.492 (-0.004%), neg=0, invalid=96777
0635: dt=0.000438, rms=0.492 (0.000%), neg=0, invalid=96777
0636: dt=0.000438, rms=0.492 (0.000%), neg=0, invalid=96777
0637: dt=0.000438, rms=0.492 (0.001%), neg=0, invalid=96777
0638: dt=0.000438, rms=0.492 (0.000%), neg=0, invalid=96777
0639: dt=0.000438, rms=0.492 (0.001%), neg=0, invalid=96777
0640: dt=0.000438, rms=0.492 (0.001%), 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=0.490, neg=0, invalid=96777
0641: dt=8.092000, rms=0.490 (0.001%), neg=0, invalid=96777
0642: dt=4.624000, rms=0.490 (0.001%), neg=0, invalid=96777
0643: dt=0.090909, rms=0.490 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.490, neg=0, invalid=96777
0644: dt=129.472000, rms=0.490 (0.043%), neg=0, invalid=96777
0645: dt=129.472000, rms=0.490 (0.028%), neg=0, invalid=96777
0646: dt=129.472000, rms=0.490 (0.014%), neg=0, invalid=96777
0647: dt=129.472000, rms=0.489 (0.016%), neg=0, invalid=96777
0648: dt=129.472000, rms=0.489 (0.076%), neg=0, invalid=96777
0649: dt=129.472000, rms=0.489 (0.032%), neg=0, invalid=96777
0650: dt=129.472000, rms=0.489 (0.005%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.489, neg=0, invalid=96777
0651: dt=31.104000, rms=0.488 (0.122%), neg=0, invalid=96777
0652: dt=36.288000, rms=0.488 (0.066%), neg=0, invalid=96777
0653: dt=36.288000, rms=0.488 (0.029%), neg=0, invalid=96777
0654: dt=36.288000, rms=0.488 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.488, neg=0, invalid=96777
0655: dt=82.944000, rms=0.486 (0.326%), neg=0, invalid=96777
0656: dt=36.288000, rms=0.486 (0.161%), neg=0, invalid=96777
0657: dt=36.288000, rms=0.485 (0.081%), neg=0, invalid=96777
0658: dt=36.288000, rms=0.485 (0.120%), neg=0, invalid=96777
0659: dt=36.288000, rms=0.484 (0.117%), neg=0, invalid=96777
0660: dt=36.288000, rms=0.483 (0.189%), neg=0, invalid=96777
0661: dt=36.288000, rms=0.482 (0.126%), neg=0, invalid=96777
0662: dt=36.288000, rms=0.482 (0.148%), neg=0, invalid=96777
0663: dt=36.288000, rms=0.481 (0.078%), neg=0, invalid=96777
0664: dt=36.288000, rms=0.481 (0.140%), neg=0, invalid=96777
0665: dt=36.288000, rms=0.480 (0.079%), neg=0, invalid=96777
0666: dt=36.288000, rms=0.480 (0.087%), neg=0, invalid=96777
0667: dt=36.288000, rms=0.480 (0.082%), neg=0, invalid=96777
0668: dt=36.288000, rms=0.479 (0.022%), neg=0, invalid=96777
0669: dt=36.288000, rms=0.479 (0.013%), neg=0, invalid=96777
0670: dt=36.288000, rms=0.479 (0.039%), neg=0, invalid=96777
0671: dt=36.288000, rms=0.479 (0.045%), neg=0, invalid=96777
0672: dt=36.288000, rms=0.479 (0.040%), neg=0, invalid=96777
0673: dt=36.288000, rms=0.479 (0.032%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.479, neg=0, invalid=96777
0674: dt=32.000000, rms=0.477 (0.436%), neg=0, invalid=96777
0675: dt=9.600000, rms=0.476 (0.167%), neg=0, invalid=96777
0676: dt=9.600000, rms=0.475 (0.184%), neg=0, invalid=96777
0677: dt=9.600000, rms=0.474 (0.218%), neg=0, invalid=96777
iter 0, gcam->neg = 5
after 7 iterations, nbhd size=1, neg = 0
0678: dt=9.600000, rms=0.473 (0.274%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0679: dt=9.600000, rms=0.472 (0.211%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0680: dt=9.600000, rms=0.471 (0.223%), neg=0, invalid=96777
0681: dt=9.600000, rms=0.470 (0.148%), neg=0, invalid=96777
0682: dt=9.600000, rms=0.469 (0.165%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0683: dt=9.600000, rms=0.469 (0.138%), neg=0, invalid=96777
0684: dt=9.600000, rms=0.468 (0.186%), neg=0, invalid=96777
0685: dt=9.600000, rms=0.467 (0.163%), neg=0, invalid=96777
0686: dt=9.600000, rms=0.466 (0.174%), neg=0, invalid=96777
0687: dt=9.600000, rms=0.465 (0.176%), neg=0, invalid=96777
0688: dt=9.600000, rms=0.465 (0.159%), neg=0, invalid=96777
0689: dt=9.600000, rms=0.464 (0.156%), neg=0, invalid=96777
0690: dt=9.600000, rms=0.463 (0.111%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0691: dt=9.600000, rms=0.463 (0.114%), neg=0, invalid=96777
0692: dt=9.600000, rms=0.462 (0.085%), neg=0, invalid=96777
0693: dt=11.200000, rms=0.462 (0.051%), neg=0, invalid=96777
0694: dt=11.200000, rms=0.462 (0.011%), neg=0, invalid=96777
0695: dt=11.200000, rms=0.462 (0.050%), neg=0, invalid=96777
0696: dt=11.200000, rms=0.462 (0.058%), neg=0, invalid=96777
0697: dt=11.200000, rms=0.461 (0.054%), neg=0, invalid=96777
0698: dt=11.200000, rms=0.461 (0.030%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.461, neg=0, invalid=96777
0699: dt=32.000000, rms=0.459 (0.582%), neg=0, invalid=96777
0700: dt=6.400000, rms=0.458 (0.174%), neg=0, invalid=96777
0701: dt=6.400000, rms=0.457 (0.102%), neg=0, invalid=96777
0702: dt=6.400000, rms=0.457 (0.111%), neg=0, invalid=96777
0703: dt=6.400000, rms=0.456 (0.126%), neg=0, invalid=96777
0704: dt=6.400000, rms=0.456 (0.132%), neg=0, invalid=96777
0705: dt=6.400000, rms=0.455 (0.130%), neg=0, invalid=96777
0706: dt=6.400000, rms=0.455 (0.125%), neg=0, invalid=96777
0707: dt=6.400000, rms=0.454 (0.100%), neg=0, invalid=96777
0708: dt=11.200000, rms=0.454 (0.020%), neg=0, invalid=96777
0709: dt=11.200000, rms=0.454 (0.024%), neg=0, invalid=96777
0710: dt=11.200000, rms=0.454 (0.044%), neg=0, invalid=96777
0711: dt=11.200000, rms=0.453 (0.054%), neg=0, invalid=96777
0712: dt=11.200000, rms=0.453 (0.071%), neg=0, invalid=96777
0713: dt=11.200000, rms=0.453 (0.057%), neg=0, invalid=96777
0714: dt=11.200000, rms=0.453 (0.065%), neg=0, invalid=96777
0715: dt=11.200000, rms=0.452 (0.072%), neg=0, invalid=96777
0716: dt=11.200000, rms=0.452 (0.046%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.456, neg=0, invalid=96777
0717: dt=1.008000, rms=0.456 (0.014%), neg=0, invalid=96777
0718: dt=1.008000, rms=0.456 (0.002%), neg=0, invalid=96777
0719: dt=1.008000, rms=0.456 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.456, neg=0, invalid=96777
0720: dt=4.032000, rms=0.456 (0.043%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0721: dt=2.880000, rms=0.456 (0.014%), neg=0, invalid=96777
0722: dt=2.880000, rms=0.456 (0.017%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0723: dt=2.880000, rms=0.456 (0.011%), neg=0, invalid=96777
0724: dt=2.880000, rms=0.456 (-0.013%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.461, neg=0, invalid=96777
0725: dt=0.000000, rms=0.461 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.461, neg=0, invalid=96777
0726: dt=0.000013, rms=0.461 (0.000%), neg=0, invalid=96777
0727: dt=0.000013, rms=0.461 (-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=0.452, neg=0, invalid=96777
iter 0, gcam->neg = 843
after 32 iterations, nbhd size=3, neg = 0
0728: dt=1.923556, rms=0.409 (9.451%), neg=0, invalid=96777
0729: dt=0.000109, rms=0.409 (-0.007%), neg=0, invalid=96777
0730: dt=0.000109, rms=0.409 (0.001%), neg=0, invalid=96777
0731: dt=0.000109, 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
0732: dt=0.000438, rms=0.409 (0.001%), neg=0, invalid=96777
0733: dt=0.000000, rms=0.409 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 80
after 9 iterations, nbhd size=1, neg = 0
0734: dt=0.050000, rms=0.409 (-0.263%), 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=0.393, neg=0, invalid=96777
0735: dt=0.007902, rms=0.394 (-0.297%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.394, neg=0, invalid=96777
0736: dt=32.368000, rms=0.394 (0.007%), neg=0, invalid=96777
0737: dt=13.872000, rms=0.394 (0.000%), neg=0, invalid=96777
0738: dt=13.872000, rms=0.394 (-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=0.395, neg=0, invalid=96777
0739: dt=0.000000, rms=0.395 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.395, neg=0, invalid=96777
0740: dt=31.104000, rms=0.394 (0.015%), neg=0, invalid=96777
0741: dt=31.104000, rms=0.394 (0.004%), neg=0, invalid=96777
0742: dt=31.104000, rms=0.394 (0.002%), neg=0, invalid=96777
0743: dt=31.104000, rms=0.394 (-0.001%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.395, neg=0, invalid=96777
iter 0, gcam->neg = 2
after 16 iterations, nbhd size=2, neg = 0
0744: dt=8.000000, rms=0.395 (0.034%), neg=0, invalid=96777
0745: dt=0.000312, rms=0.395 (0.000%), neg=0, invalid=96777
0746: dt=0.000312, rms=0.395 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.395, neg=0, invalid=96777
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0747: dt=11.200000, rms=0.395 (0.040%), neg=0, invalid=96777
iter 0, gcam->neg = 31
after 37 iterations, nbhd size=4, neg = 0
0748: dt=44.800000, rms=0.394 (0.193%), neg=0, invalid=96777
0749: dt=1.200000, rms=0.394 (0.002%), neg=0, invalid=96777
0750: dt=1.200000, rms=0.394 (0.009%), neg=0, invalid=96777
0751: dt=1.200000, rms=0.394 (0.017%), neg=0, invalid=96777
0752: dt=1.200000, rms=0.394 (0.024%), neg=0, invalid=96777
0753: dt=1.200000, rms=0.394 (0.029%), neg=0, invalid=96777
0754: dt=1.200000, rms=0.394 (0.032%), neg=0, invalid=96777
0755: dt=1.200000, rms=0.394 (0.034%), neg=0, invalid=96777
0756: dt=1.200000, rms=0.393 (0.034%), neg=0, invalid=96777
0757: dt=1.200000, rms=0.393 (0.034%), neg=0, invalid=96777
0758: dt=1.200000, rms=0.393 (0.034%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.396, neg=0, invalid=96777
iter 0, gcam->neg = 31
after 43 iterations, nbhd size=4, neg = 0
0759: dt=5.142857, rms=0.395 (0.103%), neg=0, invalid=96777
0760: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0761: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0762: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0763: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0764: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0765: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0766: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0767: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0768: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0769: dt=0.002250, rms=0.395 (0.000%), neg=0, invalid=96777
0770: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0771: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0772: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0773: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0774: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0775: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0776: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0777: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0778: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0779: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0780: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0781: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0782: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0783: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0784: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0785: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0786: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0787: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0788: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0789: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0790: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0791: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0792: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0793: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0794: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
0795: dt=0.002250, rms=0.395 (0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.395, neg=0, invalid=96777
iter 0, gcam->neg = 131
after 48 iterations, nbhd size=4, neg = 0
0796: dt=11.971429, rms=0.393 (0.565%), neg=0, invalid=96777
0797: dt=0.003938, rms=0.393 (0.000%), neg=0, invalid=96777
0798: dt=0.003938, rms=0.393 (0.000%), neg=0, invalid=96777
0799: dt=0.003938, rms=0.393 (-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=0.398, neg=0, invalid=96777
0800: dt=0.000000, rms=0.398 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.398, neg=0, invalid=96777
0801: dt=0.000160, rms=0.398 (0.000%), neg=0, invalid=96777
0802: dt=0.000000, rms=0.398 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 11
after 7 iterations, nbhd size=1, neg = 0
0803: dt=0.100000, rms=0.398 (-0.085%), 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=0.389, neg=0, invalid=96777
iter 0, gcam->neg = 498
after 31 iterations, nbhd size=3, neg = 0
0804: dt=0.754808, rms=0.377 (3.133%), neg=0, invalid=96777
0805: dt=0.000020, rms=0.377 (0.002%), neg=0, invalid=96777
0806: dt=0.000020, rms=0.377 (0.001%), neg=0, invalid=96777
0807: dt=0.000020, rms=0.377 (0.001%), neg=0, invalid=96777
0808: dt=0.000020, rms=0.377 (0.000%), neg=0, invalid=96777
0809: dt=0.000020, rms=0.377 (0.000%), neg=0, invalid=96777
0810: dt=0.000000, rms=0.377 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.377, neg=0, invalid=96777
0811: dt=0.000750, rms=0.377 (0.001%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0812: dt=0.004000, rms=0.377 (0.002%), neg=0, invalid=96777
0813: dt=0.001750, rms=0.377 (0.001%), neg=0, invalid=96777
iter 0, gcam->neg = 11
after 1 iterations, nbhd size=0, neg = 0
0814: dt=0.001750, rms=0.377 (0.001%), neg=0, invalid=96777
iter 0, gcam->neg = 11
after 1 iterations, nbhd size=0, neg = 0
0815: dt=0.001750, rms=0.377 (0.002%), neg=0, invalid=96777
iter 0, gcam->neg = 11
after 1 iterations, nbhd size=0, neg = 0
0816: dt=0.001750, rms=0.377 (0.003%), neg=0, invalid=96777
iter 0, gcam->neg = 11
after 1 iterations, nbhd size=0, neg = 0
0817: dt=0.001750, rms=0.377 (0.004%), neg=0, invalid=96777
iter 0, gcam->neg = 11
after 1 iterations, nbhd size=0, neg = 0
0818: dt=0.001750, rms=0.377 (0.005%), neg=0, invalid=96777
iter 0, gcam->neg = 20
after 1 iterations, nbhd size=0, neg = 0
0819: dt=0.001750, rms=0.377 (0.006%), neg=0, invalid=96777
iter 0, gcam->neg = 29
after 6 iterations, nbhd size=1, neg = 0
0820: dt=0.001750, rms=0.377 (0.006%), neg=0, invalid=96777
iter 0, gcam->neg = 29
after 0 iterations, nbhd size=0, neg = 0
0821: dt=0.001750, rms=0.377 (0.006%), neg=0, invalid=96777
iter 0, gcam->neg = 33
after 1 iterations, nbhd size=0, neg = 0
0822: dt=0.001750, rms=0.377 (0.006%), neg=0, invalid=96777
iter 0, gcam->neg = 31
after 1 iterations, nbhd size=0, neg = 0
0823: dt=0.001750, rms=0.377 (0.007%), neg=0, invalid=96777
iter 0, gcam->neg = 29
after 0 iterations, nbhd size=0, neg = 0
0824: dt=0.001750, rms=0.377 (0.006%), neg=0, invalid=96777
iter 0, gcam->neg = 27
after 7 iterations, nbhd size=1, neg = 0
0825: dt=0.001750, rms=0.377 (0.007%), neg=0, invalid=96777
iter 0, gcam->neg = 27
after 7 iterations, nbhd size=1, neg = 0
0826: dt=0.001750, rms=0.377 (0.007%), neg=0, invalid=96777
writing output transformation to transforms/talairach.m3z...
GCAMwrite
registration took 4 hours, 29 minutes and 22 seconds.
#--------------------------------------
#@# CA Reg Inv Thu Aug  8 16:45:53 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 16:47:27 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...
11782618 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 1 minutes and 34 seconds.
#--------------------------------------
#@# SkullLTA Thu Aug  8 16:49:01 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=10.0
skull bounding box = (52, 28, 27) --> (203, 194, 199)
using (102, 83, 113) as brain centroid...
mean wm in atlas = 126, using box (83,63,92) --> (120, 103,134) to find MRI wm
before smoothing, mri peak at 109
after smoothing, mri peak at 109, scaling input intensities by 1.156
scaling channel 0 by 1.15596
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2)
 1.095  -0.072   0.039  -10.025;
 0.055   1.276   0.255  -44.216;
-0.091  -0.284   1.027   27.244;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.095  -0.072   0.039  -10.025;
 0.055   1.276   0.255  -44.216;
-0.091  -0.284   1.027   27.244;
 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 =-4.0 (thresh=-4.0)
 1.136  -0.075   0.041  -15.117;
 0.059   1.244   0.180  -32.716;
-0.093  -0.211   1.101   11.506;
 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)
 1.136  -0.075   0.041  -15.117;
 0.059   1.244   0.180  -32.716;
-0.093  -0.211   1.101   11.506;
 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)
 1.136  -0.075   0.041  -15.117;
 0.059   1.245   0.180  -32.896;
-0.093  -0.211   1.101   11.506;
 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
 1.13637  -0.07456   0.04070  -15.11703;
 0.05882   1.24525   0.18004  -32.89606;
-0.09253  -0.21080   1.10093   11.50646;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.13637  -0.07456   0.04070  -15.11703;
 0.05882   1.24525   0.18004  -32.89606;
-0.09253  -0.21080   1.10093   11.50646;
 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: 006: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.136  -0.075   0.041  -15.117;
 0.059   1.245   0.180  -32.896;
-0.093  -0.211   1.101   11.506;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
transform before final EM align:
 1.136  -0.075   0.041  -15.117;
 0.059   1.245   0.180  -32.896;
-0.093  -0.211   1.101   11.506;
 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
 1.13637  -0.07456   0.04070  -15.11703;
 0.05882   1.24525   0.18004  -32.89606;
-0.09253  -0.21080   1.10093   11.50646;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.13637  -0.07456   0.04070  -15.11703;
 0.05882   1.24525   0.18004  -32.89606;
-0.09253  -0.21080   1.10093   11.50646;
 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: 008: -log(p) =    4.4  tol 0.000000
final transform:
 1.136  -0.075   0.041  -15.117;
 0.059   1.245   0.180  -32.896;
-0.093  -0.211   1.101   11.506;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull_2.lta...
registration took 25 minutes and 7 seconds.
#--------------------------------------
#@# SubCort Seg Thu Aug  8 17:14:08 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/sub013/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 = 0.13628 (10)
Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (536 voxels, overlap=0.006)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (536 voxels, peak =  9), gca=10.8
gca peak = 0.14982 (20)
mri peak = 0.12903 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (235 voxels, overlap=0.007)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (235 voxels, peak =  7), gca=8.0
gca peak = 0.28003 (97)
mri peak = 0.10513 (93)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (387 voxels, overlap=0.323)
Right_Pallidum (52): linear fit = 0.92 x + 0.0 (387 voxels, peak = 89), gca=88.8
gca peak = 0.18160 (96)
mri peak = 0.10819 (85)
Left_Pallidum (13): linear fit = 0.86 x + 0.0 (344 voxels, overlap=0.061)
Left_Pallidum (13): linear fit = 0.86 x + 0.0 (344 voxels, peak = 82), gca=82.1
gca peak = 0.27536 (62)
mri peak = 0.08553 (60)
Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (545 voxels, overlap=0.872)
Right_Hippocampus (53): linear fit = 0.95 x + 0.0 (545 voxels, peak = 59), gca=59.2
gca peak = 0.32745 (63)
mri peak = 0.08616 (61)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (533 voxels, overlap=0.783)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (533 voxels, peak = 58), gca=58.3
gca peak = 0.08597 (105)
mri peak = 0.09958 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (24923 voxels, overlap=0.558)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (24923 voxels, peak = 109), gca=108.7
gca peak = 0.09209 (106)
mri peak = 0.10253 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (21975 voxels, overlap=0.564)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (21975 voxels, peak = 110), gca=109.7
gca peak = 0.07826 (63)
mri peak = 0.05715 (55)
Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (9916 voxels, overlap=0.445)
Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (9916 voxels, peak = 55), gca=55.1
gca peak = 0.08598 (64)
mri peak = 0.05531 (56)
Right_Cerebral_Cortex (42): linear fit = 0.85 x + 0.0 (8262 voxels, overlap=0.343)
Right_Cerebral_Cortex (42): linear fit = 0.85 x + 0.0 (8262 voxels, peak = 54), gca=54.1
gca peak = 0.24164 (71)
mri peak = 0.11036 (68)
Right_Caudate (50): linear fit = 0.94 x + 0.0 (585 voxels, overlap=1.013)
Right_Caudate (50): linear fit = 0.94 x + 0.0 (585 voxels, peak = 67), gca=67.1
gca peak = 0.18227 (75)
mri peak = 0.08733 (75)
Left_Caudate (11): linear fit = 0.90 x + 0.0 (937 voxels, overlap=0.497)
Left_Caudate (11): linear fit = 0.90 x + 0.0 (937 voxels, peak = 68), gca=67.9
gca peak = 0.10629 (62)
mri peak = 0.05016 (63)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5280 voxels, overlap=0.988)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5280 voxels, peak = 64), gca=63.5
gca peak = 0.11668 (59)
mri peak = 0.05479 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (5271 voxels, overlap=0.999)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (5271 voxels, peak = 60), gca=60.5
gca peak = 0.17849 (88)
mri peak = 0.08720 (92)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (3452 voxels, overlap=0.815)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (3452 voxels, peak = 95), gca=94.6
gca peak = 0.16819 (86)
mri peak = 0.09189 (92)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (3976 voxels, overlap=0.896)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (3976 voxels, peak = 92), gca=91.6
gca peak = 0.41688 (64)
mri peak = 0.09705 (62)
Left_Amygdala (18): linear fit = 0.95 x + 0.0 (240 voxels, overlap=1.041)
Left_Amygdala (18): linear fit = 0.95 x + 0.0 (240 voxels, peak = 61), gca=61.1
gca peak = 0.42394 (62)
mri peak = 0.10480 (58)
Right_Amygdala (54): linear fit = 0.92 x + 0.0 (230 voxels, overlap=1.046)
Right_Amygdala (54): linear fit = 0.92 x + 0.0 (230 voxels, peak = 57), gca=56.7
gca peak = 0.10041 (96)
mri peak = 0.06634 (89)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (2711 voxels, overlap=0.909)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (2711 voxels, peak = 92), gca=91.7
gca peak = 0.13978 (88)
mri peak = 0.07587 (86)
Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2962 voxels, overlap=0.754)
Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (2962 voxels, peak = 84), gca=84.0
gca peak = 0.08514 (81)
mri peak = 0.06258 (71)
Left_Putamen (12): linear fit = 0.87 x + 0.0 (1348 voxels, overlap=0.538)
Left_Putamen (12): linear fit = 0.87 x + 0.0 (1348 voxels, peak = 70), gca=70.1
gca peak = 0.09624 (82)
mri peak = 0.07460 (75)
Right_Putamen (51): linear fit = 0.94 x + 0.0 (1674 voxels, overlap=0.685)
Right_Putamen (51): linear fit = 0.94 x + 0.0 (1674 voxels, peak = 77), gca=76.7
gca peak = 0.07543 (88)
mri peak = 0.09234 (86)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (8975 voxels, overlap=0.764)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (8975 voxels, peak = 87), gca=86.7
gca peak = 0.12757 (95)
mri peak = 0.07259 (91)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (784 voxels, overlap=0.768)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (784 voxels, peak = 92), gca=91.7
gca peak = 0.17004 (92)
mri peak = 0.06643 (94)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (935 voxels, overlap=0.942)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (935 voxels, peak = 92), gca=91.5
gca peak = 0.21361 (36)
mri peak = 0.33333 (10)
gca peak = 0.26069 (23)
mri peak = 0.25488 (10)
Fourth_Ventricle (15): linear fit = 0.40 x + 0.0 (98 voxels, overlap=0.022)
Fourth_Ventricle (15): linear fit = 0.40 x + 0.0 (98 voxels, peak =  9), gca=9.1
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 0.91 x + 0.0
estimating mean wm scale to be 1.03 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 = 0.13628 (10)
Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (536 voxels, overlap=0.968)
Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (536 voxels, peak =  9), gca=9.0
gca peak = 0.29325 ( 9)
mri peak = 0.12903 ( 9)
Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (235 voxels, overlap=0.938)
Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (235 voxels, peak =  8), gca=8.3
gca peak = 0.32314 (89)
mri peak = 0.10513 (93)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (387 voxels, overlap=1.021)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (387 voxels, peak = 89), gca=88.6
gca peak = 0.22699 (82)
mri peak = 0.10819 (85)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (344 voxels, overlap=1.015)
Left_Pallidum (13): linear fit = 1.02 x + 0.0 (344 voxels, peak = 84), gca=84.0
gca peak = 0.29992 (59)
mri peak = 0.08553 (60)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (545 voxels, overlap=1.007)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (545 voxels, peak = 59), gca=59.0
gca peak = 0.29472 (58)
mri peak = 0.08616 (61)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (533 voxels, overlap=1.007)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (533 voxels, peak = 58), gca=58.0
gca peak = 0.08269 (109)
mri peak = 0.09958 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24923 voxels, overlap=0.712)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (24923 voxels, peak = 110), gca=109.5
gca peak = 0.08544 (110)
mri peak = 0.10253 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (21975 voxels, overlap=0.685)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (21975 voxels, peak = 110), gca=110.0
gca peak = 0.08975 (55)
mri peak = 0.05715 (55)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (9916 voxels, overlap=0.922)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (9916 voxels, peak = 54), gca=54.2
gca peak = 0.09945 (54)
mri peak = 0.05531 (56)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (8262 voxels, overlap=0.977)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (8262 voxels, peak = 54), gca=54.0
gca peak = 0.23211 (69)
mri peak = 0.11036 (68)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (585 voxels, overlap=1.009)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (585 voxels, peak = 69), gca=69.0
gca peak = 0.18196 (68)
mri peak = 0.08733 (75)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (937 voxels, overlap=0.995)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (937 voxels, peak = 69), gca=69.0
gca peak = 0.10217 (62)
mri peak = 0.05016 (63)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5280 voxels, overlap=0.997)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (5280 voxels, peak = 64), gca=63.5
gca peak = 0.12512 (61)
mri peak = 0.05479 (63)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (5271 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (5271 voxels, peak = 61), gca=61.0
gca peak = 0.17137 (94)
mri peak = 0.08720 (92)
Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (3452 voxels, overlap=0.994)
Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (3452 voxels, peak = 92), gca=91.7
gca peak = 0.16105 (92)
mri peak = 0.09189 (92)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3976 voxels, overlap=0.998)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3976 voxels, peak = 92), gca=91.5
gca peak = 0.46581 (61)
mri peak = 0.09705 (62)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (240 voxels, overlap=1.032)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (240 voxels, peak = 61), gca=61.0
gca peak = 0.48938 (57)
mri peak = 0.10480 (58)
Right_Amygdala (54): linear fit = 1.10 x + 0.0 (230 voxels, overlap=1.041)
Right_Amygdala (54): linear fit = 1.10 x + 0.0 (230 voxels, peak = 62), gca=62.4
gca peak = 0.11149 (90)
mri peak = 0.06634 (89)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2711 voxels, overlap=0.963)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2711 voxels, peak = 90), gca=89.6
gca peak = 0.14413 (84)
mri peak = 0.07587 (86)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2962 voxels, overlap=0.951)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2962 voxels, peak = 84), gca=83.6
gca peak = 0.09590 (71)
mri peak = 0.06258 (71)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (1348 voxels, overlap=0.998)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (1348 voxels, peak = 73), gca=73.5
gca peak = 0.10488 (71)
mri peak = 0.07460 (75)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1674 voxels, overlap=0.991)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1674 voxels, peak = 71), gca=71.0
gca peak = 0.07636 (87)
mri peak = 0.09234 (86)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (8975 voxels, overlap=0.725)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (8975 voxels, peak = 88), gca=88.3
gca peak = 0.14282 (91)
mri peak = 0.07259 (91)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (784 voxels, overlap=0.874)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (784 voxels, peak = 92), gca=92.4
gca peak = 0.17216 (92)
mri peak = 0.06643 (94)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (935 voxels, overlap=0.943)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (935 voxels, peak = 93), gca=93.4
gca peak = 0.35640 (14)
mri peak = 0.33333 (10)
gca peak = 0.33827 ( 9)
mri peak = 0.25488 (10)
Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (98 voxels, overlap=0.866)
Fourth_Ventricle (15): linear fit = 0.94 x + 0.0 (98 voxels, peak =  9), gca=8.5
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.24950 (33)
gca peak Third_Ventricle = 0.35640 (14)
gca peak CSF = 0.30128 (18)
gca peak Left_Accumbens_area = 0.57696 (63)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.58667 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.24675 (30)
gca peak Right_Accumbens_area = 0.31095 (68)
gca peak Right_vessel = 0.56475 (60)
gca peak Right_choroid_plexus = 0.10226 (48)
gca peak Fifth_Ventricle = 0.45329 (19)
gca peak WM_hypointensities = 0.14808 (84)
gca peak non_WM_hypointensities = 0.10295 (55)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.89 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
9775 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels)
234 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 78974 changed. image ll: -2.148, PF=1.000
pass 2: 13824 changed. image ll: -2.147, PF=1.000
pass 3: 5218 changed.
pass 4: 2391 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
auto-labeling took 19 minutes and 26 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/cc_up.lta sub013 

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/sub013/mri/transforms/cc_up.lta
reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aseg.auto_noCCseg.mgz
reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/norm.mgz
30385 voxels in left wm, 28632 in right wm, xrange [122, 131]
searching rotation angles z=[-6  8], y=[-3 11]

searching scale 1 Z rot -5.8  
searching scale 1 Z rot -5.6  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.1  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.4  
searching scale 1 Z rot 6.7  
searching scale 1 Z rot 6.9  
searching scale 1 Z rot 7.2  
searching scale 1 Z rot 7.4  
searching scale 1 Z rot 7.7  
searching scale 1 Z rot 7.9  global minimum found at slice 126.1, rotations (3.53, 1.18)
final transformation (x=126.1, yr=3.532, zr=1.181):
 0.998  -0.021   0.062  -3.059;
 0.021   1.000   0.001   45.281;
-0.062   0.000   0.998   24.982;
 0.000   0.000   0.000   1.000;
updating x range to be [124, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 152 114
eigenvectors:
-0.001  -0.006   1.000;
-0.091  -0.996  -0.006;
 0.996  -0.091   0.001;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aseg.auto.mgz...
corpus callosum matter segmentation took 0.8 minutes
#--------------------------------------
#@# Merge ASeg Thu Aug  8 17:34:20 CEST 2013

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Thu Aug  8 17:34:20 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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...
2409 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 110
gm peak at 56 (56), valley at 31 (31)
csf peak at 10, setting threshold to 40
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 58 (58), valley at 32 (32)
csf peak at 10, setting threshold to 42
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 4 minutes and 9 seconds.
#--------------------------------------------
#@# Mask BFS Thu Aug  8 17:38:31 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1358979 voxels in mask (pct=  8.10)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Thu Aug  8 17:38:33 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): 107.2 +- 4.7 [80.0 --> 125.0]
GM (67.0) : 66.5 +- 9.5 [30.0 --> 96.0]
setting bottom of white matter range to 76.0
setting top of gray matter range to 85.5
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...
5757 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4922 filled
492 bright non-wm voxels segmented.
3330 diagonally connected voxels added...
white matter segmentation took 1.7 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 0.61 minutes
reading wm segmentation from wm.seg.mgz...
31 voxels added to wm to prevent paths from MTL structures to cortex
1028 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 36068 voxels turned on, 33017 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+):  13 found -  13 modified     |    TOTAL:  13
pass   2 (xy+):   0 found -  13 modified     |    TOTAL:  13
pass   1 (xy-):  14 found -  14 modified     |    TOTAL:  27
pass   2 (xy-):   0 found -  14 modified     |    TOTAL:  27
pass   1 (yz+):  20 found -  20 modified     |    TOTAL:  47
pass   2 (yz+):   0 found -  20 modified     |    TOTAL:  47
pass   1 (yz-):  21 found -  21 modified     |    TOTAL:  68
pass   2 (yz-):   0 found -  21 modified     |    TOTAL:  68
pass   1 (xz+):  12 found -  12 modified     |    TOTAL:  80
pass   2 (xz+):   0 found -  12 modified     |    TOTAL:  80
pass   1 (xz-):  15 found -  15 modified     |    TOTAL:  95
pass   2 (xz-):   0 found -  15 modified     |    TOTAL:  95
Iteration Number : 1
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  10
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  10
pass   1 (+++):  15 found -  15 modified     |    TOTAL:  25
pass   2 (+++):   0 found -  15 modified     |    TOTAL:  25
pass   1 (+++):   8 found -   8 modified     |    TOTAL:  33
pass   2 (+++):   0 found -   8 modified     |    TOTAL:  33
pass   1 (+++):  29 found -  29 modified     |    TOTAL:  62
pass   2 (+++):   0 found -  29 modified     |    TOTAL:  62
Iteration Number : 1
pass   1 (++): 158 found - 158 modified     |    TOTAL: 158
pass   2 (++):   0 found - 158 modified     |    TOTAL: 158
pass   1 (+-): 148 found - 148 modified     |    TOTAL: 306
pass   2 (+-):   1 found - 149 modified     |    TOTAL: 307
pass   3 (+-):   0 found - 149 modified     |    TOTAL: 307
pass   1 (--): 147 found - 147 modified     |    TOTAL: 454
pass   2 (--):   0 found - 147 modified     |    TOTAL: 454
pass   1 (-+): 175 found - 175 modified     |    TOTAL: 629
pass   2 (-+):   0 found - 175 modified     |    TOTAL: 629
Iteration Number : 2
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:   8
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   8
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:  11
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:  11
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:  11
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  15
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  15
pass   1 (xz-):   7 found -   7 modified     |    TOTAL:  22
pass   2 (xz-):   0 found -   7 modified     |    TOTAL:  22
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 (++):   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
pass   1 (--):   1 found -   1 modified     |    TOTAL:   5
pass   2 (--):   0 found -   1 modified     |    TOTAL:   5
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   6
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 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 = 815 (out of 458383: 0.177799)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Thu Aug  8 17:40:55 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.284   1.027   27.244;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 1.095  -0.072   0.039  -10.025;
 0.052   1.200   0.239  -34.308;
-0.091  -0.284   1.027   27.244;
 0.000   0.000   0.000   1.000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2203 (min = 350, max = 1400), aspect = 1.13 (min = 0.10, max = 0.75)
need search nearby
using seed (126, 119, 149), TAL = (2.0, 21.0, 9.0)
talairach voxel to voxel transform
 0.907   0.044  -0.045   11.817;
-0.052   0.787  -0.181   31.431;
 0.066   0.221   0.919  -16.797;
 0.000   0.000   0.000   1.000;
segmentation indicates cc at (126,  119,  149) --> (2.0, 21.0, 9.0)
done.
writing output to filled.mgz...
filling took 0.9 minutes
talairach cc position changed to (2.00, 21.00, 9.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 21.00, 9.00) SRC: (108.32, 92.43, 153.68)
search lh wm seed point around talairach space (-16.00, 21.00, 9.00), SRC: (140.98, 90.54, 156.07)
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 17:41:51 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   4
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:   8
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:   8
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   8
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  10
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  10
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 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 12 (out of 218937: 0.005481)
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 50: 2189 vertices, 2317 faces
slice 60: 8334 vertices, 8599 faces
slice 70: 17664 vertices, 17991 faces
slice 80: 27741 vertices, 28066 faces
slice 90: 38701 vertices, 39052 faces
slice 100: 49286 vertices, 49670 faces
slice 110: 61177 vertices, 61563 faces
slice 120: 72148 vertices, 72547 faces
slice 130: 82525 vertices, 82909 faces
slice 140: 94017 vertices, 94459 faces
slice 150: 103334 vertices, 103683 faces
slice 160: 111346 vertices, 111631 faces
slice 170: 118304 vertices, 118561 faces
slice 180: 124270 vertices, 124496 faces
slice 190: 128924 vertices, 129109 faces
slice 200: 130598 vertices, 130646 faces
slice 210: 130598 vertices, 130646 faces
slice 220: 130598 vertices, 130646 faces
slice 230: 130598 vertices, 130646 faces
slice 240: 130598 vertices, 130646 faces
slice 250: 130598 vertices, 130646 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...
   130598 voxel in cpt #1: X=-48 [v=130598,e=391938,f=261292] located at (-25.073286, -13.639091, 37.046310)
For the whole surface: X=-48 [v=130598,e=391938,f=261292]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Thu Aug  8 17:41:58 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 17:42:02 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts
avg radius = 44.6 mm, total surface area = 68201 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.5 minutes
Not saving sulc

step 000: RMS=0.102 (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=0.026 (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=0.023 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Thu Aug  8 17:42:33 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 1.01 +- 0.58 (0.00-->6.09) (max @ vno 95877 --> 95878)
face area 0.03 +- 0.03 (-0.11-->0.60)
scaling brain by 0.318...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.739, avgs=0
005/300: dt: 0.9000, rms radial error=176.480, avgs=0
010/300: dt: 0.9000, rms radial error=175.926, avgs=0
015/300: dt: 0.9000, rms radial error=175.198, avgs=0
020/300: dt: 0.9000, rms radial error=174.370, avgs=0
025/300: dt: 0.9000, rms radial error=173.484, avgs=0
030/300: dt: 0.9000, rms radial error=172.565, avgs=0
035/300: dt: 0.9000, rms radial error=171.631, avgs=0
040/300: dt: 0.9000, rms radial error=170.689, avgs=0
045/300: dt: 0.9000, rms radial error=169.745, avgs=0
050/300: dt: 0.9000, rms radial error=168.801, avgs=0
055/300: dt: 0.9000, rms radial error=167.860, avgs=0
060/300: dt: 0.9000, rms radial error=166.922, avgs=0
065/300: dt: 0.9000, rms radial error=165.987, avgs=0
070/300: dt: 0.9000, rms radial error=165.058, avgs=0
075/300: dt: 0.9000, rms radial error=164.133, avgs=0
080/300: dt: 0.9000, rms radial error=163.213, avgs=0
085/300: dt: 0.9000, rms radial error=162.298, avgs=0
090/300: dt: 0.9000, rms radial error=161.387, avgs=0
095/300: dt: 0.9000, rms radial error=160.481, avgs=0
100/300: dt: 0.9000, rms radial error=159.579, avgs=0
105/300: dt: 0.9000, rms radial error=158.682, avgs=0
110/300: dt: 0.9000, rms radial error=157.790, avgs=0
115/300: dt: 0.9000, rms radial error=156.903, avgs=0
120/300: dt: 0.9000, rms radial error=156.020, avgs=0
125/300: dt: 0.9000, rms radial error=155.142, avgs=0
130/300: dt: 0.9000, rms radial error=154.269, avgs=0
135/300: dt: 0.9000, rms radial error=153.401, avgs=0
140/300: dt: 0.9000, rms radial error=152.538, avgs=0
145/300: dt: 0.9000, rms radial error=151.679, avgs=0
150/300: dt: 0.9000, rms radial error=150.825, avgs=0
155/300: dt: 0.9000, rms radial error=149.975, avgs=0
160/300: dt: 0.9000, rms radial error=149.130, avgs=0
165/300: dt: 0.9000, rms radial error=148.290, avgs=0
170/300: dt: 0.9000, rms radial error=147.454, avgs=0
175/300: dt: 0.9000, rms radial error=146.623, avgs=0
180/300: dt: 0.9000, rms radial error=145.798, avgs=0
185/300: dt: 0.9000, rms radial error=144.979, avgs=0
190/300: dt: 0.9000, rms radial error=144.163, avgs=0
195/300: dt: 0.9000, rms radial error=143.352, avgs=0
200/300: dt: 0.9000, rms radial error=142.546, avgs=0
205/300: dt: 0.9000, rms radial error=141.744, avgs=0
210/300: dt: 0.9000, rms radial error=140.947, avgs=0
215/300: dt: 0.9000, rms radial error=140.153, avgs=0
220/300: dt: 0.9000, rms radial error=139.365, avgs=0
225/300: dt: 0.9000, rms radial error=138.580, avgs=0
230/300: dt: 0.9000, rms radial error=137.800, avgs=0
235/300: dt: 0.9000, rms radial error=137.024, avgs=0
240/300: dt: 0.9000, rms radial error=136.253, avgs=0
245/300: dt: 0.9000, rms radial error=135.485, avgs=0
250/300: dt: 0.9000, rms radial error=134.722, avgs=0
255/300: dt: 0.9000, rms radial error=133.964, avgs=0
260/300: dt: 0.9000, rms radial error=133.209, avgs=0
265/300: dt: 0.9000, rms radial error=132.459, avgs=0
270/300: dt: 0.9000, rms radial error=131.713, avgs=0
275/300: dt: 0.9000, rms radial error=130.971, avgs=0
280/300: dt: 0.9000, rms radial error=130.233, avgs=0
285/300: dt: 0.9000, rms radial error=129.499, avgs=0
290/300: dt: 0.9000, rms radial error=128.769, avgs=0
295/300: dt: 0.9000, rms radial error=128.044, avgs=0
300/300: dt: 0.9000, rms radial error=127.322, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 15190.87
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
epoch 2 (K=40.0), pass 1, starting sse = 2496.24
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
epoch 3 (K=160.0), pass 1, starting sse = 247.74
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.12/12 = 0.00960
epoch 4 (K=640.0), pass 1, starting sse = 13.36
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.17/17 = 0.00976
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 17:47:07 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/sub013/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub013 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=-48 (nv=130598, nf=261292, ne=391938, g=25)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
2324 ambiguous faces found in tessellation
segmenting defects...
27 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 5 into 3
26 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7427  (-4.8714)
      -vertex     loglikelihood: -6.6606  (-3.3303)
      -normal dot loglikelihood: -3.6239  (-3.6239)
      -quad curv  loglikelihood: -6.4179  (-3.2090)
      Total Loglikelihood : -26.4451

CORRECTING DEFECT 0 (vertices=28, convex hull=73)
After retessellation of defect 0, euler #=-21 (129159,386820,257640) : difference with theory (-23) = -2 

CORRECTING DEFECT 1 (vertices=31, convex hull=66)
After retessellation of defect 1, euler #=-20 (129178,386903,257705) : difference with theory (-22) = -2 

CORRECTING DEFECT 2 (vertices=6, convex hull=21)
After retessellation of defect 2, euler #=-19 (129179,386910,257712) : difference with theory (-21) = -2 

CORRECTING DEFECT 3 (vertices=149, convex hull=141)
After retessellation of defect 3, euler #=-17 (129234,387140,257889) : difference with theory (-20) = -3 

CORRECTING DEFECT 4 (vertices=35, convex hull=67)
After retessellation of defect 4, euler #=-16 (129244,387197,257937) : difference with theory (-19) = -3 

CORRECTING DEFECT 5 (vertices=50, convex hull=78)
After retessellation of defect 5, euler #=-15 (129267,387304,258022) : difference with theory (-18) = -3 

CORRECTING DEFECT 6 (vertices=18, convex hull=29)
After retessellation of defect 6, euler #=-14 (129270,387321,258037) : difference with theory (-17) = -3 

CORRECTING DEFECT 7 (vertices=102, convex hull=109)
After retessellation of defect 7, euler #=-15 (129296,387458,258147) : difference with theory (-16) = -1 

CORRECTING DEFECT 8 (vertices=11, convex hull=21)
After retessellation of defect 8, euler #=-14 (129298,387468,258156) : difference with theory (-15) = -1 

CORRECTING DEFECT 9 (vertices=18, convex hull=28)
After retessellation of defect 9, euler #=-13 (129303,387493,258177) : difference with theory (-14) = -1 

CORRECTING DEFECT 10 (vertices=256, convex hull=97)
After retessellation of defect 10, euler #=-12 (129337,387640,258291) : difference with theory (-13) = -1 

CORRECTING DEFECT 11 (vertices=34, convex hull=41)
After retessellation of defect 11, euler #=-11 (129347,387686,258328) : difference with theory (-12) = -1 

CORRECTING DEFECT 12 (vertices=223, convex hull=99)
After retessellation of defect 12, euler #=-10 (129386,387848,258452) : difference with theory (-11) = -1 

CORRECTING DEFECT 13 (vertices=8, convex hull=15)
After retessellation of defect 13, euler #=-9 (129387,387854,258458) : difference with theory (-10) = -1 

CORRECTING DEFECT 14 (vertices=95, convex hull=108)
After retessellation of defect 14, euler #=-9 (129404,387962,258549) : difference with theory (-9) = 0 

CORRECTING DEFECT 15 (vertices=9, convex hull=19)
After retessellation of defect 15, euler #=-8 (129408,387977,258561) : difference with theory (-8) = 0 

CORRECTING DEFECT 16 (vertices=28, convex hull=46)
After retessellation of defect 16, euler #=-7 (129417,388022,258598) : difference with theory (-7) = 0 

CORRECTING DEFECT 17 (vertices=89, convex hull=101)
After retessellation of defect 17, euler #=-6 (129459,388193,258728) : difference with theory (-6) = 0 

CORRECTING DEFECT 18 (vertices=48, convex hull=81)
After retessellation of defect 18, euler #=-5 (129473,388270,258792) : difference with theory (-5) = 0 

CORRECTING DEFECT 19 (vertices=11, convex hull=25)
After retessellation of defect 19, euler #=-4 (129475,388285,258806) : difference with theory (-4) = 0 

CORRECTING DEFECT 20 (vertices=7, convex hull=23)
After retessellation of defect 20, euler #=-3 (129476,388296,258817) : difference with theory (-3) = 0 

CORRECTING DEFECT 21 (vertices=25, convex hull=53)
After retessellation of defect 21, euler #=-2 (129487,388347,258858) : difference with theory (-2) = 0 

CORRECTING DEFECT 22 (vertices=32, convex hull=71)
After retessellation of defect 22, euler #=-1 (129501,388416,258914) : difference with theory (-1) = 0 

CORRECTING DEFECT 23 (vertices=23, convex hull=85)
After retessellation of defect 23, euler #=0 (129515,388489,258974) : difference with theory (0) = 0 

CORRECTING DEFECT 24 (vertices=106, convex hull=99)
After retessellation of defect 24, euler #=1 (129541,388612,259072) : difference with theory (1) = 0 

CORRECTING DEFECT 25 (vertices=7, convex hull=18)
After retessellation of defect 25, euler #=2 (129542,388620,259080) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.05-->7.46) (max @ vno 68081 --> 72523)
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 (0.05-->7.46) (max @ vno 68081 --> 72523)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
102 mutations (37.6%), 169 crossovers (62.4%), 137 vertices were eliminated
building final representation...
1056 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=129542, nf=259080, ne=388620, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 18.3 minutes
0 defective edges
removing intersecting faces
000: 160 intersecting
001: 5 intersecting

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 129542 - 388620 + 259080 = 2 --> 0 holes
      F =2V-4:          259080 = 259084-4 (0)
      2E=3F:            777240 = 777240 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 15 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make White Surf lh Thu Aug  8 18:05:32 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub013 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/sub013/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
16512 bright wm thresholded.
535 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.orig...
computing class statistics...
border white:    233793 voxels (1.39%)
border gray      268841 voxels (1.60%)
WM (92.0): 93.4 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.7 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.2 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.4 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.6 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->3.95) (max @ vno 53583 --> 57301)
face area 0.28 +- 0.12 (0.00-->2.56)
mean absolute distance = 0.67 +- 0.77
3330 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=106,    GM=60
mean inside = 93.5, mean outside = 68.9
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=73.0, 53 (53) missing vertices, mean dist 0.4 [0.5 (%31.7)->0.8 (%68.3))]
%66 local maxima, %29 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 +- 0.26 (0.07-->4.12) (max @ vno 100232 --> 99359)
face area 0.28 +- 0.13 (0.00-->1.72)
mean absolute distance = 0.32 +- 0.48
2631 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7130699.0, rms=13.86
001: dt: 0.5000, sse=6987036.5, rms=9.885 (0.000%)
002: dt: 0.5000, sse=7135044.5, rms=7.583 (0.000%)
003: dt: 0.5000, sse=7211852.0, rms=6.145 (0.000%)
004: dt: 0.5000, sse=7475402.5, rms=5.304 (0.000%)
005: dt: 0.5000, sse=7511256.0, rms=4.840 (0.000%)
006: dt: 0.5000, sse=7653010.0, rms=4.600 (0.000%)
007: dt: 0.5000, sse=7564958.0, rms=4.462 (0.000%)
008: dt: 0.5000, sse=7648770.5, rms=4.382 (0.000%)
009: dt: 0.5000, sse=7542357.5, rms=4.320 (0.000%)
rms = 4.28, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=7593083.0, rms=4.285 (0.000%)
011: dt: 0.2500, sse=4754908.5, rms=2.954 (0.000%)
012: dt: 0.2500, sse=4360588.0, rms=2.494 (0.000%)
013: dt: 0.2500, sse=4109899.0, rms=2.395 (0.000%)
014: dt: 0.2500, sse=4041897.2, rms=2.316 (0.000%)
rms = 2.29, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=3957360.0, rms=2.287 (0.000%)
016: dt: 0.1250, sse=3757942.8, rms=2.047 (0.000%)
rms = 2.02, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=3716283.8, rms=2.019 (0.000%)
positioning took 2.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=77.9, 30 (3) missing vertices, mean dist -0.2 [0.3 (%79.6)->0.2 (%20.4))]
%78 local maxima, %16 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 0.90 +- 0.25 (0.07-->3.91) (max @ vno 97766 --> 97752)
face area 0.35 +- 0.16 (0.00-->2.31)
mean absolute distance = 0.21 +- 0.29
2072 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4761450.5, rms=6.45
018: dt: 0.5000, sse=4759869.5, rms=4.346 (0.000%)
rms = 4.56, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=4331723.0, rms=3.223 (0.000%)
020: dt: 0.2500, sse=4151802.0, rms=2.524 (0.000%)
021: dt: 0.2500, sse=4099835.5, rms=2.046 (0.000%)
022: dt: 0.2500, sse=4070287.8, rms=1.943 (0.000%)
023: dt: 0.2500, sse=4002842.5, rms=1.810 (0.000%)
rms = 1.81, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=4017596.5, rms=1.805 (0.000%)
025: dt: 0.1250, sse=3880156.8, rms=1.587 (0.000%)
rms = 1.57, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=3842001.2, rms=1.569 (0.000%)
positioning took 1.1 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 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=81.6, 27 (1) missing vertices, mean dist -0.1 [0.2 (%79.9)->0.2 (%20.1))]
%88 local maxima, % 7 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 0.89 +- 0.25 (0.11-->4.27) (max @ vno 79720 --> 78608)
face area 0.34 +- 0.16 (0.00-->2.22)
mean absolute distance = 0.15 +- 0.23
2265 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4290514.5, rms=4.65
027: dt: 0.5000, sse=4456544.0, rms=4.052 (0.000%)
rms = 4.32, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=4038313.5, rms=2.507 (0.000%)
029: dt: 0.2500, sse=3931187.0, rms=2.051 (0.000%)
030: dt: 0.2500, sse=4009238.8, rms=1.695 (0.000%)
rms = 1.76, time step reduction 2 of 3 to 0.125...
031: dt: 0.1250, sse=3951694.0, rms=1.561 (0.000%)
032: dt: 0.1250, sse=3873274.2, rms=1.379 (0.000%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=3843766.0, rms=1.362 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=82.8, 36 (1) missing vertices, mean dist -0.0 [0.2 (%60.0)->0.1 (%40.0))]
%90 local maxima, % 5 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/sub013/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=3871365.2, rms=1.82
rms = 2.92, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=3924494.8, rms=1.117 (0.000%)
035: dt: 0.2500, sse=4037528.8, rms=1.025 (0.000%)
rms = 1.03, time step reduction 2 of 3 to 0.125...
rms = 1.01, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=4038617.8, rms=1.013 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
23 non-cortical segments detected
only using segment with 1910 vertices
erasing segment 1 (vno[0] = 73387)
erasing segment 2 (vno[0] = 74377)
erasing segment 3 (vno[0] = 76475)
erasing segment 4 (vno[0] = 80749)
erasing segment 5 (vno[0] = 88048)
erasing segment 6 (vno[0] = 91652)
erasing segment 7 (vno[0] = 93805)
erasing segment 8 (vno[0] = 93813)
erasing segment 9 (vno[0] = 96824)
erasing segment 10 (vno[0] = 97713)
erasing segment 11 (vno[0] = 98505)
erasing segment 12 (vno[0] = 99257)
erasing segment 13 (vno[0] = 99321)
erasing segment 14 (vno[0] = 99359)
erasing segment 15 (vno[0] = 101029)
erasing segment 16 (vno[0] = 101036)
erasing segment 17 (vno[0] = 101062)
erasing segment 18 (vno[0] = 101105)
erasing segment 19 (vno[0] = 101131)
erasing segment 20 (vno[0] = 101817)
erasing segment 21 (vno[0] = 101925)
erasing segment 22 (vno[0] = 129448)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/lh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.09-->4.23) (max @ vno 78608 --> 79720)
face area 0.33 +- 0.16 (0.00-->2.19)
refinement took 6.5 minutes
#--------------------------------------------
#@# Smooth2 lh Thu Aug  8 18:12:04 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 18:12:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

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

avg radius = 44.6 mm, total surface area = 78667 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.117 (target=0.015)   
step 005: RMS=0.081 (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)   
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
190 vertices thresholded to be in k1 ~ [-0.20 0.36], k2 ~ [-0.09 0.05]
total integrated curvature = 0.565*4pi (7.095) --> 0 handles
ICI = 1.6, FI = 10.8, variation=180.929
104 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
142 vertices thresholded to be in [-0.13 0.19]
done.
writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.025
done.

#-----------------------------------------
#@# Curvature Stats lh Thu Aug  8 18:14:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub013 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       [ sub013/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                      [ 260 ]
Gb_filter = 0

WARN:    S lookup   min:                          -1.118525
WARN:    S explicit min:                          0.000000	vertex = 59
#--------------------------------------------
#@# Sphere lh Thu Aug  8 18:14:18 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 0.294...
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 %20.49
pass 1: epoch 2 of 3 starting distance error %20.48
unfolding complete - removing small folds...
starting distance error %20.44
removing remaining folds...
final distance error %20.45
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.70 hours
#--------------------------------------------
#@# Surf Reg lh Thu Aug  8 18:56:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = 0.579
curvature mean = 0.028, std = 0.935
curvature mean = 0.025, std = 0.855
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 312486.4, tmin=1.0123
  d=32.00 min @ (0.00, 8.00, 8.00) sse = 238081.1, tmin=2.0286
  d=16.00 min @ (4.00, 0.00, -4.00) sse = 225530.0, tmin=3.0564
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 220383.2, tmin=4.1213
  d=4.00 min @ (1.00, 1.00, 1.00) sse = 219392.2, tmin=5.2053
  d=2.00 min @ (-0.50, 0.00, -0.50) sse = 219005.6, tmin=6.2935
  d=1.00 min @ (0.00, 0.00, 0.25) sse = 218944.8, tmin=7.4197
  d=0.50 min @ (0.00, -0.12, 0.00) sse = 218932.3, tmin=8.6178
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   8.62 min
curvature mean = 0.021, std = 0.951
curvature mean = 0.012, std = 0.938
curvature mean = 0.021, std = 0.964
curvature mean = 0.006, std = 0.972
curvature mean = 0.021, std = 0.966
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.024, std = 0.308
curvature mean = 0.003, std = 0.066
curvature mean = 0.071, std = 0.328
curvature mean = 0.004, std = 0.079
curvature mean = 0.028, std = 0.526
curvature mean = 0.004, std = 0.085
curvature mean = 0.015, std = 0.668
curvature mean = 0.004, std = 0.089
curvature mean = 0.005, std = 0.781
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white lh Thu Aug  8 19:23:20 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 19:23:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 19:23:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub013 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...
1058 labels changed using aseg
relabeling using gibbs priors...
000:   3089 changed, 129542 examined...
001:    702 changed, 13136 examined...
002:    160 changed, 3855 examined...
003:     53 changed, 957 examined...
004:     23 changed, 313 examined...
005:     10 changed, 136 examined...
006:      5 changed, 68 examined...
007:      1 changed, 24 examined...
008:      0 changed, 7 examined...
257 labels changed using aseg
000: 117 total segments, 74 labels (248 vertices) changed
001: 41 total segments, 2 labels (8 vertices) changed
002: 39 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...
1275 vertices marked for relabeling...
1275 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 58 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Thu Aug  8 19:24:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub013 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/sub013/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
16512 bright wm thresholded.
535 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.orig...
computing class statistics...
border white:    233793 voxels (1.39%)
border gray      268841 voxels (1.60%)
WM (92.0): 93.4 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.7 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.2 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.4 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.6 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=60
mean inside = 93.5, mean outside = 68.9
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/sub013/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->3.95) (max @ vno 53583 --> 57301)
face area 0.28 +- 0.12 (0.00-->2.56)
mean absolute distance = 0.67 +- 0.79
3408 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 12 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 593 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
deleting segment 6 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 11 points - only 0.00% unknown
mean border=73.0, 53 (53) missing vertices, mean dist 0.4 [0.5 (%31.8)->0.8 (%68.2))]
%66 local maxima, %29 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 +- 0.26 (0.07-->4.12) (max @ vno 100232 --> 99359)
face area 0.28 +- 0.13 (0.00-->1.72)
mean absolute distance = 0.32 +- 0.48
2681 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7147475.5, rms=13.84
001: dt: 0.5000, sse=7009248.0, rms=9.871 (0.000%)
002: dt: 0.5000, sse=7158732.5, rms=7.572 (0.000%)
003: dt: 0.5000, sse=7240204.5, rms=6.135 (0.000%)
004: dt: 0.5000, sse=7506868.0, rms=5.297 (0.000%)
005: dt: 0.5000, sse=7544965.0, rms=4.834 (0.000%)
006: dt: 0.5000, sse=7689598.0, rms=4.596 (0.000%)
007: dt: 0.5000, sse=7600767.5, rms=4.458 (0.000%)
008: dt: 0.5000, sse=7689428.0, rms=4.380 (0.000%)
009: dt: 0.5000, sse=7581375.5, rms=4.318 (0.000%)
rms = 4.28, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=7633552.5, rms=4.284 (0.000%)
011: dt: 0.2500, sse=4778789.5, rms=2.955 (0.000%)
012: dt: 0.2500, sse=4383876.5, rms=2.496 (0.000%)
013: dt: 0.2500, sse=4133866.5, rms=2.397 (0.000%)
014: dt: 0.2500, sse=4065484.8, rms=2.318 (0.000%)
rms = 2.29, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=3981435.0, rms=2.289 (0.000%)
016: dt: 0.1250, sse=3781352.8, rms=2.050 (0.000%)
rms = 2.02, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=3739609.2, rms=2.022 (0.000%)
positioning took 1.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
deleting segment 3 with 546 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 7 with 43 points - only 13.95% unknown
deleting segment 9 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
deleting segment 14 with 18 points - only 0.00% unknown
mean border=77.8, 31 (3) missing vertices, mean dist -0.2 [0.3 (%79.6)->0.2 (%20.4))]
%79 local maxima, %16 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 0.90 +- 0.25 (0.07-->4.12) (max @ vno 100232 --> 99359)
face area 0.35 +- 0.16 (0.00-->2.31)
mean absolute distance = 0.21 +- 0.29
2125 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4792113.5, rms=6.43
018: dt: 0.5000, sse=4793284.5, rms=4.338 (0.000%)
rms = 4.56, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=4363020.5, rms=3.217 (0.000%)
020: dt: 0.2500, sse=4183612.0, rms=2.521 (0.000%)
021: dt: 0.2500, sse=4130164.8, rms=2.045 (0.000%)
022: dt: 0.2500, sse=4101982.2, rms=1.942 (0.000%)
023: dt: 0.2500, sse=4034437.8, rms=1.811 (0.000%)
rms = 1.81, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=4049559.8, rms=1.806 (0.000%)
025: dt: 0.1250, sse=3911300.8, rms=1.589 (0.000%)
rms = 1.57, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=3873174.0, rms=1.571 (0.000%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 15 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 2 with 533 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 5 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 15 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
deleting segment 10 with 10 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 11 with 3 points - only 0.00% unknown
deleting segment 12 with 18 points - only 0.00% unknown
mean border=81.6, 27 (1) missing vertices, mean dist -0.1 [0.2 (%79.8)->0.2 (%20.2))]
%88 local maxima, % 7 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 (0.11-->4.27) (max @ vno 79720 --> 78608)
face area 0.34 +- 0.16 (0.00-->2.22)
mean absolute distance = 0.15 +- 0.23
2311 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4321524.0, rms=4.64
027: dt: 0.5000, sse=4494703.5, rms=4.046 (0.000%)
rms = 4.31, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=4072886.0, rms=2.505 (0.000%)
029: dt: 0.2500, sse=3964409.0, rms=2.050 (0.000%)
030: dt: 0.2500, sse=4042629.5, rms=1.696 (0.000%)
rms = 1.76, time step reduction 2 of 3 to 0.125...
031: dt: 0.1250, sse=3984884.0, rms=1.563 (0.000%)
032: dt: 0.1250, sse=3905737.0, rms=1.381 (0.000%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=3876139.2, rms=1.365 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 3 with 565 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 15 points - only 0.00% unknown
deleting segment 9 with 11 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 13 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 19 points - only 0.00% unknown
mean border=82.7, 39 (1) missing vertices, mean dist -0.0 [0.2 (%59.9)->0.1 (%40.1))]
%91 local maxima, % 5 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=3903740.0, rms=1.82
rms = 2.91, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=3958544.2, rms=1.119 (0.000%)
035: dt: 0.2500, sse=4072499.5, rms=1.026 (0.000%)
rms = 1.03, time step reduction 2 of 3 to 0.125...
rms = 1.01, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=4073740.2, rms=1.015 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=50.0, 36 (36) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.2 (%100.0))]
%18 local maxima, %59 large gradients and %19 min vals, 877 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=28144568.0, rms=32.08
001: dt: 0.5000, sse=20118210.0, rms=26.534 (0.000%)
002: dt: 0.5000, sse=14570806.0, rms=21.913 (0.000%)
003: dt: 0.5000, sse=10959168.0, rms=18.148 (0.000%)
004: dt: 0.5000, sse=8792371.0, rms=15.152 (0.000%)
005: dt: 0.5000, sse=7554378.0, rms=12.849 (0.000%)
006: dt: 0.5000, sse=6869221.5, rms=11.118 (0.000%)
007: dt: 0.5000, sse=6468825.0, rms=9.673 (0.000%)
008: dt: 0.5000, sse=6216899.5, rms=8.387 (0.000%)
009: dt: 0.5000, sse=6094182.5, rms=7.239 (0.000%)
010: dt: 0.5000, sse=6078420.0, rms=6.253 (0.000%)
011: dt: 0.5000, sse=6136870.5, rms=5.479 (0.000%)
012: dt: 0.5000, sse=6280323.0, rms=4.928 (0.000%)
013: dt: 0.5000, sse=6414637.5, rms=4.585 (0.000%)
014: dt: 0.5000, sse=6531262.0, rms=4.374 (0.000%)
015: dt: 0.5000, sse=6592774.5, rms=4.240 (0.000%)
016: dt: 0.5000, sse=6641923.0, rms=4.145 (0.000%)
rms = 4.10, time step reduction 1 of 3 to 0.250...
017: dt: 0.5000, sse=6636140.0, rms=4.098 (0.000%)
018: dt: 0.2500, sse=4555159.0, rms=3.308 (0.000%)
019: dt: 0.2500, sse=4351769.5, rms=3.080 (0.000%)
rms = 3.04, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=4202066.0, rms=3.042 (0.000%)
021: dt: 0.1250, sse=4031229.5, rms=2.929 (0.000%)
rms = 2.91, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=4005149.8, rms=2.915 (0.000%)
positioning took 2.4 minutes
mean border=47.3, 718 (8) missing vertices, mean dist 0.2 [0.2 (%46.8)->0.5 (%53.2))]
%36 local maxima, %44 large gradients and %15 min vals, 267 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=4722225.0, rms=5.34
023: dt: 0.5000, sse=4927027.5, rms=4.263 (0.000%)
024: dt: 0.5000, sse=6340388.0, rms=4.202 (0.000%)
rms = 4.23, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=5184394.0, rms=3.417 (0.000%)
026: dt: 0.2500, sse=4736663.5, rms=3.067 (0.000%)
027: dt: 0.2500, sse=4672562.5, rms=2.965 (0.000%)
rms = 2.92, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=4625248.0, rms=2.920 (0.000%)
029: dt: 0.1250, sse=4466912.5, rms=2.787 (0.000%)
rms = 2.77, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=4449018.5, rms=2.765 (0.000%)
positioning took 0.9 minutes
mean border=44.6, 767 (4) missing vertices, mean dist 0.1 [0.2 (%36.1)->0.4 (%63.9))]
%58 local maxima, %22 large gradients and %15 min vals, 325 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=4808164.5, rms=4.58
031: dt: 0.5000, sse=4945274.0, rms=4.124 (0.000%)
rms = 4.21, time step reduction 1 of 3 to 0.250...
032: dt: 0.2500, sse=4618629.0, rms=3.264 (0.000%)
033: dt: 0.2500, sse=4779865.5, rms=2.904 (0.000%)
034: dt: 0.2500, sse=4731651.5, rms=2.827 (0.000%)
rms = 2.78, time step reduction 2 of 3 to 0.125...
035: dt: 0.2500, sse=4766047.0, rms=2.782 (0.000%)
036: dt: 0.1250, sse=4588867.0, rms=2.632 (0.000%)
rms = 2.61, time step reduction 3 of 3 to 0.062...
037: dt: 0.1250, sse=4572699.0, rms=2.607 (0.000%)
positioning took 0.9 minutes
mean border=43.2, 1635 (4) missing vertices, mean dist 0.1 [0.2 (%43.9)->0.3 (%56.1))]
%63 local maxima, %17 large gradients and %15 min vals, 256 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/sub013/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=4640117.0, rms=3.09
rms = 3.89, time step reduction 1 of 3 to 0.250...
038: dt: 0.2500, sse=4501629.5, rms=2.739 (0.000%)
039: dt: 0.2500, sse=4616718.5, rms=2.628 (0.000%)
rms = 2.58, time step reduction 2 of 3 to 0.125...
040: dt: 0.2500, sse=4675071.0, rms=2.585 (0.000%)
041: dt: 0.1250, sse=4601915.0, rms=2.462 (0.000%)
rms = 2.44, time step reduction 3 of 3 to 0.062...
042: dt: 0.1250, sse=4605565.5, rms=2.441 (0.000%)
positioning took 0.6 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.area.pial
vertex spacing 1.01 +- 0.42 (0.07-->7.22) (max @ vno 92740 --> 92761)
face area 0.41 +- 0.30 (0.00-->6.61)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 129542 vertices processed
25000 of 129542 vertices processed
50000 of 129542 vertices processed
75000 of 129542 vertices processed
100000 of 129542 vertices processed
125000 of 129542 vertices processed
0 of 129542 vertices processed
25000 of 129542 vertices processed
50000 of 129542 vertices processed
75000 of 129542 vertices processed
100000 of 129542 vertices processed
125000 of 129542 vertices processed
thickness calculation complete, 233:474 truncations.
31903 vertices at 0 distance
94309 vertices at 1 distance
82449 vertices at 2 distance
29368 vertices at 3 distance
7354 vertices at 4 distance
1779 vertices at 5 distance
537 vertices at 6 distance
222 vertices at 7 distance
115 vertices at 8 distance
58 vertices at 9 distance
32 vertices at 10 distance
23 vertices at 11 distance
9 vertices at 12 distance
13 vertices at 13 distance
11 vertices at 14 distance
8 vertices at 15 distance
8 vertices at 16 distance
6 vertices at 17 distance
4 vertices at 18 distance
12 vertices at 19 distance
16 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.thickness
positioning took 12.4 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 19:36:48 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 19:36:48 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 pctsurfcon --s sub013 --lh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts/pctsurfcon.log
Thu Aug  8 19:36:49 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.31782/lh.wm.mgh --regheader sub013 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = 99404
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.31782/lh.wm.mgh
Dim: 129542 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.31782/lh.gm.mgh --projfrac 0.3 --regheader sub013 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = 115748
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.31782/lh.gm.mgh
Dim: 129542 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.31782/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.31782/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/lh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.w-g.pct.mgh --annot sub013 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/lh.w-g.pct.mgh --annot sub013 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/lh.w-g.pct.mgh
Vertex Area is 0.66315 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   1000                            unknown       0       0.000
  1   1001                           bankssts    1508    1012.916
  2   1002            caudalanteriorcingulate     979     653.338
  3   1003                caudalmiddlefrontal    3460    2330.627
  4   1004                     corpuscallosum       0       0.000
  5   1005                             cuneus    2248    1482.044
  6   1006                         entorhinal     710     485.420
  7   1007                           fusiform    4818    3210.506
  8   1008                   inferiorparietal    6942    4600.178
  9   1009                   inferiortemporal    5340    3513.510
 10   1010                   isthmuscingulate    1360     870.851
 11   1011                   lateraloccipital    6211    4066.261
 12   1012               lateralorbitofrontal    3383    2272.167
 13   1013                            lingual    4201    2807.980
 14   1014                medialorbitofrontal    2408    1552.804
 15   1015                     middletemporal    4361    3009.397
 16   1016                    parahippocampal     960     632.420
 17   1017                        paracentral    1658    1075.636
 18   1018                    parsopercularis    2474    1683.026
 19   1019                      parsorbitalis    1027     664.969
 20   1020                   parstriangularis    1840    1219.863
 21   1021                      pericalcarine    1534    1052.727
 22   1022                        postcentral    5619    3671.617
 23   1023                 posteriorcingulate    1820    1235.018
 24   1024                         precentral    6951    4519.928
 25   1025                          precuneus    5568    3726.566
 26   1026           rostralanteriorcingulate    1220     806.065
 27   1027               rostralmiddlefrontal    8903    5888.388
 28   1028                    superiorfrontal   10358    7039.489
 29   1029                   superiorparietal    8067    5391.097
 30   1030                   superiortemporal    5509    3624.623
 31   1031                      supramarginal    5778    3922.542
 32   1032                        frontalpole     307     206.803
 33   1033                       temporalpole     765     517.679
 34   1034                 transversetemporal     669     396.198
 35   1035                             insula    3074    2017.099

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats lh Thu Aug  8 19:37:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 sub013 lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

 1508   1013   2446  2.425 0.419     0.114     0.029       13     1.8  bankssts
  979    653   1895  2.524 0.631     0.161     0.047       24     1.7  caudalanteriorcingulate
 3460   2331   6574  2.522 0.473     0.125     0.033       40     4.8  caudalmiddlefrontal
 2248   1482   3317  1.992 0.424     0.176     0.061       45     5.8  cuneus
  710    485   2212  3.399 0.768     0.169     0.113       29     2.7  entorhinal
 4818   3211   9314  2.555 0.515     0.152     0.095      110    11.4  fusiform
 6942   4600  11263  2.233 0.404     0.140     0.044      115    12.0  inferiorparietal
 5340   3514  10387  2.537 0.578     0.147     0.064      113    12.4  inferiortemporal
 1360    871   2360  2.486 0.811     0.152     0.055       25     2.8  isthmuscingulate
 6211   4066   8667  1.908 0.397     0.157     0.060      147    15.8  lateraloccipital
 3383   2272   6287  2.395 0.645     0.159     0.069       89     9.6  lateralorbitofrontal
 4201   2808   6310  2.027 0.472     0.157     0.066      103    11.3  lingual
 2408   1553   3878  2.070 0.760     0.169     0.106       96    11.0  medialorbitofrontal
 4361   3009  10001  2.724 0.538     0.149     0.070      102    11.4  middletemporal
  960    632   2169  2.812 0.607     0.120     0.041       12     1.5  parahippocampal
 1658   1076   2875  2.358 0.603     0.114     0.027       15     2.0  paracentral
 2474   1683   5164  2.686 0.436     0.134     0.039       36     3.8  parsopercularis
 1027    665   2280  2.611 0.535     0.155     0.058       20     2.3  parsorbitalis
 1840   1220   3385  2.420 0.494     0.138     0.040       31     3.1  parstriangularis
 1534   1053   1669  1.754 0.516     0.153     0.051       20     3.1  pericalcarine
 5619   3672   8490  2.028 0.577     0.129     0.039       80     8.9  postcentral
 1820   1235   3305  2.473 0.604     0.179     0.106       63     6.7  posteriorcingulate
 6951   4520  13291  2.625 0.521     0.117     0.032       76     9.6  precentral
 5568   3727   8874  2.201 0.559     0.141     0.055      102    12.6  precuneus
 1220    806   2533  2.503 0.576     0.153     0.054       27     2.5  rostralanteriorcingulate
 8903   5888  15085  2.195 0.494     0.159     0.072      223    22.4  rostralmiddlefrontal
10358   7039  21570  2.602 0.552     0.147     0.048      174    20.6  superiorfrontal
 8067   5391  12663  2.106 0.419     0.142     0.046      163    15.9  superiorparietal
 5509   3625  10994  2.723 0.600     0.119     0.034       61     8.1  superiortemporal
 5778   3923  10311  2.359 0.509     0.142     0.045       99     9.9  supramarginal
  307    207    769  2.605 0.588     0.209     0.078       12     1.0  frontalpole
  765    518   2569  3.451 0.713     0.155     0.093       17     3.4  temporalpole
  669    396   1077  2.504 0.274     0.134     0.042        8     1.2  transversetemporal
 3074   2017   6571  3.028 0.779     0.120     0.050       38     6.1  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Thu Aug  8 19:37:18 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub013 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...
36 labels changed using aseg
relabeling using gibbs priors...
000:   9137 changed, 129542 examined...
001:   2200 changed, 34744 examined...
002:    642 changed, 11188 examined...
003:    279 changed, 3636 examined...
004:    137 changed, 1579 examined...
005:     63 changed, 756 examined...
006:     35 changed, 357 examined...
007:     17 changed, 189 examined...
008:      6 changed, 81 examined...
009:      2 changed, 30 examined...
010:      2 changed, 14 examined...
011:      1 changed, 9 examined...
012:      2 changed, 8 examined...
013:      0 changed, 6 examined...
4 labels changed using aseg
000: 276 total segments, 190 labels (1877 vertices) changed
001: 100 total segments, 14 labels (30 vertices) changed
002: 87 total segments, 1 labels (1 vertices) changed
003: 86 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 125 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
767 vertices marked for relabeling...
767 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 1 minutes and 7 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Thu Aug  8 19:38:25 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 sub013 lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

 1127    779   1985  2.140 0.582     0.180     0.071       24     3.0  G_and_S_frontomargin
 1305    862   2015  2.015 0.372     0.147     0.045       20     2.3  G_and_S_occipital_inf
 1314    827   2288  2.274 0.576     0.130     0.038       17     2.0  G_and_S_paracentral
 1341    897   2910  2.691 0.347     0.161     0.054       27     2.9  G_and_S_subcentral
  672    450   1347  2.242 0.528     0.219     0.201       50     5.0  G_and_S_transv_frontopol
 2410   1631   4419  2.376 0.596     0.136     0.041       35     3.9  G_and_S_cingul-Ant
 1334    918   2481  2.543 0.526     0.141     0.055       22     2.2  G_and_S_cingul-Mid-Ant
 1284    886   2365  2.591 0.434     0.167     0.107       43     4.8  G_and_S_cingul-Mid-Post
  451    283   1076  2.848 0.570     0.205     0.098       17     1.9  G_cingul-Post-dorsal
  304    190    612  2.762 0.967     0.155     0.073        6     0.7  G_cingul-Post-ventral
 1970   1308   2937  1.936 0.444     0.182     0.068       44     5.5  G_cuneus
 1333    884   3316  2.761 0.399     0.146     0.047       26     2.6  G_front_inf-Opercular
  253    154    642  3.101 0.346     0.139     0.057        4     0.5  G_front_inf-Orbital
 1077    706   2436  2.614 0.391     0.149     0.048       25     2.0  G_front_inf-Triangul
 4650   3053  10003  2.495 0.496     0.161     0.064      121    11.0  G_front_middle
 7053   4768  16962  2.751 0.559     0.160     0.053      141    15.9  G_front_sup
  412    262    930  2.995 0.537     0.139     0.097       11     1.8  G_Ins_lg_and_S_cent_ins
  625    407   2160  3.674 0.663     0.136     0.066       11     1.5  G_insular_short
 1843   1162   3221  2.195 0.353     0.163     0.076       70     6.6  G_occipital_middle
 1483    960   2487  2.127 0.405     0.168     0.071       61     4.7  G_occipital_sup
 1847   1174   4166  2.670 0.403     0.166     0.078       55     4.8  G_oc-temp_lat-fusifor
 2649   1744   4430  2.077 0.526     0.179     0.086       90     9.0  G_oc-temp_med-Lingual
 1177    799   3356  3.244 0.652     0.143     0.062       18     2.7  G_oc-temp_med-Parahip
 2536   1667   5777  2.577 0.653     0.190     0.094       92     9.3  G_orbital
 2408   1622   4976  2.418 0.397     0.153     0.060       57     5.1  G_pariet_inf-Angular
 3041   2034   6471  2.610 0.479     0.160     0.056       69     6.2  G_pariet_inf-Supramar
 3295   2180   6027  2.237 0.442     0.162     0.056       77     7.6  G_parietal_sup
 1999   1245   3357  2.124 0.489     0.133     0.045       36     3.7  G_postcentral
 2782   1734   6648  2.913 0.444     0.124     0.039       45     4.8  G_precentral
 2488   1660   4763  2.294 0.634     0.160     0.067       62     7.6  G_precuneus
  868    534   1663  2.135 0.648     0.215     0.158       54     5.4  G_rectus
  284    162    496  2.645 0.898     0.107     0.042        4     0.4  G_subcallosal
  485    253    883  2.639 0.286     0.118     0.041        6     0.8  G_temp_sup-G_T_transv
 1965   1221   5118  3.033 0.505     0.142     0.049       37     3.9  G_temp_sup-Lateral
  796    549   1954  3.160 0.671     0.111     0.035        6     1.1  G_temp_sup-Plan_polar
  951    682   1733  2.296 0.413     0.123     0.036       15     1.4  G_temp_sup-Plan_tempo
 2981   1916   6617  2.641 0.588     0.161     0.083       85     8.1  G_temporal_inf
 2913   1968   7414  2.785 0.505     0.159     0.088       84     9.4  G_temporal_middle
  407    262    632  2.338 0.409     0.126     0.030        4     0.6  Lat_Fis-ant-Horizont
  341    233    569  2.743 0.558     0.140     0.048        5     0.5  Lat_Fis-ant-Vertical
 1118    746   1427  2.209 0.397     0.118     0.030        8     1.4  Lat_Fis-post
 1919   1248   2444  1.728 0.404     0.176     0.065       48     5.0  Pole_occipital
 2008   1320   5667  3.130 0.780     0.172     0.186       78     9.1  Pole_temporal
 2071   1411   2626  2.037 0.592     0.138     0.042       23     3.5  S_calcarine
 2896   1936   3408  1.951 0.649     0.112     0.028       20     3.4  S_central
 1091    743   1527  2.031 0.524     0.124     0.039       14     1.5  S_cingul-Marginalis
  536    359    866  2.716 0.487     0.114     0.034        4     0.8  S_circular_insula_ant
 1381    929   2333  2.815 0.826     0.097     0.022        6     1.3  S_circular_insula_inf
 1703   1134   2544  2.516 0.467     0.119     0.032       14     2.3  S_circular_insula_sup
 1273    890   2149  2.579 0.452     0.118     0.029        9     1.6  S_collat_transv_ant
  410    284    408  1.708 0.275     0.146     0.039        4     0.7  S_collat_transv_post
 2565   1734   3515  2.123 0.406     0.122     0.034       25     3.3  S_front_inf
 1589   1047   2300  2.067 0.456     0.140     0.049       24     2.9  S_front_middle
 2930   1998   4469  2.301 0.419     0.120     0.038       33     3.7  S_front_sup
  355    244    395  1.841 0.215     0.106     0.018        2     0.4  S_interm_prim-Jensen
 3799   2536   4745  1.969 0.346     0.115     0.028       31     4.6  S_intrapariet_and_P_trans
  733    507    874  1.757 0.353     0.144     0.053       12     1.4  S_oc_middle_and_Lunatus
 1169    786   1425  1.982 0.319     0.133     0.034       12     1.6  S_oc_sup_and_transversal
  629    438    749  1.966 0.313     0.125     0.031        5     0.8  S_occipital_ant
 1048    718   1545  2.262 0.350     0.133     0.046       14     2.3  S_oc-temp_lat
 2021   1388   2818  2.169 0.434     0.122     0.034       20     2.9  S_oc-temp_med_and_Lingual
  447    295    541  1.928 0.497     0.128     0.037        4     0.7  S_orbital_lateral
  635    444   1078  2.377 0.938     0.173     0.125       34     4.1  S_orbital_med-olfact
 1189    822   1745  2.076 0.450     0.131     0.042       16     2.1  S_orbital-H_Shaped
 2129   1399   2801  2.150 0.406     0.112     0.029       17     2.6  S_parieto_occipital
 1198    748   1327  2.083 0.740     0.161     0.054       29     2.4  S_pericallosal
 2570   1737   3376  1.989 0.367     0.115     0.030       25     3.2  S_postcentral
 1835   1239   2822  2.443 0.377     0.099     0.021       11     1.6  S_precentral-inf-part
 1079    737   1439  2.239 0.418     0.102     0.022        6     0.9  S_precentral-sup-part
  517    351    633  1.680 0.453     0.144     0.052        7     1.2  S_suborbital
 1208    828   1752  2.122 0.471     0.154     0.060       23     2.6  S_subparietal
 1522   1061   2266  2.290 0.442     0.129     0.032       17     2.3  S_temporal_inf
 5606   3788   8289  2.360 0.471     0.122     0.031       58     7.3  S_temporal_sup
  397    289    609  2.310 0.304     0.102     0.021        2     0.4  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Thu Aug  8 19:38:42 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub013 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...
878 labels changed using aseg
relabeling using gibbs priors...
000:   2744 changed, 129542 examined...
001:    582 changed, 11767 examined...
002:    150 changed, 3236 examined...
003:     63 changed, 938 examined...
004:     17 changed, 362 examined...
005:      9 changed, 111 examined...
006:      5 changed, 50 examined...
007:      2 changed, 26 examined...
008:      0 changed, 12 examined...
72 labels changed using aseg
000: 68 total segments, 35 labels (224 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 28 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
571 vertices marked for relabeling...
571 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas40.annot...
classification took 0 minutes and 57 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Thu Aug  8 19:39:39 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 sub013 lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

 1520   1029   2824  2.577 0.588     0.142     0.039       27     2.2  caudalanteriorcingulate
 3579   2413   6802  2.518 0.474     0.125     0.033       43     5.0  caudalmiddlefrontal
 3123   2049   4563  2.041 0.408     0.161     0.058       83     7.9  cuneus
  612    440   1908  3.423 0.704     0.154     0.071       10     1.5  entorhinal
 4353   2926   8256  2.538 0.476     0.149     0.057       83     9.4  fusiform
 6470   4279  10405  2.226 0.401     0.138     0.045      106    11.1  inferiorparietal
 5541   3608  11263  2.565 0.617     0.151     0.103      154    15.0  inferiortemporal
 1342    866   2349  2.494 0.812     0.150     0.053       23     2.6  isthmuscingulate
 6363   4159   8866  1.906 0.401     0.159     0.062      155    16.8  lateraloccipital
 3805   2565   7352  2.431 0.698     0.168     0.083      120    13.9  lateralorbitofrontal
 4207   2814   6318  2.024 0.473     0.156     0.066      103    11.2  lingual
 2012   1286   3361  2.043 0.727     0.175     0.099       78     7.9  medialorbitofrontal
 5970   4098  12442  2.617 0.528     0.144     0.060      120    13.7  middletemporal
  957    629   2169  2.818 0.600     0.122     0.041       12     1.6  parahippocampal
 1849   1210   3281  2.416 0.610     0.115     0.027       16     2.1  paracentral
 2259   1536   4681  2.697 0.438     0.133     0.039       31     3.4  parsopercularis
 1086    696   2131  2.587 0.544     0.131     0.043       15     2.0  parsorbitalis
 2336   1535   4065  2.363 0.484     0.143     0.045       41     4.1  parstriangularis
 1546   1055   1680  1.755 0.512     0.157     0.054       22     3.3  pericalcarine
 6336   4134   9428  2.040 0.566     0.130     0.040       90    10.3  postcentral
 1970   1327   3493  2.480 0.598     0.180     0.112       70     7.6  posteriorcingulate
 6931   4503  13159  2.623 0.519     0.117     0.032       75     9.6  precentral
 5331   3598   8707  2.192 0.562     0.143     0.054       98    12.1  precuneus
 1663   1102   3316  2.452 0.607     0.148     0.051       33     3.1  rostralanteriorcingulate
 6183   4097  10770  2.215 0.514     0.154     0.065      136    13.9  rostralmiddlefrontal
11795   7970  24028  2.515 0.567     0.155     0.058      248    27.3  superiorfrontal
 6513   4373  10360  2.114 0.422     0.140     0.043      106    11.5  superiorparietal
 7498   4976  15778  2.767 0.660     0.124     0.041       94    13.1  superiortemporal
 5570   3758   9880  2.357 0.511     0.143     0.046       98     9.8  supramarginal
  661    391   1069  2.503 0.264     0.134     0.042        8     1.2  transversetemporal
 2649   1742   5851  3.074 0.751     0.114     0.047       30     5.0  insula
#--------------------------------------------
#@# Tessellate rh Thu Aug  8 19:39:56 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   5
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   7
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   7
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   9
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   9
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 (+-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (--):   1 found -   1 modified     |    TOTAL:   4
pass   2 (--):   0 found -   1 modified     |    TOTAL:   4
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   5
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 = 14 (out of 220150: 0.006359)
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 50: 2046 vertices, 2166 faces
slice 60: 7917 vertices, 8196 faces
slice 70: 17512 vertices, 17872 faces
slice 80: 28966 vertices, 29352 faces
slice 90: 40756 vertices, 41124 faces
slice 100: 52261 vertices, 52652 faces
slice 110: 63890 vertices, 64289 faces
slice 120: 75332 vertices, 75740 faces
slice 130: 86357 vertices, 86723 faces
slice 140: 96918 vertices, 97288 faces
slice 150: 106106 vertices, 106387 faces
slice 160: 113261 vertices, 113523 faces
slice 170: 120033 vertices, 120269 faces
slice 180: 125694 vertices, 125881 faces
slice 190: 129721 vertices, 129850 faces
slice 200: 130728 vertices, 130748 faces
slice 210: 130728 vertices, 130748 faces
slice 220: 130728 vertices, 130748 faces
slice 230: 130728 vertices, 130748 faces
slice 240: 130728 vertices, 130748 faces
slice 250: 130728 vertices, 130748 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...
   130728 voxel in cpt #1: X=-20 [v=130728,e=392244,f=261496] located at (28.665871, -15.635946, 35.239323)
For the whole surface: X=-20 [v=130728,e=392244,f=261496]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 rh Thu Aug  8 19:40:03 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 19:40:07 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts
avg radius = 44.1 mm, total surface area = 68530 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.5 minutes
Not saving sulc

step 000: RMS=0.101 (target=0.015)   
step 005: RMS=0.073 (target=0.015)   
step 010: RMS=0.053 (target=0.015)   
step 015: RMS=0.044 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.033 (target=0.015)   
step 030: RMS=0.029 (target=0.015)   
step 035: RMS=0.027 (target=0.015)   
step 040: RMS=0.024 (target=0.015)   
step 045: RMS=0.024 (target=0.015)   
step 050: RMS=0.023 (target=0.015)   
step 055: RMS=0.023 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Thu Aug  8 19:40:39 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 1.02 +- 0.57 (0.00-->8.45) (max @ vno 94659 --> 94660)
face area 0.03 +- 0.03 (-0.09-->0.58)
scaling brain by 0.319...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.680, avgs=0
005/300: dt: 0.9000, rms radial error=176.422, avgs=0
010/300: dt: 0.9000, rms radial error=175.868, avgs=0
015/300: dt: 0.9000, rms radial error=175.141, avgs=0
020/300: dt: 0.9000, rms radial error=174.314, avgs=0
025/300: dt: 0.9000, rms radial error=173.429, avgs=0
030/300: dt: 0.9000, rms radial error=172.512, avgs=0
035/300: dt: 0.9000, rms radial error=171.577, avgs=0
040/300: dt: 0.9000, rms radial error=170.635, avgs=0
045/300: dt: 0.9000, rms radial error=169.691, avgs=0
050/300: dt: 0.9000, rms radial error=168.748, avgs=0
055/300: dt: 0.9000, rms radial error=167.807, avgs=0
060/300: dt: 0.9000, rms radial error=166.869, avgs=0
065/300: dt: 0.9000, rms radial error=165.936, avgs=0
070/300: dt: 0.9000, rms radial error=165.007, avgs=0
075/300: dt: 0.9000, rms radial error=164.082, avgs=0
080/300: dt: 0.9000, rms radial error=163.162, avgs=0
085/300: dt: 0.9000, rms radial error=162.247, avgs=0
090/300: dt: 0.9000, rms radial error=161.337, avgs=0
095/300: dt: 0.9000, rms radial error=160.432, avgs=0
100/300: dt: 0.9000, rms radial error=159.531, avgs=0
105/300: dt: 0.9000, rms radial error=158.636, avgs=0
110/300: dt: 0.9000, rms radial error=157.744, avgs=0
115/300: dt: 0.9000, rms radial error=156.857, avgs=0
120/300: dt: 0.9000, rms radial error=155.975, avgs=0
125/300: dt: 0.9000, rms radial error=155.098, avgs=0
130/300: dt: 0.9000, rms radial error=154.226, avgs=0
135/300: dt: 0.9000, rms radial error=153.358, avgs=0
140/300: dt: 0.9000, rms radial error=152.494, avgs=0
145/300: dt: 0.9000, rms radial error=151.636, avgs=0
150/300: dt: 0.9000, rms radial error=150.782, avgs=0
155/300: dt: 0.9000, rms radial error=149.932, avgs=0
160/300: dt: 0.9000, rms radial error=149.088, avgs=0
165/300: dt: 0.9000, rms radial error=148.248, avgs=0
170/300: dt: 0.9000, rms radial error=147.413, avgs=0
175/300: dt: 0.9000, rms radial error=146.582, avgs=0
180/300: dt: 0.9000, rms radial error=145.757, avgs=0
185/300: dt: 0.9000, rms radial error=144.935, avgs=0
190/300: dt: 0.9000, rms radial error=144.118, avgs=0
195/300: dt: 0.9000, rms radial error=143.306, avgs=0
200/300: dt: 0.9000, rms radial error=142.498, avgs=0
205/300: dt: 0.9000, rms radial error=141.695, avgs=0
210/300: dt: 0.9000, rms radial error=140.896, avgs=0
215/300: dt: 0.9000, rms radial error=140.102, avgs=0
220/300: dt: 0.9000, rms radial error=139.312, avgs=0
225/300: dt: 0.9000, rms radial error=138.526, avgs=0
230/300: dt: 0.9000, rms radial error=137.745, avgs=0
235/300: dt: 0.9000, rms radial error=136.968, avgs=0
240/300: dt: 0.9000, rms radial error=136.196, avgs=0
245/300: dt: 0.9000, rms radial error=135.428, avgs=0
250/300: dt: 0.9000, rms radial error=134.664, avgs=0
255/300: dt: 0.9000, rms radial error=133.905, avgs=0
260/300: dt: 0.9000, rms radial error=133.149, avgs=0
265/300: dt: 0.9000, rms radial error=132.398, avgs=0
270/300: dt: 0.9000, rms radial error=131.652, avgs=0
275/300: dt: 0.9000, rms radial error=130.909, avgs=0
280/300: dt: 0.9000, rms radial error=130.170, avgs=0
285/300: dt: 0.9000, rms radial error=129.436, avgs=0
290/300: dt: 0.9000, rms radial error=128.706, avgs=0
295/300: dt: 0.9000, rms radial error=127.980, avgs=0
300/300: dt: 0.9000, rms radial error=127.257, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 15158.77
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
epoch 2 (K=40.0), pass 1, starting sse = 2460.67
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 = 234.73
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/11 = 0.00877
epoch 4 (K=640.0), pass 1, starting sse = 11.32
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.12/15 = 0.00825
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 19:45:21 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/sub013/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub013 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=-20 (nv=130728, nf=261496, ne=392244, g=11)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
1895 ambiguous faces found in tessellation
segmenting defects...
15 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
15 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8156  (-4.9078)
      -vertex     loglikelihood: -6.6667  (-3.3334)
      -normal dot loglikelihood: -3.6154  (-3.6154)
      -quad curv  loglikelihood: -6.4338  (-3.2169)
      Total Loglikelihood : -26.5315

CORRECTING DEFECT 0 (vertices=11, convex hull=28)
After retessellation of defect 0, euler #=-12 (129594,388388,258782) : difference with theory (-12) = 0 

CORRECTING DEFECT 1 (vertices=6, convex hull=22)
After retessellation of defect 1, euler #=-11 (129597,388405,258797) : difference with theory (-11) = 0 

CORRECTING DEFECT 2 (vertices=39, convex hull=86)
After retessellation of defect 2, euler #=-10 (129609,388473,258854) : difference with theory (-10) = 0 

CORRECTING DEFECT 3 (vertices=181, convex hull=144)
After retessellation of defect 3, euler #=-9 (129682,388762,259071) : difference with theory (-9) = 0 

CORRECTING DEFECT 4 (vertices=265, convex hull=81)
After retessellation of defect 4, euler #=-8 (129691,388821,259122) : difference with theory (-8) = 0 

CORRECTING DEFECT 5 (vertices=45, convex hull=29)
After retessellation of defect 5, euler #=-7 (129699,388857,259151) : difference with theory (-7) = 0 

CORRECTING DEFECT 6 (vertices=187, convex hull=63)
After retessellation of defect 6, euler #=-6 (129733,388986,259247) : difference with theory (-6) = 0 

CORRECTING DEFECT 7 (vertices=72, convex hull=90)
After retessellation of defect 7, euler #=-5 (129772,389143,259366) : difference with theory (-5) = 0 

CORRECTING DEFECT 8 (vertices=60, convex hull=32)
After retessellation of defect 8, euler #=-4 (129779,389174,259391) : difference with theory (-4) = 0 

CORRECTING DEFECT 9 (vertices=57, convex hull=50)
After retessellation of defect 9, euler #=-3 (129796,389247,259448) : difference with theory (-3) = 0 

CORRECTING DEFECT 10 (vertices=44, convex hull=57)
After retessellation of defect 10, euler #=-2 (129822,389349,259525) : difference with theory (-2) = 0 

CORRECTING DEFECT 11 (vertices=73, convex hull=102)
After retessellation of defect 11, euler #=-1 (129861,389508,259646) : difference with theory (-1) = 0 

CORRECTING DEFECT 12 (vertices=42, convex hull=80)
After retessellation of defect 12, euler #=0 (129887,389619,259732) : difference with theory (0) = 0 

CORRECTING DEFECT 13 (vertices=21, convex hull=40)
After retessellation of defect 13, euler #=1 (129897,389663,259767) : difference with theory (1) = 0 

CORRECTING DEFECT 14 (vertices=33, convex hull=63)
After retessellation of defect 14, euler #=2 (129914,389736,259824) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.21 (0.05-->5.34) (max @ vno 105822 --> 108664)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.21 (0.05-->5.34) (max @ vno 105822 --> 108664)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
42 mutations (32.6%), 87 crossovers (67.4%), 38 vertices were eliminated
building final representation...
814 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=129914, nf=259824, ne=389736, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 9.6 minutes
0 defective edges
removing intersecting faces
000: 93 intersecting
001: 5 intersecting

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 129914 - 389736 + 259824 = 2 --> 0 holes
      F =2V-4:          259824 = 259828-4 (0)
      2E=3F:            779472 = 779472 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 15 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Thu Aug  8 19:55:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub013 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/sub013/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
16174 bright wm thresholded.
541 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.orig...
computing class statistics...
border white:    233793 voxels (1.39%)
border gray      268841 voxels (1.60%)
WM (92.0): 93.5 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.6 +- 13.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.0 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.1 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.1 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.21 (0.04-->3.42) (max @ vno 129618 --> 129662)
face area 0.28 +- 0.12 (0.00-->2.23)
mean absolute distance = 0.64 +- 0.73
3621 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=106,    GM=60
mean inside = 93.5, mean outside = 68.5
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=72.7, 35 (35) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))]
%67 local maxima, %28 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 +- 0.26 (0.11-->3.49) (max @ vno 90908 --> 90909)
face area 0.28 +- 0.13 (0.00-->1.78)
mean absolute distance = 0.30 +- 0.43
2372 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7173814.5, rms=13.92
001: dt: 0.5000, sse=6976711.5, rms=9.981 (0.000%)
002: dt: 0.5000, sse=7137117.5, rms=7.652 (0.000%)
003: dt: 0.5000, sse=7188496.5, rms=6.154 (0.000%)
004: dt: 0.5000, sse=7492343.5, rms=5.340 (0.000%)
005: dt: 0.5000, sse=7535654.5, rms=4.891 (0.000%)
006: dt: 0.5000, sse=7683598.5, rms=4.692 (0.000%)
007: dt: 0.5000, sse=7595509.0, rms=4.545 (0.000%)
008: dt: 0.5000, sse=7705138.5, rms=4.488 (0.000%)
009: dt: 0.5000, sse=7562329.0, rms=4.419 (0.000%)
rms = 4.40, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=7636652.5, rms=4.396 (0.000%)
011: dt: 0.2500, sse=4772536.0, rms=3.045 (0.000%)
012: dt: 0.2500, sse=4367486.5, rms=2.575 (0.000%)
013: dt: 0.2500, sse=4115707.2, rms=2.477 (0.000%)
014: dt: 0.2500, sse=4038555.8, rms=2.389 (0.000%)
rms = 2.36, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=3957508.2, rms=2.362 (0.000%)
016: dt: 0.1250, sse=3742203.5, rms=2.110 (0.000%)
rms = 2.07, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=3698844.0, rms=2.074 (0.000%)
positioning took 1.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=77.5, 35 (13) missing vertices, mean dist -0.2 [0.3 (%79.3)->0.2 (%20.7))]
%80 local maxima, %15 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 0.90 +- 0.25 (0.10-->3.66) (max @ vno 64613 --> 65791)
face area 0.35 +- 0.16 (0.00-->2.30)
mean absolute distance = 0.21 +- 0.26
2675 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4718130.0, rms=6.37
018: dt: 0.5000, sse=4807513.0, rms=4.268 (0.000%)
rms = 4.58, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=4350628.5, rms=3.099 (0.000%)
020: dt: 0.2500, sse=4165308.5, rms=2.480 (0.000%)
021: dt: 0.2500, sse=4108534.0, rms=2.036 (0.000%)
022: dt: 0.2500, sse=4094235.5, rms=1.986 (0.000%)
023: dt: 0.2500, sse=4030857.5, rms=1.879 (0.000%)
rms = 1.90, time step reduction 2 of 3 to 0.125...
024: dt: 0.1250, sse=3976441.8, rms=1.800 (0.000%)
025: dt: 0.1250, sse=3901596.2, rms=1.700 (0.000%)
rms = 1.69, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=3865531.2, rms=1.691 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=81.3, 27 (7) missing vertices, mean dist -0.1 [0.2 (%80.4)->0.2 (%19.6))]
%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-->3.81) (max @ vno 64613 --> 65791)
face area 0.34 +- 0.16 (0.00-->2.26)
mean absolute distance = 0.15 +- 0.21
2067 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4313282.0, rms=4.67
027: dt: 0.5000, sse=4523312.5, rms=4.229 (0.000%)
rms = 4.36, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=4090406.8, rms=2.643 (0.000%)
029: dt: 0.2500, sse=3970298.2, rms=2.189 (0.000%)
030: dt: 0.2500, sse=4050283.2, rms=1.812 (0.000%)
rms = 1.88, time step reduction 2 of 3 to 0.125...
031: dt: 0.1250, sse=3987611.8, rms=1.674 (0.000%)
032: dt: 0.1250, sse=3902836.2, rms=1.492 (0.000%)
rms = 1.47, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=3867436.2, rms=1.466 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=82.4, 29 (6) missing vertices, mean dist -0.0 [0.1 (%59.9)->0.1 (%40.1))]
%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/sub013/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=3894580.5, rms=1.89
rms = 2.96, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=3958464.2, rms=1.235 (0.000%)
035: dt: 0.2500, sse=4072410.0, rms=1.112 (0.000%)
rms = 1.14, time step reduction 2 of 3 to 0.125...
rms = 1.10, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=4073482.0, rms=1.101 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
24 non-cortical segments detected
only using segment with 2065 vertices
erasing segment 0 (vno[0] = 47335)
erasing segment 2 (vno[0] = 58821)
erasing segment 3 (vno[0] = 76900)
erasing segment 4 (vno[0] = 80162)
erasing segment 5 (vno[0] = 80190)
erasing segment 6 (vno[0] = 82311)
erasing segment 7 (vno[0] = 84386)
erasing segment 8 (vno[0] = 86473)
erasing segment 9 (vno[0] = 92900)
erasing segment 10 (vno[0] = 94626)
erasing segment 11 (vno[0] = 95653)
erasing segment 12 (vno[0] = 96765)
erasing segment 13 (vno[0] = 96790)
erasing segment 14 (vno[0] = 96829)
erasing segment 15 (vno[0] = 97767)
erasing segment 16 (vno[0] = 98771)
erasing segment 17 (vno[0] = 99624)
erasing segment 18 (vno[0] = 104068)
erasing segment 19 (vno[0] = 105608)
erasing segment 20 (vno[0] = 105621)
erasing segment 21 (vno[0] = 105628)
erasing segment 22 (vno[0] = 129737)
erasing segment 23 (vno[0] = 129795)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/rh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.09-->3.81) (max @ vno 64613 --> 65791)
face area 0.33 +- 0.16 (0.00-->2.25)
refinement took 6.4 minutes
#--------------------------------------------
#@# Smooth2 rh Thu Aug  8 20:01:27 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 20:01:32 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

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

avg radius = 44.3 mm, total surface area = 79037 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.116 (target=0.015)   
step 005: RMS=0.080 (target=0.015)   
step 010: RMS=0.057 (target=0.015)   
step 015: RMS=0.047 (target=0.015)   
step 020: RMS=0.039 (target=0.015)   
step 025: RMS=0.032 (target=0.015)   
step 030: RMS=0.027 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.017 (target=0.015)   
step 050: RMS=0.016 (target=0.015)   
inflation complete.
inflation took 0.5 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
150 vertices thresholded to be in k1 ~ [-0.38 0.40], k2 ~ [-0.20 0.08]
total integrated curvature = 0.591*4pi (7.424) --> 0 handles
ICI = 1.6, FI = 10.4, variation=175.636
123 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
88 vertices thresholded to be in [-0.15 0.18]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.024
done.

#-----------------------------------------
#@# Curvature Stats rh Thu Aug  8 20:03:41 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub013 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       [ sub013/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                      [ 240 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.267963
WARN:    S explicit min:                          0.000000	vertex = 542
#--------------------------------------------
#@# Sphere rh Thu Aug  8 20:03:46 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 0.296...
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 %19.74
pass 1: epoch 2 of 3 starting distance error %19.61
unfolding complete - removing small folds...
starting distance error %19.53
removing remaining folds...
final distance error %19.54
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.86 hours
#--------------------------------------------
#@# Surf Reg rh Thu Aug  8 20:55:28 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = 0.584
curvature mean = 0.034, std = 0.930
curvature mean = 0.024, std = 0.853
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, 8.00) sse = 271897.9, tmin=2.0537
  d=16.00 min @ (4.00, 4.00, 0.00) sse = 240315.2, tmin=3.0859
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 239217.3, tmin=4.1521
  d=4.00 min @ (1.00, 0.00, -1.00) sse = 235922.3, tmin=5.2330
  d=1.00 min @ (-0.25, -0.25, 0.00) sse = 235774.7, tmin=7.4162
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   8.48 min
curvature mean = 0.014, std = 0.941
curvature mean = 0.011, std = 0.937
curvature mean = 0.013, std = 0.951
curvature mean = 0.005, std = 0.971
curvature mean = 0.012, std = 0.952
curvature mean = 0.001, std = 0.987
2 Reading smoothwm
curvature mean = -0.025, std = 0.294
curvature mean = 0.006, std = 0.069
curvature mean = 0.072, std = 0.349
curvature mean = 0.006, std = 0.083
curvature mean = 0.033, std = 0.542
curvature mean = 0.007, std = 0.089
curvature mean = 0.017, std = 0.687
curvature mean = 0.007, std = 0.092
curvature mean = 0.006, std = 0.796
MRISregister() return, current seed 0
writing registered surface to ../surf/rh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white rh Thu Aug  8 21:20:49 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 21:20:51 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 21:20:53 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub013 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...
1019 labels changed using aseg
relabeling using gibbs priors...
000:   2649 changed, 129914 examined...
001:    662 changed, 11474 examined...
002:    187 changed, 3800 examined...
003:     54 changed, 1116 examined...
004:     24 changed, 346 examined...
005:      6 changed, 138 examined...
006:      4 changed, 43 examined...
007:      3 changed, 24 examined...
008:      3 changed, 18 examined...
009:      3 changed, 13 examined...
010:      0 changed, 12 examined...
143 labels changed using aseg
000: 103 total segments, 63 labels (297 vertices) changed
001: 42 total segments, 3 labels (13 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 40 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1365 vertices marked for relabeling...
1365 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 58 seconds.
#--------------------------------------------
#@# Make Pial Surf rh Thu Aug  8 21:21:51 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub013 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/sub013/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
16174 bright wm thresholded.
541 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.orig...
computing class statistics...
border white:    233793 voxels (1.39%)
border gray      268841 voxels (1.60%)
WM (92.0): 93.5 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.6 +- 13.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.0 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.1 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.1 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=60
mean inside = 93.5, mean outside = 68.5
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/sub013/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.21 (0.04-->3.42) (max @ vno 129618 --> 129662)
face area 0.28 +- 0.12 (0.00-->2.23)
mean absolute distance = 0.64 +- 0.74
3691 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
deleting segment 2 with 25 points - only 0.00% unknown
deleting segment 4 with 348 points - only 0.00% unknown
deleting segment 5 with 11 points - only 0.00% unknown
deleting segment 7 with 85 points - only 0.00% unknown
removing 3 vertex label from ripped group
mean border=72.7, 35 (35) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))]
%68 local maxima, %28 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 +- 0.26 (0.11-->3.49) (max @ vno 90908 --> 90909)
face area 0.28 +- 0.13 (0.00-->1.78)
mean absolute distance = 0.31 +- 0.44
2411 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7185548.0, rms=13.90
001: dt: 0.5000, sse=6993602.0, rms=9.967 (0.000%)
002: dt: 0.5000, sse=7160777.5, rms=7.641 (0.000%)
003: dt: 0.5000, sse=7217228.5, rms=6.146 (0.000%)
004: dt: 0.5000, sse=7521716.5, rms=5.333 (0.000%)
005: dt: 0.5000, sse=7569031.0, rms=4.885 (0.000%)
006: dt: 0.5000, sse=7714246.5, rms=4.687 (0.000%)
007: dt: 0.5000, sse=7632322.5, rms=4.541 (0.000%)
008: dt: 0.5000, sse=7737699.5, rms=4.484 (0.000%)
009: dt: 0.5000, sse=7599600.5, rms=4.416 (0.000%)
rms = 4.39, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=7671330.0, rms=4.392 (0.000%)
011: dt: 0.2500, sse=4795398.5, rms=3.043 (0.000%)
012: dt: 0.2500, sse=4387526.0, rms=2.574 (0.000%)
013: dt: 0.2500, sse=4136296.5, rms=2.477 (0.000%)
014: dt: 0.2500, sse=4058662.0, rms=2.388 (0.000%)
rms = 2.36, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=3977202.2, rms=2.361 (0.000%)
016: dt: 0.1250, sse=3761514.0, rms=2.111 (0.000%)
rms = 2.07, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=3717766.5, rms=2.075 (0.000%)
positioning took 2.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 2 with 25 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 6 with 315 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 10 with 53 points - only 0.00% unknown
deleting segment 12 with 12 points - only 0.00% unknown
deleting segment 13 with 41 points - only 7.32% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
mean border=77.5, 37 (13) missing vertices, mean dist -0.2 [0.3 (%79.3)->0.2 (%20.7))]
%80 local maxima, %15 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 0.90 +- 0.25 (0.03-->3.66) (max @ vno 64613 --> 65791)
face area 0.35 +- 0.16 (0.00-->2.30)
mean absolute distance = 0.21 +- 0.27
2715 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4743984.0, rms=6.37
018: dt: 0.5000, sse=4828964.0, rms=4.267 (0.000%)
rms = 4.57, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=4371778.5, rms=3.099 (0.000%)
020: dt: 0.2500, sse=4190437.5, rms=2.482 (0.000%)
021: dt: 0.2500, sse=4131714.0, rms=2.040 (0.000%)
022: dt: 0.2500, sse=4118280.2, rms=1.989 (0.000%)
023: dt: 0.2500, sse=4054125.2, rms=1.884 (0.000%)
rms = 1.91, time step reduction 2 of 3 to 0.125...
024: dt: 0.1250, sse=3999717.0, rms=1.805 (0.000%)
025: dt: 0.1250, sse=3924737.2, rms=1.706 (0.000%)
rms = 1.70, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=3888475.2, rms=1.696 (0.000%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 1 with 26 points - only 0.00% unknown
deleting segment 2 with 349 points - only 0.00% unknown
deleting segment 3 with 17 points - only 0.00% unknown
deleting segment 4 with 91 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
mean border=81.3, 31 (7) missing vertices, mean dist -0.1 [0.2 (%80.3)->0.2 (%19.7))]
%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-->3.81) (max @ vno 64613 --> 65791)
face area 0.34 +- 0.16 (0.00-->2.26)
mean absolute distance = 0.15 +- 0.22
2117 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4337230.0, rms=4.67
027: dt: 0.5000, sse=4548303.0, rms=4.225 (0.000%)
rms = 4.36, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=4115059.2, rms=2.643 (0.000%)
029: dt: 0.2500, sse=3995613.2, rms=2.191 (0.000%)
030: dt: 0.2500, sse=4074596.2, rms=1.816 (0.000%)
rms = 1.88, time step reduction 2 of 3 to 0.125...
031: dt: 0.1250, sse=4012514.8, rms=1.679 (0.000%)
032: dt: 0.1250, sse=3929130.5, rms=1.497 (0.000%)
rms = 1.47, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=3892872.2, rms=1.471 (0.000%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
deleting segment 1 with 28 points - only 0.00% unknown
deleting segment 2 with 366 points - only 0.00% unknown
deleting segment 3 with 28 points - only 0.00% unknown
deleting segment 4 with 104 points - only 0.00% unknown
deleting segment 5 with 41 points - only 7.32% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
mean border=82.4, 33 (6) missing vertices, mean dist -0.0 [0.1 (%59.9)->0.1 (%40.1))]
%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=3920698.8, rms=1.90
rms = 2.96, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=3986362.8, rms=1.245 (0.000%)
035: dt: 0.2500, sse=4104079.2, rms=1.118 (0.000%)
rms = 1.14, time step reduction 2 of 3 to 0.125...
rms = 1.11, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=4105311.8, rms=1.107 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=50.1, 56 (56) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.1 (%100.0))]
%16 local maxima, %63 large gradients and %17 min vals, 983 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=27787974.0, rms=31.81
001: dt: 0.5000, sse=19704236.0, rms=26.180 (0.000%)
002: dt: 0.5000, sse=14122182.0, rms=21.471 (0.000%)
003: dt: 0.5000, sse=10503879.0, rms=17.665 (0.000%)
004: dt: 0.5000, sse=8458157.0, rms=14.670 (0.000%)
005: dt: 0.5000, sse=7342709.5, rms=12.376 (0.000%)
006: dt: 0.5000, sse=6730138.0, rms=10.634 (0.000%)
007: dt: 0.5000, sse=6341661.0, rms=9.164 (0.000%)
008: dt: 0.5000, sse=6109655.5, rms=7.904 (0.000%)
009: dt: 0.5000, sse=6028573.0, rms=6.802 (0.000%)
010: dt: 0.5000, sse=6066673.0, rms=5.930 (0.000%)
011: dt: 0.5000, sse=6195183.0, rms=5.248 (0.000%)
012: dt: 0.5000, sse=6307013.0, rms=4.803 (0.000%)
013: dt: 0.5000, sse=6426273.5, rms=4.467 (0.000%)
014: dt: 0.5000, sse=6500349.0, rms=4.278 (0.000%)
015: dt: 0.5000, sse=6562051.5, rms=4.127 (0.000%)
016: dt: 0.5000, sse=6621953.5, rms=4.071 (0.000%)
017: dt: 0.5000, sse=6648869.5, rms=4.001 (0.000%)
rms = 4.00, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=6647189.0, rms=3.996 (0.000%)
019: dt: 0.2500, sse=4607305.0, rms=3.227 (0.000%)
020: dt: 0.2500, sse=4415754.0, rms=3.033 (0.000%)
rms = 3.02, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=4290173.0, rms=3.017 (0.000%)
022: dt: 0.1250, sse=4128421.2, rms=2.906 (0.000%)
rms = 2.89, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=4091088.0, rms=2.895 (0.000%)
positioning took 2.6 minutes
mean border=47.2, 626 (10) missing vertices, mean dist 0.2 [0.2 (%46.7)->0.6 (%53.3))]
%36 local maxima, %46 large gradients and %14 min vals, 276 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=4846669.0, rms=5.47
024: dt: 0.5000, sse=4995649.5, rms=4.402 (0.000%)
025: dt: 0.5000, sse=6412708.0, rms=4.271 (0.000%)
rms = 4.28, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=5266280.0, rms=3.535 (0.000%)
027: dt: 0.2500, sse=4849413.5, rms=3.219 (0.000%)
028: dt: 0.2500, sse=4780988.0, rms=3.112 (0.000%)
029: dt: 0.2500, sse=4741763.0, rms=3.052 (0.000%)
rms = 3.01, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=4752761.5, rms=3.011 (0.000%)
031: dt: 0.1250, sse=4589939.5, rms=2.866 (0.000%)
rms = 2.84, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=4577623.5, rms=2.836 (0.000%)
positioning took 1.1 minutes
mean border=44.2, 735 (7) missing vertices, mean dist 0.2 [0.2 (%34.2)->0.4 (%65.8))]
%60 local maxima, %21 large gradients and %13 min vals, 315 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=4990280.5, rms=4.84
033: dt: 0.5000, sse=5064065.5, rms=4.171 (0.000%)
rms = 4.23, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=4732924.0, rms=3.338 (0.000%)
035: dt: 0.2500, sse=4865883.5, rms=2.985 (0.000%)
036: dt: 0.2500, sse=4830745.0, rms=2.904 (0.000%)
rms = 2.86, time step reduction 2 of 3 to 0.125...
037: dt: 0.2500, sse=4863233.0, rms=2.864 (0.000%)
038: dt: 0.1250, sse=4682620.5, rms=2.710 (0.000%)
rms = 2.68, time step reduction 3 of 3 to 0.062...
039: dt: 0.1250, sse=4666744.0, rms=2.685 (0.000%)
positioning took 0.9 minutes
mean border=42.8, 1669 (7) missing vertices, mean dist 0.1 [0.2 (%42.4)->0.3 (%57.6))]
%65 local maxima, %16 large gradients and %13 min vals, 235 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/sub013/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=4736420.5, rms=3.18
rms = 3.98, time step reduction 1 of 3 to 0.250...
040: dt: 0.2500, sse=4591328.0, rms=2.809 (0.000%)
041: dt: 0.2500, sse=4720313.5, rms=2.697 (0.000%)
rms = 2.66, time step reduction 2 of 3 to 0.125...
042: dt: 0.2500, sse=4794201.0, rms=2.658 (0.000%)
043: dt: 0.1250, sse=4700234.0, rms=2.532 (0.000%)
rms = 2.51, time step reduction 3 of 3 to 0.062...
044: dt: 0.1250, sse=4708578.0, rms=2.512 (0.000%)
positioning took 0.7 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.area.pial
vertex spacing 1.01 +- 0.42 (0.07-->7.42) (max @ vno 88738 --> 89882)
face area 0.41 +- 0.30 (0.00-->9.28)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 129914 vertices processed
25000 of 129914 vertices processed
50000 of 129914 vertices processed
75000 of 129914 vertices processed
100000 of 129914 vertices processed
125000 of 129914 vertices processed
0 of 129914 vertices processed
25000 of 129914 vertices processed
50000 of 129914 vertices processed
75000 of 129914 vertices processed
100000 of 129914 vertices processed
125000 of 129914 vertices processed
thickness calculation complete, 185:445 truncations.
33214 vertices at 0 distance
94125 vertices at 1 distance
82181 vertices at 2 distance
29595 vertices at 3 distance
7221 vertices at 4 distance
1731 vertices at 5 distance
515 vertices at 6 distance
196 vertices at 7 distance
71 vertices at 8 distance
54 vertices at 9 distance
35 vertices at 10 distance
30 vertices at 11 distance
25 vertices at 12 distance
17 vertices at 13 distance
10 vertices at 14 distance
11 vertices at 15 distance
6 vertices at 16 distance
12 vertices at 17 distance
3 vertices at 18 distance
6 vertices at 19 distance
8 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.thickness
positioning took 13.3 minutes
#--------------------------------------------
#@# Surf Volume rh Thu Aug  8 21:35:07 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 21:35:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 pctsurfcon --s sub013 --rh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts/pctsurfcon.log
Thu Aug  8 21:35:08 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.1763/rh.wm.mgh --regheader sub013 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = 99911
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.1763/rh.wm.mgh
Dim: 129914 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.1763/rh.gm.mgh --projfrac 0.3 --regheader sub013 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = 116074
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.1763/rh.gm.mgh
Dim: 129914 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.1763/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/tmp.pctsurfcon.1763/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/rh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.w-g.pct.mgh --annot sub013 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/rh.w-g.pct.mgh --annot sub013 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/rh.w-g.pct.mgh
Vertex Area is 0.663999 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   2000                            unknown       0       0.000
  1   2001                           bankssts    1286     909.207
  2   2002            caudalanteriorcingulate    1001     649.707
  3   2003                caudalmiddlefrontal    2775    1892.919
  4   2004                     corpuscallosum       0       0.000
  5   2005                             cuneus    2407    1562.346
  6   2006                         entorhinal     593     435.251
  7   2007                           fusiform    4355    2904.319
  8   2008                   inferiorparietal    8817    5825.207
  9   2009                   inferiortemporal    4751    3220.793
 10   2010                   isthmuscingulate    1285     832.450
 11   2011                   lateraloccipital    6108    3934.384
 12   2012               lateralorbitofrontal    4245    2690.580
 13   2013                            lingual    4309    2835.095
 14   2014                medialorbitofrontal    2276    1488.799
 15   2015                     middletemporal    4830    3289.504
 16   2016                    parahippocampal     931     611.212
 17   2017                        paracentral    2471    1620.922
 18   2018                    parsopercularis    1599    1066.128
 19   2019                      parsorbitalis    1230     822.387
 20   2020                   parstriangularis    2001    1343.618
 21   2021                      pericalcarine    1796    1212.563
 22   2022                        postcentral    6020    3919.212
 23   2023                 posteriorcingulate    1596    1087.249
 24   2024                         precentral    7853    5134.176
 25   2025                          precuneus    5758    3880.331
 26   2026           rostralanteriorcingulate    1024     669.467
 27   2027               rostralmiddlefrontal    9042    6246.322
 28   2028                    superiorfrontal   10517    7173.332
 29   2029                   superiorparietal    7615    5032.704
 30   2030                   superiortemporal    4655    3049.055
 31   2031                      supramarginal    4653    3154.145
 32   2032                        frontalpole     343     233.464
 33   2033                       temporalpole     452     310.370
 34   2034                 transversetemporal     567     317.348
 35   2035                             insula    3030    2014.824

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats rh Thu Aug  8 21:35:20 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 sub013 rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

 1286    909   2171  2.471 0.368     0.117     0.028        9     1.5  bankssts
 1001    650   1868  2.383 0.740     0.155     0.064       25     2.1  caudalanteriorcingulate
 2775   1893   5284  2.452 0.456     0.134     0.042       41     4.6  caudalmiddlefrontal
 2407   1562   3360  2.003 0.395     0.168     0.055       44     5.6  cuneus
  593    435   2199  3.460 0.704     0.176     0.067       11     1.8  entorhinal
 4355   2904   8088  2.456 0.471     0.146     0.052       84     9.5  fusiform
 8817   5825  15337  2.332 0.478     0.144     0.046      149    16.3  inferiorparietal
 4751   3221   9445  2.361 0.599     0.149     0.059       96    11.6  inferiortemporal
 1285    832   2043  2.280 0.721     0.162     0.077       30     3.8  isthmuscingulate
 6108   3934   9310  2.090 0.420     0.151     0.055      115    12.9  lateraloccipital
 4245   2691   7436  2.523 0.649     0.151     0.087      111    15.1  lateralorbitofrontal
 4309   2835   6619  2.161 0.501     0.154     0.061       77    10.4  lingual
 2276   1489   3557  2.090 0.568     0.161     0.096       89     9.0  medialorbitofrontal
 4830   3290  10040  2.546 0.629     0.150     0.061      103    11.6  middletemporal
  931    611   1803  2.586 0.526     0.129     0.049       11     1.6  parahippocampal
 2471   1621   4443  2.424 0.505     0.118     0.032       26     3.3  paracentral
 1599   1066   3215  2.626 0.376     0.120     0.039       19     2.1  parsopercularis
 1230    822   2630  2.483 0.592     0.154     0.058       25     2.6  parsorbitalis
 2001   1344   3698  2.392 0.491     0.131     0.044       32     3.4  parstriangularis
 1796   1213   2107  1.722 0.403     0.141     0.053       24     3.8  pericalcarine
 6020   3919   8862  2.006 0.572     0.125     0.041       83     8.6  postcentral
 1596   1087   2805  2.401 0.608     0.155     0.046       33     2.7  posteriorcingulate
 7853   5134  14358  2.525 0.508     0.122     0.039      119    13.3  precentral
 5758   3880   9733  2.293 0.541     0.143     0.046       94    10.4  precuneus
 1024    669   1943  2.507 0.584     0.160     0.059       27     2.4  rostralanteriorcingulate
 9042   6246  16511  2.255 0.532     0.166     0.081      264    26.4  rostralmiddlefrontal
10517   7173  22336  2.637 0.519     0.142     0.048      164    19.0  superiorfrontal
 7615   5033  11673  2.069 0.399     0.137     0.050      126    13.2  superiorparietal
 4655   3049  10102  2.778 0.614     0.112     0.031       49     6.4  superiortemporal
 4653   3154   8620  2.452 0.503     0.153     0.060       96    10.4  supramarginal
  343    233    688  2.219 0.515     0.266     0.182       27     2.5  frontalpole
  452    310   1501  3.263 0.849     0.185     0.116       15     2.1  temporalpole
  567    317    909  2.550 0.260     0.130     0.082        7     1.1  transversetemporal
 3030   2015   5812  2.783 0.713     0.147     0.114      129    15.7  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Thu Aug  8 21:35:37 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub013 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...
0 labels changed using aseg
relabeling using gibbs priors...
000:   9230 changed, 129914 examined...
001:   2207 changed, 35337 examined...
002:    683 changed, 11266 examined...
003:    252 changed, 3700 examined...
004:    147 changed, 1482 examined...
005:     75 changed, 837 examined...
006:     34 changed, 437 examined...
007:     15 changed, 169 examined...
008:     12 changed, 95 examined...
009:     12 changed, 67 examined...
010:      7 changed, 59 examined...
011:      3 changed, 39 examined...
012:      1 changed, 21 examined...
013:      1 changed, 7 examined...
014:      0 changed, 8 examined...
1 labels changed using aseg
000: 280 total segments, 195 labels (2696 vertices) changed
001: 104 total segments, 22 labels (140 vertices) changed
002: 84 total segments, 2 labels (4 vertices) changed
003: 82 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 117 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
879 vertices marked for relabeling...
879 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 1 minutes and 8 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Thu Aug  8 21:36:45 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 sub013 rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

  816    555   1654  2.349 0.588     0.177     0.079       21     2.4  G_and_S_frontomargin
  926    614   1700  2.353 0.445     0.154     0.078       18     1.7  G_and_S_occipital_inf
 1461    950   2615  2.316 0.560     0.121     0.034       17     1.9  G_and_S_paracentral
 1260    826   2617  2.703 0.511     0.156     0.049       24     2.5  G_and_S_subcentral
  846    634   1913  2.326 0.486     0.248     0.199       70     7.4  G_and_S_transv_frontopol
 2289   1542   4186  2.451 0.550     0.140     0.046       38     4.2  G_and_S_cingul-Ant
 1433    968   2775  2.619 0.508     0.135     0.049       24     2.5  G_and_S_cingul-Mid-Ant
 1616   1100   2929  2.441 0.459     0.142     0.040       24     2.7  G_and_S_cingul-Mid-Post
  463    296    988  2.734 0.623     0.197     0.104       20     1.5  G_cingul-Post-dorsal
  240    153    545  2.776 0.675     0.180     0.103        7     0.8  G_cingul-Post-ventral
 2255   1461   3267  1.990 0.398     0.166     0.057       41     5.3  G_cuneus
 1130    736   2795  2.821 0.303     0.140     0.054       21     2.0  G_front_inf-Opercular
  407    252   1126  2.988 0.411     0.177     0.067       12     1.2  G_front_inf-Orbital
  730    513   1786  2.654 0.369     0.165     0.071       21     1.9  G_front_inf-Triangul
 3903   2610   8070  2.459 0.509     0.166     0.068      106     9.8  G_front_middle
 7273   4887  17229  2.736 0.514     0.158     0.067      174    18.5  G_front_sup
  490    314   1020  2.779 0.562     0.136     0.117       14     1.8  G_Ins_lg_and_S_cent_ins
  564    390   1737  3.243 0.748     0.236     0.303       86     9.6  G_insular_short
 1909   1220   3831  2.447 0.384     0.169     0.063       51     4.6  G_occipital_middle
 1588   1023   2677  2.082 0.378     0.142     0.044       27     2.8  G_occipital_sup
 2003   1276   4351  2.632 0.413     0.169     0.063       51     5.7  G_oc-temp_lat-fusifor
 2984   1913   4875  2.222 0.508     0.172     0.076       67     8.5  G_oc-temp_med-Lingual
 1222    839   3548  3.170 0.756     0.157     0.072       30     3.5  G_oc-temp_med-Parahip
 2825   1790   6087  2.600 0.628     0.175     0.109      102    12.6  G_orbital
 3433   2278   7373  2.494 0.487     0.165     0.065       83     8.1  G_pariet_inf-Angular
 2478   1666   5366  2.643 0.488     0.177     0.076       73     7.5  G_pariet_inf-Supramar
 2311   1560   4199  2.220 0.382     0.159     0.077       59     5.3  G_parietal_sup
 2187   1352   3685  2.147 0.532     0.131     0.053       39     3.5  G_postcentral
 2967   1877   6707  2.741 0.486     0.124     0.046       56     5.7  G_precentral
 2526   1689   5176  2.384 0.513     0.164     0.058       59     5.5  G_precuneus
  636    396    984  2.017 0.499     0.199     0.125       33     3.0  G_rectus
  350    215    582  2.432 0.902     0.087     0.071        6     0.9  G_subcallosal
  443    241    813  2.620 0.263     0.125     0.090        6     0.9  G_temp_sup-G_T_transv
 1452    897   4196  3.123 0.593     0.137     0.046       25     2.8  G_temp_sup-Lateral
  766    501   1841  3.121 0.641     0.095     0.033        5     1.0  G_temp_sup-Plan_polar
  734    521   1367  2.405 0.350     0.104     0.023        5     0.7  G_temp_sup-Plan_tempo
 2598   1769   6170  2.514 0.654     0.171     0.076       75     8.4  G_temporal_inf
 2914   1963   7225  2.759 0.610     0.166     0.080       86     9.0  G_temporal_middle
  467    304    716  2.327 0.429     0.099     0.019        2     0.5  Lat_Fis-ant-Horizont
  234    163    314  2.245 0.420     0.098     0.019        1     0.2  Lat_Fis-ant-Vertical
 1258    834   1638  2.269 0.382     0.113     0.030        8     1.6  Lat_Fis-post
 2912   1853   4265  1.997 0.390     0.160     0.057       63     6.9  Pole_occipital
 1536   1052   4104  2.767 0.734     0.170     0.083       37     5.1  Pole_temporal
 2330   1560   2791  1.938 0.544     0.133     0.045       29     4.4  S_calcarine
 3010   2043   3652  1.937 0.610     0.113     0.036       44     4.7  S_central
 1411    961   2096  2.274 0.388     0.112     0.026       10     1.5  S_cingul-Marginalis
  719    482   1298  2.881 0.525     0.139     0.091       12     1.6  S_circular_insula_ant
 1163    769   1821  2.801 0.545     0.096     0.028        6     1.1  S_circular_insula_inf
 1209    805   1687  2.291 0.401     0.113     0.033        8     1.6  S_circular_insula_sup
  943    646   1350  2.219 0.371     0.097     0.022        5     0.9  S_collat_transv_ant
  518    340    588  2.016 0.283     0.141     0.045        5     1.0  S_collat_transv_post
 2032   1398   3014  2.137 0.456     0.121     0.030       21     2.4  S_front_inf
 2660   1843   4307  2.089 0.506     0.162     0.098       78     7.8  S_front_middle
 2691   1863   4426  2.299 0.453     0.132     0.037       35     4.1  S_front_sup
  248    162    278  2.079 0.262     0.110     0.025        1     0.3  S_interm_prim-Jensen
 2845   1867   3683  1.958 0.357     0.125     0.038       34     4.2  S_intrapariet_and_P_trans
  745    520    864  1.769 0.286     0.116     0.024        4     0.8  S_oc_middle_and_Lunatus
 1660   1107   1957  1.926 0.364     0.125     0.033       15     2.3  S_oc_sup_and_transversal
  756    495   1164  2.188 0.468     0.123     0.031        7     1.0  S_occipital_ant
 1044    715   1341  2.081 0.400     0.127     0.042       11     1.7  S_oc-temp_lat
 1512   1047   2338  2.375 0.447     0.110     0.027       10     1.7  S_oc-temp_med_and_Lingual
  579    383    915  2.152 0.566     0.137     0.041        7     1.0  S_orbital_lateral
  884    598   1184  2.099 0.658     0.134     0.064       23     2.6  S_orbital_med-olfact
 1501    987   2379  2.436 0.570     0.129     0.039       14     2.5  S_orbital-H_Shaped
 2514   1697   3356  2.103 0.533     0.133     0.036       31     3.8  S_parieto_occipital
 1446    911   1457  1.877 0.627     0.150     0.052       28     3.1  S_pericallosal
 2380   1643   3030  1.980 0.324     0.115     0.028       20     2.8  S_postcentral
 1351    935   2153  2.490 0.282     0.108     0.025        9     1.4  S_precentral-inf-part
 1982   1334   2770  2.208 0.374     0.108     0.024       16     2.0  S_precentral-sup-part
  238    165    294  1.857 0.285     0.142     0.032        2     0.4  S_suborbital
 1003    688   1534  2.197 0.568     0.137     0.039       12     1.7  S_subparietal
 1337    922   1713  2.008 0.400     0.128     0.033       11     1.8  S_temporal_inf
 6314   4260   9524  2.336 0.444     0.119     0.032       58     8.3  S_temporal_sup
  331    234    498  2.401 0.318     0.111     0.026        2     0.4  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Thu Aug  8 21:37:02 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub013 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...
927 labels changed using aseg
relabeling using gibbs priors...
000:   2661 changed, 129914 examined...
001:    664 changed, 11258 examined...
002:    144 changed, 3516 examined...
003:     62 changed, 839 examined...
004:     30 changed, 383 examined...
005:     10 changed, 174 examined...
006:      6 changed, 66 examined...
007:      2 changed, 34 examined...
008:      1 changed, 10 examined...
009:      3 changed, 7 examined...
010:      1 changed, 13 examined...
011:      1 changed, 7 examined...
012:      0 changed, 7 examined...
110 labels changed using aseg
000: 62 total segments, 29 labels (208 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 54 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
638 vertices marked for relabeling...
638 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 0 minutes and 57 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Thu Aug  8 21:37:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 sub013 rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

 1028    667   1918  2.377 0.746     0.154     0.063       25     2.2  caudalanteriorcingulate
 2868   1939   5291  2.438 0.454     0.133     0.042       42     4.7  caudalmiddlefrontal
 3026   1976   4264  1.995 0.397     0.158     0.049       51     6.2  cuneus
  606    447   2324  3.498 0.676     0.178     0.075       11     1.9  entorhinal
 3806   2553   7183  2.486 0.454     0.145     0.049       73     7.9  fusiform
 8225   5421  14202  2.313 0.475     0.146     0.047      142    15.7  inferiorparietal
 5236   3532  10133  2.347 0.590     0.148     0.059      103    13.0  inferiortemporal
 1284    832   2051  2.273 0.709     0.161     0.079       31     3.9  isthmuscingulate
 6438   4135   9836  2.095 0.417     0.151     0.055      121    13.5  lateraloccipital
 4447   2853   8074  2.495 0.646     0.154     0.081      120    15.9  lateralorbitofrontal
 4346   2857   6680  2.160 0.499     0.154     0.062       77    10.5  lingual
 1878   1214   2832  2.042 0.607     0.163     0.104       77     8.5  medialorbitofrontal
 5775   3957  11775  2.554 0.597     0.146     0.056      112    12.7  middletemporal
  894    585   1747  2.605 0.519     0.126     0.045       10     1.5  parahippocampal
 2576   1693   4649  2.426 0.501     0.120     0.033       28     3.5  paracentral
 1666   1112   3293  2.609 0.376     0.120     0.039       20     2.3  parsopercularis
 1322    876   2732  2.525 0.530     0.154     0.076       26     2.7  parsorbitalis
 2121   1430   3826  2.342 0.525     0.131     0.043       33     3.6  parstriangularis
 1777   1206   2087  1.718 0.406     0.140     0.052       23     3.7  pericalcarine
 6489   4243   9628  2.023 0.571     0.125     0.040       89     9.2  postcentral
 1810   1228   3359  2.454 0.606     0.157     0.042       34     3.2  posteriorcingulate
 7469   4864  13833  2.542 0.508     0.123     0.040      117    12.8  precentral
 5816   3934   9870  2.286 0.539     0.140     0.045       94    10.1  precuneus
 1111    720   2059  2.500 0.554     0.162     0.060       29     2.7  rostralanteriorcingulate
 6431   4389  11713  2.272 0.551     0.160     0.076      169    16.6  rostralmiddlefrontal
13190   9085  27121  2.541 0.537     0.150     0.061      281    30.3  superiorfrontal
 6392   4212   9717  2.072 0.402     0.142     0.055      113    11.9  superiorparietal
 6206   4103  13537  2.778 0.641     0.121     0.039       77    10.4  superiortemporal
 4459   3022   8180  2.441 0.500     0.153     0.061       93    10.2  supramarginal
  569    322    917  2.555 0.258     0.133     0.082        7     1.2  transversetemporal
 2930   1962   5674  2.788 0.673     0.145     0.109      122    14.8  insula
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR Thu Aug  8 21:38:16 CEST 2013

 bbregister --s sub013 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.lta --init-fsl --T2 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.dat.log
Thu Aug  8 21:38:16 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub013 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996032, 0.0582575, 0.0672728)
j_ras = (0.0588709, 0.99824, 0.00717099)
k_ras = (0.0667366, -0.011103, 0.997709)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii...
fslregister --s sub013 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat.fslregister.log

Thu Aug  8 21:38:20 CEST 2013
--s sub013 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -5.12227e-09, -7.45058e-09)
j_ras = (-7.45058e-09, -9.31323e-10, -1)
k_ras = (-5.99539e-09, 1, -9.31323e-10)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/mri/transforms/tmp.bbregister.1926/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996032, 0.0582575, 0.0672728)
j_ras = (0.0588709, 0.99824, 0.00717099)
k_ras = (0.0667366, -0.011103, 0.997709)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311062
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/reg0.1967.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat.fsl.mat0 --s sub013 --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/sub013/mri/transforms/tmp.bbregister.1926/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/reg0.1967.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/sub013/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/sub013/mri/transforms/tmp.bbregister.1926/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.885;
 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) --------
 0.996  -0.058  -0.067  -0.000;
 0.067  -0.011   0.998   0.000;
-0.059  -0.998  -0.007   0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.996  -0.058  -0.067  -0.000;
 0.067  -0.011   0.998   0.000;
-0.059  -0.998  -0.007   0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub013
RegMat ---------------------------
 0.996  -0.058  -0.067  -0.000;
 0.067  -0.011   0.998   0.000;
-0.059  -0.998  -0.007   0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311062, ref det = -1
Thu Aug  8 21:38:29 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/mri/transforms/tmp.bbregister.1926/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat.fsl.mat0
Thu Aug  8 21:42:56 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub013 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.996  -0.059  -0.069   48.895;
-0.069  -0.003  -0.998   262.366;
 0.059   0.998  -0.007  -4.941;
 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/sub013/mri/transforms/tmp.bbregister.1926/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/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/sub013/mri/transforms/tmp.bbregister.1926/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.885;
 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 = -0.311062, ref det = -1
---- Input registration matrix (computed) --------
 0.996  -0.059  -0.069   0.053;
 0.069  -0.007   0.998  -0.318;
-0.059  -0.998  -0.003  -0.447;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.996  -0.059  -0.069   0.053;
 0.069  -0.007   0.998  -0.318;
-0.059  -0.998  -0.003  -0.447;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub013
RegMat ---------------------------
 0.996  -0.059  -0.069   0.053;
 0.069  -0.007   0.998  -0.318;
-0.059  -0.998  -0.003  -0.447;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 21:38:20 CEST 2013 
Ended   at Thu Aug  8 21:48:41 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/mri/transforms/tmp.bbregister.1926/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/reg.init.dat
subject sub013
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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 1376072236
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.996  -0.059  -0.069   0.053;
 0.069  -0.007   0.998  -0.318;
-0.059  -0.998  -0.003  -0.447;
 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   0.972231
 1  -25.0 -25.0  25.0   1.028446
 2  -25.0  25.0 -25.0   1.019947
 3  -25.0  25.0  25.0   0.986119
 4   25.0 -25.0 -25.0   1.044645
 5   25.0 -25.0  25.0   1.035140
 6   25.0  25.0 -25.0   1.040034
 7   25.0  25.0  25.0   1.009784
REL:  8  0.199005    8.136345  1.017043 rel = 0.195671 
Initial costs ----------------
Number of surface hits 2437
WM  Intensity    62.3080 +/-  10.2189
Ctx Intensity    78.4240 +/-   9.8221
Pct Contrast     23.1306 +/-  17.3793
Cost   0.1990
RelCost   0.1957

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9663   0.9663  0.0
     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      0.9421   0.9421  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8810   0.8810  0.0
    21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.8633   0.8633  0.0
    99  -4.0000   0.0000  -4.0000   4.0000  -4.0000  -4.0000      0.8372   0.8372  0.0
   102  -4.0000   0.0000  -4.0000   4.0000   0.0000  -4.0000      0.7984   0.7984  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.6843   0.6843  0.0
   346   0.0000   0.0000  -4.0000   4.0000   0.0000   0.0000      0.6577   0.6577  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.1990   0.1990  0.0
Brute Force --------------------------
Min cost was 0.199005
Number of iterations   729
Search time 2.008000 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   0.1982535587
   7  0.205  0.000  0.000  0.000  0.000  0.000   0.1943027456
   8  0.199  0.000  0.000  0.000  0.000  0.000   0.1942611206
   9  0.158  0.000  0.000  0.000  0.000  0.000   0.1937524912
  11  0.135  0.000  0.000  0.000  0.000  0.000   0.1936678826
  13  0.143  0.000  0.000  0.000  0.000  0.000   0.1936439196
  15  0.142  0.000  0.000  0.000  0.000  0.000   0.1936438361
  21  0.142 -0.618  0.000  0.000  0.000  0.000   0.1657325207
  23  0.142 -0.460  0.000  0.000  0.000  0.000   0.1560781155
  24  0.142 -0.407  0.000  0.000  0.000  0.000   0.1549360548
  25  0.142 -0.377  0.000  0.000  0.000  0.000   0.1548001138
  26  0.142 -0.381  0.000  0.000  0.000  0.000   0.1547944348
  27  0.142 -0.382  0.000  0.000  0.000  0.000   0.1547936044
  30  0.142 -0.382  1.000  0.000  0.000  0.000   0.1229966860
  34  0.142 -0.382  0.618  0.000  0.000  0.000   0.1076755561
  35  0.142 -0.382  0.641  0.000  0.000  0.000   0.1075856362
  36  0.142 -0.382  0.646  0.000  0.000  0.000   0.1075382154
  38  0.142 -0.382  0.697  0.000  0.000  0.000   0.1067615839
  40  0.142 -0.382  0.699  0.000  0.000  0.000   0.1067539974
  41  0.142 -0.382  0.703  0.000  0.000  0.000   0.1067503945
  42  0.142 -0.382  0.702  0.000  0.000  0.000   0.1067500112
  51  0.142 -0.382  0.702  0.020  0.000  0.000   0.1066433208
  60  0.142 -0.382  0.702  0.020 -0.145  0.000   0.1050170889
  61  0.142 -0.382  0.702  0.020 -0.111  0.000   0.1041409249
  62  0.142 -0.382  0.702  0.020 -0.089  0.000   0.1037462441
  64  0.142 -0.382  0.702  0.020 -0.084  0.000   0.1037429921
  65  0.142 -0.382  0.702  0.020 -0.086  0.000   0.1037393929
  74  0.142 -0.382  0.702  0.020 -0.086  0.096   0.1036813602
  75  0.142 -0.382  0.702  0.020 -0.086  0.051   0.1033583009
  76  0.142 -0.382  0.702  0.020 -0.086  0.050   0.1033467584
  77  0.142 -0.382  0.702  0.020 -0.086  0.031   0.1032760635
  87  0.153 -0.382  0.702  0.020 -0.086  0.031   0.1028705701
  89  0.179 -0.382  0.702  0.020 -0.086  0.031   0.1024035417
  90  0.184 -0.382  0.702  0.020 -0.086  0.031   0.1023876730
 100  0.184 -0.379  0.702  0.020 -0.086  0.031   0.1023842681
 101  0.184 -0.377  0.702  0.020 -0.086  0.031   0.1023820184
 114  0.184 -0.377  0.628  0.020 -0.086  0.031   0.1020420236
 119  0.184 -0.377  0.626  0.020 -0.086  0.031   0.1020407094
 128  0.184 -0.377  0.626  0.071 -0.086  0.031   0.1011136248
 129  0.184 -0.377  0.626  0.083 -0.086  0.031   0.1010014543
 132  0.184 -0.377  0.626  0.093 -0.086  0.031   0.1009888236
 135  0.184 -0.377  0.626  0.096 -0.086  0.031   0.1009876110
 137  0.184 -0.377  0.626  0.097 -0.086  0.031   0.1009868929
 146  0.184 -0.377  0.626  0.097 -0.114  0.031   0.1009258257
 147  0.184 -0.377  0.626  0.097 -0.107  0.031   0.1008687199
 148  0.184 -0.377  0.626  0.097 -0.103  0.031   0.1008448537
 150  0.184 -0.377  0.626  0.097 -0.100  0.031   0.1008384255
 159  0.184 -0.377  0.626  0.097 -0.100  0.133   0.1005889609
 160  0.184 -0.377  0.626  0.097 -0.100  0.096   0.1005402290
 163  0.184 -0.377  0.626  0.097 -0.100  0.098   0.1005392967
 164  0.184 -0.377  0.626  0.097 -0.100  0.099   0.1005392315
 166  0.225 -0.373  0.549  0.174 -0.114  0.167   0.0986016390
 173  0.238 -0.371  0.526  0.197 -0.118  0.188   0.0983519357
 175  0.237 -0.371  0.526  0.197 -0.118  0.188   0.0983517018
 177  0.236 -0.371  0.530  0.194 -0.117  0.185   0.0983515185
 178  0.237 -0.371  0.528  0.195 -0.117  0.186   0.0983500191
 179  0.237 -0.371  0.528  0.195 -0.117  0.186   0.0983499633
 181  0.237 -0.371  0.528  0.195 -0.117  0.186   0.0983498389
 183  0.237 -0.371  0.528  0.195 -0.117  0.186   0.0983498040
 190  0.252 -0.371  0.528  0.195 -0.117  0.186   0.0978493408
 192  0.275 -0.371  0.528  0.195 -0.117  0.186   0.0975504975
 194  0.271 -0.371  0.528  0.195 -0.117  0.186   0.0975256774
 196  0.270 -0.371  0.528  0.195 -0.117  0.186   0.0975248228
 206  0.270 -0.432  0.528  0.195 -0.117  0.186   0.0963414289
 207  0.270 -0.489  0.528  0.195 -0.117  0.186   0.0963297225
 208  0.270 -0.461  0.528  0.195 -0.117  0.186   0.0960463997
 210  0.270 -0.465  0.528  0.195 -0.117  0.186   0.0960349158
 212  0.270 -0.468  0.528  0.195 -0.117  0.186   0.0960304495
 214  0.270 -0.467  0.528  0.195 -0.117  0.186   0.0960302291
 222  0.270 -0.467  0.494  0.195 -0.117  0.186   0.0959847427
 225  0.270 -0.467  0.499  0.195 -0.117  0.186   0.0959793014
 238  0.270 -0.467  0.499  0.195 -0.117  0.194   0.0959435265
 239  0.270 -0.467  0.499  0.195 -0.117  0.195   0.0959433137
 260  0.269 -0.467  0.500  0.195 -0.117  0.194   0.0959422909
 261  0.269 -0.467  0.499  0.195 -0.117  0.194   0.0959421310
 262  0.269 -0.467  0.499  0.195 -0.117  0.195   0.0959421295
 273  0.281 -0.467  0.499  0.195 -0.117  0.195   0.0959047986
 274  0.277 -0.467  0.499  0.195 -0.117  0.195   0.0958835427
 286  0.277 -0.458  0.499  0.195 -0.117  0.195   0.0958807946
 287  0.277 -0.461  0.499  0.195 -0.117  0.195   0.0958731412
 288  0.277 -0.462  0.499  0.195 -0.117  0.195   0.0958722814
 297  0.277 -0.462  0.497  0.195 -0.117  0.195   0.0958708586
 309  0.277 -0.462  0.497  0.195 -0.117  0.202   0.0958436446
 310  0.277 -0.462  0.497  0.195 -0.117  0.201   0.0958426653
 319  0.277 -0.462  0.497  0.195 -0.121  0.201   0.0958228382
 321  0.277 -0.462  0.497  0.195 -0.124  0.201   0.0958215856
 323  0.277 -0.462  0.497  0.195 -0.123  0.201   0.0958203784
 330  0.274 -0.462  0.504  0.189 -0.122  0.195   0.0958097485
 331  0.274 -0.462  0.502  0.190 -0.122  0.197   0.0958038908
 338  0.280 -0.458  0.505  0.185 -0.126  0.199   0.0956715103
 341  0.288 -0.450  0.509  0.177 -0.134  0.202   0.0955144890
 344  0.293 -0.445  0.512  0.172 -0.139  0.205   0.0954951981
 346  0.292 -0.446  0.511  0.174 -0.137  0.204   0.0954908820
 347  0.292 -0.446  0.511  0.173 -0.137  0.204   0.0954905818
 360  0.298 -0.446  0.500  0.185 -0.139  0.215   0.0954676115
 363  0.300 -0.445  0.497  0.188 -0.140  0.217   0.0954629964
 364  0.300 -0.445  0.497  0.188 -0.140  0.217   0.0954627163
 365  0.300 -0.445  0.496  0.189 -0.140  0.218   0.0954624577
 381  0.300 -0.447  0.496  0.189 -0.140  0.218   0.0954621411
 389  0.300 -0.447  0.503  0.189 -0.140  0.218   0.0953791791
 390  0.300 -0.447  0.532  0.189 -0.140  0.218   0.0953752427
 392  0.300 -0.447  0.518  0.189 -0.140  0.218   0.0953114187
 395  0.300 -0.447  0.516  0.189 -0.140  0.218   0.0953094998
 405  0.300 -0.447  0.516  0.189 -0.140  0.219   0.0953088945
 414  0.300 -0.447  0.516  0.189 -0.142  0.219   0.0953011707
 416  0.300 -0.447  0.516  0.189 -0.145  0.219   0.0952958854
 420  0.305 -0.442  0.519  0.184 -0.149  0.221   0.0952224949
 421  0.314 -0.434  0.523  0.176 -0.157  0.225   0.0952181869
 422  0.310 -0.438  0.521  0.180 -0.153  0.223   0.0952081729
 424  0.308 -0.439  0.520  0.182 -0.152  0.223   0.0952075212
 428  0.308 -0.439  0.520  0.181 -0.152  0.223   0.0952072693
 431  0.308 -0.439  0.520  0.181 -0.152  0.223   0.0952072016
 433  0.308 -0.439  0.520  0.181 -0.152  0.223   0.0952071637
 444  0.312 -0.439  0.513  0.188 -0.153  0.229   0.0951838342
 445  0.312 -0.439  0.513  0.189 -0.153  0.229   0.0951827663
 448  0.313 -0.439  0.511  0.190 -0.153  0.231   0.0951824748
 449  0.313 -0.439  0.512  0.190 -0.153  0.230   0.0951822989
 450  0.313 -0.439  0.512  0.190 -0.153  0.230   0.0951822278
 462  0.313 -0.441  0.512  0.190 -0.153  0.230   0.0951815147
 464  0.313 -0.440  0.512  0.190 -0.153  0.230   0.0951814433
 473  0.313 -0.440  0.517  0.190 -0.153  0.230   0.0951802039
 474  0.313 -0.440  0.514  0.190 -0.153  0.230   0.0951786466
 485  0.313 -0.440  0.514  0.190 -0.153  0.224   0.0951564239
 487  0.313 -0.440  0.514  0.190 -0.153  0.225   0.0951561667
 498  0.313 -0.440  0.514  0.190 -0.154  0.225   0.0951555165
 501  0.318 -0.436  0.517  0.185 -0.159  0.227   0.0951450903
 505  0.316 -0.438  0.516  0.187 -0.157  0.227   0.0951401775
 506  0.316 -0.437  0.516  0.187 -0.157  0.227   0.0951400426
 507  0.316 -0.437  0.516  0.186 -0.157  0.227   0.0951399079
 510  0.316 -0.437  0.516  0.186 -0.157  0.227   0.0951396984
 516  0.324 -0.435  0.513  0.191 -0.163  0.231   0.0951023771
 519  0.337 -0.432  0.506  0.199 -0.172  0.237   0.0951012662
 520  0.331 -0.434  0.509  0.196 -0.168  0.234   0.0950884853
 524  0.330 -0.434  0.510  0.195 -0.167  0.234   0.0950877871
 525  0.330 -0.434  0.510  0.195 -0.167  0.234   0.0950877163
 527  0.330 -0.434  0.510  0.195 -0.167  0.233   0.0950875332
 538  0.326 -0.437  0.508  0.198 -0.164  0.232   0.0950868505
 540  0.328 -0.436  0.509  0.196 -0.165  0.233   0.0950830987
 541  0.328 -0.436  0.509  0.196 -0.165  0.233   0.0950827721
 559  0.328 -0.441  0.509  0.196 -0.165  0.233   0.0950800710
 560  0.328 -0.439  0.509  0.196 -0.165  0.233   0.0950769174
 569  0.328 -0.439  0.504  0.196 -0.165  0.233   0.0950727105
 571  0.328 -0.439  0.506  0.196 -0.165  0.233   0.0950702282
 593  0.328 -0.439  0.506  0.196 -0.163  0.233   0.0950684177
 596  0.336 -0.437  0.502  0.201 -0.169  0.237   0.0950604466
 604  0.336 -0.437  0.502  0.201 -0.169  0.237   0.0950603018
 606  0.336 -0.437  0.502  0.201 -0.169  0.237   0.0950601668
 616  0.338 -0.435  0.503  0.199 -0.170  0.238   0.0950592442
 617  0.337 -0.436  0.503  0.200 -0.170  0.237   0.0950577665
 618  0.337 -0.436  0.503  0.200 -0.170  0.237   0.0950574535
 621  0.337 -0.436  0.503  0.200 -0.170  0.237   0.0950573218
 623  0.337 -0.436  0.503  0.200 -0.169  0.237   0.0950572834
 638  0.337 -0.441  0.503  0.200 -0.169  0.237   0.0950513524
 639  0.337 -0.440  0.503  0.200 -0.169  0.237   0.0950497348
 647  0.337 -0.440  0.501  0.200 -0.169  0.237   0.0950479782
 659  0.337 -0.440  0.501  0.200 -0.169  0.239   0.0950451786
 670  0.337 -0.440  0.501  0.200 -0.167  0.239   0.0950361125
 674  0.345 -0.438  0.498  0.205 -0.172  0.243   0.0950306743
 678  0.342 -0.438  0.499  0.203 -0.170  0.241   0.0950283269
 681  0.341 -0.439  0.499  0.203 -0.170  0.241   0.0950282125
 691  0.347 -0.440  0.496  0.205 -0.171  0.246   0.0949997431
 694  0.355 -0.443  0.491  0.208 -0.173  0.253   0.0949550960
 698  0.387 -0.454  0.474  0.219 -0.180  0.279   0.0943767921
 699  0.392 -0.456  0.471  0.220 -0.181  0.283   0.0942459072
 701  0.400 -0.458  0.467  0.223 -0.183  0.289   0.0941860031
 702  0.400 -0.458  0.467  0.223 -0.182  0.289   0.0941853953
 704  0.399 -0.458  0.467  0.223 -0.182  0.289   0.0941852744
 707  0.399 -0.458  0.467  0.223 -0.182  0.289   0.0941851658
 720  0.399 -0.458  0.468  0.222 -0.183  0.289   0.0941851206
 725  0.399 -0.458  0.468  0.222 -0.183  0.289   0.0941848544
 742  0.399 -0.460  0.468  0.222 -0.183  0.289   0.0941796066
 751  0.399 -0.460  0.476  0.222 -0.183  0.289   0.0941098465
 763  0.399 -0.460  0.476  0.222 -0.183  0.301   0.0941070243
 764  0.399 -0.460  0.476  0.222 -0.183  0.295   0.0940813692
 772  0.402 -0.459  0.475  0.224 -0.185  0.296   0.0940789319
 775  0.404 -0.459  0.474  0.226 -0.186  0.297   0.0940781981
 780  0.404 -0.459  0.474  0.226 -0.186  0.297   0.0940779381
 791  0.401 -0.458  0.476  0.224 -0.185  0.295   0.0940710890
 793  0.401 -0.458  0.475  0.225 -0.186  0.295   0.0940705756
 804  0.406 -0.453  0.478  0.220 -0.190  0.297   0.0940659920
 808  0.405 -0.455  0.477  0.222 -0.188  0.296   0.0940566667
 809  0.404 -0.455  0.477  0.222 -0.188  0.296   0.0940566007
 810  0.404 -0.455  0.477  0.222 -0.188  0.296   0.0940563914
 817  0.404 -0.455  0.477  0.222 -0.188  0.296   0.0940562946
 838  0.404 -0.455  0.480  0.222 -0.188  0.296   0.0940546006
 839  0.404 -0.455  0.479  0.222 -0.188  0.296   0.0940535533
 850  0.404 -0.455  0.479  0.222 -0.188  0.298   0.0940454353
 851  0.404 -0.455  0.479  0.222 -0.188  0.300   0.0940438479
 854  0.412 -0.453  0.476  0.227 -0.194  0.304   0.0940160621
 857  0.417 -0.452  0.473  0.230 -0.197  0.306   0.0939997968
 858  0.420 -0.451  0.472  0.232 -0.199  0.308   0.0939951179
 860  0.420 -0.451  0.472  0.231 -0.199  0.307   0.0939946699
 865  0.420 -0.451  0.472  0.231 -0.199  0.307   0.0939944196
 872  0.416 -0.450  0.474  0.230 -0.198  0.305   0.0939843512
 893  0.416 -0.450  0.474  0.230 -0.198  0.305   0.0939843233
 896  0.417 -0.450  0.474  0.230 -0.198  0.305   0.0939842467
 907  0.417 -0.443  0.474  0.230 -0.198  0.305   0.0939332319
 909  0.417 -0.444  0.474  0.230 -0.198  0.305   0.0939321910
 917  0.417 -0.444  0.473  0.230 -0.198  0.305   0.0939314924
 927  0.417 -0.444  0.473  0.230 -0.198  0.321   0.0939285648
 928  0.417 -0.444  0.473  0.230 -0.198  0.313   0.0938909902
 932  0.425 -0.442  0.469  0.235 -0.204  0.317   0.0938901181
 936  0.421 -0.443  0.471  0.233 -0.202  0.315   0.0938791567
 937  0.421 -0.443  0.471  0.233 -0.201  0.315   0.0938784247
 939  0.421 -0.443  0.471  0.233 -0.201  0.315   0.0938784152
 941  0.421 -0.443  0.471  0.233 -0.201  0.315   0.0938783764
 942  0.420 -0.443  0.471  0.233 -0.201  0.315   0.0938783580
 953  0.421 -0.444  0.470  0.233 -0.201  0.316   0.0938777360
 958  0.421 -0.444  0.470  0.233 -0.201  0.316   0.0938775638
 966  0.418 -0.446  0.469  0.236 -0.199  0.314   0.0938649224
 968  0.419 -0.446  0.469  0.236 -0.199  0.314   0.0938642090
 969  0.419 -0.446  0.469  0.235 -0.199  0.315   0.0938640295
 970  0.419 -0.446  0.469  0.235 -0.199  0.315   0.0938639745
 972  0.419 -0.446  0.469  0.235 -0.199  0.315   0.0938639611
 986  0.419 -0.442  0.469  0.235 -0.199  0.315   0.0938432426
1008  0.419 -0.442  0.469  0.235 -0.199  0.316   0.0938432026
1016  0.420 -0.442  0.469  0.236 -0.200  0.316   0.0938420459
1032  0.422 -0.442  0.468  0.236 -0.200  0.318   0.0938399772
1033  0.421 -0.442  0.468  0.236 -0.200  0.317   0.0938396614
1037  0.421 -0.442  0.468  0.236 -0.200  0.317   0.0938396576
1044  0.421 -0.441  0.466  0.239 -0.199  0.319   0.0938199370
1049  0.421 -0.440  0.464  0.241 -0.198  0.320   0.0938167123
1052  0.421 -0.440  0.464  0.242 -0.198  0.320   0.0938166927
1056  0.421 -0.440  0.464  0.242 -0.198  0.320   0.0938166807
1057  0.421 -0.440  0.464  0.242 -0.198  0.320   0.0938164740
1082  0.421 -0.440  0.464  0.242 -0.198  0.320   0.0938162741
1083  0.421 -0.440  0.464  0.242 -0.198  0.320   0.0938162558
1086  0.421 -0.440  0.464  0.242 -0.198  0.320   0.0938162153
1110  0.421 -0.440  0.464  0.242 -0.198  0.318   0.0938131115
1116  0.416 -0.441  0.466  0.239 -0.194  0.316   0.0938068997
1119  0.417 -0.441  0.466  0.239 -0.195  0.316   0.0938067727
1120  0.417 -0.441  0.466  0.239 -0.195  0.316   0.0938066238
1121  0.417 -0.441  0.466  0.239 -0.195  0.316   0.0938065600
1130  0.417 -0.440  0.465  0.241 -0.195  0.317   0.0938058145
1131  0.417 -0.441  0.465  0.240 -0.195  0.317   0.0938055315
1146  0.417 -0.441  0.465  0.241 -0.194  0.316   0.0938044124
1160  0.418 -0.441  0.464  0.241 -0.194  0.317   0.0938029317
1163  0.418 -0.442  0.464  0.241 -0.194  0.317   0.0938028449
1189  0.418 -0.442  0.464  0.241 -0.194  0.316   0.0938018046
1197  0.417 -0.442  0.464  0.241 -0.194  0.315   0.0938007197
1198  0.416 -0.442  0.465  0.240 -0.193  0.315   0.0938000972
1223  0.416 -0.442  0.465  0.240 -0.193  0.315   0.0937999371
Powell done niters = 13
Computing relative cost
 0  -25.0 -25.0 -25.0   0.994116
 1  -25.0 -25.0  25.0   1.021778
 2  -25.0  25.0 -25.0   1.019457
 3  -25.0  25.0  25.0   1.012021
 4   25.0 -25.0 -25.0   1.049738
 5   25.0 -25.0  25.0   1.004247
 6   25.0  25.0 -25.0   1.055087
 7   25.0  25.0  25.0   1.033732
REL:  8  0.093800    8.190176  1.023772 rel = 0.0916219 
Number of iterations    13
Min cost was 0.093800
Number of FunctionCalls  1227
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 3.244000 sec
Parameters at optimum (transmm)  0.41590 -0.44198  0.46493
Parameters at optimum (rotdeg)  0.24002 -0.19320  0.31488 
Final costs ----------------
Number of surface hits 2437
WM  Intensity    61.7728 +/-   8.9882
Ctx Intensity    78.1765 +/-   8.7876
Pct Contrast     23.6733 +/-  14.7923
Cost   0.0938
RelCost   0.1957
Reg at min cost was 
 0.996  -0.055  -0.074   0.472;
 0.074  -0.003   0.997  -0.758;
-0.055  -0.998   0.001   0.017;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/bbr.pass1.dat, type = 14 
Original Reg 
 0.996  -0.059  -0.069   0.053;
 0.069  -0.007   0.998  -0.318;
-0.059  -0.998  -0.003  -0.447;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000  -0.003   0.005  -0.419;
-0.006  -0.004   0.000   0.440;
-0.004   0.000  -0.004  -0.464;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.889233
Computing change in rh position
Surface RMS Diff (mm) 0.869118 1.074054
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/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/sub013/mri/transforms/tmp.bbregister.1926/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/tmp.bbregister.1926/bbr.pass1.dat
subject sub013
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 1376409012
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.996  -0.055  -0.074   0.472;
 0.074  -0.003   0.997  -0.758;
-0.055  -0.998   0.001   0.017;
 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   1.007479
 1  -25.0 -25.0  25.0   1.008766
 2  -25.0  25.0 -25.0   1.020152
 3  -25.0  25.0  25.0   1.006316
 4   25.0 -25.0 -25.0   1.014987
 5   25.0 -25.0  25.0   1.008678
 6   25.0  25.0 -25.0   1.013304
 7   25.0  25.0  25.0   1.024505
REL:  8  0.113576    8.104188  1.013023 rel = 0.112116 
Initial costs ----------------
Number of surface hits 244221
WM  Intensity    62.0302 +/-   8.9942
Ctx Intensity    78.0510 +/-   8.8041
Pct Contrast     23.0917 +/-  14.9004
Cost   0.1136
RelCost   0.1121

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.1116   0.1116  0.0
     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.1092   0.1092  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.1055   0.1055  0.0
     6  -0.1000  -0.1000  -0.1000  -0.1000   0.1000  -0.1000      0.1009   0.1009  0.0
    15  -0.1000  -0.1000  -0.1000   0.0000   0.1000  -0.1000      0.0995   0.0995  0.0
    33  -0.1000  -0.1000   0.0000  -0.1000   0.1000  -0.1000      0.0993   0.0993  0.0
    40  -0.1000  -0.1000   0.0000   0.0000   0.0000   0.0000      0.0988   0.0988  0.0
    42  -0.1000  -0.1000   0.0000   0.0000   0.1000  -0.1000      0.0987   0.0987  0.0
   114  -0.1000   0.0000   0.0000  -0.1000   0.1000  -0.1000      0.0979   0.0979  0.0
   120  -0.1000   0.0000   0.0000   0.0000   0.0000  -0.1000      0.0964   0.0964  0.0
   138  -0.1000   0.0000   0.1000  -0.1000   0.0000  -0.1000      0.0964   0.0964  0.0
   139  -0.1000   0.0000   0.1000  -0.1000   0.0000   0.0000      0.0963   0.0963  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0938   0.0938  0.0
Brute Force --------------------------
Min cost was 0.093800
Number of iterations   729
Search time 1.870000 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 -0.021  0.000  0.000  0.000  0.000  0.000   0.1135294176
   8 -0.020  0.000  0.000  0.000  0.000  0.000   0.1135286163
   9 -0.018  0.000  0.000  0.000  0.000  0.000   0.1135278911
  11 -0.017  0.000  0.000  0.000  0.000  0.000   0.1135277892
  19 -0.017  0.132  0.000  0.000  0.000  0.000   0.1113011632
  20 -0.017  0.129  0.000  0.000  0.000  0.000   0.1112914511
  21 -0.017  0.121  0.000  0.000  0.000  0.000   0.1112776303
  23 -0.017  0.118  0.000  0.000  0.000  0.000   0.1112767325
  35 -0.017  0.118 -0.016  0.000  0.000  0.000   0.1112382715
  45 -0.017  0.118 -0.016  0.019  0.000  0.000   0.1111700638
  46 -0.017  0.118 -0.016  0.017  0.000  0.000   0.1111684413
  47 -0.017  0.118 -0.016  0.016  0.000  0.000   0.1111683171
  55 -0.017  0.118 -0.016  0.016 -0.027  0.000   0.1110699042
  64 -0.017  0.118 -0.016  0.016 -0.027 -0.119   0.1091519266
  65 -0.017  0.118 -0.016  0.016 -0.027 -0.123   0.1091500701
  66 -0.017  0.118 -0.016  0.016 -0.027 -0.122   0.1091498946
  75 -0.091  0.118 -0.016  0.016 -0.027 -0.122   0.1088259361
  76 -0.072  0.118 -0.016  0.016 -0.027 -0.122   0.1087821778
  78 -0.069  0.118 -0.016  0.016 -0.027 -0.122   0.1087818911
  81 -0.070  0.118 -0.016  0.016 -0.027 -0.122   0.1087817409
  90 -0.070  0.122 -0.016  0.016 -0.027 -0.122   0.1087780995
  92 -0.070  0.123 -0.016  0.016 -0.027 -0.122   0.1087780450
 100 -0.070  0.123 -0.045  0.016 -0.027 -0.122   0.1087712278
 101 -0.070  0.123 -0.031  0.016 -0.027 -0.122   0.1087554945
 111 -0.070  0.123 -0.031  0.029 -0.027 -0.122   0.1087044490
 112 -0.070  0.123 -0.031  0.032 -0.027 -0.122   0.1087042297
 114 -0.070  0.123 -0.031  0.031 -0.027 -0.122   0.1087039119
 122 -0.070  0.123 -0.031  0.031 -0.020 -0.122   0.1086871914
 123 -0.070  0.123 -0.031  0.031 -0.014 -0.122   0.1086836675
 124 -0.070  0.123 -0.031  0.031 -0.015 -0.122   0.1086834943
 125 -0.070  0.123 -0.031  0.031 -0.016 -0.122   0.1086834931
 133 -0.070  0.123 -0.031  0.031 -0.016 -0.150   0.1084903958
 135 -0.070  0.123 -0.031  0.031 -0.016 -0.155   0.1084862670
 138 -0.124  0.128 -0.047  0.047 -0.005 -0.188   0.1081821744
 145 -0.138  0.130 -0.051  0.051 -0.002 -0.197   0.1081694152
 146 -0.137  0.130 -0.050  0.051 -0.002 -0.197   0.1081692485
 147 -0.136  0.129 -0.050  0.050 -0.002 -0.196   0.1081688487
 150 -0.135  0.129 -0.050  0.050 -0.003 -0.195   0.1081688077
 154 -0.135  0.129 -0.050  0.050 -0.003 -0.195   0.1081688042
 162 -0.135  0.129 -0.050  0.050 -0.003 -0.205   0.1081646812
 164 -0.135  0.129 -0.050  0.050 -0.003 -0.202   0.1081623440
 174 -0.135  0.136 -0.050  0.050 -0.003 -0.202   0.1081504458
 175 -0.135  0.138 -0.050  0.050 -0.003 -0.202   0.1081499277
 176 -0.135  0.139 -0.050  0.050 -0.003 -0.202   0.1081498112
 184 -0.135  0.139 -0.073  0.050 -0.003 -0.202   0.1081089469
 186 -0.135  0.139 -0.072  0.050 -0.003 -0.202   0.1081089091
 195 -0.135  0.139 -0.072  0.051 -0.003 -0.202   0.1081088372
 205 -0.135  0.139 -0.072  0.051 -0.001 -0.202   0.1081086162
 212 -0.140  0.139 -0.074  0.053 -0.000 -0.205   0.1081036750
 213 -0.142  0.139 -0.074  0.053 -0.000 -0.206   0.1081032060
 229 -0.142  0.139 -0.074  0.053 -0.000 -0.207   0.1081030070
 247 -0.142  0.139 -0.076  0.053 -0.000 -0.207   0.1081028009
 256 -0.142  0.139 -0.076  0.052 -0.000 -0.207   0.1081025567
 266 -0.142  0.139 -0.076  0.052  0.001 -0.207   0.1081021056
 274 -0.143  0.139 -0.076  0.052  0.001 -0.208   0.1081020312
 276 -0.143  0.139 -0.076  0.052  0.001 -0.207   0.1081019884
 280 -0.143  0.139 -0.076  0.052  0.001 -0.207   0.1081019876
 300 -0.143  0.138 -0.076  0.052  0.001 -0.207   0.1081019387
 308 -0.143  0.138 -0.075  0.052  0.001 -0.207   0.1081017032
 317 -0.143  0.138 -0.075  0.051  0.001 -0.207   0.1081014471
 328 -0.143  0.138 -0.075  0.051  0.002 -0.207   0.1081013979
 336 -0.144  0.138 -0.075  0.051  0.002 -0.208   0.1081013652
 337 -0.143  0.138 -0.075  0.051  0.002 -0.208   0.1081013280
 349 -0.143  0.138 -0.075  0.051  0.002 -0.207   0.1081011917
 367 -0.143  0.138 -0.074  0.051  0.002 -0.207   0.1081008778
 368 -0.143  0.138 -0.073  0.051  0.002 -0.207   0.1081008578
 378 -0.143  0.138 -0.073  0.050  0.002 -0.207   0.1081008337
 396 -0.144  0.138 -0.074  0.051  0.003 -0.207   0.1081005968
 431 -0.144  0.138 -0.073  0.051  0.003 -0.207   0.1081005519
 459 -0.145  0.138 -0.073  0.051  0.003 -0.207   0.1081005364
Powell done niters = 7
Computing relative cost
 0  -25.0 -25.0 -25.0   1.006662
 1  -25.0 -25.0  25.0   1.007795
 2  -25.0  25.0 -25.0   1.019355
 3  -25.0  25.0  25.0   1.007909
 4   25.0 -25.0 -25.0   1.014188
 5   25.0 -25.0  25.0   1.009912
 6   25.0  25.0 -25.0   1.012267
 7   25.0  25.0  25.0   1.025412
REL:  8  0.108101    8.103502  1.012938 rel = 0.10672 
Number of iterations     7
Min cost was 0.108101
Number of FunctionCalls   522
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 50.756000 sec
Parameters at optimum (transmm) -0.14454  0.13806 -0.07267
Parameters at optimum (rotdeg)  0.05057  0.00263 -0.20736 
Final costs ----------------
Number of surface hits 244221
WM  Intensity    62.0535 +/-   9.0422
Ctx Intensity    78.0245 +/-   8.7600
Pct Contrast     23.0325 +/-  14.8099
Cost   0.1081
RelCost   0.1121
Reg at min cost was 
 0.996  -0.055  -0.071   0.324;
 0.071  -0.002   0.997  -0.622;
-0.055  -0.998   0.002  -0.056;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.996  -0.055  -0.074   0.472;
 0.074  -0.003   0.997  -0.758;
-0.055  -0.998   0.001   0.017;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000   0.000  -0.004   0.147;
 0.004  -0.001  -0.000  -0.136;
-0.000  -0.000  -0.001   0.073;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.241364
Computing change in rh position
Surface RMS Diff (mm) 0.175645 0.372936
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 --------
 0.996  -0.055  -0.071   0.324;
 0.071  -0.002   0.997  -0.622;
-0.055  -0.998   0.002  -0.056;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.885;
 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 --------
 0.996  -0.055  -0.071   0.324;
 0.071  -0.002   0.997  -0.622;
-0.055  -0.998   0.002  -0.056;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub013
RegMat ---------------------------
 0.996  -0.055  -0.071   0.324;
 0.071  -0.002   0.997  -0.622;
-0.055  -0.998   0.002  -0.056;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000  -0.004   0.004  -0.142;
 0.004   1.000   0.009   0.099;
-0.004  -0.009   1.000   0.825;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.697  -0.037  -0.047   48.923;
-0.050   0.001  -0.665   261.588;
 0.039   0.666  -0.001  -4.878;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 21:38:16 CEST 2013 
Ended   at Thu Aug  8 21:50:23 CEST 2013
BBR-Run-Time-Sec 727
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.dat --surf
 

 mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/T2.mgz 

mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996032, 0.0582575, 0.0672728)
j_ras = (0.0588709, 0.99824, 0.00717099)
k_ras = (0.0667366, -0.011103, 0.997709)
INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
reading extra input line subject sub013
reading extra input line fscale 0.150000
reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/orig.mgz...
INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/transforms/T2raw.lta...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
 1.000  -0.004   0.004  -0.142;
 0.004   1.000   0.009   0.099;
-0.004  -0.009   1.000   0.825;
 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/sub013/mri/T2.mgz...

 mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/T2.mgz...
computing distance transform
computing distance transform
computing nonmaximum suppression
9014 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/sub013/mri/T2.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub013 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/sub013/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
16512 bright wm thresholded.
535 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.orig...
computing class statistics...
border white:    233793 voxels (1.39%)
border gray      268841 voxels (1.60%)
WM (92.0): 93.4 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.7 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.2 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.4 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.6 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=60
mean inside = 93.5, mean outside = 68.9
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/sub013/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.26 (0.04-->4.23) (max @ vno 78608 --> 79720)
face area 0.33 +- 0.16 (0.00-->2.18)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
deleting segment 4 with 615 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 17 points - only 0.00% unknown
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 8 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 11 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 0.89 +- 0.25 (0.09-->4.23) (max @ vno 79720 --> 78608)
face area 0.33 +- 0.16 (0.00-->2.18)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4033813.8, rms=0.00
rms = 1.18, time step reduction 1 of 3 to 0.250...
rms = 0.30, 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=4033813.8, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
deleting segment 3 with 615 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
deleting segment 6 with 17 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
deleting segment 10 with 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 0.89 +- 0.25 (0.09-->4.23) (max @ vno 79720 --> 78608)
face area 0.33 +- 0.16 (0.00-->2.18)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4033813.8, rms=0.00
rms = 1.19, time step reduction 1 of 3 to 0.250...
rms = 0.30, 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=4033813.8, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
deleting segment 3 with 615 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
deleting segment 6 with 17 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
deleting segment 10 with 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 0.89 +- 0.25 (0.09-->4.23) (max @ vno 79720 --> 78608)
face area 0.33 +- 0.16 (0.00-->2.18)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4033813.8, rms=0.00
rms = 1.18, time step reduction 1 of 3 to 0.250...
rms = 0.30, 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=4033813.8, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
deleting segment 3 with 615 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
deleting segment 6 with 17 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
deleting segment 10 with 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=4033813.8, rms=0.00
rms = 1.19, time step reduction 1 of 3 to 0.250...
rms = 0.30, 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=4033813.8, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 1 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 [94.50 229.50], gm=162.00+-22.50, and vertices in regions > 150.7
39800 surface locations found to contain inconsistent values (1896 in, 37904 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=454444.2, rms=0.23
001: dt: 0.5000, sse=428222.2, rms=0.225 (0.000%)
002: dt: 0.5000, sse=413110.7, rms=0.210 (0.000%)
003: dt: 0.5000, sse=404198.5, rms=0.200 (0.000%)
004: dt: 0.5000, sse=396875.7, rms=0.190 (0.000%)
005: dt: 0.5000, sse=392016.7, rms=0.182 (0.000%)
006: dt: 0.5000, sse=388435.3, rms=0.175 (0.000%)
007: dt: 0.5000, sse=385701.8, rms=0.169 (0.000%)
008: dt: 0.5000, sse=383489.9, rms=0.164 (0.000%)
009: dt: 0.5000, sse=382212.8, rms=0.160 (0.000%)
010: dt: 0.5000, sse=381004.8, rms=0.156 (0.000%)
011: dt: 0.5000, sse=379632.8, rms=0.153 (0.000%)
012: dt: 0.5000, sse=378393.1, rms=0.151 (0.000%)
013: dt: 0.5000, sse=377101.0, rms=0.149 (0.000%)
014: dt: 0.5000, sse=376103.8, rms=0.147 (0.000%)
015: dt: 0.5000, sse=374978.3, rms=0.146 (0.000%)
016: dt: 0.5000, sse=373812.6, rms=0.145 (0.000%)
017: dt: 0.5000, sse=372737.4, rms=0.144 (0.000%)
018: dt: 0.5000, sse=371562.1, rms=0.144 (0.000%)
019: dt: 0.5000, sse=370604.7, rms=0.143 (0.000%)
020: dt: 0.5000, sse=369591.7, rms=0.143 (0.000%)
021: dt: 0.5000, sse=368616.1, rms=0.143 (0.000%)
022: dt: 0.5000, sse=367468.5, rms=0.143 (0.000%)
023: dt: 0.5000, sse=366367.5, rms=0.143 (0.000%)
024: dt: 0.5000, sse=365452.3, rms=0.143 (0.000%)
025: dt: 0.5000, sse=364480.9, rms=0.143 (0.000%)
026: dt: 0.5000, sse=363675.7, rms=0.143 (0.000%)
027: dt: 0.5000, sse=362561.3, rms=0.144 (0.000%)
028: dt: 0.5000, sse=361918.6, rms=0.144 (0.000%)
029: dt: 0.5000, sse=360871.0, rms=0.144 (0.000%)
030: dt: 0.5000, sse=359905.8, rms=0.145 (0.000%)
positioning took 3.5 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [91.50 232.50], gm=162.00+-23.50, and vertices in regions > 150.2
34191 surface locations found to contain inconsistent values (591 in, 33600 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=37443.2, rms=0.12
031: dt: 0.5000, sse=37181.7, rms=0.119 (0.000%)
032: dt: 0.5000, sse=38211.2, rms=0.108 (0.000%)
033: dt: 0.5000, sse=39378.7, rms=0.100 (0.000%)
034: dt: 0.5000, sse=40342.6, rms=0.095 (0.000%)
035: dt: 0.5000, sse=41138.9, rms=0.090 (0.000%)
036: dt: 0.5000, sse=41875.1, rms=0.085 (0.000%)
037: dt: 0.5000, sse=42554.7, rms=0.081 (0.000%)
038: dt: 0.5000, sse=43248.4, rms=0.077 (0.000%)
039: dt: 0.5000, sse=43897.7, rms=0.073 (0.000%)
040: dt: 0.5000, sse=44533.6, rms=0.070 (0.000%)
041: dt: 0.5000, sse=45140.2, rms=0.067 (0.000%)
042: dt: 0.5000, sse=45694.1, rms=0.064 (0.000%)
043: dt: 0.5000, sse=46204.2, rms=0.062 (0.000%)
044: dt: 0.5000, sse=46689.9, rms=0.059 (0.000%)
045: dt: 0.5000, sse=47147.0, rms=0.057 (0.000%)
046: dt: 0.5000, sse=47568.7, rms=0.055 (0.000%)
047: dt: 0.5000, sse=47962.0, rms=0.053 (0.000%)
048: dt: 0.5000, sse=48307.7, rms=0.051 (0.000%)
049: dt: 0.5000, sse=48638.2, rms=0.050 (0.000%)
050: dt: 0.5000, sse=48952.7, rms=0.048 (0.000%)
051: dt: 0.5000, sse=49229.6, rms=0.047 (0.000%)
052: dt: 0.5000, sse=49502.2, rms=0.046 (0.000%)
053: dt: 0.5000, sse=49757.7, rms=0.045 (0.000%)
054: dt: 0.5000, sse=49971.7, rms=0.044 (0.000%)
055: dt: 0.5000, sse=50200.5, rms=0.043 (0.000%)
056: dt: 0.5000, sse=50398.1, rms=0.042 (0.000%)
057: dt: 0.5000, sse=50562.8, rms=0.041 (0.000%)
058: dt: 0.5000, sse=50722.2, rms=0.040 (0.000%)
059: dt: 0.5000, sse=50878.3, rms=0.039 (0.000%)
060: dt: 0.5000, sse=51017.2, rms=0.039 (0.000%)
positioning took 3.5 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [90.00 234.00], gm=162.00+-24.00, and vertices in regions > 150.0
33700 surface locations found to contain inconsistent values (122 in, 33578 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=5441.6, rms=0.05
061: dt: 0.5000, sse=5426.9, rms=0.051 (0.000%)
062: dt: 0.5000, sse=5501.3, rms=0.045 (0.000%)
063: dt: 0.5000, sse=5568.7, rms=0.042 (0.000%)
064: dt: 0.5000, sse=5619.8, rms=0.040 (0.000%)
065: dt: 0.5000, sse=5652.5, rms=0.038 (0.000%)
066: dt: 0.5000, sse=5667.3, rms=0.036 (0.000%)
067: dt: 0.5000, sse=5675.3, rms=0.035 (0.000%)
068: dt: 0.5000, sse=5682.0, rms=0.034 (0.000%)
069: dt: 0.5000, sse=5687.4, rms=0.033 (0.000%)
070: dt: 0.5000, sse=5693.0, rms=0.032 (0.000%)
071: dt: 0.5000, sse=5697.0, rms=0.032 (0.000%)
072: dt: 0.5000, sse=5701.9, rms=0.031 (0.000%)
073: dt: 0.5000, sse=5706.6, rms=0.030 (0.000%)
074: dt: 0.5000, sse=5711.7, rms=0.030 (0.000%)
075: dt: 0.5000, sse=5715.0, rms=0.029 (0.000%)
076: dt: 0.5000, sse=5719.1, rms=0.029 (0.000%)
077: dt: 0.5000, sse=5721.6, rms=0.028 (0.000%)
078: dt: 0.5000, sse=5724.9, rms=0.028 (0.000%)
079: dt: 0.5000, sse=5726.4, rms=0.027 (0.000%)
080: dt: 0.5000, sse=5728.7, rms=0.027 (0.000%)
081: dt: 0.5000, sse=5731.0, rms=0.027 (0.000%)
082: dt: 0.5000, sse=5732.3, rms=0.026 (0.000%)
083: dt: 0.5000, sse=5734.2, rms=0.026 (0.000%)
084: dt: 0.5000, sse=5735.6, rms=0.026 (0.000%)
085: dt: 0.5000, sse=5736.7, rms=0.026 (0.000%)
086: dt: 0.5000, sse=5738.5, rms=0.025 (0.000%)
087: dt: 0.5000, sse=5740.5, rms=0.025 (0.000%)
088: dt: 0.5000, sse=5741.6, rms=0.025 (0.000%)
089: dt: 0.5000, sse=5742.5, rms=0.025 (0.000%)
090: dt: 0.5000, sse=5744.2, rms=0.025 (0.000%)
positioning took 3.5 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [32.00 284.00], gm=158.00+-42.00, and vertices in regions > 137.0
19081 surface locations found to contain inconsistent values (0 in, 19081 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/sub013/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=5452.7, rms=0.20
091: dt: 0.5000, sse=4940.3, rms=0.188 (0.000%)
092: dt: 0.5000, sse=4196.4, rms=0.171 (0.000%)
093: dt: 0.5000, sse=3550.6, rms=0.155 (0.000%)
094: dt: 0.5000, sse=2993.2, rms=0.139 (0.000%)
095: dt: 0.5000, sse=2543.7, rms=0.125 (0.000%)
096: dt: 0.5000, sse=2181.6, rms=0.113 (0.000%)
097: dt: 0.5000, sse=1897.5, rms=0.102 (0.000%)
098: dt: 0.5000, sse=1678.6, rms=0.092 (0.000%)
099: dt: 0.5000, sse=1501.6, rms=0.083 (0.000%)
100: dt: 0.5000, sse=1356.5, rms=0.075 (0.000%)
101: dt: 0.5000, sse=1243.3, rms=0.068 (0.000%)
102: dt: 0.5000, sse=1157.0, rms=0.062 (0.000%)
103: dt: 0.5000, sse=1090.8, rms=0.056 (0.000%)
104: dt: 0.5000, sse=1041.0, rms=0.051 (0.000%)
105: dt: 0.5000, sse=1002.0, rms=0.047 (0.000%)
106: dt: 0.5000, sse=971.8, rms=0.044 (0.000%)
107: dt: 0.5000, sse=948.7, rms=0.041 (0.000%)
108: dt: 0.5000, sse=931.3, rms=0.038 (0.000%)
109: dt: 0.5000, sse=918.1, rms=0.036 (0.000%)
110: dt: 0.5000, sse=908.1, rms=0.034 (0.000%)
111: dt: 0.5000, sse=901.3, rms=0.032 (0.000%)
112: dt: 0.5000, sse=896.3, rms=0.031 (0.000%)
113: dt: 0.5000, sse=892.7, rms=0.030 (0.000%)
114: dt: 0.5000, sse=890.4, rms=0.029 (0.000%)
115: dt: 0.5000, sse=889.2, rms=0.028 (0.000%)
116: dt: 0.5000, sse=888.5, rms=0.028 (0.000%)
117: dt: 0.5000, sse=888.4, rms=0.028 (0.000%)
118: dt: 0.5000, sse=888.1, rms=0.027 (0.000%)
119: dt: 0.5000, sse=888.2, rms=0.027 (0.000%)
120: dt: 0.5000, sse=888.1, rms=0.027 (0.000%)
positioning took 3.5 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.area.pial
vertex spacing 1.04 +- 0.45 (0.07-->7.32) (max @ vno 92762 --> 92787)
face area 0.41 +- 0.31 (0.00-->6.39)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 129542 vertices processed
25000 of 129542 vertices processed
50000 of 129542 vertices processed
75000 of 129542 vertices processed
100000 of 129542 vertices processed
125000 of 129542 vertices processed
0 of 129542 vertices processed
25000 of 129542 vertices processed
50000 of 129542 vertices processed
75000 of 129542 vertices processed
100000 of 129542 vertices processed
125000 of 129542 vertices processed
thickness calculation complete, 227:612 truncations.
29842 vertices at 0 distance
92972 vertices at 1 distance
83168 vertices at 2 distance
30660 vertices at 3 distance
8199 vertices at 4 distance
2213 vertices at 5 distance
643 vertices at 6 distance
269 vertices at 7 distance
121 vertices at 8 distance
63 vertices at 9 distance
41 vertices at 10 distance
21 vertices at 11 distance
18 vertices at 12 distance
11 vertices at 13 distance
17 vertices at 14 distance
11 vertices at 15 distance
19 vertices at 16 distance
10 vertices at 17 distance
9 vertices at 18 distance
14 vertices at 19 distance
19 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.thickness
positioning took 17.5 minutes
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub013 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/sub013/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
16174 bright wm thresholded.
541 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.orig...
computing class statistics...
border white:    233793 voxels (1.39%)
border gray      268841 voxels (1.60%)
WM (92.0): 93.5 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.6 +- 13.0 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.0 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.1 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.5 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.1 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=60
mean inside = 93.5, mean outside = 68.5
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/sub013/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.26 (0.04-->3.81) (max @ vno 64613 --> 65791)
face area 0.33 +- 0.16 (0.00-->2.23)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
deleting segment 2 with 25 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 333 points - only 0.00% unknown
deleting segment 6 with 25 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 9 with 93 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 0.89 +- 0.25 (0.09-->3.81) (max @ vno 64613 --> 65791)
face area 0.33 +- 0.16 (0.00-->2.23)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4055689.8, rms=0.00
rms = 1.25, time step reduction 1 of 3 to 0.250...
rms = 0.32, 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=4055689.8, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
deleting segment 1 with 25 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 333 points - only 0.00% unknown
deleting segment 4 with 25 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 93 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 0.89 +- 0.25 (0.09-->3.81) (max @ vno 64613 --> 65791)
face area 0.33 +- 0.16 (0.00-->2.23)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4055689.8, rms=0.00
rms = 1.25, time step reduction 1 of 3 to 0.250...
rms = 0.32, 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=4055689.8, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
deleting segment 1 with 25 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 333 points - only 0.00% unknown
deleting segment 4 with 25 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 93 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 0.89 +- 0.25 (0.09-->3.81) (max @ vno 64613 --> 65791)
face area 0.33 +- 0.16 (0.00-->2.23)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4055689.8, rms=0.00
rms = 1.25, time step reduction 1 of 3 to 0.250...
rms = 0.32, 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=4055689.8, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 22 points - only 0.00% unknown
deleting segment 1 with 25 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 333 points - only 0.00% unknown
deleting segment 4 with 25 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
deleting segment 6 with 93 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=4055689.8, rms=0.00
rms = 1.25, time step reduction 1 of 3 to 0.250...
rms = 0.32, 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=4055689.8, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 1 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 [98.00 236.00], gm=167.00+-23.00, and vertices in regions > 155.5
39824 surface locations found to contain inconsistent values (2451 in, 37373 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=465036.6, rms=0.25
001: dt: 0.5000, sse=438802.8, rms=0.241 (0.000%)
002: dt: 0.5000, sse=421870.3, rms=0.226 (0.000%)
003: dt: 0.5000, sse=412086.6, rms=0.215 (0.000%)
004: dt: 0.5000, sse=404466.1, rms=0.205 (0.000%)
005: dt: 0.5000, sse=399787.9, rms=0.196 (0.000%)
006: dt: 0.5000, sse=395952.5, rms=0.189 (0.000%)
007: dt: 0.5000, sse=393065.3, rms=0.182 (0.000%)
008: dt: 0.5000, sse=391865.6, rms=0.177 (0.000%)
009: dt: 0.5000, sse=390833.2, rms=0.172 (0.000%)
010: dt: 0.5000, sse=389349.1, rms=0.168 (0.000%)
011: dt: 0.5000, sse=388125.6, rms=0.165 (0.000%)
012: dt: 0.5000, sse=387429.6, rms=0.162 (0.000%)
013: dt: 0.5000, sse=386652.7, rms=0.160 (0.000%)
014: dt: 0.5000, sse=385373.6, rms=0.158 (0.000%)
015: dt: 0.5000, sse=384236.1, rms=0.156 (0.000%)
016: dt: 0.5000, sse=383600.7, rms=0.155 (0.000%)
017: dt: 0.5000, sse=382012.7, rms=0.154 (0.000%)
018: dt: 0.5000, sse=381371.2, rms=0.153 (0.000%)
019: dt: 0.5000, sse=379927.1, rms=0.152 (0.000%)
020: dt: 0.5000, sse=379214.4, rms=0.152 (0.000%)
021: dt: 0.5000, sse=378057.5, rms=0.151 (0.000%)
022: dt: 0.5000, sse=377220.5, rms=0.151 (0.000%)
023: dt: 0.5000, sse=376034.4, rms=0.151 (0.000%)
024: dt: 0.5000, sse=375225.1, rms=0.151 (0.000%)
025: dt: 0.5000, sse=374323.9, rms=0.151 (0.000%)
026: dt: 0.5000, sse=373472.8, rms=0.151 (0.000%)
027: dt: 0.5000, sse=372187.7, rms=0.151 (0.000%)
028: dt: 0.5000, sse=371462.2, rms=0.151 (0.000%)
029: dt: 0.5000, sse=370301.0, rms=0.151 (0.000%)
030: dt: 0.5000, sse=369975.5, rms=0.151 (0.000%)
positioning took 3.3 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [96.00 240.00], gm=168.00+-24.00, and vertices in regions > 156.0
33435 surface locations found to contain inconsistent values (591 in, 32844 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=38849.5, rms=0.14
031: dt: 0.5000, sse=38547.2, rms=0.132 (0.000%)
032: dt: 0.5000, sse=39657.3, rms=0.120 (0.000%)
033: dt: 0.5000, sse=40905.2, rms=0.112 (0.000%)
034: dt: 0.5000, sse=41946.9, rms=0.106 (0.000%)
035: dt: 0.5000, sse=42832.8, rms=0.101 (0.000%)
036: dt: 0.5000, sse=43694.5, rms=0.096 (0.000%)
037: dt: 0.5000, sse=44496.6, rms=0.091 (0.000%)
038: dt: 0.5000, sse=45241.1, rms=0.087 (0.000%)
039: dt: 0.5000, sse=45997.9, rms=0.083 (0.000%)
040: dt: 0.5000, sse=46691.4, rms=0.079 (0.000%)
041: dt: 0.5000, sse=47337.6, rms=0.076 (0.000%)
042: dt: 0.5000, sse=47995.1, rms=0.073 (0.000%)
043: dt: 0.5000, sse=48583.3, rms=0.070 (0.000%)
044: dt: 0.5000, sse=49184.4, rms=0.067 (0.000%)
045: dt: 0.5000, sse=49679.5, rms=0.065 (0.000%)
046: dt: 0.5000, sse=50211.6, rms=0.062 (0.000%)
047: dt: 0.5000, sse=50675.8, rms=0.060 (0.000%)
048: dt: 0.5000, sse=51118.3, rms=0.058 (0.000%)
049: dt: 0.5000, sse=51505.8, rms=0.056 (0.000%)
050: dt: 0.5000, sse=51897.1, rms=0.054 (0.000%)
051: dt: 0.5000, sse=52226.5, rms=0.053 (0.000%)
052: dt: 0.5000, sse=52553.5, rms=0.051 (0.000%)
053: dt: 0.5000, sse=52858.7, rms=0.050 (0.000%)
054: dt: 0.5000, sse=53129.0, rms=0.049 (0.000%)
055: dt: 0.5000, sse=53380.6, rms=0.048 (0.000%)
056: dt: 0.5000, sse=53604.3, rms=0.046 (0.000%)
057: dt: 0.5000, sse=53810.6, rms=0.045 (0.000%)
058: dt: 0.5000, sse=53985.6, rms=0.044 (0.000%)
059: dt: 0.5000, sse=54170.3, rms=0.044 (0.000%)
060: dt: 0.5000, sse=54335.8, rms=0.043 (0.000%)
positioning took 3.3 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [57.60 272.40], gm=165.00+-35.80, and vertices in regions > 147.1
23640 surface locations found to contain inconsistent values (7 in, 23633 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=8517.9, rms=0.16
061: dt: 0.5000, sse=8153.9, rms=0.148 (0.000%)
062: dt: 0.5000, sse=7629.7, rms=0.131 (0.000%)
063: dt: 0.5000, sse=7256.2, rms=0.116 (0.000%)
064: dt: 0.5000, sse=7010.9, rms=0.103 (0.000%)
065: dt: 0.5000, sse=6880.9, rms=0.092 (0.000%)
066: dt: 0.5000, sse=6819.9, rms=0.083 (0.000%)
067: dt: 0.5000, sse=6797.4, rms=0.076 (0.000%)
068: dt: 0.5000, sse=6789.9, rms=0.071 (0.000%)
069: dt: 0.5000, sse=6809.9, rms=0.066 (0.000%)
070: dt: 0.5000, sse=6844.3, rms=0.062 (0.000%)
071: dt: 0.5000, sse=6891.3, rms=0.058 (0.000%)
072: dt: 0.5000, sse=6939.9, rms=0.054 (0.000%)
073: dt: 0.5000, sse=6987.3, rms=0.052 (0.000%)
074: dt: 0.5000, sse=7032.4, rms=0.049 (0.000%)
075: dt: 0.5000, sse=7073.8, rms=0.046 (0.000%)
076: dt: 0.5000, sse=7114.1, rms=0.044 (0.000%)
077: dt: 0.5000, sse=7154.3, rms=0.042 (0.000%)
078: dt: 0.5000, sse=7190.1, rms=0.040 (0.000%)
079: dt: 0.5000, sse=7228.1, rms=0.039 (0.000%)
080: dt: 0.5000, sse=7262.7, rms=0.037 (0.000%)
081: dt: 0.5000, sse=7298.9, rms=0.036 (0.000%)
082: dt: 0.5000, sse=7324.7, rms=0.035 (0.000%)
083: dt: 0.5000, sse=7354.9, rms=0.034 (0.000%)
084: dt: 0.5000, sse=7381.1, rms=0.033 (0.000%)
085: dt: 0.5000, sse=7405.7, rms=0.032 (0.000%)
086: dt: 0.5000, sse=7427.9, rms=0.032 (0.000%)
087: dt: 0.5000, sse=7450.5, rms=0.031 (0.000%)
088: dt: 0.5000, sse=7469.6, rms=0.031 (0.000%)
089: dt: 0.5000, sse=7487.3, rms=0.031 (0.000%)
090: dt: 0.5000, sse=7501.5, rms=0.030 (0.000%)
positioning took 3.4 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [87.30 242.70], gm=165.00+-25.90, and vertices in regions > 152.0
14488 surface locations found to contain inconsistent values (126 in, 14362 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/sub013/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1066.2, rms=0.05
091: dt: 0.5000, sse=1055.5, rms=0.050 (0.000%)
092: dt: 0.5000, sse=1010.1, rms=0.046 (0.000%)
093: dt: 0.5000, sse=984.5, rms=0.043 (0.000%)
094: dt: 0.5000, sse=964.4, rms=0.040 (0.000%)
095: dt: 0.5000, sse=949.5, rms=0.039 (0.000%)
096: dt: 0.5000, sse=937.9, rms=0.037 (0.000%)
097: dt: 0.5000, sse=928.4, rms=0.036 (0.000%)
098: dt: 0.5000, sse=920.2, rms=0.035 (0.000%)
099: dt: 0.5000, sse=912.5, rms=0.034 (0.000%)
100: dt: 0.5000, sse=905.7, rms=0.033 (0.000%)
101: dt: 0.5000, sse=899.5, rms=0.032 (0.000%)
102: dt: 0.5000, sse=893.8, rms=0.031 (0.000%)
103: dt: 0.5000, sse=890.9, rms=0.031 (0.000%)
104: dt: 0.5000, sse=886.1, rms=0.030 (0.000%)
105: dt: 0.5000, sse=881.3, rms=0.029 (0.000%)
106: dt: 0.5000, sse=877.4, rms=0.029 (0.000%)
107: dt: 0.5000, sse=873.4, rms=0.028 (0.000%)
108: dt: 0.5000, sse=870.9, rms=0.028 (0.000%)
109: dt: 0.5000, sse=867.3, rms=0.027 (0.000%)
110: dt: 0.5000, sse=864.6, rms=0.027 (0.000%)
111: dt: 0.5000, sse=863.4, rms=0.026 (0.000%)
112: dt: 0.5000, sse=861.4, rms=0.026 (0.000%)
113: dt: 0.5000, sse=859.9, rms=0.026 (0.000%)
114: dt: 0.5000, sse=859.4, rms=0.026 (0.000%)
115: dt: 0.5000, sse=859.1, rms=0.026 (0.000%)
116: dt: 0.5000, sse=857.6, rms=0.025 (0.000%)
117: dt: 0.5000, sse=855.9, rms=0.025 (0.000%)
118: dt: 0.5000, sse=854.6, rms=0.025 (0.000%)
119: dt: 0.5000, sse=854.5, rms=0.025 (0.000%)
120: dt: 0.5000, sse=854.0, rms=0.025 (0.000%)
positioning took 3.5 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.area.pial
vertex spacing 1.04 +- 0.45 (0.09-->7.37) (max @ vno 85549 --> 85566)
face area 0.42 +- 0.32 (0.00-->8.63)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 129914 vertices processed
25000 of 129914 vertices processed
50000 of 129914 vertices processed
75000 of 129914 vertices processed
100000 of 129914 vertices processed
125000 of 129914 vertices processed
0 of 129914 vertices processed
25000 of 129914 vertices processed
50000 of 129914 vertices processed
75000 of 129914 vertices processed
100000 of 129914 vertices processed
125000 of 129914 vertices processed
thickness calculation complete, 195:581 truncations.
30992 vertices at 0 distance
92961 vertices at 1 distance
83386 vertices at 2 distance
30649 vertices at 3 distance
7938 vertices at 4 distance
2004 vertices at 5 distance
625 vertices at 6 distance
195 vertices at 7 distance
107 vertices at 8 distance
47 vertices at 9 distance
39 vertices at 10 distance
34 vertices at 11 distance
42 vertices at 12 distance
18 vertices at 13 distance
13 vertices at 14 distance
16 vertices at 15 distance
10 vertices at 16 distance
14 vertices at 17 distance
12 vertices at 18 distance
4 vertices at 19 distance
14 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.thickness
positioning took 16.8 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 22:26:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 22:26:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 22:26:17 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub013 

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 = 9
writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/ribbon.mgz
 writing ribbon files
#--------------------------------------------
#@# ASeg Stats Thu Aug  8 22:39:43 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013

 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 sub013 


$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 sub013 
sysname  Linux
hostname snake4
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 993260 mm^3    (det: 1.961323 )
Computing euler number
orig.nofix lheno =  -48, rheno = -20
orig.nofix lhholes =   25, rhholes = 11
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 236564.460 233631.000  diff= 2933.5  pctdiff= 1.240
rhCtxGM: 236162.270 233484.000  diff= 2678.3  pctdiff= 1.134
lhCtxWM: 184426.963 184718.000  diff= -291.0  pctdiff=-0.158
rhCtxWM: 187146.071 186840.000  diff=  306.1  pctdiff= 0.164
SubCortGMVol  58857.000
SupraTentVol  916029.765 (909765.000) diff=6264.765 pctdiff=0.684
SupraTentVolNotVent  904012.765 (897748.000) diff=6264.765 pctdiff=0.693
BrainSegVol  1015563.000 (1013735.000) diff=1828.000 pctdiff=0.180
BrainSegVolNotVent  1001019.000 (1006420.765) diff=-5401.765 pctdiff=-0.540
BrainSegVolNotVent  1001019.000
CerebellumVol 103046.000
VentChorVol   12017.000
3rd4th5thCSF   2527.000
CSFVol   711.000, OptChiasmVol   213.000
MaskVol 1454550.000
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    5142    5142.240
  4     5                  Left-Inf-Lat-Vent     282     281.810
  5     7       Left-Cerebellum-White-Matter   12460   12459.542
  6     8             Left-Cerebellum-Cortex   38470   38469.914
  7    10               Left-Thalamus-Proper    6900    6899.712
  8    11                       Left-Caudate    3733    3732.688
  9    12                       Left-Putamen    5647    5646.615
 10    13                      Left-Pallidum    2109    2109.158
 11    14                      3rd-Ventricle     779     778.757
 12    15                      4th-Ventricle    1206    1206.138
 13    16                         Brain-Stem   20741   20741.012
 14    17                   Left-Hippocampus    3744    3743.823
 15    18                      Left-Amygdala    1472    1471.668
 16    24                                CSF     713     713.025
 17    26                Left-Accumbens-area     682     682.284
 18    28                     Left-VentralDC    3616    3615.875
 19    30                        Left-vessel     103     103.238
 20    31                Left-choroid-plexus    1072    1071.960
 23    43            Right-Lateral-Ventricle    3592    3591.786
 24    44                 Right-Inf-Lat-Vent     748     748.147
 25    46      Right-Cerebellum-White-Matter   13477   13476.980
 26    47            Right-Cerebellum-Cortex   40846   40845.898
 27    49              Right-Thalamus-Proper    6351    6351.053
 28    50                      Right-Caudate    4053    4053.184
 29    51                      Right-Putamen    6199    6199.393
 30    52                     Right-Pallidum    2049    2048.520
 31    53                  Right-Hippocampus    3746    3745.798
 32    54                     Right-Amygdala    1743    1742.629
 33    58               Right-Accumbens-area     863     862.818
 34    60                    Right-VentralDC    3906    3905.602
 35    62                       Right-vessel     100      99.611
 36    63               Right-choroid-plexus    1256    1255.857
 37    72                      5th-Ventricle       0       0.000
 38    77                 WM-hypointensities     711     710.868
 39    78            Left-WM-hypointensities       0       0.000
 40    79           Right-WM-hypointensities       0       0.000
 41    80             non-WM-hypointensities       9       9.453
 42    81        Left-non-WM-hypointensities       0       0.000
 43    82       Right-non-WM-hypointensities       0       0.000
 44    85                       Optic-Chiasm     221     221.414
 45   251                       CC_Posterior     787     786.693
 46   252                   CC_Mid_Posterior     389     388.697
 47   253                         CC_Central     362     362.136
 48   254                    CC_Mid_Anterior     342     341.828
 49   255                        CC_Anterior     681     681.194

Reporting on  45 segmentations
mri_segstats done
#-----------------------------------------
#@# AParc-to-ASeg Thu Aug  8 22:42:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013

 mri_aparc2aseg --s sub013 --volmask 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub013
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/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/sub013/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 = 465529
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aparc+aseg.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013

 mri_aparc2aseg --s sub013 --volmask --a2009s 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub013
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/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/sub013/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 = 465529
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Thu Aug  8 22:47:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013

 mri_aparc2aseg --s sub013 --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 sub013
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/sub013/mri/aparc+aseg.mgz

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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/sub013/mri/ribbon.mgz
Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 7512 vertices from left hemi
Ripped 7723 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/sub013/mri/aseg.mgz
Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 = 836078
Used brute-force search on 28 voxels
Fixing Parahip LH WM
  Found 11 clusters
     0 k 2.000000
     1 k 1.000000
     2 k 1.000000
     3 k 5.000000
     4 k 1.000000
     5 k 1499.000000
     6 k 6.000000
     7 k 1.000000
     8 k 21.000000
     9 k 1.000000
     10 k 1.000000
Fixing Parahip RH WM
  Found 9 clusters
     0 k 1.000000
     1 k 2.000000
     2 k 3.000000
     3 k 13.000000
     4 k 2.000000
     5 k 3.000000
     6 k 1.000000
     7 k 1.000000
     8 k 1315.000000
Writing output aseg to mri/wmparc.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013

 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 sub013 --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 sub013 --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) = 993260 mm^3    (det: 1.961323 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 236564.460 233631.000  diff= 2933.5  pctdiff= 1.240
rhCtxGM: 236162.270 233484.000  diff= 2678.3  pctdiff= 1.134
lhCtxWM: 184426.963 184718.000  diff= -291.0  pctdiff=-0.158
rhCtxWM: 187146.071 186840.000  diff=  306.1  pctdiff= 0.164
SubCortGMVol  58857.000
SupraTentVol  916029.765 (909765.000) diff=6264.765 pctdiff=0.684
SupraTentVolNotVent  904012.765 (897748.000) diff=6264.765 pctdiff=0.693
BrainSegVol  1015563.000 (1013735.000) diff=1828.000 pctdiff=0.180
BrainSegVolNotVent  1001019.000 (1006420.765) diff=-5401.765 pctdiff=-0.540
BrainSegVolNotVent  1001019.000
CerebellumVol 103046.000
VentChorVol   12017.000
3rd4th5thCSF   2527.000
CSFVol   711.000, OptChiasmVol   213.000
MaskVol 1454550.000
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    2641    2640.714
  2   3002      wm-lh-caudalanteriorcingulate    2529    2529.086
  3   3003          wm-lh-caudalmiddlefrontal    6525    6524.855
  4   3004               wm-lh-corpuscallosum       0       0.000
  5   3005                       wm-lh-cuneus    2199    2198.521
  6   3006                   wm-lh-entorhinal     878     877.751
  7   3007                     wm-lh-fusiform    6700    6699.555
  8   3008             wm-lh-inferiorparietal    8891    8890.831
  9   3009             wm-lh-inferiortemporal    5794    5794.061
 10   3010             wm-lh-isthmuscingulate    3113    3112.600
 11   3011             wm-lh-lateraloccipital    6697    6696.663
 12   3012         wm-lh-lateralorbitofrontal    5292    5291.687
 13   3013                      wm-lh-lingual    4571    4570.642
 14   3014          wm-lh-medialorbitofrontal    2860    2860.101
 15   3015               wm-lh-middletemporal    4338    4338.062
 16   3016              wm-lh-parahippocampal    1562    1562.303
 17   3017                  wm-lh-paracentral    2978    2977.714
 18   3018              wm-lh-parsopercularis    3431    3430.899
 19   3019                wm-lh-parsorbitalis     786     786.093
 20   3020             wm-lh-parstriangularis    2462    2461.940
 21   3021                wm-lh-pericalcarine    2192    2192.009
 22   3022                  wm-lh-postcentral    5852    5851.892
 23   3023           wm-lh-posteriorcingulate    4104    4104.079
 24   3024                   wm-lh-precentral   11489   11489.182
 25   3025                    wm-lh-precuneus    7776    7776.311
 26   3026     wm-lh-rostralanteriorcingulate    2274    2274.238
 27   3027         wm-lh-rostralmiddlefrontal   10706   10705.638
 28   3028              wm-lh-superiorfrontal   15561   15561.468
 29   3029             wm-lh-superiorparietal   10437   10436.664
 30   3030             wm-lh-superiortemporal    6528    6527.583
 31   3031                wm-lh-supramarginal    7326    7326.491
 32   3032                  wm-lh-frontalpole     173     172.588
 33   3033                 wm-lh-temporalpole     568     568.259
 34   3034           wm-lh-transversetemporal     674     673.619
 35   3035                       wm-lh-insula    7410    7409.543
 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    2578    2578.328
120   4002      wm-rh-caudalanteriorcingulate    2178    2178.417
121   4003          wm-rh-caudalmiddlefrontal    4464    4463.698
122   4004               wm-rh-corpuscallosum       0       0.000
123   4005                       wm-rh-cuneus    2379    2379.486
124   4006                   wm-rh-entorhinal     703     703.146
125   4007                     wm-rh-fusiform    5967    5967.033
126   4008             wm-rh-inferiorparietal   11588   11588.154
127   4009             wm-rh-inferiortemporal    5144    5144.041
128   4010             wm-rh-isthmuscingulate    2922    2922.324
129   4011             wm-rh-lateraloccipital    6816    6816.442
130   4012         wm-rh-lateralorbitofrontal    5774    5774.073
131   4013                      wm-rh-lingual    4878    4878.103
132   4014          wm-rh-medialorbitofrontal    2831    2831.492
133   4015               wm-rh-middletemporal    5330    5330.169
134   4016              wm-rh-parahippocampal    1388    1387.874
135   4017                  wm-rh-paracentral    4467    4467.446
136   4018              wm-rh-parsopercularis    2124    2124.319
137   4019                wm-rh-parsorbitalis    1046    1046.072
138   4020             wm-rh-parstriangularis    2839    2839.432
139   4021                wm-rh-pericalcarine    2187    2186.981
140   4022                  wm-rh-postcentral    6622    6621.937
141   4023           wm-rh-posteriorcingulate    3940    3939.714
142   4024                   wm-rh-precentral   12930   12929.946
143   4025                    wm-rh-precuneus    8352    8352.497
144   4026     wm-rh-rostralanteriorcingulate    1975    1975.340
145   4027         wm-rh-rostralmiddlefrontal   11482   11482.115
146   4028              wm-rh-superiorfrontal   15958   15958.345
147   4029             wm-rh-superiorparietal    9145    9144.646
148   4030             wm-rh-superiortemporal    4893    4893.062
149   4031                wm-rh-supramarginal    6335    6334.636
150   4032                  wm-rh-frontalpole     194     194.357
151   4033                 wm-rh-temporalpole     418     418.013
152   4034           wm-rh-transversetemporal     561     561.300
153   4035                       wm-rh-insula    7199    7199.450
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   19495   19494.689
237   5002       Right-UnsegmentedWhiteMatter   21819   21819.035
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/sub013/label
#--------------------------------------------
#@# BA Labels lh Thu Aug  8 22:58:47 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 138
Checking for and removing duplicates
Writing label file ./lh.BA1.label 4267
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 247
Checking for and removing duplicates
Writing label file ./lh.BA2.label 8156
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 114
Checking for and removing duplicates
Writing label file ./lh.BA3a.label 4191
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 277
Checking for and removing duplicates
Writing label file ./lh.BA3b.label 6260
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 184
Checking for and removing duplicates
Writing label file ./lh.BA4a.label 5968
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 133
Checking for and removing duplicates
Writing label file ./lh.BA4p.label 4203
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 958
Checking for and removing duplicates
Writing label file ./lh.BA6.label 14547
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 458
Checking for and removing duplicates
Writing label file ./lh.BA44.label 4639
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 870
Checking for and removing duplicates
Writing label file ./lh.BA45.label 4292
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 808
Checking for and removing duplicates
Writing label file ./lh.V1.label 5449
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 2141
Checking for and removing duplicates
Writing label file ./lh.V2.label 10255
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 310
Checking for and removing duplicates
Writing label file ./lh.MT.label 2328
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 220
Checking for and removing duplicates
Writing label file ./lh.perirhinal.label 1419
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 32
Checking for and removing duplicates
Writing label file ./lh.BA1.thresh.label 1046
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 36
Checking for and removing duplicates
Writing label file ./lh.BA2.thresh.label 2128
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 28
Checking for and removing duplicates
Writing label file ./lh.BA3a.thresh.label 1532
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 126
Checking for and removing duplicates
Writing label file ./lh.BA3b.thresh.label 2122
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 61
Checking for and removing duplicates
Writing label file ./lh.BA4a.thresh.label 2380
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 57
Checking for and removing duplicates
Writing label file ./lh.BA4p.thresh.label 1606
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 313
Checking for and removing duplicates
Writing label file ./lh.BA6.thresh.label 7348
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 230
Checking for and removing duplicates
Writing label file ./lh.BA44.thresh.label 2142
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 306
Checking for and removing duplicates
Writing label file ./lh.BA45.thresh.label 1457
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 535
Checking for and removing duplicates
Writing label file ./lh.V1.thresh.label 3940
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 992
Checking for and removing duplicates
Writing label file ./lh.V2.thresh.label 4326
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129542
Number of reverse mapping hits = 61
Checking for and removing duplicates
Writing label file ./lh.MT.thresh.label 574
mri_label2label: Done


 mris_label2annot --s sub013 --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/sub013/label
cmdline mris_label2annot --s sub013 --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 sub013
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/sub013/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 91791 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/lh.BA.annot

 mris_label2annot --s sub013 --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/sub013/label
cmdline mris_label2annot --s sub013 --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 sub013
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/sub013/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 108540 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/lh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub013 lh white 

computing statistics for each annotation in ./lh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

  876    490   1806  2.442 0.432     0.157     0.059       25     2.4  BA1
 3236   2187   5763  2.353 0.502     0.121     0.033       34     4.1  BA2
  914    606    923  1.970 0.485     0.143     0.042        9     1.6  BA3a
 2314   1523   3627  2.030 0.653     0.123     0.037       30     3.4  BA3b
 1300    826   3366  3.124 0.457     0.119     0.029       13     1.7  BA4a
 1216    788   2356  2.870 0.503     0.106     0.032       11     1.6  BA4p
 8803   5866  22082  2.903 0.559     0.133     0.037      123    14.2  BA6
 2538   1714   5758  2.827 0.467     0.117     0.033       29     3.3  BA44
 3287   2183   6493  2.483 0.524     0.144     0.046       58     5.9  BA45
 2843   1906   3494  1.764 0.484     0.161     0.071       69     7.6  V1
 7521   4989  11052  2.032 0.447     0.168     0.062      186    19.6  V2
 1784   1200   2808  2.167 0.373     0.147     0.045       27     3.2  MT
 1119    747   3274  3.295 0.757     0.159     0.099       37     4.0  perirhinal

 mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub013 lh white 

computing statistics for each annotation in ./lh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

  573    273   1126  2.501 0.374     0.166     0.069       19     1.7  BA1
 1226    845   2341  2.332 0.503     0.095     0.021        7     1.0  BA2
  771    507    690  1.920 0.464     0.146     0.044        7     1.4  BA3a
 1453    991   1940  1.715 0.466     0.099     0.022        9     1.2  BA3b
 1302    850   3396  3.161 0.448     0.110     0.026       10     1.5  BA4a
  975    636   1713  2.753 0.473     0.108     0.034        9     1.3  BA4p
 4529   2961  11409  2.893 0.599     0.128     0.035       58     6.8  BA6
 1668   1124   3806  2.870 0.448     0.122     0.035       21     2.2  BA44
 1272    837   3101  2.684 0.397     0.154     0.055       29     2.6  BA45
 3038   2046   3817  1.767 0.476     0.165     0.071       75     8.6  V1
 3769   2542   5242  1.926 0.421     0.177     0.065       80     9.5  V2
  426    290    632  2.097 0.403     0.140     0.046        5     0.7  MT
#--------------------------------------------
#@# BA Labels rh Thu Aug  8 23:03:05 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 245
Checking for and removing duplicates
Writing label file ./rh.BA1.label 4207
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 324
Checking for and removing duplicates
Writing label file ./rh.BA2.label 7011
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 259
Checking for and removing duplicates
Writing label file ./rh.BA3a.label 4239
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 295
Checking for and removing duplicates
Writing label file ./rh.BA3b.label 4817
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 529
Checking for and removing duplicates
Writing label file ./rh.BA4a.label 6276
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 339
Checking for and removing duplicates
Writing label file ./rh.BA4p.label 4812
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 1548
Checking for and removing duplicates
Writing label file ./rh.BA6.label 13804
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 452
Checking for and removing duplicates
Writing label file ./rh.BA44.label 7364
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 1017
Checking for and removing duplicates
Writing label file ./rh.BA45.label 6372
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 1038
Checking for and removing duplicates
Writing label file ./rh.V1.label 5765
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 2598
Checking for and removing duplicates
Writing label file ./rh.V2.label 10614
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 242
Checking for and removing duplicates
Writing label file ./rh.MT.label 2174
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 123
Checking for and removing duplicates
Writing label file ./rh.perirhinal.label 875
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 62
Checking for and removing duplicates
Writing label file ./rh.BA1.thresh.label 938
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 116
Checking for and removing duplicates
Writing label file ./rh.BA2.thresh.label 2804
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 50
Checking for and removing duplicates
Writing label file ./rh.BA3a.thresh.label 1748
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 199
Checking for and removing duplicates
Writing label file ./rh.BA3b.thresh.label 2382
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 68
Checking for and removing duplicates
Writing label file ./rh.BA4a.thresh.label 1456
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 176
Checking for and removing duplicates
Writing label file ./rh.BA4p.thresh.label 1665
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 850
Checking for and removing duplicates
Writing label file ./rh.BA6.thresh.label 7809
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 72
Checking for and removing duplicates
Writing label file ./rh.BA44.thresh.label 1084
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 78
Checking for and removing duplicates
Writing label file ./rh.BA45.thresh.label 1256
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 610
Checking for and removing duplicates
Writing label file ./rh.V1.thresh.label 3842
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 1316
Checking for and removing duplicates
Writing label file ./rh.V2.thresh.label 4753
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub013 --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 = sub013
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/sub013/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 129914
Number of reverse mapping hits = 21
Checking for and removing duplicates
Writing label file ./rh.MT.thresh.label 289
mri_label2label: Done


 mris_label2annot --s sub013 --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/sub013/label
cmdline mris_label2annot --s sub013 --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 sub013
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/sub013/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 89651 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/rh.BA.annot

 mris_label2annot --s sub013 --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/sub013/label
cmdline mris_label2annot --s sub013 --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 sub013
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/sub013/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 107732 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label/rh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub013 rh white 

computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

  850    476   1819  2.532 0.455     0.165     0.092       25     2.1  BA1
 3099   2127   5623  2.358 0.490     0.120     0.030       35     3.8  BA2
 1094    735   1066  1.891 0.481     0.130     0.035        8     1.6  BA3a
 2087   1380   3248  1.960 0.556     0.116     0.034       27     2.7  BA3b
 1548    996   3875  3.007 0.436     0.106     0.028       13     1.9  BA4a
 1211    799   2303  2.761 0.410     0.112     0.045       32     2.7  BA4p
 9137   6118  21409  2.768 0.585     0.128     0.038      127    14.5  BA6
 3035   2048   6543  2.830 0.396     0.126     0.039       37     4.3  BA44
 4287   2902   9280  2.582 0.539     0.144     0.049       83     8.0  BA45
 3390   2220   4539  1.876 0.425     0.153     0.063       68     8.4  V1
 8136   5281  12412  2.164 0.441     0.158     0.056      146    18.6  V2
 1717   1141   2749  2.337 0.456     0.135     0.041       20     2.7  MT
  672    473   2102  3.296 0.680     0.170     0.074       13     2.2  perirhinal

 mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub013 rh white 

computing statistics for each annotation in ./rh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

  576    291   1158  2.549 0.422     0.148     0.104       16     1.2  BA1
 1786   1225   3422  2.380 0.464     0.113     0.027       18     2.0  BA2
  959    640    903  1.917 0.466     0.133     0.037        7     1.5  BA3a
 1748   1179   2430  1.827 0.508     0.103     0.027       17     1.7  BA3b
  857    566   2166  2.992 0.436     0.112     0.031        8     1.2  BA4a
 1052    700   2016  2.795 0.406     0.106     0.047       29     2.5  BA4p
 5861   3945  13249  2.691 0.599     0.126     0.038       84     9.4  BA6
  746    500   1855  2.899 0.336     0.131     0.052       12     1.3  BA44
  836    592   2200  2.814 0.419     0.155     0.057       21     1.8  BA45
 3204   2122   4245  1.868 0.435     0.149     0.059       59     7.2  V1
 4334   2787   6344  2.091 0.445     0.165     0.061       85    11.1  V2
  223    160    391  2.267 0.332     0.123     0.028        2     0.3  MT
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label lh Thu Aug  8 23:07:23 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub013 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

painting output onto subject sub013.
processing subject lh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 sub013 lh white 

limiting computations to label ./lh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

  358    233   1248  3.491 0.544     0.119     0.039        4     0.5  ./lh.entorhinal_exvivo.label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label rh Thu Aug  8 23:07:38 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub013 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 

painting output onto subject sub013.
processing subject rh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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 869 points to rh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub013 rh white 

limiting computations to label ./rh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub013/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

  330    244   1198  3.508 0.633     0.127     0.039        2     0.6  ./rh.entorhinal_exvivo.label

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

Started at Thu Aug 8 10:53:42 CEST 2013 
Ended   at Thu Aug 8 23:07:52 CEST 2013
#@#%# recon-all-run-time-hours 12.236
recon-all -s sub013 finished without error at Thu Aug  8 23:07:52 CEST 2013