cortical-surfaces-freesurfer/sub-11/scripts/recon-all.log

Thu Aug  8 10:54:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011
/opt/freesurfer/5.3.0/bin/recon-all
-i /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/other/t2w001.nii.gz -T2pial -subjid sub011 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subjid sub011
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 snake6 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   96979616    2222076          0     118440   94733892
-/+ buffers/cache:    2127284   97074408
Swap:     25165780       2780   25163000

########################################
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: 2013/08/08-08:54:16-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: snake6  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: 2013/08/08-08:54:17-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: snake6  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: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  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: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  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: 2013/08/08-08:54:20-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: snake6  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: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  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/sub011

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/001.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/anatomy/highres001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998102, -0.0611237, 0.00753358)
j_ras = (-0.0606425, 0.996759, 0.0528636)
k_ras = (0.0107404, -0.0523064, 0.998573)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Thu Aug  8 10:54:37 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub011/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/anatomy/other/t2w001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998102, -0.0611237, 0.00753358)
j_ras = (-0.0606425, 0.996759, 0.0528636)
k_ras = (0.0107404, -0.0523064, 0.998573)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Thu Aug  8 10:54:54 CEST 2013
Found 1 runs
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz 

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz --conform --cw256 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998102, -0.0611237, 0.00753358)
j_ras = (-0.0606425, 0.996759, 0.0528636)
k_ras = (0.0107404, -0.0523064, 0.998573)
Original Data has (0.699913, 0.666667, 0.666667) mm size and (274, 384, 384) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz...

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Aug  8 10:55:34 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri

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


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


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

#--------------------------------------------
#@# Talairach Failure Detection Thu Aug  8 10:58:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6269, pval=0.3663 >= threshold=0.0050)

 awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/talairach_avi.log 


 tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/talairach_avi.log 

TalAviQA: 0.96663
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Thu Aug  8 10:58:14 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/sub011/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 snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
Thu Aug  8 10:58:14 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.24474
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24474/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24474/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, 1.31549e-08, 0)
j_ras = (0, -1.11759e-08, -1)
k_ras = (5.47152e-09, 1, -3.72529e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.24474/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Thu Aug  8 10:58:17 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.24474/nu0.mnc ./tmp.mri_nu_correct.mni.24474/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24474/0/
[fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/] [2013-08-08 10:58:18] running:
  /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24474/0/ ./tmp.mri_nu_correct.mni.24474/nu0.mnc ./tmp.mri_nu_correct.mni.24474/nu1.imp

Processing:.................................................................Done
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Number of iterations: 32 
CV of field change: 0.000995292
[fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/] [2013-08-08 10:58:58] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24474/nu0.mnc ./tmp.mri_nu_correct.mni.24474/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Thu Aug  8 10:59:06 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.24474/nu1.mnc ./tmp.mri_nu_correct.mni.24474/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24474/1/
[fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/] [2013-08-08 10:59:06] 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.24474/1/ ./tmp.mri_nu_correct.mni.24474/nu1.mnc ./tmp.mri_nu_correct.mni.24474/nu2.imp

Processing:.................................................................Done
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Number of iterations: 32 
CV of field change: 0.000992195
[fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/] [2013-08-08 10:59:45] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24474/nu1.mnc ./tmp.mri_nu_correct.mni.24474/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.24474/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24474/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/sub011/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24474/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24474/ones.mgz 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule

input      ./tmp.mri_nu_correct.mni.24474/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.24474/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.24474/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24474/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24474/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.24474/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24474/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24474/input.mean.dat 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.24474/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.24474/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24474/ones.mgz --i ./tmp.mri_nu_correct.mni.24474/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24474/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24474/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.24474/ones.mgz --i ./tmp.mri_nu_correct.mni.24474/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24474/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24474/output.mean.dat 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.24474/ones.mgz
Loading ./tmp.mri_nu_correct.mni.24474/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.24474/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.24474/nu2.mnc ./tmp.mri_nu_correct.mni.24474/nu2.mnc mul .93847485184404357313
Saving result to './tmp.mri_nu_correct.mni.24474/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.24474/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.24474/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.24474/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.31549e-08, 0)
j_ras = (0, -1.11759e-08, -1)
k_ras = (5.47152e-09, 1, -3.72529e-09)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 7 seconds.
mapping ( 7, 150) to ( 3, 110)
 
 
Thu Aug  8 11:00:31 CEST 2013
mri_nu_correct.mni done

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Aug  8 11:00:32 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri

 mri_normalize -g 1 nu.mgz T1.mgz 

using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
 1.096   0.129   0.014   2.157;
-0.159   1.026   0.259  -40.388;
 0.042  -0.399   1.140   2.207;
 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 = 19
Starting OpenSpline(): npoints = 19
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 11, 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 77 (77), valley at  0 (-1)
csf peak at 38, setting threshold to 64
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 48 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Aug  8 11:03:21 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = (49, 16, 0) --> (210, 255, 194)
using (103, 96, 97) as brain centroid...
mean wm in atlas = 126, using box (83,66,73) --> (122, 125,120) to find MRI wm
before smoothing, mri peak at 110
after smoothing, mri peak at 109, scaling input intensities by 1.156
scaling channel 0 by 1.15596
initial log_p = -4.7
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.447860 @ (-9.091, 27.273, -9.091)
max log p =    -4.353130 @ (4.545, -4.545, 4.545)
max log p =    -4.298753 @ (2.273, -2.273, 2.273)
max log p =    -4.271574 @ (1.136, -1.136, 3.409)
max log p =    -4.270184 @ (0.568, 0.568, -0.568)
max log p =    -4.245293 @ (0.284, -1.989, -1.989)
Found translation: (-0.3, 17.9, -1.4): log p = -4.245
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2)
 1.140   0.057  -0.139  -11.174;
 0.000   1.142   0.473  -33.728;
 0.139  -0.404   0.974   33.423;
 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 =-4.1 (thresh=-4.0)
 1.055   0.053  -0.128  -0.904;
-0.017   1.096   0.316  -19.623;
 0.127  -0.232   0.951   13.249;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.055   0.053  -0.128  -0.904;
-0.017   1.096   0.316  -19.623;
 0.127  -0.232   0.951   13.249;
 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=-3.9, old_max_log_p =-4.0 (thresh=-4.0)
 1.019   0.008  -0.100   5.060;
 0.012   1.084   0.275  -14.089;
 0.096  -0.203   0.981   13.069;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.000   0.043  -0.088   2.950;
-0.019   1.096   0.316  -17.426;
 0.094  -0.234   0.953   19.202;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.000   0.043  -0.088   2.950;
-0.019   1.096   0.316  -17.426;
 0.094  -0.234   0.953   19.202;
 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=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.002   0.043  -0.088   2.663;
-0.017   1.094   0.333  -19.156;
 0.095  -0.252   0.949   20.443;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.002   0.043  -0.088   2.663;
-0.017   1.094   0.333  -19.156;
 0.095  -0.252   0.949   20.443;
 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
 1.00219   0.04278  -0.08846   2.66256;
-0.01700   1.09433   0.33261  -19.15604;
 0.09452  -0.25172   0.94899   20.44276;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.00219   0.04278  -0.08846   2.66256;
-0.01700   1.09433   0.33261  -19.15604;
 0.09452  -0.25172   0.94899   20.44276;
 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:
 1.002   0.043  -0.088   2.663;
-0.017   1.094   0.333  -19.156;
 0.095  -0.252   0.949   20.443;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.9 (old=-4.7)
transform before final EM align:
 1.002   0.043  -0.088   2.663;
-0.017   1.094   0.333  -19.156;
 0.095  -0.252   0.949   20.443;
 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
 1.00219   0.04278  -0.08846   2.66256;
-0.01700   1.09433   0.33261  -19.15604;
 0.09452  -0.25172   0.94899   20.44276;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.00219   0.04278  -0.08846   2.66256;
-0.01700   1.09433   0.33261  -19.15604;
 0.09452  -0.25172   0.94899   20.44276;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 011: -log(p) = 4.3
after pass:transform: ( 1.00, 0.04, -0.09, 2.66)
                      ( -0.02, 1.09, 0.33, -19.16)
                      ( 0.09, -0.25, 0.95, 20.44)
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) =    4.3  tol 0.000000
final transform:
 1.002   0.043  -0.088   2.663;
-0.017   1.094   0.333  -19.156;
 0.095  -0.252   0.949   20.443;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 38 minutes and 36 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=129 y=84 z=107 r=95
      first estimation of the main basin volume: 3642261 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=145, y=88, z=62, Imax=255
      CSF=13, 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=22614982755 voxels, voxel volume =1.000 
                     = 22614982755 mmm3 = 22614982.656 cm3
done.
PostAnalyze...Basin Prior
 164 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=97, z=103, r=10360 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 45460
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = -1031416867
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = 1100756446
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = -1071523831
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = 1083001950
    OTHER      CSF_MIN=0, CSF_intensity=10, CSF_MAX=41 , nb = 1063265510
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    9,      12,        25,   55
  after  analyzing :    9,      20,        25,   28
   RIGHT_CER   
  before analyzing :    19,      17,        15,   63
  after  analyzing :    17,      22,        25,   32
   LEFT_CER    
  before analyzing :    20,      21,        26,   64
  after  analyzing :    20,      24,        26,   34
  RIGHT_BRAIN  
  before analyzing :    8,      11,        26,   55
  after  analyzing :    8,      21,        26,   29
  LEFT_BRAIN   
  before analyzing :    8,      10,        24,   54
  after  analyzing :    8,      20,        25,   28
     OTHER     
  before analyzing :    41,      74,        85,   95
  after  analyzing :    41,      81,        85,   84
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...76 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.012
curvature mean = 73.052, std = 9.262

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.05, sigma = 5.82
      after  rotation: sse = 3.05, sigma = 5.82
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  3.35, its var is  5.32   
      before Erosion-Dilatation  1.06% of inacurate vertices
      after  Erosion-Dilatation  1.76% 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...42 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1940057 voxels, voxel volume = 1.000 mm3
           = 1940057 mmm3 = 1940.057 cm3


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

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Thu Aug  8 11:42:26 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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=22.0
skull bounding box = (56, 33, 27) --> (192, 178, 196)
using (101, 81, 112) as brain centroid...
mean wm in atlas = 107, using box (84,63,91) --> (117, 98,132) to find MRI wm
before smoothing, mri peak at 107
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.5
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.004340 @ (-9.091, 27.273, -9.091)
max log p =    -3.789185 @ (4.545, -4.545, 4.545)
max log p =    -3.770103 @ (2.273, -2.273, 2.273)
max log p =    -3.748410 @ (-1.136, 1.136, -1.136)
max log p =    -3.720674 @ (1.705, -0.568, 1.705)
max log p =    -3.720674 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, 21.0, -1.7): log p = -3.721
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.7 (thresh=-3.7)
 0.991   0.034  -0.126   9.584;
 0.000   1.038   0.278  -12.511;
 0.121  -0.237   0.886   18.222;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 0.991   0.034  -0.126   9.584;
 0.000   1.038   0.278  -12.511;
 0.121  -0.237   0.886   18.222;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.4 (thresh=-3.4)
 1.032   0.026  -0.102   2.669;
 0.004   1.069   0.317  -16.343;
 0.089  -0.279   0.896   28.969;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.032   0.026  -0.102   2.669;
 0.004   1.069   0.317  -16.343;
 0.089  -0.279   0.896   28.969;
 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=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.106  -0.243   0.904   22.566;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.106  -0.243   0.904   22.566;
 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
 1.03164   0.03013  -0.11703   3.86285;
 0.00105   1.08130   0.28901  -14.23942;
 0.10554  -0.24302   0.90434   22.56604;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2772
Quasinewton: input matrix
 1.03164   0.03013  -0.11703   3.86285;
 0.00105   1.08130   0.28901  -14.23942;
 0.10554  -0.24302   0.90434   22.56604;
 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: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.106  -0.243   0.904   22.566;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.2 (old=-4.5)
transform before final EM align:
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.106  -0.243   0.904   22.566;
 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
 1.03164   0.03013  -0.11703   3.86285;
 0.00105   1.08130   0.28901  -14.23942;
 0.10554  -0.24302   0.90434   22.56604;
 0.00000   0.00000   0.00000   1.00000;
nsamples 312841
Quasinewton: input matrix
 1.03164   0.03013  -0.11703   3.86285;
 0.00105   1.08130   0.28901  -14.23942;
 0.10554  -0.24302   0.90434   22.56604;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 009: -log(p) = 3.7
after pass:transform: ( 1.03, 0.03, -0.12, 3.86)
                      ( 0.00, 1.08, 0.29, -14.24)
                      ( 0.11, -0.24, 0.90, 22.57)
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =    3.7  tol 0.000000
final transform:
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.106  -0.243   0.904   22.566;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 22 minutes and 56 seconds.
#--------------------------------------
#@# CA Normalize Thu Aug  8 12:05:23 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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=22.0
skull bounding box = (56, 33, 27) --> (192, 178, 196)
using (101, 81, 112) as brain centroid...
mean wm in atlas = 107, using box (84,63,91) --> (117, 98,132) to find MRI wm
before smoothing, mri peak at 107
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 244171 sample points...
INFO: compute sample coordinates transform
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.106  -0.243   0.904   22.566;
 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 (116, 36, 22) --> (189, 144, 194)
Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 182.0
0 of 13 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (64, 35, 24) --> (134, 134, 197)
Right_Cerebral_White_Matter: limiting intensities to 102.0 --> 182.0
0 of 11 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (123, 117, 51) --> (171, 159, 107)
Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 182.0
0 of 7 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (79, 117, 52) --> (124, 156, 112)
Right_Cerebellum_White_Matter: limiting intensities to 93.0 --> 182.0
0 of 19 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (112, 106, 89) --> (142, 169, 121)
Brain_Stem: limiting intensities to 82.0 --> 182.0
1 of 9 (11.1%) samples deleted
using 59 total control points for intensity normalization...
bias field = 0.923 +- 0.074
0 of 58 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (116, 36, 22) --> (189, 144, 194)
Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 167.0
0 of 86 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (64, 35, 24) --> (134, 134, 197)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 167.0
0 of 108 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (123, 117, 51) --> (171, 159, 107)
Left_Cerebellum_White_Matter: limiting intensities to 76.0 --> 167.0
0 of 59 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (79, 117, 52) --> (124, 156, 112)
Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 167.0
0 of 33 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (112, 106, 89) --> (142, 169, 121)
Brain_Stem: limiting intensities to 73.0 --> 167.0
0 of 43 (0.0%) samples deleted
using 329 total control points for intensity normalization...
bias field = 1.003 +- 0.054
1 of 329 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (116, 36, 22) --> (189, 144, 194)
Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 165.0
0 of 212 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (64, 35, 24) --> (134, 134, 197)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 165.0
0 of 188 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (123, 117, 51) --> (171, 159, 107)
Left_Cerebellum_White_Matter: limiting intensities to 73.0 --> 165.0
0 of 50 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (79, 117, 52) --> (124, 156, 112)
Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 165.0
0 of 24 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (112, 106, 89) --> (142, 169, 121)
Brain_Stem: limiting intensities to 68.0 --> 165.0
0 of 82 (0.0%) samples deleted
using 556 total control points for intensity normalization...
bias field = 1.008 +- 0.050
1 of 556 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 2 minutes and 5 seconds.
#--------------------------------------
#@# CA Reg Thu Aug  8 12:07:27 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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) = 1.10 (predicted orig area = 7.3)
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=0.831, neg=0, invalid=96777
0001: dt=129.472000, rms=0.776 (6.635%), neg=0, invalid=96777
0002: dt=129.472000, rms=0.763 (1.672%), neg=0, invalid=96777
0003: dt=129.472000, rms=0.757 (0.773%), neg=0, invalid=96777
0004: dt=221.952000, rms=0.750 (0.973%), neg=0, invalid=96777
0005: dt=92.480000, rms=0.746 (0.559%), neg=0, invalid=96777
0006: dt=295.936000, rms=0.741 (0.712%), neg=0, invalid=96777
0007: dt=73.984000, rms=0.737 (0.533%), neg=0, invalid=96777
0008: dt=517.888000, rms=0.730 (0.962%), neg=0, invalid=96777
0009: dt=73.984000, rms=0.727 (0.409%), neg=0, invalid=96777
0010: dt=887.808000, rms=0.721 (0.803%), neg=0, invalid=96777
0011: dt=110.976000, rms=0.717 (0.573%), neg=0, invalid=96777
0012: dt=221.952000, rms=0.715 (0.164%), neg=0, invalid=96777
0013: dt=221.952000, rms=0.714 (0.181%), neg=0, invalid=96777
0014: dt=221.952000, rms=0.711 (0.444%), neg=0, invalid=96777
0015: dt=221.952000, rms=0.709 (0.295%), neg=0, invalid=96777
0016: dt=221.952000, rms=0.705 (0.559%), neg=0, invalid=96777
0017: dt=221.952000, rms=0.701 (0.499%), neg=0, invalid=96777
0018: dt=221.952000, rms=0.699 (0.279%), neg=0, invalid=96777
0019: dt=221.952000, rms=0.695 (0.609%), neg=0, invalid=96777
0020: dt=221.952000, rms=0.693 (0.379%), neg=0, invalid=96777
0021: dt=221.952000, rms=0.691 (0.215%), neg=0, invalid=96777
0022: dt=221.952000, rms=0.688 (0.453%), neg=0, invalid=96777
0023: dt=221.952000, rms=0.686 (0.311%), neg=0, invalid=96777
0024: dt=221.952000, rms=0.684 (0.320%), neg=0, invalid=96777
0025: dt=221.952000, rms=0.682 (0.269%), neg=0, invalid=96777
0026: dt=221.952000, rms=0.680 (0.254%), neg=0, invalid=96777
0027: dt=221.952000, rms=0.678 (0.317%), neg=0, invalid=96777
0028: dt=221.952000, rms=0.676 (0.206%), neg=0, invalid=96777
0029: dt=221.952000, rms=0.676 (0.067%), neg=0, invalid=96777
0030: dt=221.952000, rms=0.674 (0.302%), neg=0, invalid=96777
0031: dt=221.952000, rms=0.673 (0.158%), neg=0, invalid=96777
0032: dt=221.952000, rms=0.673 (0.017%), neg=0, invalid=96777
0033: dt=221.952000, rms=0.671 (0.221%), neg=0, invalid=96777
0034: dt=221.952000, rms=0.671 (0.085%), neg=0, invalid=96777
0035: dt=221.952000, rms=0.670 (0.138%), neg=0, invalid=96777
0036: dt=221.952000, rms=0.669 (0.145%), neg=0, invalid=96777
0037: dt=221.952000, rms=0.669 (0.023%), neg=0, invalid=96777
0038: dt=221.952000, rms=0.667 (0.193%), neg=0, invalid=96777
0039: dt=221.952000, rms=0.667 (0.069%), neg=0, invalid=96777
0040: dt=221.952000, rms=0.667 (-0.004%), neg=0, invalid=96777
0041: dt=0.000000, rms=0.667 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.667, neg=0, invalid=96777
0042: dt=73.984000, rms=0.667 (0.023%), neg=0, invalid=96777
0043: dt=295.936000, rms=0.666 (0.115%), neg=0, invalid=96777
0044: dt=73.984000, rms=0.666 (0.006%), neg=0, invalid=96777
0045: dt=73.984000, rms=0.666 (0.007%), neg=0, invalid=96777
0046: dt=73.984000, rms=0.666 (0.000%), neg=0, invalid=96777
0047: dt=73.984000, rms=0.666 (-0.004%), neg=0, invalid=96777
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.674, neg=0, invalid=96777
0048: dt=145.152000, rms=0.665 (1.274%), neg=0, invalid=96777
0049: dt=82.944000, rms=0.661 (0.602%), neg=0, invalid=96777
0050: dt=36.288000, rms=0.658 (0.583%), neg=0, invalid=96777
0051: dt=62.208000, rms=0.656 (0.248%), neg=0, invalid=96777
0052: dt=62.208000, rms=0.653 (0.448%), neg=0, invalid=96777
0053: dt=62.208000, rms=0.649 (0.589%), neg=0, invalid=96777
0054: dt=62.208000, rms=0.643 (0.928%), neg=0, invalid=96777
0055: dt=62.208000, rms=0.637 (0.906%), neg=0, invalid=96777
0056: dt=62.208000, rms=0.632 (0.799%), neg=0, invalid=96777
0057: dt=62.208000, rms=0.627 (0.833%), neg=0, invalid=96777
0058: dt=62.208000, rms=0.623 (0.626%), neg=0, invalid=96777
0059: dt=62.208000, rms=0.620 (0.506%), neg=0, invalid=96777
0060: dt=62.208000, rms=0.617 (0.440%), neg=0, invalid=96777
0061: dt=62.208000, rms=0.614 (0.434%), neg=0, invalid=96777
0062: dt=62.208000, rms=0.612 (0.346%), neg=0, invalid=96777
0063: dt=62.208000, rms=0.611 (0.289%), neg=0, invalid=96777
0064: dt=62.208000, rms=0.609 (0.202%), neg=0, invalid=96777
0065: dt=62.208000, rms=0.608 (0.190%), neg=0, invalid=96777
0066: dt=62.208000, rms=0.607 (0.143%), neg=0, invalid=96777
0067: dt=62.208000, rms=0.606 (0.143%), neg=0, invalid=96777
0068: dt=62.208000, rms=0.606 (0.106%), neg=0, invalid=96777
0069: dt=62.208000, rms=0.605 (0.155%), neg=0, invalid=96777
0070: dt=62.208000, rms=0.604 (0.155%), neg=0, invalid=96777
0071: dt=62.208000, rms=0.603 (0.132%), neg=0, invalid=96777
0072: dt=62.208000, rms=0.602 (0.139%), neg=0, invalid=96777
0073: dt=62.208000, rms=0.601 (0.162%), neg=0, invalid=96777
0074: dt=62.208000, rms=0.601 (0.122%), neg=0, invalid=96777
0075: dt=62.208000, rms=0.600 (0.120%), neg=0, invalid=96777
0076: dt=62.208000, rms=0.600 (0.026%), neg=0, invalid=96777
0077: dt=62.208000, rms=0.600 (-0.039%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.600, neg=0, invalid=96777
0078: dt=31.104000, rms=0.600 (0.029%), neg=0, invalid=96777
0079: dt=36.288000, rms=0.599 (0.027%), neg=0, invalid=96777
0080: dt=36.288000, rms=0.599 (-0.027%), neg=0, invalid=96777
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.628, neg=0, invalid=96777
0081: dt=0.700000, rms=0.628 (0.002%), neg=0, invalid=96777
0082: dt=0.175000, rms=0.628 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.628, neg=0, invalid=96777
0083: dt=0.500000, rms=0.628 (0.001%), neg=0, invalid=96777
0084: dt=0.150000, rms=0.628 (0.001%), neg=0, invalid=96777
0085: dt=0.007812, rms=0.628 (-0.001%), neg=0, invalid=96777
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.712, neg=0, invalid=96777
0086: dt=4.998117, rms=0.686 (3.602%), neg=0, invalid=96777
0087: dt=3.159091, rms=0.684 (0.251%), neg=0, invalid=96777
0088: dt=0.864000, rms=0.684 (0.010%), neg=0, invalid=96777
0089: dt=0.864000, rms=0.684 (0.000%), neg=0, invalid=96777
0090: dt=0.864000, rms=0.684 (-0.040%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.684, neg=0, invalid=96777
0091: dt=0.000000, rms=0.684 (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=0.749, neg=0, invalid=96777
0092: dt=0.924883, rms=0.746 (0.378%), neg=0, invalid=96777
0093: dt=1.974522, rms=0.741 (0.645%), neg=0, invalid=96777
0094: dt=1.024000, rms=0.741 (0.097%), neg=0, invalid=96777
0095: dt=1.024000, rms=0.740 (0.165%), neg=0, invalid=96777
0096: dt=1.024000, rms=0.739 (0.089%), neg=0, invalid=96777
0097: dt=1.024000, rms=0.739 (-0.183%), neg=0, invalid=96777
0098: dt=0.112000, rms=0.739 (0.001%), neg=0, invalid=96777
0099: dt=0.112000, rms=0.739 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.739, neg=0, invalid=96777
0100: dt=1.024000, rms=0.738 (0.090%), neg=0, invalid=96777
0101: dt=0.000000, rms=0.738 (-0.003%), 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=0.697, neg=0, invalid=96777
0102: dt=0.157895, rms=0.689 (1.171%), neg=0, invalid=96777
0103: dt=0.000000, rms=0.689 (0.002%), neg=0, invalid=96777
0104: dt=0.050000, rms=0.689 (-0.034%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.689, neg=0, invalid=96777
0105: dt=0.250000, rms=0.687 (0.289%), neg=0, invalid=96777
0106: dt=0.096000, rms=0.686 (0.130%), neg=0, invalid=96777
0107: dt=0.096000, rms=0.686 (0.041%), neg=0, invalid=96777
0108: dt=0.096000, rms=0.686 (0.070%), neg=0, invalid=96777
0109: dt=0.096000, rms=0.685 (0.111%), neg=0, invalid=96777
0110: dt=0.096000, rms=0.684 (0.128%), neg=0, invalid=96777
0111: dt=0.096000, rms=0.683 (0.121%), neg=0, invalid=96777
0112: dt=0.096000, rms=0.682 (0.105%), neg=0, invalid=96777
0113: dt=0.000000, rms=0.682 (0.001%), neg=0, invalid=96777
0114: dt=0.050000, rms=0.682 (-0.001%), neg=0, invalid=96777
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.11725 (24)
mri peak = 0.11688 ( 8)
Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (1727 voxels, overlap=0.006)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1727 voxels, peak =  7), gca=9.6
gca peak = 0.14022 (22)
mri peak = 0.13743 (10)
Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (1428 voxels, overlap=0.007)
Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (1428 voxels, peak =  9), gca=8.9
gca peak = 0.24234 (100)
mri peak = 0.09243 (81)
Right_Pallidum (52): linear fit = 0.81 x + 0.0 (472 voxels, overlap=0.049)
Right_Pallidum (52): linear fit = 0.81 x + 0.0 (472 voxels, peak = 80), gca=80.5
gca peak = 0.19192 (97)
mri peak = 0.10526 (77)
Left_Pallidum (13): linear fit = 0.79 x + 0.0 (399 voxels, overlap=0.047)
Left_Pallidum (13): linear fit = 0.79 x + 0.0 (399 voxels, peak = 76), gca=76.1
gca peak = 0.24007 (63)
mri peak = 0.07313 (59)
Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (543 voxels, overlap=0.783)
Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (543 voxels, peak = 58), gca=58.3
gca peak = 0.29892 (64)
mri peak = 0.06841 (59)
Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (581 voxels, overlap=0.710)
Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (581 voxels, peak = 58), gca=57.9
gca peak = 0.12541 (104)
mri peak = 0.07006 (106)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (78113 voxels, overlap=0.812)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (78113 voxels, peak = 108), gca=107.6
gca peak = 0.13686 (104)
mri peak = 0.07853 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (80588 voxels, overlap=0.713)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (80588 voxels, peak = 109), gca=108.7
gca peak = 0.11691 (63)
mri peak = 0.04927 (50)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (22125 voxels, overlap=0.067)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (22125 voxels, peak = 50), gca=50.1
gca peak = 0.13270 (63)
mri peak = 0.05019 (54)
Right_Cerebral_Cortex (42): linear fit = 0.83 x + 0.0 (20580 voxels, overlap=0.290)
Right_Cerebral_Cortex (42): linear fit = 0.83 x + 0.0 (20580 voxels, peak = 53), gca=52.6
gca peak = 0.15182 (70)
mri peak = 0.08925 (65)
Right_Caudate (50): linear fit = 0.88 x + 0.0 (670 voxels, overlap=0.471)
Right_Caudate (50): linear fit = 0.88 x + 0.0 (670 voxels, peak = 62), gca=62.0
gca peak = 0.14251 (76)
mri peak = 0.07479 (66)
Left_Caudate (11): linear fit = 0.85 x + 0.0 (813 voxels, overlap=0.091)
Left_Caudate (11): linear fit = 0.85 x + 0.0 (813 voxels, peak = 64), gca=64.2
gca peak = 0.12116 (60)
mri peak = 0.03908 (57)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (15431 voxels, overlap=0.932)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (15431 voxels, peak = 56), gca=56.1
gca peak = 0.12723 (61)
mri peak = 0.03990 (56)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (13758 voxels, overlap=0.972)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (13758 voxels, peak = 59), gca=58.9
gca peak = 0.22684 (88)
mri peak = 0.07232 (87)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8311 voxels, overlap=0.976)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8311 voxels, peak = 88), gca=87.6
gca peak = 0.21067 (87)
mri peak = 0.06918 (86)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7539 voxels, overlap=0.965)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (7539 voxels, peak = 89), gca=89.2
gca peak = 0.25455 (62)
mri peak = 0.10207 (56)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (379 voxels, overlap=0.619)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (379 voxels, peak = 54), gca=54.2
gca peak = 0.39668 (62)
mri peak = 0.11971 (53)
Right_Amygdala (54): linear fit = 0.83 x + 0.0 (311 voxels, overlap=0.417)
Right_Amygdala (54): linear fit = 0.83 x + 0.0 (311 voxels, peak = 52), gca=51.8
gca peak = 0.10129 (93)
mri peak = 0.06025 (89)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5703 voxels, overlap=0.937)
Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (5703 voxels, peak = 89), gca=88.8
gca peak = 0.12071 (89)
mri peak = 0.05848 (87)
Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (4707 voxels, overlap=0.972)
Right_Thalamus_Proper (49): linear fit = 0.96 x + 0.0 (4707 voxels, peak = 86), gca=85.9
gca peak = 0.13716 (82)
mri peak = 0.06062 (72)
Left_Putamen (12): linear fit = 0.90 x + 0.0 (2119 voxels, overlap=0.788)
Left_Putamen (12): linear fit = 0.90 x + 0.0 (2119 voxels, peak = 74), gca=74.2
gca peak = 0.15214 (84)
mri peak = 0.06504 (75)
Right_Putamen (51): linear fit = 0.92 x + 0.0 (2378 voxels, overlap=0.457)
Right_Putamen (51): linear fit = 0.92 x + 0.0 (2378 voxels, peak = 77), gca=76.9
gca peak = 0.08983 (85)
mri peak = 0.07193 (87)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (11713 voxels, overlap=0.778)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (11713 voxels, peak = 88), gca=88.0
gca peak = 0.11809 (92)
mri peak = 0.06034 (88)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (862 voxels, overlap=0.905)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (862 voxels, peak = 93), gca=93.4
gca peak = 0.12914 (94)
mri peak = 0.05874 (92)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (943 voxels, overlap=0.937)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (943 voxels, peak = 93), gca=92.6
gca peak = 0.21100 (36)
mri peak = 0.05263 (53)
gca peak = 0.13542 (27)
mri peak = 0.12683 ( 8)
Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (479 voxels, overlap=0.024)
Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (479 voxels, peak =  9), gca=8.8
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 0.86 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=0.724, neg=0, invalid=96777
0115: dt=129.472000, rms=0.719 (0.699%), neg=0, invalid=96777
0116: dt=295.936000, rms=0.714 (0.657%), neg=0, invalid=96777
0117: dt=110.976000, rms=0.712 (0.316%), neg=0, invalid=96777
0118: dt=129.472000, rms=0.711 (0.170%), neg=0, invalid=96777
0119: dt=295.936000, rms=0.708 (0.298%), neg=0, invalid=96777
0120: dt=73.984000, rms=0.707 (0.155%), neg=0, invalid=96777
0121: dt=517.888000, rms=0.705 (0.340%), neg=0, invalid=96777
0122: dt=73.984000, rms=0.704 (0.111%), neg=0, invalid=96777
0123: dt=295.936000, rms=0.704 (0.084%), neg=0, invalid=96777
0124: dt=55.488000, rms=0.703 (0.101%), neg=0, invalid=96777
0125: dt=1183.744000, rms=0.700 (0.345%), neg=0, invalid=96777
0126: dt=55.488000, rms=0.699 (0.183%), neg=0, invalid=96777
0127: dt=92.480000, rms=0.699 (0.041%), neg=0, invalid=96777
0128: dt=92.480000, rms=0.699 (0.024%), neg=0, invalid=96777
0129: dt=92.480000, rms=0.698 (0.041%), neg=0, invalid=96777
0130: dt=92.480000, rms=0.698 (0.075%), neg=0, invalid=96777
0131: dt=92.480000, rms=0.697 (0.104%), neg=0, invalid=96777
0132: dt=92.480000, rms=0.696 (0.119%), neg=0, invalid=96777
0133: dt=92.480000, rms=0.696 (0.116%), neg=0, invalid=96777
0134: dt=92.480000, rms=0.695 (0.110%), neg=0, invalid=96777
0135: dt=92.480000, rms=0.694 (0.119%), neg=0, invalid=96777
0136: dt=92.480000, rms=0.693 (0.118%), neg=0, invalid=96777
0137: dt=92.480000, rms=0.692 (0.116%), neg=0, invalid=96777
0138: dt=92.480000, rms=0.692 (0.100%), neg=0, invalid=96777
0139: dt=92.480000, rms=0.691 (0.091%), neg=0, invalid=96777
0140: dt=92.480000, rms=0.690 (0.096%), neg=0, invalid=96777
0141: dt=92.480000, rms=0.690 (0.103%), neg=0, invalid=96777
0142: dt=92.480000, rms=0.689 (0.103%), neg=0, invalid=96777
0143: dt=92.480000, rms=0.688 (0.091%), neg=0, invalid=96777
0144: dt=92.480000, rms=0.688 (0.085%), neg=0, invalid=96777
0145: dt=92.480000, rms=0.687 (0.081%), neg=0, invalid=96777
0146: dt=92.480000, rms=0.687 (0.091%), neg=0, invalid=96777
0147: dt=92.480000, rms=0.686 (0.081%), neg=0, invalid=96777
0148: dt=92.480000, rms=0.685 (0.075%), neg=0, invalid=96777
0149: dt=92.480000, rms=0.685 (0.067%), neg=0, invalid=96777
0150: dt=92.480000, rms=0.684 (0.071%), neg=0, invalid=96777
0151: dt=92.480000, rms=0.684 (0.085%), neg=0, invalid=96777
0152: dt=92.480000, rms=0.683 (0.082%), neg=0, invalid=96777
0153: dt=92.480000, rms=0.683 (0.067%), neg=0, invalid=96777
0154: dt=92.480000, rms=0.683 (0.055%), neg=0, invalid=96777
0155: dt=92.480000, rms=0.682 (0.052%), neg=0, invalid=96777
0156: dt=92.480000, rms=0.682 (0.062%), neg=0, invalid=96777
0157: dt=92.480000, rms=0.681 (0.064%), neg=0, invalid=96777
0158: dt=92.480000, rms=0.681 (0.050%), neg=0, invalid=96777
0159: dt=92.480000, rms=0.681 (0.043%), neg=0, invalid=96777
0160: dt=92.480000, rms=0.680 (0.041%), neg=0, invalid=96777
0161: dt=92.480000, rms=0.680 (0.048%), neg=0, invalid=96777
0162: dt=92.480000, rms=0.680 (0.052%), neg=0, invalid=96777
0163: dt=92.480000, rms=0.679 (0.051%), neg=0, invalid=96777
0164: dt=92.480000, rms=0.679 (0.049%), neg=0, invalid=96777
0165: dt=92.480000, rms=0.679 (0.044%), neg=0, invalid=96777
0166: dt=92.480000, rms=0.678 (0.042%), neg=0, invalid=96777
0167: dt=92.480000, rms=0.678 (0.034%), neg=0, invalid=96777
0168: dt=92.480000, rms=0.678 (0.038%), neg=0, invalid=96777
0169: dt=92.480000, rms=0.678 (0.039%), neg=0, invalid=96777
0170: dt=92.480000, rms=0.677 (0.042%), neg=0, invalid=96777
0171: dt=92.480000, rms=0.677 (0.033%), neg=0, invalid=96777
0172: dt=92.480000, rms=0.677 (0.031%), neg=0, invalid=96777
0173: dt=92.480000, rms=0.677 (0.031%), neg=0, invalid=96777
0174: dt=92.480000, rms=0.677 (0.035%), neg=0, invalid=96777
0175: dt=92.480000, rms=0.676 (0.036%), neg=0, invalid=96777
0176: dt=92.480000, rms=0.676 (0.039%), neg=0, invalid=96777
0177: dt=92.480000, rms=0.676 (0.034%), neg=0, invalid=96777
0178: dt=92.480000, rms=0.676 (0.028%), neg=0, invalid=96777
0179: dt=92.480000, rms=0.675 (0.032%), neg=0, invalid=96777
0180: dt=92.480000, rms=0.675 (0.034%), neg=0, invalid=96777
0181: dt=92.480000, rms=0.675 (0.024%), neg=0, invalid=96777
0182: dt=92.480000, rms=0.675 (0.023%), neg=0, invalid=96777
0183: dt=221.952000, rms=0.675 (0.004%), neg=0, invalid=96777
0184: dt=221.952000, rms=0.675 (0.009%), neg=0, invalid=96777
0185: dt=221.952000, rms=0.675 (-0.010%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.675, neg=0, invalid=96777
0186: dt=443.904000, rms=0.673 (0.200%), neg=0, invalid=96777
0187: dt=32.368000, rms=0.673 (-0.004%), neg=0, invalid=96777
0188: dt=32.368000, rms=0.673 (0.004%), neg=0, invalid=96777
0189: dt=32.368000, rms=0.673 (-0.006%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.674, neg=0, invalid=96777
0190: dt=124.416000, rms=0.670 (0.688%), neg=0, invalid=96777
0191: dt=82.944000, rms=0.662 (1.131%), neg=0, invalid=96777
0192: dt=25.920000, rms=0.661 (0.218%), neg=0, invalid=96777
0193: dt=145.152000, rms=0.657 (0.520%), neg=0, invalid=96777
0194: dt=36.288000, rms=0.654 (0.483%), neg=0, invalid=96777
0195: dt=331.776000, rms=0.648 (0.955%), neg=0, invalid=96777
0196: dt=20.736000, rms=0.644 (0.573%), neg=0, invalid=96777
0197: dt=145.152000, rms=0.642 (0.321%), neg=0, invalid=96777
0198: dt=36.288000, rms=0.640 (0.259%), neg=0, invalid=96777
0199: dt=62.208000, rms=0.640 (0.098%), neg=0, invalid=96777
0200: dt=36.288000, rms=0.639 (0.162%), neg=0, invalid=96777
0201: dt=103.680000, rms=0.638 (0.149%), neg=0, invalid=96777
0202: dt=25.920000, rms=0.637 (0.149%), neg=0, invalid=96777
0203: dt=145.152000, rms=0.635 (0.247%), neg=0, invalid=96777
0204: dt=20.736000, rms=0.634 (0.149%), neg=0, invalid=96777
0205: dt=580.608000, rms=0.627 (1.134%), neg=0, invalid=96777
0206: dt=36.288000, rms=0.627 (0.075%), neg=0, invalid=96777
0207: dt=82.944000, rms=0.626 (0.152%), neg=0, invalid=96777
0208: dt=20.736000, rms=0.625 (0.047%), neg=0, invalid=96777
0209: dt=20.736000, rms=0.625 (0.026%), neg=0, invalid=96777
0210: dt=20.736000, rms=0.625 (0.049%), neg=0, invalid=96777
0211: dt=20.736000, rms=0.624 (0.088%), neg=0, invalid=96777
0212: dt=20.736000, rms=0.624 (0.110%), neg=0, invalid=96777
0213: dt=20.736000, rms=0.623 (0.117%), neg=0, invalid=96777
0214: dt=20.736000, rms=0.622 (0.125%), neg=0, invalid=96777
0215: dt=20.736000, rms=0.621 (0.136%), neg=0, invalid=96777
0216: dt=20.736000, rms=0.621 (0.029%), neg=0, invalid=96777
0217: dt=20.736000, rms=0.621 (0.051%), neg=0, invalid=96777
0218: dt=10.368000, rms=0.621 (0.010%), neg=0, invalid=96777
0219: dt=5.184000, rms=0.621 (0.007%), neg=0, invalid=96777
0220: dt=1.620000, rms=0.621 (0.002%), neg=0, invalid=96777
0221: dt=0.202500, rms=0.621 (0.000%), neg=0, invalid=96777
0222: dt=0.025312, rms=0.621 (0.000%), neg=0, invalid=96777
0223: dt=0.003164, rms=0.621 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.621, neg=0, invalid=96777
0224: dt=145.152000, rms=0.618 (0.437%), neg=0, invalid=96777
0225: dt=36.288000, rms=0.617 (0.137%), neg=0, invalid=96777
0226: dt=103.680000, rms=0.616 (0.123%), neg=0, invalid=96777
0227: dt=36.288000, rms=0.616 (0.121%), neg=0, invalid=96777
0228: dt=36.288000, rms=0.615 (0.041%), neg=0, invalid=96777
0229: dt=36.288000, rms=0.615 (0.070%), neg=0, invalid=96777
0230: dt=36.288000, rms=0.615 (0.089%), neg=0, invalid=96777
0231: dt=36.288000, rms=0.614 (0.115%), neg=0, invalid=96777
0232: dt=36.288000, rms=0.613 (0.151%), neg=0, invalid=96777
0233: dt=36.288000, rms=0.612 (0.173%), neg=0, invalid=96777
0234: dt=36.288000, rms=0.611 (0.177%), neg=0, invalid=96777
0235: dt=36.288000, rms=0.610 (0.180%), neg=0, invalid=96777
0236: dt=36.288000, rms=0.609 (0.173%), neg=0, invalid=96777
0237: dt=36.288000, rms=0.607 (0.186%), neg=0, invalid=96777
0238: dt=36.288000, rms=0.606 (0.177%), neg=0, invalid=96777
0239: dt=36.288000, rms=0.605 (0.179%), neg=0, invalid=96777
0240: dt=36.288000, rms=0.604 (0.172%), neg=0, invalid=96777
0241: dt=36.288000, rms=0.603 (0.177%), neg=0, invalid=96777
0242: dt=36.288000, rms=0.602 (0.178%), neg=0, invalid=96777
0243: dt=36.288000, rms=0.601 (0.167%), neg=0, invalid=96777
0244: dt=36.288000, rms=0.600 (0.158%), neg=0, invalid=96777
0245: dt=36.288000, rms=0.599 (0.157%), neg=0, invalid=96777
0246: dt=36.288000, rms=0.598 (0.157%), neg=0, invalid=96777
0247: dt=36.288000, rms=0.597 (0.136%), neg=0, invalid=96777
0248: dt=36.288000, rms=0.597 (0.121%), neg=0, invalid=96777
0249: dt=36.288000, rms=0.596 (0.112%), neg=0, invalid=96777
0250: dt=36.288000, rms=0.595 (0.139%), neg=0, invalid=96777
0251: dt=36.288000, rms=0.594 (0.135%), neg=0, invalid=96777
0252: dt=36.288000, rms=0.594 (0.103%), neg=0, invalid=96777
0253: dt=18.144000, rms=0.594 (0.021%), neg=0, invalid=96777
0254: dt=18.144000, rms=0.594 (0.006%), neg=0, invalid=96777
0255: dt=36.288000, rms=0.594 (0.012%), neg=0, invalid=96777
0256: dt=9.072000, rms=0.594 (0.004%), neg=0, invalid=96777
0257: dt=9.072000, rms=0.594 (0.005%), neg=0, invalid=96777
0258: dt=4.536000, rms=0.594 (0.001%), neg=0, invalid=96777
0259: dt=2.268000, rms=0.594 (0.001%), neg=0, invalid=96777
0260: dt=0.567000, rms=0.594 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.600, neg=0, invalid=96777
0261: dt=44.800000, rms=0.592 (1.295%), neg=0, invalid=96777
0262: dt=8.000000, rms=0.591 (0.259%), neg=0, invalid=96777
0263: dt=44.800000, rms=0.583 (1.221%), neg=0, invalid=96777
0264: dt=11.200000, rms=0.582 (0.224%), neg=0, invalid=96777
0265: dt=44.800000, rms=0.578 (0.784%), neg=0, invalid=96777
0266: dt=9.600000, rms=0.576 (0.206%), neg=0, invalid=96777
0267: dt=19.200000, rms=0.575 (0.249%), neg=0, invalid=96777
0268: dt=8.272109, rms=0.574 (0.201%), neg=0, invalid=96777
0269: dt=44.800000, rms=0.572 (0.304%), neg=0, invalid=96777
0270: dt=7.799544, rms=0.570 (0.383%), neg=0, invalid=96777
0271: dt=32.000000, rms=0.568 (0.363%), neg=0, invalid=96777
0272: dt=8.242424, rms=0.567 (0.128%), neg=0, invalid=96777
0273: dt=38.400000, rms=0.565 (0.301%), neg=0, invalid=96777
0274: dt=5.532710, rms=0.564 (0.153%), neg=0, invalid=96777
0275: dt=44.800000, rms=0.563 (0.286%), neg=0, invalid=96777
0276: dt=11.200000, rms=0.562 (0.208%), neg=0, invalid=96777
0277: dt=11.200000, rms=0.561 (0.097%), neg=0, invalid=96777
0278: dt=128.000000, rms=0.559 (0.411%), neg=0, invalid=96777
0279: dt=2.800000, rms=0.558 (0.199%), neg=0, invalid=96777
0280: dt=2.800000, rms=0.557 (0.180%), neg=0, invalid=96777
0281: dt=7.140187, rms=0.556 (0.192%), neg=0, invalid=96777
0282: dt=25.600000, rms=0.555 (0.147%), neg=0, invalid=96777
0283: dt=8.000000, rms=0.555 (0.046%), neg=0, invalid=96777
0284: dt=8.000000, rms=0.554 (0.068%), neg=0, invalid=96777
0285: dt=8.000000, rms=0.554 (0.075%), neg=0, invalid=96777
0286: dt=8.000000, rms=0.553 (0.107%), neg=0, invalid=96777
0287: dt=8.000000, rms=0.553 (0.117%), neg=0, invalid=96777
0288: dt=8.000000, rms=0.552 (0.153%), neg=0, invalid=96777
0289: dt=8.000000, rms=0.551 (0.175%), neg=0, invalid=96777
0290: dt=8.000000, rms=0.550 (0.178%), neg=0, invalid=96777
0291: dt=8.000000, rms=0.549 (0.177%), neg=0, invalid=96777
0292: dt=8.000000, rms=0.548 (0.175%), neg=0, invalid=96777
0293: dt=8.000000, rms=0.547 (0.197%), neg=0, invalid=96777
0294: dt=8.000000, rms=0.546 (0.205%), neg=0, invalid=96777
0295: dt=8.000000, rms=0.545 (0.188%), neg=0, invalid=96777
0296: dt=8.000000, rms=0.544 (0.168%), neg=0, invalid=96777
0297: dt=8.000000, rms=0.543 (0.154%), neg=0, invalid=96777
0298: dt=8.000000, rms=0.542 (0.145%), neg=0, invalid=96777
0299: dt=8.000000, rms=0.541 (0.140%), neg=0, invalid=96777
0300: dt=8.000000, rms=0.541 (0.134%), neg=0, invalid=96777
0301: dt=8.000000, rms=0.540 (0.139%), neg=0, invalid=96777
0302: dt=8.000000, rms=0.539 (0.122%), neg=0, invalid=96777
0303: dt=8.000000, rms=0.539 (0.120%), neg=0, invalid=96777
0304: dt=8.000000, rms=0.538 (0.113%), neg=0, invalid=96777
0305: dt=8.000000, rms=0.537 (0.099%), neg=0, invalid=96777
0306: dt=8.000000, rms=0.537 (0.097%), neg=0, invalid=96777
0307: dt=8.000000, rms=0.536 (0.094%), neg=0, invalid=96777
0308: dt=8.000000, rms=0.536 (0.086%), neg=0, invalid=96777
0309: dt=8.000000, rms=0.535 (0.089%), neg=0, invalid=96777
0310: dt=8.000000, rms=0.535 (0.076%), neg=0, invalid=96777
0311: dt=8.000000, rms=0.535 (0.067%), neg=0, invalid=96777
0312: dt=8.000000, rms=0.534 (0.056%), neg=0, invalid=96777
0313: dt=8.000000, rms=0.534 (0.060%), neg=0, invalid=96777
0314: dt=8.000000, rms=0.534 (0.059%), neg=0, invalid=96777
0315: dt=8.000000, rms=0.533 (0.064%), neg=0, invalid=96777
0316: dt=8.000000, rms=0.533 (0.054%), neg=0, invalid=96777
0317: dt=8.000000, rms=0.533 (0.053%), neg=0, invalid=96777
0318: dt=8.000000, rms=0.533 (0.040%), neg=0, invalid=96777
0319: dt=8.000000, rms=0.532 (0.037%), neg=0, invalid=96777
0320: dt=8.000000, rms=0.532 (0.050%), neg=0, invalid=96777
0321: dt=8.000000, rms=0.532 (0.050%), neg=0, invalid=96777
0322: dt=8.000000, rms=0.532 (0.043%), neg=0, invalid=96777
0323: dt=8.000000, rms=0.531 (0.041%), neg=0, invalid=96777
0324: dt=8.000000, rms=0.531 (0.041%), neg=0, invalid=96777
0325: dt=8.000000, rms=0.531 (0.036%), neg=0, invalid=96777
0326: dt=8.000000, rms=0.531 (0.038%), neg=0, invalid=96777
0327: dt=8.000000, rms=0.531 (0.034%), neg=0, invalid=96777
0328: dt=8.000000, rms=0.530 (0.037%), neg=0, invalid=96777
0329: dt=8.000000, rms=0.530 (0.044%), neg=0, invalid=96777
0330: dt=8.000000, rms=0.530 (0.042%), neg=0, invalid=96777
0331: dt=8.000000, rms=0.530 (0.036%), neg=0, invalid=96777
0332: dt=8.000000, rms=0.530 (0.038%), neg=0, invalid=96777
0333: dt=8.000000, rms=0.529 (0.033%), neg=0, invalid=96777
0334: dt=8.000000, rms=0.529 (0.025%), neg=0, invalid=96777
0335: dt=8.000000, rms=0.529 (0.026%), neg=0, invalid=96777
0336: dt=8.000000, rms=0.529 (0.027%), neg=0, invalid=96777
0337: dt=8.000000, rms=0.529 (0.032%), neg=0, invalid=96777
0338: dt=8.000000, rms=0.529 (0.034%), neg=0, invalid=96777
0339: dt=8.000000, rms=0.528 (0.031%), neg=0, invalid=96777
0340: dt=8.000000, rms=0.528 (0.032%), neg=0, invalid=96777
0341: dt=8.000000, rms=0.528 (0.027%), neg=0, invalid=96777
0342: dt=8.000000, rms=0.528 (0.020%), neg=0, invalid=96777
0343: dt=8.000000, rms=0.528 (0.023%), neg=0, invalid=96777
0344: dt=8.000000, rms=0.528 (0.021%), neg=0, invalid=96777
0345: dt=32.000000, rms=0.528 (0.017%), neg=0, invalid=96777
0346: dt=32.000000, rms=0.528 (-0.137%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.528, neg=0, invalid=96777
0347: dt=25.600000, rms=0.527 (0.159%), neg=0, invalid=96777
0348: dt=11.200000, rms=0.526 (0.115%), neg=0, invalid=96777
0349: dt=11.200000, rms=0.526 (0.052%), neg=0, invalid=96777
0350: dt=11.200000, rms=0.526 (0.037%), neg=0, invalid=96777
0351: dt=11.200000, rms=0.526 (0.027%), neg=0, invalid=96777
0352: dt=11.200000, rms=0.526 (0.042%), neg=0, invalid=96777
0353: dt=11.200000, rms=0.525 (0.042%), neg=0, invalid=96777
0354: dt=11.200000, rms=0.525 (0.041%), neg=0, invalid=96777
0355: dt=11.200000, rms=0.525 (0.020%), neg=0, invalid=96777
0356: dt=11.200000, rms=0.525 (0.007%), neg=0, invalid=96777
0357: dt=11.200000, rms=0.525 (0.011%), neg=0, invalid=96777
0358: dt=19.200000, rms=0.525 (0.033%), neg=0, invalid=96777
0359: dt=2.800000, rms=0.525 (0.005%), neg=0, invalid=96777
0360: dt=2.800000, rms=0.525 (-0.004%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.548, neg=0, invalid=96777
0361: dt=0.000000, rms=0.548 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.548, neg=0, invalid=96777
0362: dt=0.000000, rms=0.548 (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=0.594, neg=0, invalid=96777
0363: dt=1.436747, rms=0.588 (0.918%), neg=0, invalid=96777
0364: dt=0.320000, rms=0.588 (0.025%), neg=0, invalid=96777
0365: dt=0.320000, rms=0.588 (-0.010%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.588, neg=0, invalid=96777
0366: dt=0.500000, rms=0.588 (0.087%), neg=0, invalid=96777
0367: dt=0.384000, rms=0.588 (0.022%), neg=0, invalid=96777
0368: dt=0.384000, rms=0.588 (-0.006%), 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=0.540, neg=0, invalid=96777
0369: dt=0.170500, rms=0.532 (1.405%), neg=0, invalid=96777
0370: dt=0.143079, rms=0.528 (0.801%), neg=0, invalid=96777
0371: dt=0.126550, rms=0.525 (0.528%), neg=0, invalid=96777
0372: dt=0.118172, rms=0.523 (0.388%), neg=0, invalid=96777
0373: dt=0.112000, rms=0.522 (0.303%), neg=0, invalid=96777
0374: dt=0.112000, rms=0.521 (0.249%), neg=0, invalid=96777
0375: dt=0.112000, rms=0.519 (0.209%), neg=0, invalid=96777
0376: dt=0.320000, rms=0.517 (0.510%), neg=0, invalid=96777
0377: dt=0.005000, rms=0.517 (0.008%), neg=0, invalid=96777
0378: dt=0.005000, rms=0.517 (0.005%), neg=0, invalid=96777
0379: dt=0.005000, rms=0.517 (0.009%), neg=0, invalid=96777
0380: dt=0.005000, rms=0.517 (0.013%), neg=0, invalid=96777
0381: dt=0.005000, rms=0.517 (0.015%), neg=0, invalid=96777
0382: dt=0.005000, rms=0.516 (0.018%), neg=0, invalid=96777
0383: dt=0.005000, rms=0.516 (0.020%), neg=0, invalid=96777
0384: dt=0.005000, rms=0.516 (0.024%), neg=0, invalid=96777
0385: dt=0.005000, rms=0.516 (0.026%), neg=0, invalid=96777
0386: dt=0.005000, rms=0.516 (0.027%), neg=0, invalid=96777
0387: dt=0.005000, rms=0.516 (0.028%), neg=0, invalid=96777
0388: dt=0.005000, rms=0.516 (0.029%), neg=0, invalid=96777
0389: dt=0.005000, rms=0.515 (0.030%), neg=0, invalid=96777
0390: dt=0.005000, rms=0.515 (0.031%), neg=0, invalid=96777
0391: dt=0.005000, rms=0.515 (0.031%), neg=0, invalid=96777
0392: dt=0.005000, rms=0.515 (0.032%), neg=0, invalid=96777
0393: dt=0.005000, rms=0.515 (0.030%), neg=0, invalid=96777
0394: dt=0.005000, rms=0.515 (0.031%), neg=0, invalid=96777
0395: dt=0.005000, rms=0.515 (0.032%), neg=0, invalid=96777
0396: dt=0.005000, rms=0.514 (0.029%), neg=0, invalid=96777
0397: dt=0.005000, rms=0.514 (0.033%), neg=0, invalid=96777
0398: dt=0.005000, rms=0.514 (0.028%), neg=0, invalid=96777
0399: dt=0.005000, rms=0.514 (0.029%), neg=0, invalid=96777
0400: dt=0.005000, rms=0.514 (0.028%), neg=0, invalid=96777
0401: dt=0.005000, rms=0.514 (0.029%), neg=0, invalid=96777
0402: dt=0.005000, rms=0.513 (0.027%), neg=0, invalid=96777
0403: dt=0.005000, rms=0.513 (0.026%), neg=0, invalid=96777
0404: dt=0.005000, rms=0.513 (0.027%), neg=0, invalid=96777
0405: dt=0.005000, rms=0.513 (0.024%), neg=0, invalid=96777
0406: dt=0.005000, rms=0.513 (0.023%), neg=0, invalid=96777
0407: dt=0.112000, rms=0.513 (0.036%), neg=0, invalid=96777
0408: dt=0.112000, rms=0.513 (0.037%), neg=0, invalid=96777
0409: dt=0.112000, rms=0.512 (0.031%), neg=0, invalid=96777
0410: dt=0.014000, rms=0.512 (0.006%), neg=0, invalid=96777
0411: dt=0.014000, rms=0.512 (0.004%), neg=0, invalid=96777
0412: dt=0.014000, rms=0.512 (0.006%), neg=0, invalid=96777
0413: dt=0.014000, rms=0.512 (0.009%), neg=0, invalid=96777
0414: dt=0.014000, rms=0.512 (0.014%), neg=0, invalid=96777
0415: dt=0.014000, rms=0.512 (0.012%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.512, neg=0, invalid=96777
0416: dt=0.112000, rms=0.511 (0.316%), neg=0, invalid=96777
0417: dt=0.112000, rms=0.509 (0.243%), neg=0, invalid=96777
0418: dt=0.112000, rms=0.508 (0.177%), neg=0, invalid=96777
0419: dt=0.112000, rms=0.508 (0.144%), neg=0, invalid=96777
0420: dt=0.028000, rms=0.508 (0.033%), neg=0, invalid=96777
0421: dt=0.028000, rms=0.507 (0.023%), neg=0, invalid=96777
0422: dt=0.028000, rms=0.507 (0.047%), neg=0, invalid=96777
0423: dt=0.028000, rms=0.507 (0.068%), neg=0, invalid=96777
0424: dt=0.028000, rms=0.506 (0.077%), neg=0, invalid=96777
0425: dt=0.014000, rms=0.506 (0.006%), neg=0, invalid=96777
0426: dt=0.003500, rms=0.506 (0.003%), neg=0, invalid=96777
0427: dt=0.028000, rms=0.506 (0.015%), neg=0, invalid=96777
0428: dt=0.024000, rms=0.506 (0.012%), neg=0, invalid=96777
0429: dt=0.024000, rms=0.506 (0.011%), neg=0, invalid=96777
0430: dt=0.024000, rms=0.506 (0.012%), neg=0, invalid=96777
0431: dt=0.024000, rms=0.506 (0.022%), neg=0, invalid=96777
0432: dt=0.024000, rms=0.506 (0.024%), neg=0, invalid=96777
0433: dt=0.024000, rms=0.506 (0.033%), neg=0, invalid=96777
0434: dt=0.024000, rms=0.506 (0.039%), neg=0, invalid=96777
0435: dt=0.024000, rms=0.505 (0.044%), neg=0, invalid=96777
0436: dt=0.024000, rms=0.505 (0.037%), neg=0, invalid=96777
0437: dt=0.024000, rms=0.505 (0.040%), neg=0, invalid=96777
0438: dt=0.024000, rms=0.505 (0.040%), neg=0, invalid=96777
0439: dt=0.024000, rms=0.505 (0.032%), neg=0, invalid=96777
0440: dt=0.024000, rms=0.504 (0.031%), neg=0, invalid=96777
0441: dt=0.024000, rms=0.504 (0.030%), neg=0, invalid=96777
0442: dt=0.024000, rms=0.504 (0.028%), neg=0, invalid=96777
0443: dt=0.024000, rms=0.504 (0.013%), neg=0, invalid=96777
0444: dt=0.024000, rms=0.504 (0.014%), neg=0, invalid=96777
0445: dt=0.024000, rms=0.504 (0.012%), neg=0, invalid=96777
0446: dt=0.000000, rms=0.504 (0.002%), neg=0, invalid=96777
0447: dt=0.050000, rms=0.504 (-0.003%), 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=0.502, neg=0, invalid=96777
0448: dt=0.000000, rms=0.502 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.502, neg=0, invalid=96777
0449: dt=129.472000, rms=0.502 (0.051%), neg=0, invalid=96777
0450: dt=110.976000, rms=0.502 (0.014%), neg=0, invalid=96777
0451: dt=110.976000, rms=0.501 (0.006%), neg=0, invalid=96777
0452: dt=110.976000, rms=0.501 (0.043%), neg=0, invalid=96777
0453: dt=110.976000, rms=0.501 (0.015%), neg=0, invalid=96777
0454: dt=110.976000, rms=0.501 (0.003%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.501, neg=0, invalid=96777
0455: dt=36.288000, rms=0.500 (0.176%), neg=0, invalid=96777
0456: dt=36.288000, rms=0.500 (0.049%), neg=0, invalid=96777
0457: dt=36.288000, rms=0.500 (0.066%), neg=0, invalid=96777
0458: dt=36.288000, rms=0.500 (0.025%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0459: dt=36.288000, rms=0.500 (-0.060%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.500, neg=0, invalid=96777
0460: dt=103.680000, rms=0.498 (0.347%), neg=0, invalid=96777
0461: dt=36.288000, rms=0.497 (0.150%), neg=0, invalid=96777
0462: dt=36.288000, rms=0.497 (0.007%), neg=0, invalid=96777
0463: dt=36.288000, rms=0.497 (0.108%), neg=0, invalid=96777
0464: dt=36.288000, rms=0.496 (0.156%), neg=0, invalid=96777
0465: dt=36.288000, rms=0.495 (0.120%), neg=0, invalid=96777
0466: dt=36.288000, rms=0.495 (0.067%), neg=0, invalid=96777
0467: dt=25.920000, rms=0.495 (0.074%), neg=0, invalid=96777
0468: dt=15.552000, rms=0.495 (-0.002%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.495, neg=0, invalid=96777
iter 0, gcam->neg = 8
after 7 iterations, nbhd size=1, neg = 0
0469: dt=44.800000, rms=0.490 (0.886%), neg=0, invalid=96777
0470: dt=9.134752, rms=0.489 (0.310%), neg=0, invalid=96777
0471: dt=11.200000, rms=0.488 (0.204%), neg=0, invalid=96777
0472: dt=11.200000, rms=0.487 (0.183%), neg=0, invalid=96777
0473: dt=11.200000, rms=0.486 (0.292%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 6 iterations, nbhd size=1, neg = 0
0474: dt=11.200000, rms=0.484 (0.306%), neg=0, invalid=96777
0475: dt=11.200000, rms=0.483 (0.316%), neg=0, invalid=96777
0476: dt=11.200000, rms=0.481 (0.300%), neg=0, invalid=96777
0477: dt=11.200000, rms=0.480 (0.251%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0478: dt=11.200000, rms=0.479 (0.193%), neg=0, invalid=96777
0479: dt=11.200000, rms=0.478 (0.202%), neg=0, invalid=96777
0480: dt=11.200000, rms=0.477 (0.201%), neg=0, invalid=96777
0481: dt=11.200000, rms=0.476 (0.179%), neg=0, invalid=96777
0482: dt=11.200000, rms=0.475 (0.190%), neg=0, invalid=96777
0483: dt=11.200000, rms=0.475 (0.158%), neg=0, invalid=96777
0484: dt=11.200000, rms=0.474 (0.167%), neg=0, invalid=96777
0485: dt=11.200000, rms=0.473 (0.145%), neg=0, invalid=96777
0486: dt=11.200000, rms=0.473 (0.118%), neg=0, invalid=96777
0487: dt=11.200000, rms=0.472 (0.088%), neg=0, invalid=96777
0488: dt=11.200000, rms=0.472 (0.025%), neg=0, invalid=96777
0489: dt=11.200000, rms=0.472 (0.035%), neg=0, invalid=96777
0490: dt=11.200000, rms=0.472 (0.025%), neg=0, invalid=96777
0491: dt=11.200000, rms=0.472 (0.040%), neg=0, invalid=96777
0492: dt=11.200000, rms=0.471 (0.033%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.471, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0493: dt=44.800000, rms=0.469 (0.499%), neg=0, invalid=96777
0494: dt=7.306358, rms=0.468 (0.191%), neg=0, invalid=96777
0495: dt=7.306358, rms=0.468 (0.076%), neg=0, invalid=96777
0496: dt=7.306358, rms=0.467 (0.081%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0497: dt=7.306358, rms=0.467 (0.114%), neg=0, invalid=96777
iter 0, gcam->neg = 5
after 7 iterations, nbhd size=1, neg = 0
0498: dt=7.306358, rms=0.466 (0.101%), neg=0, invalid=96777
0499: dt=7.306358, rms=0.466 (0.093%), neg=0, invalid=96777
0500: dt=11.200000, rms=0.466 (0.033%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.472, neg=0, invalid=96777
iter 0, gcam->neg = 12
after 7 iterations, nbhd size=1, neg = 0
0501: dt=4.032000, rms=0.472 (0.096%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0502: dt=1.008000, rms=0.472 (0.008%), neg=0, invalid=96777
0503: dt=1.008000, rms=0.471 (0.016%), neg=0, invalid=96777
0504: dt=1.008000, rms=0.471 (0.020%), neg=0, invalid=96777
iter 0, gcam->neg = 6
after 7 iterations, nbhd size=1, neg = 0
0505: dt=1.008000, rms=0.471 (-0.005%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.471, neg=0, invalid=96777
iter 0, gcam->neg = 18
after 10 iterations, nbhd size=1, neg = 0
0506: dt=7.759657, rms=0.471 (0.171%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0507: dt=3.456000, rms=0.470 (0.026%), neg=0, invalid=96777
0508: dt=3.456000, rms=0.470 (0.074%), neg=0, invalid=96777
iter 0, gcam->neg = 24
after 16 iterations, nbhd size=2, neg = 0
0509: dt=3.456000, rms=0.470 (0.090%), neg=0, invalid=96777
iter 0, gcam->neg = 13
after 8 iterations, nbhd size=1, neg = 0
0510: dt=3.456000, rms=0.469 (0.075%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 7 iterations, nbhd size=1, neg = 0
0511: dt=3.456000, rms=0.469 (0.055%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.474, neg=0, invalid=96777
0512: dt=0.000000, rms=0.474 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.474, neg=0, invalid=96777
0513: dt=0.000000, rms=0.474 (0.000%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.466, neg=0, invalid=96777
iter 0, gcam->neg = 757
after 200 iterations, nbhd size=3, neg = 1
starting rms=0.006, neg=1, removing folds in lattice....
iter 1, dt=0.000039: new neg 0, old_neg 1, delta 1, rms=0.006 (10.584%)
0514: dt=2.001663, rms=0.422 (9.388%), neg=0, invalid=96777
0515: dt=0.000250, rms=0.422 (0.007%), neg=0, invalid=96777
0516: dt=0.000250, rms=0.422 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.422, neg=0, invalid=96777
0517: dt=0.000438, rms=0.422 (0.000%), neg=0, invalid=96777
0518: dt=0.000000, rms=0.422 (-0.000%), neg=0, invalid=96777
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.404, neg=0, invalid=96777
0519: dt=0.005645, rms=0.405 (-0.300%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.405, neg=0, invalid=96777
0520: dt=73.984000, rms=0.405 (0.014%), neg=0, invalid=96777
0521: dt=32.368000, rms=0.405 (0.001%), neg=0, invalid=96777
0522: dt=32.368000, rms=0.405 (0.000%), neg=0, invalid=96777
0523: dt=32.368000, rms=0.405 (-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=0.405, neg=0, invalid=96777
0524: dt=0.972000, rms=0.405 (0.000%), neg=0, invalid=96777
0525: dt=0.002215, rms=0.405 (0.000%), neg=0, invalid=96777
0526: dt=0.002215, rms=0.405 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.405, neg=0, invalid=96777
0527: dt=36.288000, rms=0.405 (0.028%), neg=0, invalid=96777
0528: dt=82.944000, rms=0.405 (0.026%), neg=0, invalid=96777
0529: dt=82.944000, rms=0.405 (0.024%), neg=0, invalid=96777
0530: dt=82.944000, rms=0.405 (0.018%), neg=0, invalid=96777
0531: dt=82.944000, rms=0.405 (-0.006%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.405, neg=0, invalid=96777
iter 0, gcam->neg = 4
after 23 iterations, nbhd size=3, neg = 0
0532: dt=11.200000, rms=0.405 (0.075%), neg=0, invalid=96777
0533: dt=2.800000, rms=0.405 (0.006%), neg=0, invalid=96777
0534: dt=2.800000, rms=0.405 (0.016%), neg=0, invalid=96777
0535: dt=2.800000, rms=0.405 (0.024%), neg=0, invalid=96777
0536: dt=2.800000, rms=0.405 (0.020%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 26 iterations, nbhd size=4, neg = 0
0537: dt=2.800000, rms=0.405 (-0.022%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.405, neg=0, invalid=96777
iter 0, gcam->neg = 15
after 44 iterations, nbhd size=4, neg = 0
0538: dt=44.800000, rms=0.403 (0.349%), neg=0, invalid=96777
0539: dt=11.200000, rms=0.403 (0.042%), neg=0, invalid=96777
0540: dt=11.200000, rms=0.403 (0.106%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 200 iterations, nbhd size=1, neg = 1
starting rms=0.010, neg=1, removing folds in lattice....
iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.003 (66.915%)
iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.003 (11.475%)
0541: dt=11.200000, rms=0.402 (0.138%), neg=0, invalid=96777
0542: dt=11.200000, rms=0.402 (0.057%), neg=0, invalid=96777
iter 0, gcam->neg = 5
after 200 iterations, nbhd size=1, neg = 1
starting rms=0.010, neg=1, removing folds in lattice....
iter 1, dt=0.000023: new neg 1, old_neg 1, delta 0, rms=0.003 (67.666%)
iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.003 (15.840%)
0543: dt=11.200000, rms=0.402 (0.091%), neg=0, invalid=96777
0544: dt=11.200000, rms=0.401 (0.052%), neg=0, invalid=96777
iter 0, gcam->neg = 18
after 200 iterations, nbhd size=2, neg = 2
starting rms=0.003, neg=2, removing folds in lattice....
iter 1, dt=0.000025: new neg 0, old_neg 2, delta 2, rms=0.003 (12.616%)
0545: dt=44.800000, rms=0.401 (0.138%), neg=0, invalid=96777
iter 0, gcam->neg = 26
after 200 iterations, nbhd size=1, neg = 2
starting rms=0.010, neg=2, removing folds in lattice....
iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.004 (64.107%)
iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.003 (25.453%)
0546: dt=102.400000, rms=0.400 (0.105%), neg=0, invalid=96777
iter 0, gcam->neg = 210
after 200 iterations, nbhd size=2, neg = 6
starting rms=0.008, neg=6, removing folds in lattice....
iter 1, dt=0.000094: new neg 1, old_neg 6, delta 5, rms=0.004 (46.454%)
iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.004 (18.148%)
0547: dt=102.400000, rms=0.400 (-0.423%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.404, neg=0, invalid=96777
iter 0, gcam->neg = 18
after 21 iterations, nbhd size=2, neg = 0
0548: dt=4.032000, rms=0.403 (0.140%), neg=0, invalid=96777
0549: dt=0.063000, rms=0.403 (0.000%), neg=0, invalid=96777
0550: dt=0.063000, rms=0.403 (0.002%), neg=0, invalid=96777
0551: dt=0.063000, rms=0.403 (0.003%), neg=0, invalid=96777
0552: dt=0.063000, rms=0.403 (0.005%), neg=0, invalid=96777
0553: dt=0.063000, rms=0.403 (0.006%), neg=0, invalid=96777
0554: dt=0.063000, rms=0.403 (0.006%), neg=0, invalid=96777
0555: dt=0.063000, rms=0.403 (0.007%), neg=0, invalid=96777
0556: dt=0.063000, rms=0.403 (0.008%), neg=0, invalid=96777
0557: dt=0.063000, rms=0.403 (0.008%), neg=0, invalid=96777
0558: dt=0.063000, rms=0.403 (0.009%), neg=0, invalid=96777
0559: dt=0.063000, rms=0.403 (0.009%), neg=0, invalid=96777
0560: dt=0.063000, rms=0.403 (0.008%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.403, neg=0, invalid=96777
iter 0, gcam->neg = 35
after 31 iterations, nbhd size=3, neg = 0
0561: dt=9.216000, rms=0.402 (0.284%), neg=0, invalid=96777
0562: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777
0563: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777
0564: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777
0565: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777
0566: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777
0567: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777
0568: dt=0.009000, rms=0.402 (0.000%), neg=0, invalid=96777
0569: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0570: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0571: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0572: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0573: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0574: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0575: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0576: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0577: dt=0.009000, rms=0.402 (0.001%), neg=0, invalid=96777
0578: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0579: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0580: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0581: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0582: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0583: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0584: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0585: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0586: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0587: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0588: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0589: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0590: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0591: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0592: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0593: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0594: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0595: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0596: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0597: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
0598: dt=0.009000, rms=0.402 (0.002%), neg=0, invalid=96777
iter 0, gcam->neg = 60
after 38 iterations, nbhd size=4, neg = 0
0599: dt=11.520000, rms=0.401 (0.128%), neg=0, invalid=96777
0600: dt=0.002250, rms=0.401 (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=0.408, neg=0, invalid=96777
0601: dt=0.000250, rms=0.408 (0.000%), neg=0, invalid=96777
0602: dt=0.000000, rms=0.408 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.408, neg=0, invalid=96777
0603: dt=0.000000, rms=0.408 (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=0.397, neg=0, invalid=96777
iter 0, gcam->neg = 442
after 46 iterations, nbhd size=4, neg = 0
0604: dt=0.768000, rms=0.384 (3.140%), neg=0, invalid=96777
0605: dt=0.000020, rms=0.384 (0.001%), neg=0, invalid=96777
0606: dt=0.000020, rms=0.384 (0.001%), neg=0, invalid=96777
0607: dt=0.000020, rms=0.384 (0.001%), neg=0, invalid=96777
0608: dt=0.000020, rms=0.384 (0.000%), neg=0, invalid=96777
0609: dt=0.000109, rms=0.384 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.384, neg=0, invalid=96777
0610: dt=0.000438, rms=0.384 (0.000%), neg=0, invalid=96777
0611: dt=0.001750, rms=0.384 (0.000%), neg=0, invalid=96777
0612: dt=0.001750, rms=0.384 (0.001%), neg=0, invalid=96777
0613: dt=0.001750, rms=0.384 (0.001%), neg=0, invalid=96777
0614: dt=0.001750, rms=0.384 (0.002%), neg=0, invalid=96777
0615: dt=0.001750, rms=0.384 (0.003%), neg=0, invalid=96777
0616: dt=0.001750, rms=0.384 (0.003%), neg=0, invalid=96777
0617: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777
0618: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0619: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0620: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0621: dt=0.001750, rms=0.384 (0.004%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0622: dt=0.001750, rms=0.384 (0.005%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 5 iterations, nbhd size=1, neg = 0
0623: dt=0.001750, rms=0.384 (0.005%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 5 iterations, nbhd size=1, neg = 0
0624: dt=0.001750, rms=0.384 (0.005%), neg=0, invalid=96777
writing output transformation to transforms/talairach.m3z...
GCAMwrite
registration took 4 hours, 15 minutes and 50 seconds.
#--------------------------------------
#@# CA Reg Inv Thu Aug  8 16:23:18 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 16:24:42 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...
10751868 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 1 minutes and 26 seconds.
#--------------------------------------
#@# SkullLTA Thu Aug  8 16:26:08 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=8.0
skull bounding box = (41, 16, 0) --> (210, 203, 194)
using (97, 78, 97) as brain centroid...
mean wm in atlas = 126, using box (76,55,73) --> (117, 101,120) 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=-3.9, old_max_log_p =-4.1 (thresh=-4.0)
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.113  -0.261   0.972   16.306;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.113  -0.261   0.972   16.306;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.032   0.030  -0.117   3.863;
 0.001   1.041   0.278  -9.164;
 0.113  -0.261   0.972   16.306;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.032   0.030  -0.117   3.863;
 0.001   1.041   0.278  -9.164;
 0.113  -0.261   0.972   16.306;
 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=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.034   0.036  -0.107   1.460;
-0.006   1.037   0.295  -9.760;
 0.105  -0.278   0.965   19.749;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.034   0.036  -0.107   1.460;
-0.006   1.036   0.295  -9.606;
 0.105  -0.277   0.964   19.850;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9)
 1.034   0.036  -0.107   1.460;
-0.006   1.036   0.295  -9.606;
 0.105  -0.277   0.964   19.850;
 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
 1.03373   0.03636  -0.10679   1.46017;
-0.00558   1.03607   0.29492  -9.60604;
 0.10453  -0.27718   0.96387   19.85009;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.03373   0.03636  -0.10679   1.46017;
-0.00558   1.03607   0.29492  -9.60604;
 0.10453  -0.27718   0.96387   19.85009;
 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: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.034   0.036  -0.107   1.460;
-0.006   1.036   0.295  -9.606;
 0.105  -0.277   0.964   19.850;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.9 (old=-4.1)
transform before final EM align:
 1.034   0.036  -0.107   1.460;
-0.006   1.036   0.295  -9.606;
 0.105  -0.277   0.964   19.850;
 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
 1.03373   0.03636  -0.10679   1.46017;
-0.00558   1.03607   0.29492  -9.60604;
 0.10453  -0.27718   0.96387   19.85009;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.03373   0.03636  -0.10679   1.46017;
-0.00558   1.03607   0.29492  -9.60604;
 0.10453  -0.27718   0.96387   19.85009;
 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: 010: -log(p) =    4.3  tol 0.000000
final transform:
 1.034   0.036  -0.107   1.460;
-0.006   1.036   0.295  -9.606;
 0.105  -0.277   0.964   19.850;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull_2.lta...
registration took 37 minutes and 49 seconds.
#--------------------------------------
#@# SubCort Seg Thu Aug  8 17:03:57 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 snake6
machine  x86_64

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 0.09989 (11)
Left_Lateral_Ventricle (4): linear fit = 0.38 x + 0.0 (2756 voxels, overlap=0.007)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2756 voxels, peak = 10), gca=10.8
gca peak = 0.14982 (20)
mri peak = 0.12652 (10)
Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (1226 voxels, overlap=0.007)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1226 voxels, peak =  7), gca=8.0
gca peak = 0.28003 (97)
mri peak = 0.09471 (90)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (353 voxels, overlap=0.049)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (353 voxels, peak = 86), gca=85.8
gca peak = 0.18160 (96)
mri peak = 0.08256 (87)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (379 voxels, overlap=0.084)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (379 voxels, peak = 84), gca=84.0
gca peak = 0.27536 (62)
mri peak = 0.09570 (56)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (578 voxels, overlap=0.631)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (578 voxels, peak = 55), gca=54.9
gca peak = 0.32745 (63)
mri peak = 0.07680 (59)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (607 voxels, overlap=0.786)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (607 voxels, peak = 58), gca=58.3
gca peak = 0.08597 (105)
mri peak = 0.06944 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (46078 voxels, overlap=0.701)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (46078 voxels, peak = 109), gca=108.7
gca peak = 0.09209 (106)
mri peak = 0.07869 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48429 voxels, overlap=0.613)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48429 voxels, peak = 111), gca=110.8
gca peak = 0.07826 (63)
mri peak = 0.05008 (50)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (17863 voxels, overlap=0.236)
Left_Cerebral_Cortex (3): linear fit = 0.80 x + 0.0 (17863 voxels, peak = 50), gca=50.1
gca peak = 0.08598 (64)
mri peak = 0.05013 (51)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (16328 voxels, overlap=0.347)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (16328 voxels, peak = 53), gca=52.8
gca peak = 0.24164 (71)
mri peak = 0.10371 (66)
Right_Caudate (50): linear fit = 0.90 x + 0.0 (914 voxels, overlap=0.428)
Right_Caudate (50): linear fit = 0.90 x + 0.0 (914 voxels, peak = 64), gca=64.3
gca peak = 0.18227 (75)
mri peak = 0.08705 (68)
Left_Caudate (11): linear fit = 0.87 x + 0.0 (966 voxels, overlap=0.149)
Left_Caudate (11): linear fit = 0.87 x + 0.0 (966 voxels, peak = 65), gca=64.9
gca peak = 0.10629 (62)
mri peak = 0.04937 (57)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (11432 voxels, overlap=0.971)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (11432 voxels, peak = 60), gca=59.8
gca peak = 0.11668 (59)
mri peak = 0.04903 (57)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8595 voxels, overlap=0.987)
Right_Cerebellum_Cortex (47): linear fit = 0.96 x + 0.0 (8595 voxels, peak = 57), gca=56.9
gca peak = 0.17849 (88)
mri peak = 0.08428 (87)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5743 voxels, overlap=0.990)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5743 voxels, peak = 88), gca=87.6
gca peak = 0.16819 (86)
mri peak = 0.07910 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5090 voxels, overlap=0.973)
Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (5090 voxels, peak = 88), gca=88.2
gca peak = 0.41688 (64)
mri peak = 0.09510 (58)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (350 voxels, overlap=1.040)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (350 voxels, peak = 57), gca=56.6
gca peak = 0.42394 (62)
mri peak = 0.08621 (57)
Right_Amygdala (54): linear fit = 0.90 x + 0.0 (247 voxels, overlap=1.040)
Right_Amygdala (54): linear fit = 0.90 x + 0.0 (247 voxels, peak = 56), gca=56.1
gca peak = 0.10041 (96)
mri peak = 0.07499 (89)
Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (3945 voxels, overlap=0.713)
Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (3945 voxels, peak = 90), gca=89.8
gca peak = 0.13978 (88)
mri peak = 0.07177 (87)
Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3802 voxels, overlap=0.887)
Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3802 voxels, peak = 86), gca=85.8
gca peak = 0.08514 (81)
mri peak = 0.07651 (72)
Left_Putamen (12): linear fit = 0.87 x + 0.0 (1749 voxels, overlap=0.342)
Left_Putamen (12): linear fit = 0.87 x + 0.0 (1749 voxels, peak = 70), gca=70.1
gca peak = 0.09624 (82)
mri peak = 0.07106 (75)
Right_Putamen (51): linear fit = 0.87 x + 0.0 (1944 voxels, overlap=0.377)
Right_Putamen (51): linear fit = 0.87 x + 0.0 (1944 voxels, peak = 71), gca=70.9
gca peak = 0.07543 (88)
mri peak = 0.06908 (87)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11648 voxels, overlap=0.765)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11648 voxels, peak = 89), gca=89.3
gca peak = 0.12757 (95)
mri peak = 0.06821 (93)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (988 voxels, overlap=0.883)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (988 voxels, peak = 94), gca=93.6
gca peak = 0.17004 (92)
mri peak = 0.07131 (90)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1269 voxels, overlap=0.905)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1269 voxels, peak = 91), gca=90.6
gca peak = 0.21361 (36)
mri peak = 0.08855 (12)
gca peak = 0.26069 (23)
mri peak = 0.12416 ( 8)
Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (297 voxels, overlap=0.027)
Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (297 voxels, peak =  7), gca=7.0
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 0.87 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 aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.31600 (11)
mri peak = 0.09989 (11)
Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (2756 voxels, overlap=0.988)
Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (2756 voxels, peak = 11), gca=11.5
gca peak = 0.29325 ( 9)
mri peak = 0.12652 (10)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (1226 voxels, overlap=0.968)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (1226 voxels, peak =  9), gca=9.5
gca peak = 0.26036 (86)
mri peak = 0.09471 (90)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (353 voxels, overlap=1.015)
Right_Pallidum (52): linear fit = 0.99 x + 0.0 (353 voxels, peak = 85), gca=84.7
gca peak = 0.18878 (84)
mri peak = 0.08256 (87)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (379 voxels, overlap=1.018)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (379 voxels, peak = 84), gca=84.0
gca peak = 0.31426 (55)
mri peak = 0.09570 (56)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (578 voxels, overlap=1.008)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (578 voxels, peak = 55), gca=55.0
gca peak = 0.30737 (58)
mri peak = 0.07680 (59)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (607 voxels, overlap=1.005)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (607 voxels, peak = 58), gca=58.0
gca peak = 0.08268 (109)
mri peak = 0.06944 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46078 voxels, overlap=0.809)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (46078 voxels, peak = 109), gca=109.0
gca peak = 0.08584 (111)
mri peak = 0.07869 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48429 voxels, overlap=0.753)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48429 voxels, peak = 111), gca=111.0
gca peak = 0.09726 (50)
mri peak = 0.05008 (50)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17863 voxels, overlap=0.990)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (17863 voxels, peak = 49), gca=49.2
gca peak = 0.10559 (53)
mri peak = 0.05013 (51)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16328 voxels, overlap=0.986)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16328 voxels, peak = 53), gca=53.0
gca peak = 0.24091 (64)
mri peak = 0.10371 (66)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (914 voxels, overlap=1.004)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (914 voxels, peak = 64), gca=64.0
gca peak = 0.16577 (65)
mri peak = 0.08705 (68)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (966 voxels, overlap=0.991)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (966 voxels, peak = 65), gca=65.0
gca peak = 0.10996 (60)
mri peak = 0.04937 (57)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (11432 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (11432 voxels, peak = 59), gca=59.1
gca peak = 0.12346 (58)
mri peak = 0.04903 (57)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (8595 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (8595 voxels, peak = 59), gca=59.4
gca peak = 0.18530 (87)
mri peak = 0.08428 (87)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5743 voxels, overlap=0.987)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5743 voxels, peak = 87), gca=86.6
gca peak = 0.14595 (89)
mri peak = 0.07910 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5090 voxels, overlap=0.996)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5090 voxels, peak = 89), gca=88.6
gca peak = 0.31177 (57)
mri peak = 0.09510 (58)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (350 voxels, overlap=1.032)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (350 voxels, peak = 57), gca=57.0
gca peak = 0.43549 (57)
mri peak = 0.08621 (57)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (247 voxels, overlap=1.032)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (247 voxels, peak = 57), gca=57.0
gca peak = 0.11773 (90)
mri peak = 0.07499 (89)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3945 voxels, overlap=0.968)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3945 voxels, peak = 90), gca=89.6
gca peak = 0.11840 (83)
mri peak = 0.07177 (87)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3802 voxels, overlap=0.968)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3802 voxels, peak = 83), gca=82.6
gca peak = 0.09485 (74)
mri peak = 0.07651 (72)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1749 voxels, overlap=1.001)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1749 voxels, peak = 74), gca=74.0
gca peak = 0.09818 (66)
mri peak = 0.07106 (75)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (1944 voxels, overlap=1.001)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (1944 voxels, peak = 65), gca=65.0
gca peak = 0.07609 (87)
mri peak = 0.06908 (87)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11648 voxels, overlap=0.797)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11648 voxels, peak = 87), gca=86.6
gca peak = 0.13957 (93)
mri peak = 0.06821 (93)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (988 voxels, overlap=0.878)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (988 voxels, peak = 94), gca=94.4
gca peak = 0.16991 (91)
mri peak = 0.07131 (90)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1269 voxels, overlap=0.921)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1269 voxels, peak = 91), gca=90.5
gca peak = 0.35640 (14)
mri peak = 0.08855 (12)
gca peak = 0.33827 ( 9)
mri peak = 0.12416 ( 8)
Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (297 voxels, overlap=0.932)
Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (297 voxels, peak =  9), gca=9.5
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 = 0.44858 (60)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.62149 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.33369 (28)
gca peak Right_Accumbens_area = 0.35953 (65)
gca peak Right_vessel = 0.57697 (60)
gca peak Right_choroid_plexus = 0.10381 (48)
gca peak Fifth_Ventricle = 0.45329 (19)
gca peak WM_hypointensities = 0.16968 (85)
gca peak non_WM_hypointensities = 0.11242 (55)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.05 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
14278 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels)
284 hippocampal voxels changed.
6 amygdala voxels changed.
pass 1: 98947 changed. image ll: -2.247, PF=1.000
pass 2: 18221 changed. image ll: -2.244, PF=1.000
pass 3: 6753 changed.
pass 4: 3188 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
auto-labeling took 18 minutes and 11 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/cc_up.lta sub011 

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/sub011/mri/transforms/cc_up.lta
reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.auto_noCCseg.mgz
reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/norm.mgz
66835 voxels in left wm, 149031 in right wm, xrange [112, 135]
searching rotation angles z=[-9  5], y=[-14  0]

searching scale 1 Z rot -9.5  
searching scale 1 Z rot -9.2  
searching scale 1 Z rot -9.0  
searching scale 1 Z rot -8.7  
searching scale 1 Z rot -8.5  
searching scale 1 Z rot -8.2  
searching scale 1 Z rot -8.0  
searching scale 1 Z rot -7.7  
searching scale 1 Z rot -7.5  
searching scale 1 Z rot -7.2  
searching scale 1 Z rot -7.0  
searching scale 1 Z rot -6.7  
searching scale 1 Z rot -6.5  
searching scale 1 Z rot -6.2  
searching scale 1 Z rot -6.0  
searching scale 1 Z rot -5.7  
searching scale 1 Z rot -5.5  
searching scale 1 Z rot -5.2  
searching scale 1 Z rot -5.0  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.5  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -4.0  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.5  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.0  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.5  
searching scale 1 Z rot 4.8  global minimum found at slice 127.0, rotations (-7.01, -2.00)
final transformation (x=127.0, yr=-7.012, zr=-1.998):
 0.992   0.035  -0.122   11.106;
-0.035   0.999   0.004   53.030;
 0.122   0.000   0.993   16.222;
 0.000   0.000   0.000   1.000;
updating x range to be [125, 130] in xformed coordinates
best xformed slice 128
cc center is found at 128 155 117
eigenvectors:
 0.000   0.000   1.000;
-0.179  -0.984   0.000;
 0.984  -0.179   0.000;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.auto.mgz...
corpus callosum matter segmentation took 3.3 minutes
#--------------------------------------
#@# Merge ASeg Thu Aug  8 17:25:25 CEST 2013

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Thu Aug  8 17:25:25 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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...
1794 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 109
gm peak at 56 (56), valley at 23 (23)
csf peak at 28, setting threshold to 46
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 58 (58), valley at 24 (24)
csf peak at 29, setting threshold to 48
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 4 minutes and 18 seconds.
#--------------------------------------------
#@# Mask BFS Thu Aug  8 17:29:44 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1798706 voxels in mask (pct= 10.72)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Thu Aug  8 17:29:46 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 +- 4.6 [80.0 --> 125.0]
GM (68.0) : 66.7 +- 9.7 [30.0 --> 96.0]
setting bottom of white matter range to 76.5
setting top of gray matter range to 86.2
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
6816 sparsely connected voxels removed...
thickening thin strands....
20 segments, 6489 filled
859 bright non-wm voxels segmented.
3959 diagonally connected voxels added...
white matter segmentation took 1.8 minutes
writing output to wm.seg.mgz...

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

preserving editing changes in input volume...
auto filling took 0.64 minutes
reading wm segmentation from wm.seg.mgz...
88 voxels added to wm to prevent paths from MTL structures to cortex
1313 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 63908 voxels turned on, 41859 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  17 found -  17 modified     |    TOTAL:  17
pass   2 (xy+):   0 found -  17 modified     |    TOTAL:  17
pass   1 (xy-):  17 found -  17 modified     |    TOTAL:  34
pass   2 (xy-):   0 found -  17 modified     |    TOTAL:  34
pass   1 (yz+):  26 found -  26 modified     |    TOTAL:  60
pass   2 (yz+):   0 found -  26 modified     |    TOTAL:  60
pass   1 (yz-):  23 found -  23 modified     |    TOTAL:  83
pass   2 (yz-):   0 found -  23 modified     |    TOTAL:  83
pass   1 (xz+):  26 found -  26 modified     |    TOTAL: 109
pass   2 (xz+):   0 found -  26 modified     |    TOTAL: 109
pass   1 (xz-):  24 found -  24 modified     |    TOTAL: 133
pass   2 (xz-):   0 found -  24 modified     |    TOTAL: 133
Iteration Number : 1
pass   1 (+++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+++):  21 found -  21 modified     |    TOTAL:  29
pass   2 (+++):   0 found -  21 modified     |    TOTAL:  29
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  39
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  39
pass   1 (+++):  19 found -  19 modified     |    TOTAL:  58
pass   2 (+++):   0 found -  19 modified     |    TOTAL:  58
Iteration Number : 1
pass   1 (++): 202 found - 202 modified     |    TOTAL: 202
pass   2 (++):   0 found - 202 modified     |    TOTAL: 202
pass   1 (+-): 157 found - 157 modified     |    TOTAL: 359
pass   2 (+-):   0 found - 157 modified     |    TOTAL: 359
pass   1 (--): 173 found - 173 modified     |    TOTAL: 532
pass   2 (--):   0 found - 173 modified     |    TOTAL: 532
pass   1 (-+): 157 found - 157 modified     |    TOTAL: 689
pass   2 (-+):   0 found - 157 modified     |    TOTAL: 689
Iteration Number : 2
pass   1 (xy+):   5 found -   5 modified     |    TOTAL:   5
pass   2 (xy+):   0 found -   5 modified     |    TOTAL:   5
pass   1 (xy-):   6 found -   6 modified     |    TOTAL:  11
pass   2 (xy-):   0 found -   6 modified     |    TOTAL:  11
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:  15
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:  15
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:  17
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:  17
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  21
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  21
pass   1 (xz-):  12 found -  12 modified     |    TOTAL:  33
pass   2 (xz-):   0 found -  12 modified     |    TOTAL:  33
Iteration Number : 2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (--):   5 found -   5 modified     |    TOTAL:   8
pass   2 (--):   0 found -   5 modified     |    TOTAL:   8
pass   1 (-+):   2 found -   2 modified     |    TOTAL:  10
pass   2 (-+):   0 found -   2 modified     |    TOTAL:  10
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   3
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   3
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 (--):   3 found -   3 modified     |    TOTAL:   3
pass   2 (--):   0 found -   3 modified     |    TOTAL:   3
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   3
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 = 933 (out of 649256: 0.143703)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Thu Aug  8 17:32:21 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.106  -0.243   0.904   22.566;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 1.032   0.030  -0.117   3.863;
 0.001   1.081   0.289  -14.239;
 0.106  -0.243   0.904   22.566;
 0.000   0.000   0.000   1.000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1559 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75)
need search nearby
using seed (127, 119, 155), TAL = (1.0, 27.0, 9.0)
talairach voxel to voxel transform
 0.957   0.001   0.123  -6.466;
 0.027   0.863  -0.272   18.327;
-0.104   0.232   1.018  -19.274;
 0.000   0.000   0.000   1.000;
segmentation indicates cc at (127,  119,  155) --> (1.0, 27.0, 9.0)
done.
writing output to filled.mgz...
filling took 0.9 minutes
talairach cc position changed to (1.00, 27.00, 9.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, 27.00, 9.00) SRC: (117.08, 81.75, 154.75)
search lh wm seed point around talairach space (-17.00, 27.00, 9.00), SRC: (151.52, 82.72, 150.99)
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 17:33:17 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

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


Iteration Number : 1
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:   8
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:   8
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   9
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   9
pass   1 (yz-):   5 found -   5 modified     |    TOTAL:  14
pass   2 (yz-):   0 found -   5 modified     |    TOTAL:  14
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:  14
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  17
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  17
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 (++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   7
pass   1 (--):   0 found -   0 modified     |    TOTAL:   7
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   8
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   8
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 = 25 (out of 315607: 0.007921)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 30: 2005 vertices, 2154 faces
slice 40: 11569 vertices, 11951 faces
slice 50: 23411 vertices, 23864 faces
slice 60: 36580 vertices, 36993 faces
slice 70: 49105 vertices, 49506 faces
slice 80: 61274 vertices, 61684 faces
slice 90: 74008 vertices, 74419 faces
slice 100: 85915 vertices, 86313 faces
slice 110: 97610 vertices, 98021 faces
slice 120: 108997 vertices, 109389 faces
slice 130: 120046 vertices, 120460 faces
slice 140: 129736 vertices, 130074 faces
slice 150: 138007 vertices, 138311 faces
slice 160: 144626 vertices, 144879 faces
slice 170: 150573 vertices, 150787 faces
slice 180: 155773 vertices, 155979 faces
slice 190: 159365 vertices, 159483 faces
slice 200: 159812 vertices, 159848 faces
slice 210: 159812 vertices, 159848 faces
slice 220: 159812 vertices, 159848 faces
slice 230: 159812 vertices, 159848 faces
slice 240: 159812 vertices, 159848 faces
slice 250: 159812 vertices, 159848 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...
   159812 voxel in cpt #1: X=-36 [v=159812,e=479544,f=319696] located at (-26.925438, -30.900133, 37.848133)
For the whole surface: X=-36 [v=159812,e=479544,f=319696]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Thu Aug  8 17:33:24 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 17:33:29 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
avg radius = 51.1 mm, total surface area = 83945 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.6 minutes
Not saving sulc

step 000: RMS=0.100 (target=0.015)   
step 005: RMS=0.073 (target=0.015)   
step 010: RMS=0.053 (target=0.015)   
step 015: RMS=0.043 (target=0.015)   
step 020: RMS=0.037 (target=0.015)   
step 025: RMS=0.031 (target=0.015)   
step 030: RMS=0.028 (target=0.015)   
step 035: RMS=0.025 (target=0.015)   
step 040: RMS=0.023 (target=0.015)   
step 045: RMS=0.022 (target=0.015)   
step 050: RMS=0.021 (target=0.015)   
step 055: RMS=0.020 (target=0.015)   
step 060: RMS=0.019 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Thu Aug  8 17:34:07 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.90 +- 0.54 (0.00-->7.98) (max @ vno 110943 --> 110944)
face area 0.02 +- 0.03 (-0.12-->0.52)
scaling brain by 0.293...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.860, avgs=0
005/300: dt: 0.9000, rms radial error=175.611, avgs=0
010/300: dt: 0.9000, rms radial error=175.075, avgs=0
015/300: dt: 0.9000, rms radial error=174.368, avgs=0
020/300: dt: 0.9000, rms radial error=173.560, avgs=0
025/300: dt: 0.9000, rms radial error=172.693, avgs=0
030/300: dt: 0.9000, rms radial error=171.793, avgs=0
035/300: dt: 0.9000, rms radial error=170.857, avgs=0
040/300: dt: 0.9000, rms radial error=169.913, avgs=0
045/300: dt: 0.9000, rms radial error=168.967, avgs=0
050/300: dt: 0.9000, rms radial error=168.021, avgs=0
055/300: dt: 0.9000, rms radial error=167.080, avgs=0
060/300: dt: 0.9000, rms radial error=166.143, avgs=0
065/300: dt: 0.9000, rms radial error=165.211, avgs=0
070/300: dt: 0.9000, rms radial error=164.284, avgs=0
075/300: dt: 0.9000, rms radial error=163.362, avgs=0
080/300: dt: 0.9000, rms radial error=162.445, avgs=0
085/300: dt: 0.9000, rms radial error=161.533, avgs=0
090/300: dt: 0.9000, rms radial error=160.626, avgs=0
095/300: dt: 0.9000, rms radial error=159.723, avgs=0
100/300: dt: 0.9000, rms radial error=158.826, avgs=0
105/300: dt: 0.9000, rms radial error=157.933, avgs=0
110/300: dt: 0.9000, rms radial error=157.045, avgs=0
115/300: dt: 0.9000, rms radial error=156.162, avgs=0
120/300: dt: 0.9000, rms radial error=155.283, avgs=0
125/300: dt: 0.9000, rms radial error=154.410, avgs=0
130/300: dt: 0.9000, rms radial error=153.541, avgs=0
135/300: dt: 0.9000, rms radial error=152.677, avgs=0
140/300: dt: 0.9000, rms radial error=151.818, avgs=0
145/300: dt: 0.9000, rms radial error=150.963, avgs=0
150/300: dt: 0.9000, rms radial error=150.113, avgs=0
155/300: dt: 0.9000, rms radial error=149.268, avgs=0
160/300: dt: 0.9000, rms radial error=148.427, avgs=0
165/300: dt: 0.9000, rms radial error=147.591, avgs=0
170/300: dt: 0.9000, rms radial error=146.760, avgs=0
175/300: dt: 0.9000, rms radial error=145.934, avgs=0
180/300: dt: 0.9000, rms radial error=145.112, avgs=0
185/300: dt: 0.9000, rms radial error=144.294, avgs=0
190/300: dt: 0.9000, rms radial error=143.481, avgs=0
195/300: dt: 0.9000, rms radial error=142.673, avgs=0
200/300: dt: 0.9000, rms radial error=141.869, avgs=0
205/300: dt: 0.9000, rms radial error=141.069, avgs=0
210/300: dt: 0.9000, rms radial error=140.274, avgs=0
215/300: dt: 0.9000, rms radial error=139.483, avgs=0
220/300: dt: 0.9000, rms radial error=138.696, avgs=0
225/300: dt: 0.9000, rms radial error=137.914, avgs=0
230/300: dt: 0.9000, rms radial error=137.136, avgs=0
235/300: dt: 0.9000, rms radial error=136.362, avgs=0
240/300: dt: 0.9000, rms radial error=135.593, avgs=0
245/300: dt: 0.9000, rms radial error=134.828, avgs=0
250/300: dt: 0.9000, rms radial error=134.067, avgs=0
255/300: dt: 0.9000, rms radial error=133.311, avgs=0
260/300: dt: 0.9000, rms radial error=132.560, avgs=0
265/300: dt: 0.9000, rms radial error=131.813, avgs=0
270/300: dt: 0.9000, rms radial error=131.070, avgs=0
275/300: dt: 0.9000, rms radial error=130.332, avgs=0
280/300: dt: 0.9000, rms radial error=129.597, avgs=0
285/300: dt: 0.9000, rms radial error=128.867, avgs=0
290/300: dt: 0.9000, rms radial error=128.141, avgs=0
295/300: dt: 0.9000, rms radial error=127.419, avgs=0
300/300: dt: 0.9000, rms radial error=126.701, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19093.60
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
epoch 2 (K=40.0), pass 1, starting sse = 3373.40
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
epoch 3 (K=160.0), pass 1, starting sse = 366.48
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.03/10 = 0.00288
epoch 4 (K=640.0), pass 1, starting sse = 22.40
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/10 = 0.00211
final writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.09 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology lh Thu Aug  8 17:39:25 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/sub011/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub011 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=-36 (nv=159812, nf=319696, ne=479544, g=19)
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...
2626 ambiguous faces found in tessellation
segmenting defects...
25 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 18 into 15
24 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7532  (-4.8766)
      -vertex     loglikelihood: -6.6481  (-3.3240)
      -normal dot loglikelihood: -3.5987  (-3.5987)
      -quad curv  loglikelihood: -6.5286  (-3.2643)
      Total Loglikelihood : -26.5286

CORRECTING DEFECT 0 (vertices=5, convex hull=25)
After retessellation of defect 0, euler #=-22 (158178,473831,315631) : difference with theory (-21) = 1 

CORRECTING DEFECT 1 (vertices=144, convex hull=93)
After retessellation of defect 1, euler #=-21 (158217,473990,315752) : difference with theory (-20) = 1 

CORRECTING DEFECT 2 (vertices=184, convex hull=105)
After retessellation of defect 2, euler #=-20 (158243,474115,315852) : difference with theory (-19) = 1 

CORRECTING DEFECT 3 (vertices=53, convex hull=79)
After retessellation of defect 3, euler #=-19 (158269,474226,315938) : difference with theory (-18) = 1 

CORRECTING DEFECT 4 (vertices=45, convex hull=66)
After retessellation of defect 4, euler #=-18 (158286,474301,315997) : difference with theory (-17) = 1 

CORRECTING DEFECT 5 (vertices=61, convex hull=63)
After retessellation of defect 5, euler #=-17 (158311,474400,316072) : difference with theory (-16) = 1 

CORRECTING DEFECT 6 (vertices=11, convex hull=19)
After retessellation of defect 6, euler #=-16 (158312,474409,316081) : difference with theory (-15) = 1 

CORRECTING DEFECT 7 (vertices=341, convex hull=252)
normal vector of length zero at vertex 158902 with 4 faces
normal vector of length zero at vertex 158902 with 4 faces
normal vector of length zero at vertex 158836 with 3 faces
normal vector of length zero at vertex 158836 with 3 faces
normal vector of length zero at vertex 158836 with 3 faces
After retessellation of defect 7, euler #=-15 (158325,474572,316232) : difference with theory (-14) = 1 

CORRECTING DEFECT 8 (vertices=42, convex hull=40)
After retessellation of defect 8, euler #=-14 (158340,474632,316278) : difference with theory (-13) = 1 

CORRECTING DEFECT 9 (vertices=12, convex hull=22)
After retessellation of defect 9, euler #=-13 (158341,474640,316286) : difference with theory (-12) = 1 

CORRECTING DEFECT 10 (vertices=155, convex hull=185)
After retessellation of defect 10, euler #=-12 (158379,474850,316459) : difference with theory (-11) = 1 

CORRECTING DEFECT 11 (vertices=52, convex hull=45)
After retessellation of defect 11, euler #=-11 (158384,474887,316492) : difference with theory (-10) = 1 

CORRECTING DEFECT 12 (vertices=10, convex hull=27)
After retessellation of defect 12, euler #=-10 (158387,474903,316506) : difference with theory (-9) = 1 

CORRECTING DEFECT 13 (vertices=25, convex hull=59)
After retessellation of defect 13, euler #=-9 (158400,474966,316557) : difference with theory (-8) = 1 

CORRECTING DEFECT 14 (vertices=29, convex hull=57)
After retessellation of defect 14, euler #=-8 (158410,475019,316601) : difference with theory (-7) = 1 

CORRECTING DEFECT 15 (vertices=150, convex hull=121)
After retessellation of defect 15, euler #=-6 (158435,475150,316709) : difference with theory (-6) = 0 

CORRECTING DEFECT 16 (vertices=143, convex hull=64)
After retessellation of defect 16, euler #=-5 (158446,475206,316755) : difference with theory (-5) = 0 

CORRECTING DEFECT 17 (vertices=10, convex hull=20)
After retessellation of defect 17, euler #=-4 (158450,475222,316768) : difference with theory (-4) = 0 

CORRECTING DEFECT 18 (vertices=22, convex hull=55)
After retessellation of defect 18, euler #=-3 (158460,475273,316810) : difference with theory (-3) = 0 

CORRECTING DEFECT 19 (vertices=9, convex hull=15)
After retessellation of defect 19, euler #=-2 (158460,475274,316812) : difference with theory (-2) = 0 

CORRECTING DEFECT 20 (vertices=42, convex hull=55)
After retessellation of defect 20, euler #=-1 (158463,475307,316843) : difference with theory (-1) = 0 

CORRECTING DEFECT 21 (vertices=40, convex hull=79)
After retessellation of defect 21, euler #=0 (158473,475369,316896) : difference with theory (0) = 0 

CORRECTING DEFECT 22 (vertices=17, convex hull=44)
After retessellation of defect 22, euler #=1 (158481,475409,316929) : difference with theory (1) = 0 

CORRECTING DEFECT 23 (vertices=31, convex hull=74)
After retessellation of defect 23, euler #=2 (158499,475491,316994) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.14-->8.09) (max @ vno 39825 --> 48461)
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 (0.14-->8.09) (max @ vno 39825 --> 48461)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
115 mutations (36.9%), 197 crossovers (63.1%), 265 vertices were eliminated
building final representation...
1313 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=158499, nf=316994, ne=475491, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 30.7 minutes
0 defective edges
removing intersecting faces
000: 217 intersecting
001: 2 intersecting

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 158499 - 475491 + 316994 = 2 --> 0 holes
      F =2V-4:          316994 = 316998-4 (0)
      2E=3F:            950982 = 950982 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 15 intersecting
001: 2 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make White Surf lh Thu Aug  8 18:10:15 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub011 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/sub011/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
19648 bright wm thresholded.
948 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.orig...
computing class statistics...
border white:    292650 voxels (1.74%)
border gray      329335 voxels (1.96%)
WM (92.0): 93.5 +- 9.7 [70.0 --> 110.0]
GM (76.0) : 74.2 +- 13.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.9 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 33.8 (was 40)
setting MAX_GRAY to 94.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.6 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.04-->3.88) (max @ vno 158222 --> 158228)
face area 0.28 +- 0.12 (0.00-->2.78)
mean absolute distance = 0.66 +- 0.80
3670 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104,    GM=60
mean inside = 93.0, mean outside = 69.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=73.8, 21 (21) missing vertices, mean dist 0.3 [0.5 (%33.0)->0.7 (%67.0))]
%71 local maxima, %24 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 (0.10-->4.35) (max @ vno 120419 --> 121336)
face area 0.28 +- 0.13 (0.00-->2.15)
mean absolute distance = 0.30 +- 0.49
2711 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8318902.5, rms=13.42
001: dt: 0.5000, sse=8307937.0, rms=9.642 (0.000%)
002: dt: 0.5000, sse=8591579.0, rms=7.447 (0.000%)
003: dt: 0.5000, sse=8766030.0, rms=6.072 (0.000%)
004: dt: 0.5000, sse=9069262.0, rms=5.281 (0.000%)
005: dt: 0.5000, sse=9156258.0, rms=4.856 (0.000%)
006: dt: 0.5000, sse=9343889.0, rms=4.639 (0.000%)
007: dt: 0.5000, sse=9309365.0, rms=4.519 (0.000%)
008: dt: 0.5000, sse=9397955.0, rms=4.439 (0.000%)
009: dt: 0.5000, sse=9293000.0, rms=4.388 (0.000%)
rms = 4.34, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9352230.0, rms=4.341 (0.000%)
011: dt: 0.2500, sse=5813038.5, rms=3.017 (0.000%)
012: dt: 0.2500, sse=5305349.0, rms=2.553 (0.000%)
013: dt: 0.2500, sse=4999034.5, rms=2.457 (0.000%)
014: dt: 0.2500, sse=4903991.5, rms=2.364 (0.000%)
rms = 2.34, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4803816.5, rms=2.336 (0.000%)
016: dt: 0.1250, sse=4559721.0, rms=2.092 (0.000%)
rms = 2.06, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4510840.5, rms=2.059 (0.000%)
positioning took 2.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=77.6, 38 (6) missing vertices, mean dist -0.2 [0.3 (%74.0)->0.2 (%26.0))]
%79 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 0.91 +- 0.25 (0.04-->3.86) (max @ vno 76660 --> 75430)
face area 0.35 +- 0.16 (0.00-->2.74)
mean absolute distance = 0.23 +- 0.34
3623 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5472760.5, rms=5.60
018: dt: 0.5000, sse=5867451.0, rms=3.879 (0.000%)
rms = 4.33, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=5308465.5, rms=2.790 (0.000%)
020: dt: 0.2500, sse=5096968.0, rms=2.229 (0.000%)
021: dt: 0.2500, sse=5010209.5, rms=1.895 (0.000%)
rms = 1.86, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=4981557.0, rms=1.857 (0.000%)
023: dt: 0.1250, sse=4819734.5, rms=1.658 (0.000%)
rms = 1.63, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=4769812.5, rms=1.629 (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 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=80.8, 21 (2) missing vertices, mean dist -0.1 [0.2 (%74.9)->0.2 (%25.1))]
%87 local maxima, % 8 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 (0.07-->4.03) (max @ vno 76660 --> 75430)
face area 0.34 +- 0.16 (0.00-->2.83)
mean absolute distance = 0.18 +- 0.27
3431 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5183580.5, rms=4.14
025: dt: 0.5000, sse=5573927.5, rms=3.929 (0.000%)
rms = 4.16, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=5074547.0, rms=2.517 (0.000%)
027: dt: 0.2500, sse=4948327.0, rms=2.015 (0.000%)
028: dt: 0.2500, sse=4992215.0, rms=1.684 (0.000%)
rms = 1.72, time step reduction 2 of 3 to 0.125...
029: dt: 0.1250, sse=4927405.5, rms=1.571 (0.000%)
030: dt: 0.1250, sse=4839932.5, rms=1.416 (0.000%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=4800880.5, rms=1.403 (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 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=81.9, 21 (0) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))]
%89 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/sub011/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=4836710.5, rms=1.89
rms = 2.65, time step reduction 1 of 3 to 0.250...
032: dt: 0.2500, sse=4933057.0, rms=1.250 (0.000%)
033: dt: 0.2500, sse=5104526.5, rms=1.050 (0.000%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
rms = 1.04, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=5106081.0, rms=1.041 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
generating cortex label...
12 non-cortical segments detected
only using segment with 2427 vertices
erasing segment 1 (vno[0] = 95387)
erasing segment 2 (vno[0] = 101027)
erasing segment 3 (vno[0] = 106685)
erasing segment 4 (vno[0] = 109983)
erasing segment 5 (vno[0] = 110103)
erasing segment 6 (vno[0] = 115282)
erasing segment 7 (vno[0] = 119443)
erasing segment 8 (vno[0] = 122296)
erasing segment 9 (vno[0] = 125224)
erasing segment 10 (vno[0] = 126154)
erasing segment 11 (vno[0] = 127067)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.area
vertex spacing 0.90 +- 0.25 (0.06-->4.35) (max @ vno 121336 --> 120419)
face area 0.34 +- 0.16 (0.00-->2.87)
refinement took 7.7 minutes
#--------------------------------------------
#@# Smooth2 lh Thu Aug  8 18:17:56 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 18:18:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

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

avg radius = 51.4 mm, total surface area = 97210 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=0.080 (target=0.015)   
step 010: RMS=0.058 (target=0.015)   
step 015: RMS=0.047 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.031 (target=0.015)   
step 030: RMS=0.026 (target=0.015)   
step 035: RMS=0.022 (target=0.015)   
step 040: RMS=0.019 (target=0.015)   
step 045: RMS=0.017 (target=0.015)   
step 050: RMS=0.016 (target=0.015)   
inflation complete.
inflation took 0.6 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
207 vertices thresholded to be in k1 ~ [-0.65 0.43], k2 ~ [-0.19 0.17]
total integrated curvature = 0.492*4pi (6.186) --> 1 handles
ICI = 1.7, FI = 11.5, variation=194.498
173 vertices thresholded to be in [-0.06 0.01]
writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
128 vertices thresholded to be in [-0.21 0.15]
done.
writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.023
done.

#-----------------------------------------
#@# Curvature Stats lh Thu Aug  8 18:20:35 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub011 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       [ sub011/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                      [ 299 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.455109
WARN:    S explicit min:                          0.000000	vertex = 208
#--------------------------------------------
#@# Sphere lh Thu Aug  8 18:20:40 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 0.272...
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 %20.25
pass 1: epoch 2 of 3 starting distance error %20.17
unfolding complete - removing small folds...
starting distance error %20.06
removing remaining folds...
final distance error %20.07
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.09 hours
#--------------------------------------------
#@# Surf Reg lh Thu Aug  8 19:26:18 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 0.577
curvature mean = 0.049, std = 0.947
curvature mean = 0.023, std = 0.838
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 374760.5, tmin=1.2742
  d=32.00 min @ (8.00, 8.00, -8.00) sse = 301320.9, tmin=2.6405
  d=16.00 min @ (0.00, -4.00, 4.00) sse = 270303.3, tmin=4.1247
  d=8.00 min @ (0.00, 0.00, -2.00) sse = 265071.2, tmin=5.6329
  d=4.00 min @ (-1.00, 0.00, 1.00) sse = 264140.4, tmin=7.1627
  d=2.00 min @ (0.50, 0.50, -0.50) sse = 263578.5, tmin=8.7226
  d=1.00 min @ (-0.25, -0.25, 0.00) sse = 263508.4, tmin=10.2998
  d=0.50 min @ (0.00, 0.12, 0.00) sse = 263492.1, tmin=11.8797
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  11.88 min
curvature mean = 0.024, std = 0.942
curvature mean = 0.012, std = 0.926
curvature mean = 0.024, std = 0.954
curvature mean = 0.006, std = 0.965
curvature mean = 0.021, std = 0.952
curvature mean = 0.002, std = 0.984
2 Reading smoothwm
curvature mean = -0.022, std = 0.287
curvature mean = 0.005, std = 0.066
curvature mean = 0.071, std = 0.325
curvature mean = 0.005, std = 0.078
curvature mean = 0.037, std = 0.522
curvature mean = 0.005, std = 0.083
curvature mean = 0.020, std = 0.673
curvature mean = 0.005, std = 0.085
curvature mean = 0.005, std = 0.791
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
#--------------------------------------------
#@# Jacobian white lh Thu Aug  8 20:03:11 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 20:03:14 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 20:03:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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...
1224 labels changed using aseg
relabeling using gibbs priors...
000:   3407 changed, 158499 examined...
001:    794 changed, 14561 examined...
002:    187 changed, 4441 examined...
003:     68 changed, 1119 examined...
004:     31 changed, 394 examined...
005:     15 changed, 176 examined...
006:      6 changed, 96 examined...
007:      4 changed, 32 examined...
008:      3 changed, 24 examined...
009:      1 changed, 15 examined...
010:      1 changed, 7 examined...
011:      1 changed, 7 examined...
012:      2 changed, 7 examined...
013:      1 changed, 10 examined...
014:      2 changed, 9 examined...
015:      0 changed, 6 examined...
278 labels changed using aseg
000: 121 total segments, 75 labels (278 vertices) changed
001: 46 total segments, 1 labels (2 vertices) changed
002: 45 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 64 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1053 vertices marked for relabeling...
1053 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 1 minutes and 10 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Thu Aug  8 20:04:26 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub011 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/sub011/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
19648 bright wm thresholded.
948 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.orig...
computing class statistics...
border white:    292650 voxels (1.74%)
border gray      329335 voxels (1.96%)
WM (92.0): 93.5 +- 9.7 [70.0 --> 110.0]
GM (76.0) : 74.2 +- 13.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.9 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 33.8 (was 40)
setting MAX_GRAY to 94.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.6 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104,    GM=60
mean inside = 93.0, mean outside = 69.3
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/sub011/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.04-->3.88) (max @ vno 158222 --> 158228)
face area 0.28 +- 0.12 (0.00-->2.78)
mean absolute distance = 0.66 +- 0.81
3708 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 0.00% unknown
deleting segment 3 with 12 points - only 0.00% unknown
deleting segment 4 with 16 points - only 0.00% unknown
deleting segment 5 with 816 points - only 0.00% unknown
deleting segment 7 with 27 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
deleting segment 12 with 35 points - only 0.00% unknown
deleting segment 13 with 7 points - only 0.00% unknown
mean border=73.8, 21 (21) missing vertices, mean dist 0.3 [0.5 (%33.0)->0.7 (%67.0))]
%71 local maxima, %24 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 (0.10-->4.35) (max @ vno 120419 --> 121336)
face area 0.28 +- 0.13 (0.00-->2.15)
mean absolute distance = 0.30 +- 0.49
2735 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8344084.5, rms=13.40
001: dt: 0.5000, sse=8342708.5, rms=9.623 (0.000%)
002: dt: 0.5000, sse=8628524.0, rms=7.433 (0.000%)
003: dt: 0.5000, sse=8807791.0, rms=6.061 (0.000%)
004: dt: 0.5000, sse=9112575.0, rms=5.273 (0.000%)
005: dt: 0.5000, sse=9201597.0, rms=4.849 (0.000%)
006: dt: 0.5000, sse=9394261.0, rms=4.633 (0.000%)
007: dt: 0.5000, sse=9357459.0, rms=4.513 (0.000%)
008: dt: 0.5000, sse=9448341.0, rms=4.433 (0.000%)
009: dt: 0.5000, sse=9340989.0, rms=4.383 (0.000%)
rms = 4.34, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9404186.0, rms=4.337 (0.000%)
011: dt: 0.2500, sse=5838742.0, rms=3.013 (0.000%)
012: dt: 0.2500, sse=5329213.5, rms=2.550 (0.000%)
013: dt: 0.2500, sse=5020564.5, rms=2.454 (0.000%)
014: dt: 0.2500, sse=4924177.5, rms=2.361 (0.000%)
rms = 2.33, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4825814.0, rms=2.334 (0.000%)
016: dt: 0.1250, sse=4581110.0, rms=2.090 (0.000%)
rms = 2.06, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4532082.0, rms=2.057 (0.000%)
positioning took 2.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
deleting segment 3 with 13 points - only 0.00% unknown
deleting segment 5 with 659 points - only 0.00% unknown
deleting segment 7 with 7 points - only 42.86% unknown
deleting segment 8 with 37 points - only 0.00% unknown
deleting segment 10 with 24 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 6 points - only 0.00% unknown
deleting segment 13 with 6 points - only 0.00% unknown
deleting segment 15 with 13 points - only 0.00% unknown
deleting segment 16 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 17 with 3 points - only 0.00% unknown
deleting segment 18 with 25 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 19 with 2 points - only 0.00% unknown
deleting segment 20 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 21 with 1 points - only 0.00% unknown
mean border=77.5, 34 (6) missing vertices, mean dist -0.2 [0.3 (%74.0)->0.2 (%26.0))]
%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 0.91 +- 0.25 (0.04-->3.86) (max @ vno 76660 --> 75430)
face area 0.35 +- 0.16 (0.00-->2.74)
mean absolute distance = 0.23 +- 0.34
3649 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5499196.5, rms=5.59
018: dt: 0.5000, sse=5902466.5, rms=3.872 (0.000%)
rms = 4.32, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=5341033.5, rms=2.785 (0.000%)
020: dt: 0.2500, sse=5125767.0, rms=2.226 (0.000%)
021: dt: 0.2500, sse=5039339.5, rms=1.892 (0.000%)
rms = 1.86, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=5010136.5, rms=1.856 (0.000%)
023: dt: 0.1250, sse=4847970.0, rms=1.657 (0.000%)
rms = 1.63, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=4798316.0, rms=1.629 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
deleting segment 3 with 18 points - only 0.00% unknown
deleting segment 4 with 701 points - only 0.00% unknown
deleting segment 5 with 14 points - only 50.00% unknown
deleting segment 6 with 37 points - only 0.00% unknown
deleting segment 7 with 24 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 12 with 13 points - only 0.00% unknown
deleting segment 13 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
deleting segment 15 with 26 points - only 0.00% unknown
deleting segment 16 with 5 points - only 0.00% unknown
deleting segment 17 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 18 with 1 points - only 0.00% unknown
mean border=80.8, 18 (2) missing vertices, mean dist -0.1 [0.2 (%74.8)->0.2 (%25.2))]
%87 local maxima, % 8 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 (0.09-->4.03) (max @ vno 76660 --> 75430)
face area 0.34 +- 0.16 (0.00-->2.83)
mean absolute distance = 0.18 +- 0.27
3447 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5213834.5, rms=4.13
025: dt: 0.5000, sse=5606552.5, rms=3.922 (0.000%)
rms = 4.15, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=5106193.5, rms=2.513 (0.000%)
027: dt: 0.2500, sse=4981098.5, rms=2.011 (0.000%)
028: dt: 0.2500, sse=5025713.0, rms=1.682 (0.000%)
rms = 1.72, time step reduction 2 of 3 to 0.125...
029: dt: 0.1250, sse=4960682.0, rms=1.570 (0.000%)
030: dt: 0.1250, sse=4872179.5, rms=1.415 (0.000%)
rms = 1.40, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=4832665.0, rms=1.402 (0.000%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 9 points - only 0.00% unknown
deleting segment 3 with 16 points - only 0.00% unknown
deleting segment 4 with 695 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 6 with 7 points - only 42.86% unknown
deleting segment 7 with 38 points - only 0.00% unknown
deleting segment 8 with 28 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 6 points - only 0.00% unknown
deleting segment 14 with 11 points - only 0.00% unknown
deleting segment 15 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 16 with 3 points - only 0.00% unknown
deleting segment 17 with 39 points - only 0.00% unknown
deleting segment 18 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 19 with 1 points - only 0.00% unknown
mean border=81.9, 16 (0) missing vertices, mean dist -0.0 [0.2 (%58.8)->0.2 (%41.2))]
%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
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=4868709.0, rms=1.89
rms = 2.65, time step reduction 1 of 3 to 0.250...
032: dt: 0.2500, sse=4968167.5, rms=1.250 (0.000%)
033: dt: 0.2500, sse=5143750.5, rms=1.050 (0.000%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
rms = 1.04, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=5145442.5, rms=1.041 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
smoothing surface for 5 iterations...
mean border=49.7, 30 (30) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.2 (%100.0))]
%15 local maxima, %55 large gradients and %25 min vals, 2003 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=33518586.0, rms=31.61
001: dt: 0.5000, sse=24194100.0, rms=26.277 (0.000%)
002: dt: 0.5000, sse=17649570.0, rms=21.793 (0.000%)
003: dt: 0.5000, sse=13347920.0, rms=18.130 (0.000%)
004: dt: 0.5000, sse=10711668.0, rms=15.159 (0.000%)
005: dt: 0.5000, sse=9134480.0, rms=12.780 (0.000%)
006: dt: 0.5000, sse=8178029.5, rms=10.891 (0.000%)
007: dt: 0.5000, sse=7607395.0, rms=9.296 (0.000%)
008: dt: 0.5000, sse=7317464.5, rms=7.938 (0.000%)
009: dt: 0.5000, sse=7206807.0, rms=6.790 (0.000%)
010: dt: 0.5000, sse=7238428.5, rms=5.880 (0.000%)
011: dt: 0.5000, sse=7345923.5, rms=5.188 (0.000%)
012: dt: 0.5000, sse=7461944.5, rms=4.712 (0.000%)
013: dt: 0.5000, sse=7658667.5, rms=4.398 (0.000%)
014: dt: 0.5000, sse=7777544.5, rms=4.209 (0.000%)
015: dt: 0.5000, sse=7851391.5, rms=4.070 (0.000%)
016: dt: 0.5000, sse=7894189.5, rms=3.977 (0.000%)
017: dt: 0.5000, sse=7915245.5, rms=3.912 (0.000%)
rms = 3.87, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=7919688.5, rms=3.868 (0.000%)
019: dt: 0.2500, sse=5621893.0, rms=3.208 (0.000%)
020: dt: 0.2500, sse=5419712.0, rms=3.031 (0.000%)
rms = 3.01, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=5272483.0, rms=3.008 (0.000%)
022: dt: 0.1250, sse=5063806.5, rms=2.909 (0.000%)
rms = 2.90, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=5032504.5, rms=2.896 (0.000%)
positioning took 3.2 minutes
mean border=47.5, 849 (2) missing vertices, mean dist 0.2 [0.2 (%50.5)->0.6 (%49.5))]
%32 local maxima, %42 large gradients and %21 min vals, 675 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=5802002.5, rms=5.03
024: dt: 0.5000, sse=6088457.5, rms=4.199 (0.000%)
025: dt: 0.5000, sse=7779875.5, rms=4.069 (0.000%)
026: dt: 0.5000, sse=7626329.0, rms=4.004 (0.000%)
rms = 3.99, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=8631633.0, rms=3.995 (0.000%)
028: dt: 0.2500, sse=6093355.0, rms=3.143 (0.000%)
029: dt: 0.2500, sse=6053249.5, rms=2.899 (0.000%)
rms = 2.88, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=5870870.0, rms=2.876 (0.000%)
031: dt: 0.1250, sse=5674088.5, rms=2.735 (0.000%)
rms = 2.71, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=5644993.5, rms=2.714 (0.000%)
positioning took 1.2 minutes
mean border=45.3, 1140 (2) missing vertices, mean dist 0.1 [0.2 (%40.2)->0.4 (%59.8))]
%52 local maxima, %23 large gradients and %20 min vals, 874 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=5974194.5, rms=4.13
033: dt: 0.5000, sse=6191870.0, rms=3.798 (0.000%)
rms = 3.89, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=5836179.5, rms=3.152 (0.000%)
035: dt: 0.2500, sse=6059987.5, rms=2.858 (0.000%)
036: dt: 0.2500, sse=5971970.0, rms=2.794 (0.000%)
rms = 2.76, time step reduction 2 of 3 to 0.125...
037: dt: 0.2500, sse=6033795.0, rms=2.761 (0.000%)
038: dt: 0.1250, sse=5836756.5, rms=2.639 (0.000%)
rms = 2.62, time step reduction 3 of 3 to 0.062...
039: dt: 0.1250, sse=5823511.5, rms=2.620 (0.000%)
positioning took 1.1 minutes
mean border=44.1, 2188 (2) missing vertices, mean dist 0.1 [0.2 (%45.0)->0.3 (%55.0))]
%57 local maxima, %17 large gradients and %20 min vals, 629 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/sub011/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=5895207.0, rms=3.03
rms = 3.50, time step reduction 1 of 3 to 0.250...
040: dt: 0.2500, sse=5738429.0, rms=2.755 (0.000%)
041: dt: 0.2500, sse=5903055.5, rms=2.638 (0.000%)
rms = 2.60, time step reduction 2 of 3 to 0.125...
042: dt: 0.2500, sse=5993334.0, rms=2.605 (0.000%)
043: dt: 0.1250, sse=5885290.5, rms=2.505 (0.000%)
rms = 2.49, time step reduction 3 of 3 to 0.062...
044: dt: 0.1250, sse=5896572.0, rms=2.490 (0.000%)
positioning took 0.9 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.area.pial
vertex spacing 1.01 +- 0.42 (0.05-->8.06) (max @ vno 124187 --> 123190)
face area 0.41 +- 0.30 (0.00-->6.08)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 158499 vertices processed
25000 of 158499 vertices processed
50000 of 158499 vertices processed
75000 of 158499 vertices processed
100000 of 158499 vertices processed
125000 of 158499 vertices processed
150000 of 158499 vertices processed
0 of 158499 vertices processed
25000 of 158499 vertices processed
50000 of 158499 vertices processed
75000 of 158499 vertices processed
100000 of 158499 vertices processed
125000 of 158499 vertices processed
150000 of 158499 vertices processed
thickness calculation complete, 312:719 truncations.
34945 vertices at 0 distance
111349 vertices at 1 distance
101295 vertices at 2 distance
40385 vertices at 3 distance
10937 vertices at 4 distance
2991 vertices at 5 distance
915 vertices at 6 distance
319 vertices at 7 distance
111 vertices at 8 distance
44 vertices at 9 distance
33 vertices at 10 distance
22 vertices at 11 distance
21 vertices at 12 distance
12 vertices at 13 distance
12 vertices at 14 distance
9 vertices at 15 distance
9 vertices at 16 distance
3 vertices at 17 distance
1 vertices at 18 distance
3 vertices at 19 distance
6 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.thickness
positioning took 15.6 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 20:20:03 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 20:20:04 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 pctsurfcon --s sub011 --lh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts/pctsurfcon.log
Thu Aug  8 20:20:04 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake6 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/sub011/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.wm.mgh --regheader sub011 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 123232
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.wm.mgh
Dim: 158499 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.gm.mgh --projfrac 0.3 --regheader sub011 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 141256
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.gm.mgh
Dim: 158499 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.9432/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/lh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.w-g.pct.mgh --annot sub011 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/lh.w-g.pct.mgh --annot sub011 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname snake6
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/sub011/surf/lh.w-g.pct.mgh
Vertex Area is 0.6705 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   1000                            unknown       0       0.000
  1   1001                           bankssts    1878    1289.351
  2   1002            caudalanteriorcingulate    1043     700.011
  3   1003                caudalmiddlefrontal    4455    3031.344
  4   1004                     corpuscallosum       0       0.000
  5   1005                             cuneus    2390    1594.805
  6   1006                         entorhinal     561     401.584
  7   1007                           fusiform    5670    3840.466
  8   1008                   inferiorparietal    8553    5876.876
  9   1009                   inferiortemporal    5958    4031.534
 10   1010                   isthmuscingulate    1768    1187.077
 11   1011                   lateraloccipital    9014    5842.801
 12   1012               lateralorbitofrontal    4512    2979.639
 13   1013                            lingual    4734    3210.272
 14   1014                medialorbitofrontal    2356    1614.399
 15   1015                     middletemporal    5337    3682.813
 16   1016                    parahippocampal    1069     690.702
 17   1017                        paracentral    2077    1311.524
 18   1018                    parsopercularis    2582    1737.566
 19   1019                      parsorbitalis    1203     817.763
 20   1020                   parstriangularis    2302    1579.925
 21   1021                      pericalcarine    2110    1399.025
 22   1022                        postcentral    8318    5502.695
 23   1023                 posteriorcingulate    1974    1318.320
 24   1024                         precentral    8922    5912.194
 25   1025                          precuneus    6914    4614.999
 26   1026           rostralanteriorcingulate    1620    1084.376
 27   1027               rostralmiddlefrontal   10552    7285.981
 28   1028                    superiorfrontal   13157    8934.941
 29   1029                   superiorparietal   10453    6834.004
 30   1030                   superiortemporal    6228    4148.080
 31   1031                      supramarginal    5888    4015.426
 32   1032                        frontalpole     393     264.547
 33   1033                       temporalpole     614     443.185
 34   1034                 transversetemporal     786     486.986
 35   1035                             insula    3500    2312.378

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats lh Thu Aug  8 20:20:19 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

 1878   1289   3342  2.643 0.393     0.114     0.027       14     2.1  bankssts
 1043    700   1702  2.365 0.516     0.146     0.033       20     1.4  caudalanteriorcingulate
 4455   3031   7998  2.379 0.499     0.131     0.037       56     6.6  caudalmiddlefrontal
 2390   1595   3154  1.755 0.380     0.169     0.064       48     6.2  cuneus
  561    402   1674  3.359 0.921     0.147     0.059        6     1.2  entorhinal
 5670   3840  11847  2.693 0.598     0.154     0.066      123    12.8  fusiform
 8553   5877  15416  2.363 0.466     0.141     0.052      139    15.8  inferiorparietal
 5958   4032  11764  2.553 0.600     0.147     0.062      122    14.5  inferiortemporal
 1768   1187   3317  2.664 0.689     0.168     0.066       42     4.6  isthmuscingulate
 9014   5843  12474  1.940 0.433     0.149     0.050      135    18.5  lateraloccipital
 4512   2980   8593  2.492 0.650     0.164     0.074      113    13.0  lateralorbitofrontal
 4734   3210   7371  2.095 0.541     0.164     0.085       95    13.2  lingual
 2356   1614   4165  2.117 0.613     0.170     0.124       88     7.7  medialorbitofrontal
 5337   3683  12426  2.763 0.608     0.153     0.051      102    11.0  middletemporal
 1069    691   2202  2.790 0.787     0.126     0.044       22     2.1  parahippocampal
 2077   1312   3264  2.330 0.468     0.133     0.052       30     3.6  paracentral
 2582   1738   4938  2.610 0.483     0.140     0.046       47     4.6  parsopercularis
 1203    818   2875  2.587 0.563     0.159     0.060       27     2.7  parsorbitalis
 2302   1580   4525  2.454 0.554     0.147     0.048       38     4.4  parstriangularis
 2110   1399   2129  1.665 0.435     0.165     0.079       37     5.7  pericalcarine
 8318   5503  11729  1.906 0.612     0.138     0.046      121    15.1  postcentral
 1974   1318   3630  2.564 0.588     0.164     0.067       49     5.3  posteriorcingulate
 8922   5912  15907  2.420 0.562     0.128     0.040      110    14.7  precentral
 6914   4615  12540  2.491 0.519     0.147     0.057      125    16.0  precuneus
 1620   1084   3426  2.590 0.653     0.172     0.138       49     5.6  rostralanteriorcingulate
10552   7286  18991  2.203 0.535     0.167     0.071      272    30.5  rostralmiddlefrontal
13157   8935  26591  2.563 0.585     0.140     0.049      248    25.4  superiorfrontal
10453   6834  16197  2.141 0.493     0.132     0.040      131    16.9  superiorparietal
 6228   4148  12791  2.738 0.600     0.125     0.044       84    10.8  superiortemporal
 5888   4015  11164  2.513 0.504     0.143     0.045       93    10.3  supramarginal
  393    265    920  2.552 0.477     0.238     0.153       21     2.1  frontalpole
  614    443   2173  3.580 0.760     0.161     0.120       13     1.9  temporalpole
  786    487   1265  2.298 0.365     0.128     0.042        9     1.4  transversetemporal
 3500   2312   7472  2.982 0.853     0.128     0.076       62     7.6  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Thu Aug  8 20:20:42 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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...
61 labels changed using aseg
relabeling using gibbs priors...
000:  11151 changed, 158499 examined...
001:   2649 changed, 42437 examined...
002:    784 changed, 13494 examined...
003:    346 changed, 4453 examined...
004:    150 changed, 1867 examined...
005:     79 changed, 866 examined...
006:     39 changed, 457 examined...
007:     20 changed, 209 examined...
008:      6 changed, 112 examined...
009:      6 changed, 35 examined...
010:      3 changed, 27 examined...
011:      1 changed, 18 examined...
012:      0 changed, 7 examined...
28 labels changed using aseg
000: 369 total segments, 287 labels (4861 vertices) changed
001: 128 total segments, 47 labels (449 vertices) changed
002: 84 total segments, 3 labels (7 vertices) changed
003: 81 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 149 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
386 vertices marked for relabeling...
386 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 1 minutes and 21 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Thu Aug  8 20:22:03 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

 1526   1047   2497  2.074 0.526     0.170     0.071       44     4.9  G_and_S_frontomargin
 1844   1235   2709  1.996 0.416     0.149     0.049       28     3.6  G_and_S_occipital_inf
 1703   1006   2720  2.268 0.514     0.130     0.059       24     3.7  G_and_S_paracentral
 2009   1334   3827  2.591 0.533     0.152     0.054       37     4.1  G_and_S_subcentral
 1082    746   2321  2.369 0.522     0.198     0.091       40     4.0  G_and_S_transv_frontopol
 2553   1746   4811  2.396 0.614     0.156     0.104       59     6.9  G_and_S_cingul-Ant
 2153   1471   4042  2.586 0.567     0.130     0.031       27     2.9  G_and_S_cingul-Mid-Ant
 1603   1101   2943  2.625 0.453     0.147     0.058       31     3.8  G_and_S_cingul-Mid-Post
  620    439   1612  2.958 0.446     0.188     0.072       19     1.8  G_cingul-Post-dorsal
  303    199    532  2.399 0.760     0.163     0.071        6     0.8  G_cingul-Post-ventral
 2079   1406   2844  1.754 0.371     0.181     0.075       48     6.3  G_cuneus
 1699   1137   4069  2.816 0.459     0.165     0.067       49     4.3  G_front_inf-Opercular
  460    311   1080  2.636 0.482     0.155     0.055        9     1.1  G_front_inf-Orbital
 1310    895   3061  2.637 0.530     0.162     0.060       28     3.0  G_front_inf-Triangul
 5103   3522  10829  2.434 0.548     0.169     0.071      133    14.3  G_front_middle
 8485   5737  19109  2.650 0.581     0.152     0.061      214    20.1  G_front_sup
  476    290   1079  2.894 0.604     0.150     0.091       11     1.9  G_Ins_lg_and_S_cent_ins
  895    539   2799  3.668 0.846     0.140     0.156       34     2.6  G_insular_short
 2786   1787   5097  2.228 0.504     0.156     0.063       57     6.5  G_occipital_middle
 1682   1079   2708  2.149 0.541     0.149     0.049       27     3.1  G_occipital_sup
 2415   1585   5539  2.860 0.550     0.171     0.087       79     6.5  G_oc-temp_lat-fusifor
 3288   2202   5303  2.036 0.545     0.178     0.105       79    11.1  G_oc-temp_med-Lingual
 1218    814   3010  2.983 0.893     0.137     0.056       25     2.8  G_oc-temp_med-Parahip
 2875   1898   7144  2.741 0.562     0.184     0.090       88    10.6  G_orbital
 3005   2039   6528  2.526 0.481     0.164     0.062       71     7.4  G_pariet_inf-Angular
 2748   1897   6215  2.589 0.521     0.157     0.053       56     5.6  G_pariet_inf-Supramar
 3645   2374   6921  2.320 0.542     0.136     0.043       53     6.3  G_parietal_sup
 3352   2197   5095  1.919 0.567     0.147     0.057       64     7.4  G_postcentral
 3534   2271   7646  2.614 0.550     0.129     0.039       51     5.4  G_precentral
 3607   2374   7767  2.619 0.486     0.164     0.075       96    11.1  G_precuneus
 1074    713   2325  2.378 0.589     0.225     0.233       82     5.7  G_rectus
  324    221    691  2.753 0.477     0.179     0.089        9     1.0  G_subcallosal
  552    338    995  2.325 0.277     0.130     0.044        8     1.0  G_temp_sup-G_T_transv
 2403   1590   6567  2.966 0.542     0.152     0.065       52     5.8  G_temp_sup-Lateral
  754    518   1921  3.376 0.910     0.108     0.036        6     1.0  G_temp_sup-Plan_polar
  757    557   1533  2.447 0.427     0.112     0.030        7     0.8  G_temp_sup-Plan_tempo
 3211   2165   7573  2.703 0.646     0.167     0.078       87     9.7  G_temporal_inf
 3777   2590   9925  2.847 0.558     0.159     0.056       85     8.3  G_temporal_middle
  441    310    766  2.324 0.407     0.145     0.037        6     0.8  Lat_Fis-ant-Horizont
  332    221    518  2.392 0.526     0.142     0.039        4     0.6  Lat_Fis-ant-Vertical
 1387    933   1851  2.293 0.531     0.127     0.037       12     2.2  Lat_Fis-post
 2599   1636   3410  1.822 0.416     0.162     0.058       48     6.3  Pole_occipital
 1822   1284   5448  3.155 0.792     0.175     0.097       42     6.0  Pole_temporal
 2722   1829   3365  2.037 0.738     0.155     0.066       43     6.3  S_calcarine
 3416   2315   3546  1.689 0.506     0.122     0.036       27     5.4  S_central
 1194    815   1764  2.280 0.483     0.122     0.033       11     1.6  S_cingul-Marginalis
  807    520   1134  2.665 0.543     0.115     0.031        6     1.1  S_circular_insula_ant
 1561   1039   2369  2.600 0.540     0.092     0.026        9     1.8  S_circular_insula_inf
 1907   1296   2969  2.560 0.512     0.115     0.032       13     2.6  S_circular_insula_sup
 1064    784   1936  2.542 0.507     0.109     0.025        7     1.1  S_collat_transv_ant
  300    198    451  2.080 0.376     0.122     0.039        2     0.4  S_collat_transv_post
 2736   1883   3984  2.090 0.403     0.132     0.036       33     3.9  S_front_inf
 2286   1602   3783  2.075 0.495     0.157     0.064       51     5.9  S_front_middle
 3566   2402   5584  2.279 0.450     0.122     0.039       43     5.6  S_front_sup
  349    230    580  2.347 0.495     0.130     0.038        6     0.6  S_interm_prim-Jensen
 4149   2779   5514  2.096 0.415     0.117     0.029       35     5.0  S_intrapariet_and_P_trans
 1903   1253   2158  1.917 0.354     0.150     0.050       24     4.0  S_oc_middle_and_Lunatus
 1537   1017   1944  2.040 0.396     0.122     0.055       13     2.0  S_oc_sup_and_transversal
 1296    858   1580  1.992 0.421     0.112     0.033       10     1.7  S_occipital_ant
 1419    937   2069  2.558 0.413     0.126     0.039       14     2.1  S_oc-temp_lat
 2189   1506   3485  2.413 0.515     0.128     0.038       22     3.3  S_oc-temp_med_and_Lingual
  583    397    698  1.928 0.402     0.136     0.044        7     0.9  S_orbital_lateral
  394    275    574  1.913 0.427     0.151     0.051        7     0.7  S_orbital_med-olfact
 1584   1092   2568  2.137 0.642     0.156     0.060       29     3.5  S_orbital-H_Shaped
 2193   1439   2973  2.241 0.591     0.131     0.039       23     3.2  S_parieto_occipital
 1346    802   1522  2.219 0.742     0.150     0.053       30     2.8  S_pericallosal
 4230   2816   5432  2.044 0.498     0.126     0.034       41     5.7  S_postcentral
 1941   1362   2917  2.251 0.512     0.120     0.029       19     2.4  S_precentral-inf-part
 1602   1105   2335  2.429 0.435     0.120     0.031       14     2.0  S_precentral-sup-part
  782    543    957  1.729 0.379     0.113     0.024        5     0.8  S_suborbital
 1611   1095   2494  2.348 0.440     0.135     0.043       16     2.8  S_subparietal
 1627   1112   2296  2.176 0.515     0.134     0.043       23     2.8  S_temporal_inf
 6746   4675  11155  2.511 0.482     0.127     0.036       71    10.0  S_temporal_sup
  360    244    461  2.250 0.425     0.116     0.022        2     0.4  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Thu Aug  8 20:22:27 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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...
1480 labels changed using aseg
relabeling using gibbs priors...
000:   3330 changed, 158499 examined...
001:    830 changed, 13806 examined...
002:    200 changed, 4542 examined...
003:     86 changed, 1187 examined...
004:     40 changed, 496 examined...
005:     19 changed, 223 examined...
006:      6 changed, 98 examined...
007:      1 changed, 41 examined...
008:      1 changed, 7 examined...
009:      0 changed, 5 examined...
188 labels changed using aseg
000: 80 total segments, 47 labels (283 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 60 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
413 vertices marked for relabeling...
413 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas40.annot...
classification took 1 minutes and 11 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Thu Aug  8 20:23:38 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

 2002   1331   3919  2.649 0.619     0.143     0.039       34     3.2  caudalanteriorcingulate
 4561   3096   8208  2.387 0.500     0.132     0.037       57     6.8  caudalmiddlefrontal
 3203   2132   4202  1.829 0.437     0.161     0.057       58     7.4  cuneus
  494    357   1352  3.228 0.898     0.146     0.053        5     1.1  entorhinal
 5234   3530  10446  2.658 0.567     0.151     0.066      112    11.3  fusiform
 8013   5463  14372  2.358 0.466     0.141     0.053      133    14.9  inferiorparietal
 6023   4097  12725  2.619 0.644     0.151     0.064      125    14.8  inferiortemporal
 1780   1197   3370  2.679 0.689     0.168     0.067       43     4.7  isthmuscingulate
 9171   5937  12729  1.939 0.434     0.149     0.050      136    19.1  lateraloccipital
 4419   2936   8699  2.437 0.689     0.170     0.078      120    13.5  lateralorbitofrontal
 4721   3198   7346  2.089 0.539     0.164     0.085       95    13.2  lingual
 1943   1330   3441  2.126 0.618     0.174     0.135       77     6.6  medialorbitofrontal
 7371   5099  15912  2.661 0.588     0.144     0.047      124    14.1  middletemporal
 1062    688   2195  2.789 0.788     0.126     0.044       21     2.1  parahippocampal
 2338   1490   3747  2.364 0.469     0.131     0.050       32     3.9  paracentral
 2299   1546   4486  2.660 0.460     0.141     0.045       42     4.3  parsopercularis
 1308    875   2824  2.625 0.541     0.152     0.052       25     2.9  parsorbitalis
 2964   2024   5375  2.338 0.540     0.145     0.049       53     5.5  parstriangularis
 2116   1399   2129  1.664 0.431     0.166     0.079       38     5.8  pericalcarine
 9342   6184  13311  1.933 0.616     0.138     0.046      136    16.9  postcentral
 2121   1415   3793  2.560 0.576     0.159     0.064       49     5.4  posteriorcingulate
 8899   5887  15827  2.423 0.562     0.128     0.040      110    14.8  precentral
 6696   4467  12394  2.514 0.495     0.149     0.059      126    15.9  precuneus
 2106   1404   4120  2.482 0.658     0.164     0.118       56     6.5  rostralanteriorcingulate
 7274   5002  13153  2.219 0.566     0.167     0.073      188    21.1  rostralmiddlefrontal
14844  10198  29913  2.481 0.572     0.148     0.057      326    33.1  superiorfrontal
 8525   5578  13243  2.151 0.485     0.130     0.039      104    13.5  superiorparietal
 8298   5599  17770  2.819 0.650     0.129     0.049      114    15.0  superiortemporal
 5652   3865  10707  2.510 0.510     0.142     0.044       85     9.8  supramarginal
  784    487   1264  2.301 0.364     0.127     0.042        9     1.4  transversetemporal
 3328   2169   7001  2.965 0.810     0.127     0.074       59     7.1  insula
#--------------------------------------------
#@# Tessellate rh Thu Aug  8 20:24:00 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

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


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

Total Number of Modified Voxels = 5 (out of 309686: 0.001615)
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 30: 92 vertices, 114 faces
slice 40: 3456 vertices, 3664 faces
slice 50: 11243 vertices, 11550 faces
slice 60: 21962 vertices, 22395 faces
slice 70: 34016 vertices, 34424 faces
slice 80: 46310 vertices, 46739 faces
slice 90: 58869 vertices, 59300 faces
slice 100: 71468 vertices, 71890 faces
slice 110: 83859 vertices, 84308 faces
slice 120: 96212 vertices, 96680 faces
slice 130: 108894 vertices, 109383 faces
slice 140: 121013 vertices, 121423 faces
slice 150: 131602 vertices, 131952 faces
slice 160: 139935 vertices, 140221 faces
slice 170: 146934 vertices, 147205 faces
slice 180: 153698 vertices, 153904 faces
slice 190: 159000 vertices, 159208 faces
slice 200: 160904 vertices, 160934 faces
slice 210: 160904 vertices, 160934 faces
slice 220: 160904 vertices, 160934 faces
slice 230: 160904 vertices, 160934 faces
slice 240: 160904 vertices, 160934 faces
slice 250: 160904 vertices, 160934 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...
   160904 voxel in cpt #1: X=-30 [v=160904,e=482802,f=321868] located at (29.328512, -20.287563, 41.081017)
For the whole surface: X=-30 [v=160904,e=482802,f=321868]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 rh Thu Aug  8 20:24:08 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 rh Thu Aug  8 20:24:13 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
avg radius = 49.0 mm, total surface area = 84350 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.6 minutes
Not saving sulc

step 000: RMS=0.100 (target=0.015)   
step 005: RMS=0.073 (target=0.015)   
step 010: RMS=0.053 (target=0.015)   
step 015: RMS=0.043 (target=0.015)   
step 020: RMS=0.037 (target=0.015)   
step 025: RMS=0.032 (target=0.015)   
step 030: RMS=0.029 (target=0.015)   
step 035: RMS=0.026 (target=0.015)   
step 040: RMS=0.024 (target=0.015)   
step 045: RMS=0.023 (target=0.015)   
step 050: RMS=0.022 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Thu Aug  8 20:24:52 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.92 +- 0.53 (0.00-->5.59) (max @ vno 107171 --> 108458)
face area 0.02 +- 0.03 (-0.22-->0.60)
scaling brain by 0.295...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.393, avgs=0
005/300: dt: 0.9000, rms radial error=176.135, avgs=0
010/300: dt: 0.9000, rms radial error=175.581, avgs=0
015/300: dt: 0.9000, rms radial error=174.852, avgs=0
020/300: dt: 0.9000, rms radial error=174.020, avgs=0
025/300: dt: 0.9000, rms radial error=173.130, avgs=0
030/300: dt: 0.9000, rms radial error=172.207, avgs=0
035/300: dt: 0.9000, rms radial error=171.273, avgs=0
040/300: dt: 0.9000, rms radial error=170.331, avgs=0
045/300: dt: 0.9000, rms radial error=169.386, avgs=0
050/300: dt: 0.9000, rms radial error=168.441, avgs=0
055/300: dt: 0.9000, rms radial error=167.499, avgs=0
060/300: dt: 0.9000, rms radial error=166.561, avgs=0
065/300: dt: 0.9000, rms radial error=165.627, avgs=0
070/300: dt: 0.9000, rms radial error=164.698, avgs=0
075/300: dt: 0.9000, rms radial error=163.775, avgs=0
080/300: dt: 0.9000, rms radial error=162.856, avgs=0
085/300: dt: 0.9000, rms radial error=161.943, avgs=0
090/300: dt: 0.9000, rms radial error=161.035, avgs=0
095/300: dt: 0.9000, rms radial error=160.132, avgs=0
100/300: dt: 0.9000, rms radial error=159.233, avgs=0
105/300: dt: 0.9000, rms radial error=158.340, avgs=0
110/300: dt: 0.9000, rms radial error=157.452, avgs=0
115/300: dt: 0.9000, rms radial error=156.568, avgs=0
120/300: dt: 0.9000, rms radial error=155.690, avgs=0
125/300: dt: 0.9000, rms radial error=154.816, avgs=0
130/300: dt: 0.9000, rms radial error=153.947, avgs=0
135/300: dt: 0.9000, rms radial error=153.082, avgs=0
140/300: dt: 0.9000, rms radial error=152.223, avgs=0
145/300: dt: 0.9000, rms radial error=151.368, avgs=0
150/300: dt: 0.9000, rms radial error=150.517, avgs=0
155/300: dt: 0.9000, rms radial error=149.672, avgs=0
160/300: dt: 0.9000, rms radial error=148.830, avgs=0
165/300: dt: 0.9000, rms radial error=147.994, avgs=0
170/300: dt: 0.9000, rms radial error=147.162, avgs=0
175/300: dt: 0.9000, rms radial error=146.334, avgs=0
180/300: dt: 0.9000, rms radial error=145.511, avgs=0
185/300: dt: 0.9000, rms radial error=144.693, avgs=0
190/300: dt: 0.9000, rms radial error=143.879, avgs=0
195/300: dt: 0.9000, rms radial error=143.070, avgs=0
200/300: dt: 0.9000, rms radial error=142.265, avgs=0
205/300: dt: 0.9000, rms radial error=141.464, avgs=0
210/300: dt: 0.9000, rms radial error=140.668, avgs=0
215/300: dt: 0.9000, rms radial error=139.876, avgs=0
220/300: dt: 0.9000, rms radial error=139.089, avgs=0
225/300: dt: 0.9000, rms radial error=138.307, avgs=0
230/300: dt: 0.9000, rms radial error=137.528, avgs=0
235/300: dt: 0.9000, rms radial error=136.754, avgs=0
240/300: dt: 0.9000, rms radial error=135.984, avgs=0
245/300: dt: 0.9000, rms radial error=135.219, avgs=0
250/300: dt: 0.9000, rms radial error=134.458, avgs=0
255/300: dt: 0.9000, rms radial error=133.701, avgs=0
260/300: dt: 0.9000, rms radial error=132.949, avgs=0
265/300: dt: 0.9000, rms radial error=132.201, avgs=0
270/300: dt: 0.9000, rms radial error=131.457, avgs=0
275/300: dt: 0.9000, rms radial error=130.718, avgs=0
280/300: dt: 0.9000, rms radial error=129.982, avgs=0
285/300: dt: 0.9000, rms radial error=129.251, avgs=0
290/300: dt: 0.9000, rms radial error=128.523, avgs=0
295/300: dt: 0.9000, rms radial error=127.800, avgs=0
300/300: dt: 0.9000, rms radial error=127.081, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19134.30
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 = 3289.60
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00003
epoch 3 (K=160.0), pass 1, starting sse = 350.71
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/11 = 0.00762
epoch 4 (K=640.0), pass 1, starting sse = 20.94
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.18/15 = 0.01187
final writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.10 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology rh Thu Aug  8 20:30:34 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/sub011/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub011 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=-30 (nv=160904, nf=321868, ne=482802, g=16)
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 8 iterations
marking ambiguous vertices...
2422 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/sub011/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.9098  (-4.9549)
      -vertex     loglikelihood: -6.6368  (-3.3184)
      -normal dot loglikelihood: -3.5669  (-3.5669)
      -quad curv  loglikelihood: -6.4444  (-3.2222)
      Total Loglikelihood : -26.5580

CORRECTING DEFECT 0 (vertices=551, convex hull=180)
After retessellation of defect 0, euler #=-9 (159529,478130,318592) : difference with theory (-12) = -3 

CORRECTING DEFECT 1 (vertices=31, convex hull=74)
After retessellation of defect 1, euler #=-8 (159539,478190,318643) : difference with theory (-11) = -3 

CORRECTING DEFECT 2 (vertices=33, convex hull=69)
After retessellation of defect 2, euler #=-7 (159552,478253,318694) : difference with theory (-10) = -3 

CORRECTING DEFECT 3 (vertices=49, convex hull=37)
After retessellation of defect 3, euler #=-6 (159557,478282,318719) : difference with theory (-9) = -3 

CORRECTING DEFECT 4 (vertices=9, convex hull=28)
After retessellation of defect 4, euler #=-5 (159561,478301,318735) : difference with theory (-8) = -3 

CORRECTING DEFECT 5 (vertices=56, convex hull=71)
After retessellation of defect 5, euler #=-4 (159574,478375,318797) : difference with theory (-7) = -3 

CORRECTING DEFECT 6 (vertices=438, convex hull=259)
After retessellation of defect 6, euler #=-5 (159621,478668,319042) : difference with theory (-6) = -1 

CORRECTING DEFECT 7 (vertices=53, convex hull=53)
After retessellation of defect 7, euler #=-5 (159645,478765,319115) : difference with theory (-5) = 0 

CORRECTING DEFECT 8 (vertices=27, convex hull=55)
After retessellation of defect 8, euler #=-4 (159658,478822,319160) : difference with theory (-4) = 0 

CORRECTING DEFECT 9 (vertices=6, convex hull=13)
After retessellation of defect 9, euler #=-3 (159659,478828,319166) : difference with theory (-3) = 0 

CORRECTING DEFECT 10 (vertices=55, convex hull=63)
After retessellation of defect 10, euler #=-2 (159672,478895,319221) : difference with theory (-2) = 0 

CORRECTING DEFECT 11 (vertices=33, convex hull=72)
After retessellation of defect 11, euler #=-1 (159689,478973,319283) : difference with theory (-1) = 0 

CORRECTING DEFECT 12 (vertices=57, convex hull=94)
After retessellation of defect 12, euler #=0 (159702,479051,319349) : difference with theory (0) = 0 

CORRECTING DEFECT 13 (vertices=33, convex hull=66)
After retessellation of defect 13, euler #=1 (159714,479115,319402) : difference with theory (1) = 0 

CORRECTING DEFECT 14 (vertices=29, convex hull=58)
After retessellation of defect 14, euler #=2 (159726,479172,319448) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.06-->12.32) (max @ vno 45728 --> 48072)
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 (0.06-->12.32) (max @ vno 45728 --> 48072)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
54 mutations (36.5%), 94 crossovers (63.5%), 193 vertices were eliminated
building final representation...
1178 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=159726, nf=319448, ne=479172, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 20.2 minutes
0 defective edges
removing intersecting faces
000: 187 intersecting

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 159726 - 479172 + 319448 = 2 --> 0 holes
      F =2V-4:          319448 = 319452-4 (0)
      2E=3F:            958344 = 958344 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 43 intersecting
001: 2 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Thu Aug  8 20:50:54 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub011 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/sub011/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
20244 bright wm thresholded.
947 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.orig...
computing class statistics...
border white:    292650 voxels (1.74%)
border gray      329335 voxels (1.96%)
WM (92.0): 93.5 +- 10.0 [70.0 --> 110.0]
GM (76.0) : 74.1 +- 12.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
setting MAX_BORDER_WHITE to 115.0 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.2 (was 40)
setting MAX_GRAY to 95.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.04-->4.59) (max @ vno 159481 --> 159517)
face area 0.28 +- 0.12 (0.00-->5.21)
mean absolute distance = 0.65 +- 0.77
4463 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 93.3, mean outside = 69.4
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=73.6, 23 (23) missing vertices, mean dist 0.4 [0.5 (%31.7)->0.7 (%68.3))]
%74 local maxima, %21 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-->4.50) (max @ vno 159481 --> 159517)
face area 0.28 +- 0.14 (0.00-->5.12)
mean absolute distance = 0.31 +- 0.49
2837 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8456153.0, rms=13.48
001: dt: 0.5000, sse=8474094.0, rms=9.726 (0.000%)
002: dt: 0.5000, sse=8757679.0, rms=7.574 (0.000%)
003: dt: 0.5000, sse=8942017.0, rms=6.208 (0.000%)
004: dt: 0.5000, sse=9234185.0, rms=5.389 (0.000%)
005: dt: 0.5000, sse=9309302.0, rms=4.899 (0.000%)
006: dt: 0.5000, sse=9489659.0, rms=4.653 (0.000%)
007: dt: 0.5000, sse=9469956.0, rms=4.485 (0.000%)
008: dt: 0.5000, sse=9528877.0, rms=4.413 (0.000%)
009: dt: 0.5000, sse=9441498.0, rms=4.340 (0.000%)
rms = 4.31, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9503375.0, rms=4.312 (0.000%)
011: dt: 0.2500, sse=5980742.5, rms=2.994 (0.000%)
012: dt: 0.2500, sse=5464564.5, rms=2.546 (0.000%)
013: dt: 0.2500, sse=5147420.5, rms=2.449 (0.000%)
014: dt: 0.2500, sse=5059029.5, rms=2.366 (0.000%)
rms = 2.34, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4957086.5, rms=2.341 (0.000%)
016: dt: 0.1250, sse=4739545.5, rms=2.156 (0.000%)
rms = 2.14, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4691896.0, rms=2.138 (0.000%)
positioning took 2.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=77.6, 19 (3) missing vertices, mean dist -0.2 [0.3 (%74.8)->0.2 (%25.2))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.06-->4.43) (max @ vno 45728 --> 159526)
face area 0.35 +- 0.17 (0.00-->6.38)
mean absolute distance = 0.23 +- 0.34
3605 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5716901.0, rms=5.75
018: dt: 0.5000, sse=6051761.5, rms=3.898 (0.000%)
rms = 4.32, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=5489718.5, rms=2.815 (0.000%)
020: dt: 0.2500, sse=5282124.0, rms=2.248 (0.000%)
021: dt: 0.2500, sse=5185390.5, rms=1.919 (0.000%)
022: dt: 0.2500, sse=5156414.5, rms=1.862 (0.000%)
023: dt: 0.2500, sse=5086782.5, rms=1.802 (0.000%)
rms = 1.80, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=5098622.0, rms=1.796 (0.000%)
025: dt: 0.1250, sse=4955181.5, rms=1.651 (0.000%)
rms = 1.64, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=4916362.0, rms=1.643 (0.000%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=81.1, 16 (3) missing vertices, mean dist -0.1 [0.2 (%76.6)->0.2 (%23.4))]
%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 (0.10-->5.37) (max @ vno 159481 --> 159523)
face area 0.34 +- 0.17 (0.00-->8.84)
mean absolute distance = 0.18 +- 0.27
3338 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5399405.5, rms=4.41
027: dt: 0.5000, sse=5728430.0, rms=3.974 (0.000%)
rms = 4.20, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=5210938.0, rms=2.556 (0.000%)
029: dt: 0.2500, sse=5081435.0, rms=2.055 (0.000%)
030: dt: 0.2500, sse=5132253.0, rms=1.704 (0.000%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
031: dt: 0.1250, sse=5065830.5, rms=1.594 (0.000%)
032: dt: 0.1250, sse=4977651.5, rms=1.442 (0.000%)
rms = 1.43, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=4938956.5, rms=1.429 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=82.2, 15 (3) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))]
%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/sub011/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=4974679.5, rms=1.91
rms = 2.70, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=5072500.0, rms=1.253 (0.000%)
035: dt: 0.2500, sse=5248130.0, rms=1.068 (0.000%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
rms = 1.06, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=5249605.5, rms=1.059 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
7 non-cortical segments detected
only using segment with 1989 vertices
erasing segment 1 (vno[0] = 96989)
erasing segment 2 (vno[0] = 103184)
erasing segment 3 (vno[0] = 109704)
erasing segment 4 (vno[0] = 112267)
erasing segment 5 (vno[0] = 117234)
erasing segment 6 (vno[0] = 118242)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.area
vertex spacing 0.90 +- 0.25 (0.05-->5.62) (max @ vno 159481 --> 159523)
face area 0.34 +- 0.16 (0.00-->9.06)
refinement took 8.2 minutes
#--------------------------------------------
#@# Smooth2 rh Thu Aug  8 20:59:03 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 20:59:09 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

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

avg radius = 49.2 mm, total surface area = 97696 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.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=0.047 (target=0.015)   
step 020: RMS=0.039 (target=0.015)   
step 025: RMS=0.032 (target=0.015)   
step 030: RMS=0.028 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.018 (target=0.015)   
step 050: RMS=0.016 (target=0.015)   
step 055: RMS=0.015 (target=0.015)   
inflation complete.
inflation took 0.6 minutes

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

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
205 vertices thresholded to be in k1 ~ [-0.42 0.37], k2 ~ [-0.17 0.14]
total integrated curvature = 0.527*4pi (6.626) --> 0 handles
ICI = 1.7, FI = 12.1, variation=201.736
165 vertices thresholded to be in [-0.04 0.01]
writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
165 vertices thresholded to be in [-0.14 0.17]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.024
done.

#-----------------------------------------
#@# Curvature Stats rh Thu Aug  8 21:01:47 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub011 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       [ sub011/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                      [ 308 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.857142
WARN:    S explicit min:                          0.000000	vertex = 464
#--------------------------------------------
#@# Sphere rh Thu Aug  8 21:01:53 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 0.274...
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 %20.02
pass 1: epoch 2 of 3 starting distance error %19.95
unfolding complete - removing small folds...
starting distance error %19.82
removing remaining folds...
final distance error %19.84
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.05 hours
#--------------------------------------------
#@# Surf Reg rh Thu Aug  8 22:04:43 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 0.587
curvature mean = 0.029, std = 0.932
curvature mean = 0.025, std = 0.841
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 412018.2, tmin=1.3498
  d=32.00 min @ (0.00, -8.00, 0.00) sse = 293392.5, tmin=2.8062
  d=16.00 min @ (0.00, 0.00, 4.00) sse = 279558.9, tmin=4.1143
  d=8.00 min @ (0.00, 2.00, -2.00) sse = 273814.4, tmin=5.4315
  d=4.00 min @ (0.00, -1.00, 1.00) sse = 269481.1, tmin=6.7803
  d=2.00 min @ (0.00, 0.00, -0.50) sse = 269029.4, tmin=8.1483
  d=1.00 min @ (0.00, 0.00, 0.25) sse = 269027.5, tmin=9.5028
  d=0.50 min @ (0.00, 0.00, -0.12) sse = 268967.0, tmin=10.8516
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  10.85 min
curvature mean = -0.000, std = 0.937
curvature mean = 0.012, std = 0.929
curvature mean = -0.007, std = 0.944
curvature mean = 0.006, std = 0.966
curvature mean = -0.011, std = 0.941
curvature mean = 0.002, std = 0.984
2 Reading smoothwm
curvature mean = -0.024, std = 0.291
curvature mean = 0.005, std = 0.069
curvature mean = 0.074, std = 0.317
curvature mean = 0.005, std = 0.082
curvature mean = 0.041, std = 0.510
curvature mean = 0.006, std = 0.088
curvature mean = 0.023, std = 0.660
curvature mean = 0.006, std = 0.090
curvature mean = 0.007, std = 0.780
MRISregister() return, current seed 0
writing registered surface to ../surf/rh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white rh Thu Aug  8 22:38:06 CEST 2013

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

reading surface from ../surf/rh.white...
writing curvature file ../surf/rh.jacobian_white
#--------------------------------------------
#@# AvgCurv rh Thu Aug  8 22:38:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv 

averaging curvature patterns 5 times...
reading surface from ../surf/rh.sphere.reg...
reading template parameterization from /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
writing curvature file to ../surf/rh.avg_curv...
#-----------------------------------------
#@# Cortical Parc rh Thu Aug  8 22:38:11 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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...
1501 labels changed using aseg
relabeling using gibbs priors...
000:   3392 changed, 159726 examined...
001:    735 changed, 14448 examined...
002:    190 changed, 4118 examined...
003:     70 changed, 1110 examined...
004:     35 changed, 395 examined...
005:     12 changed, 192 examined...
006:      5 changed, 75 examined...
007:      5 changed, 41 examined...
008:      3 changed, 31 examined...
009:      0 changed, 15 examined...
217 labels changed using aseg
000: 131 total segments, 91 labels (418 vertices) changed
001: 44 total segments, 4 labels (20 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 41 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1971 vertices marked for relabeling...
1971 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 1 minutes and 12 seconds.
#--------------------------------------------
#@# Make Pial Surf rh Thu Aug  8 22:39:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub011 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/sub011/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
20244 bright wm thresholded.
947 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.orig...
computing class statistics...
border white:    292650 voxels (1.74%)
border gray      329335 voxels (1.96%)
WM (92.0): 93.5 +- 10.0 [70.0 --> 110.0]
GM (76.0) : 74.1 +- 12.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
setting MAX_BORDER_WHITE to 115.0 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.2 (was 40)
setting MAX_GRAY to 95.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 93.3, mean outside = 69.4
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/sub011/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.04-->4.59) (max @ vno 159481 --> 159517)
face area 0.28 +- 0.12 (0.00-->5.21)
mean absolute distance = 0.66 +- 0.77
4512 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 6 with 537 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 8 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 12 with 6 points - only 0.00% unknown
deleting segment 13 with 16 points - only 0.00% unknown
mean border=73.6, 23 (23) missing vertices, mean dist 0.4 [0.5 (%31.7)->0.7 (%68.3))]
%75 local maxima, %21 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-->4.50) (max @ vno 159481 --> 159517)
face area 0.28 +- 0.13 (0.00-->5.11)
mean absolute distance = 0.31 +- 0.49
2843 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8473527.0, rms=13.47
001: dt: 0.5000, sse=8494065.0, rms=9.717 (0.000%)
002: dt: 0.5000, sse=8777156.0, rms=7.568 (0.000%)
003: dt: 0.5000, sse=8969415.0, rms=6.203 (0.000%)
004: dt: 0.5000, sse=9261748.0, rms=5.386 (0.000%)
005: dt: 0.5000, sse=9342896.0, rms=4.896 (0.000%)
006: dt: 0.5000, sse=9521777.0, rms=4.651 (0.000%)
007: dt: 0.5000, sse=9505386.0, rms=4.482 (0.000%)
008: dt: 0.5000, sse=9562392.0, rms=4.410 (0.000%)
009: dt: 0.5000, sse=9477041.0, rms=4.337 (0.000%)
rms = 4.31, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9537380.0, rms=4.309 (0.000%)
011: dt: 0.2500, sse=5998708.5, rms=2.992 (0.000%)
012: dt: 0.2500, sse=5481670.0, rms=2.545 (0.000%)
013: dt: 0.2500, sse=5163551.0, rms=2.448 (0.000%)
014: dt: 0.2500, sse=5076406.0, rms=2.365 (0.000%)
rms = 2.34, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4973673.0, rms=2.340 (0.000%)
016: dt: 0.1250, sse=4756675.0, rms=2.156 (0.000%)
rms = 2.14, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4708796.0, rms=2.138 (0.000%)
positioning took 2.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 266 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 10 with 14 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 14 with 44 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
deleting segment 16 with 6 points - only 0.00% unknown
deleting segment 17 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 18 with 1 points - only 0.00% unknown
deleting segment 19 with 17 points - only 0.00% unknown
mean border=77.6, 19 (3) missing vertices, mean dist -0.2 [0.3 (%74.7)->0.2 (%25.3))]
%81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.91 +- 0.25 (0.06-->4.43) (max @ vno 45728 --> 159526)
face area 0.35 +- 0.17 (0.00-->6.38)
mean absolute distance = 0.23 +- 0.34
3631 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5735269.5, rms=5.75
018: dt: 0.5000, sse=6073061.5, rms=3.893 (0.000%)
rms = 4.32, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=5509810.5, rms=2.812 (0.000%)
020: dt: 0.2500, sse=5302589.0, rms=2.247 (0.000%)
021: dt: 0.2500, sse=5205111.0, rms=1.919 (0.000%)
022: dt: 0.2500, sse=5175737.5, rms=1.862 (0.000%)
023: dt: 0.2500, sse=5106272.5, rms=1.802 (0.000%)
rms = 1.80, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=5118582.0, rms=1.796 (0.000%)
025: dt: 0.1250, sse=4974942.5, rms=1.652 (0.000%)
rms = 1.64, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=4935998.5, rms=1.644 (0.000%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
deleting segment 4 with 263 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
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 11 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 11 with 64 points - only 0.00% unknown
deleting segment 12 with 6 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
deleting segment 14 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 with 1 points - only 0.00% unknown
deleting segment 16 with 19 points - only 0.00% unknown
mean border=81.0, 17 (3) missing vertices, mean dist -0.1 [0.2 (%76.6)->0.2 (%23.4))]
%89 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 (0.10-->5.37) (max @ vno 159481 --> 159523)
face area 0.34 +- 0.16 (0.00-->8.83)
mean absolute distance = 0.18 +- 0.27
3380 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5420578.0, rms=4.41
027: dt: 0.5000, sse=5748837.5, rms=3.969 (0.000%)
rms = 4.20, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=5229811.5, rms=2.554 (0.000%)
029: dt: 0.2500, sse=5100590.0, rms=2.054 (0.000%)
030: dt: 0.2500, sse=5150585.5, rms=1.705 (0.000%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
031: dt: 0.1250, sse=5084212.0, rms=1.596 (0.000%)
032: dt: 0.1250, sse=4996539.0, rms=1.444 (0.000%)
rms = 1.43, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=4958009.0, rms=1.431 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 272 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
deleting segment 7 with 14 points - only 0.00% unknown
deleting segment 9 with 64 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
deleting segment 13 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
deleting segment 15 with 20 points - only 0.00% unknown
mean border=82.2, 16 (3) missing vertices, mean dist -0.0 [0.2 (%59.2)->0.2 (%40.8))]
%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=4993643.0, rms=1.91
rms = 2.69, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=5093207.0, rms=1.254 (0.000%)
035: dt: 0.2500, sse=5270818.0, rms=1.069 (0.000%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
rms = 1.06, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=5272450.5, rms=1.060 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=49.2, 17 (17) missing vertices, mean dist 1.7 [0.6 (%0.0)->2.3 (%100.0))]
%14 local maxima, %56 large gradients and %26 min vals, 1614 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=35291056.0, rms=32.37
001: dt: 0.5000, sse=25554212.0, rms=26.991 (0.000%)
002: dt: 0.5000, sse=18703494.0, rms=22.476 (0.000%)
003: dt: 0.5000, sse=14080444.0, rms=18.788 (0.000%)
004: dt: 0.5000, sse=11205035.0, rms=15.804 (0.000%)
005: dt: 0.5000, sse=9506431.0, rms=13.410 (0.000%)
006: dt: 0.5000, sse=8555902.0, rms=11.498 (0.000%)
007: dt: 0.5000, sse=8009868.0, rms=9.870 (0.000%)
008: dt: 0.5000, sse=7710829.0, rms=8.476 (0.000%)
009: dt: 0.5000, sse=7555609.0, rms=7.273 (0.000%)
010: dt: 0.5000, sse=7583803.5, rms=6.330 (0.000%)
011: dt: 0.5000, sse=7692817.5, rms=5.586 (0.000%)
012: dt: 0.5000, sse=7841051.0, rms=5.065 (0.000%)
013: dt: 0.5000, sse=7985915.5, rms=4.690 (0.000%)
014: dt: 0.5000, sse=8164496.0, rms=4.486 (0.000%)
015: dt: 0.5000, sse=8183933.5, rms=4.315 (0.000%)
016: dt: 0.5000, sse=8308496.5, rms=4.216 (0.000%)
017: dt: 0.5000, sse=8267888.5, rms=4.126 (0.000%)
rms = 4.10, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=8374602.0, rms=4.099 (0.000%)
019: dt: 0.2500, sse=5795720.5, rms=3.372 (0.000%)
020: dt: 0.2500, sse=5567222.5, rms=3.178 (0.000%)
rms = 3.16, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=5413352.0, rms=3.156 (0.000%)
022: dt: 0.1250, sse=5182234.0, rms=3.043 (0.000%)
rms = 3.03, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=5153348.0, rms=3.031 (0.000%)
positioning took 3.2 minutes
mean border=47.2, 1057 (4) missing vertices, mean dist 0.1 [0.2 (%50.7)->0.6 (%49.3))]
%32 local maxima, %41 large gradients and %21 min vals, 431 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=5823663.5, rms=4.74
024: dt: 0.5000, sse=6182866.0, rms=4.048 (0.000%)
rms = 4.08, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=5768704.0, rms=3.505 (0.000%)
026: dt: 0.2500, sse=5884238.0, rms=3.256 (0.000%)
027: dt: 0.2500, sse=5806965.0, rms=3.143 (0.000%)
028: dt: 0.2500, sse=5854576.5, rms=3.078 (0.000%)
rms = 3.04, time step reduction 2 of 3 to 0.125...
029: dt: 0.2500, sse=5855774.0, rms=3.036 (0.000%)
030: dt: 0.1250, sse=5680723.5, rms=2.912 (0.000%)
rms = 2.89, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=5671070.0, rms=2.886 (0.000%)
positioning took 1.2 minutes
mean border=45.0, 1285 (3) missing vertices, mean dist 0.1 [0.2 (%38.6)->0.4 (%61.4))]
%54 local maxima, %20 large gradients and %21 min vals, 637 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=5984866.5, rms=4.21
032: dt: 0.5000, sse=6290843.0, rms=3.934 (0.000%)
rms = 4.03, time step reduction 1 of 3 to 0.250...
033: dt: 0.2500, sse=5918775.0, rms=3.224 (0.000%)
034: dt: 0.2500, sse=6174302.5, rms=2.942 (0.000%)
035: dt: 0.2500, sse=6104891.0, rms=2.882 (0.000%)
rms = 2.85, time step reduction 2 of 3 to 0.125...
036: dt: 0.2500, sse=6180108.0, rms=2.848 (0.000%)
037: dt: 0.1250, sse=5965229.0, rms=2.722 (0.000%)
rms = 2.70, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=5953201.5, rms=2.702 (0.000%)
positioning took 1.1 minutes
mean border=43.8, 2543 (3) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.3 (%55.7))]
%58 local maxima, %15 large gradients and %21 min vals, 533 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/sub011/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=6021390.0, rms=3.07
rms = 3.71, time step reduction 1 of 3 to 0.250...
039: dt: 0.2500, sse=5856422.0, rms=2.786 (0.000%)
040: dt: 0.2500, sse=6058540.0, rms=2.704 (0.000%)
rms = 2.67, time step reduction 2 of 3 to 0.125...
041: dt: 0.2500, sse=6139736.5, rms=2.673 (0.000%)
042: dt: 0.1250, sse=6035495.5, rms=2.572 (0.000%)
rms = 2.56, time step reduction 3 of 3 to 0.062...
043: dt: 0.1250, sse=6047119.0, rms=2.556 (0.000%)
positioning took 0.8 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.area.pial
vertex spacing 1.01 +- 0.42 (0.04-->8.87) (max @ vno 111253 --> 109961)
face area 0.41 +- 0.30 (0.00-->15.02)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 159726 vertices processed
25000 of 159726 vertices processed
50000 of 159726 vertices processed
75000 of 159726 vertices processed
100000 of 159726 vertices processed
125000 of 159726 vertices processed
150000 of 159726 vertices processed
0 of 159726 vertices processed
25000 of 159726 vertices processed
50000 of 159726 vertices processed
75000 of 159726 vertices processed
100000 of 159726 vertices processed
125000 of 159726 vertices processed
150000 of 159726 vertices processed
thickness calculation complete, 283:749 truncations.
36993 vertices at 0 distance
111818 vertices at 1 distance
101992 vertices at 2 distance
39995 vertices at 3 distance
10838 vertices at 4 distance
2673 vertices at 5 distance
772 vertices at 6 distance
293 vertices at 7 distance
126 vertices at 8 distance
71 vertices at 9 distance
35 vertices at 10 distance
11 vertices at 11 distance
18 vertices at 12 distance
14 vertices at 13 distance
22 vertices at 14 distance
8 vertices at 15 distance
9 vertices at 16 distance
8 vertices at 17 distance
13 vertices at 18 distance
3 vertices at 19 distance
8 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.thickness
positioning took 16.1 minutes
#--------------------------------------------
#@# Surf Volume rh Thu Aug  8 22:55:28 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf

 mris_calc -o rh.area.mid rh.area add rh.area.pial 

Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]

 mris_calc -o rh.area.mid rh.area.mid div 2 

Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]

 mris_calc -o rh.volume rh.area.mid mul rh.thickness 

Saving result to 'rh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#-----------------------------------------
#@# WM/GM Contrast rh Thu Aug  8 22:55:31 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 pctsurfcon --s sub011 --rh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts/pctsurfcon.log
Thu Aug  8 22:55:31 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake6 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/sub011/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.wm.mgh --regheader sub011 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 123745
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.wm.mgh
Dim: 159726 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.gm.mgh --projfrac 0.3 --regheader sub011 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 142347
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.gm.mgh
Dim: 159726 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/tmp.pctsurfcon.22373/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.w-g.pct.mgh --annot sub011 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.w-g.pct.mgh --annot sub011 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname snake6
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/sub011/surf/rh.w-g.pct.mgh
Vertex Area is 0.669092 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   2000                            unknown       0       0.000
  1   2001                           bankssts    1444    1006.144
  2   2002            caudalanteriorcingulate    1713    1135.003
  3   2003                caudalmiddlefrontal    3644    2389.215
  4   2004                     corpuscallosum       0       0.000
  5   2005                             cuneus    2396    1574.379
  6   2006                         entorhinal     572     421.194
  7   2007                           fusiform    5110    3446.380
  8   2008                   inferiorparietal    9379    6447.679
  9   2009                   inferiortemporal    5201    3558.020
 10   2010                   isthmuscingulate    1900    1247.385
 11   2011                   lateraloccipital    7738    5040.951
 12   2012               lateralorbitofrontal    4217    2842.153
 13   2013                            lingual    4731    3373.175
 14   2014                medialorbitofrontal    2926    1983.715
 15   2015                     middletemporal    5821    4035.433
 16   2016                    parahippocampal    1046     705.774
 17   2017                        paracentral    2912    1822.906
 18   2018                    parsopercularis    3475    2366.997
 19   2019                      parsorbitalis    1400     949.602
 20   2020                   parstriangularis    3276    2220.425
 21   2021                      pericalcarine    2260    1544.378
 22   2022                        postcentral    6873    4418.708
 23   2023                 posteriorcingulate    2288    1569.428
 24   2024                         precentral    9038    5721.352
 25   2025                          precuneus    7451    4972.561
 26   2026           rostralanteriorcingulate    1597    1057.024
 27   2027               rostralmiddlefrontal   10541    7216.732
 28   2028                    superiorfrontal   12639    8537.286
 29   2029                   superiorparietal   10631    6954.118
 30   2030                   superiortemporal    6297    4245.163
 31   2031                      supramarginal    6728    4451.228
 32   2032                        frontalpole     481     319.452
 33   2033                       temporalpole     527     400.592
 34   2034                 transversetemporal     676     430.078
 35   2035                             insula    3748    2465.553

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats rh Thu Aug  8 22:55:46 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

 1444   1006   2504  2.461 0.433     0.129     0.038       19     2.5  bankssts
 1713   1135   3201  2.510 0.624     0.134     0.030       28     2.2  caudalanteriorcingulate
 3644   2389   6596  2.457 0.478     0.129     0.038       50     5.9  caudalmiddlefrontal
 2396   1574   3204  1.850 0.453     0.176     0.069       44     6.9  cuneus
  572    421   1865  3.317 0.877     0.150     0.063        8     1.3  entorhinal
 5110   3446  10213  2.569 0.554     0.147     0.064       98    11.4  fusiform
 9379   6448  17193  2.404 0.504     0.150     0.054      170    20.0  inferiorparietal
 5201   3558  10531  2.379 0.680     0.165     0.079      124    14.8  inferiortemporal
 1900   1247   3334  2.414 0.860     0.154     0.056       33     4.3  isthmuscingulate
 7738   5041  11474  2.048 0.420     0.160     0.066      153    22.1  lateraloccipital
 4217   2842   8516  2.656 0.617     0.157     0.069       85    12.0  lateralorbitofrontal
 4731   3373   6910  1.935 0.535     0.181     0.080      107    15.3  lingual
 2926   1984   5459  2.341 0.706     0.158     0.074       88     8.6  medialorbitofrontal
 5821   4035  13614  2.741 0.634     0.149     0.059      122    15.4  middletemporal
 1046    706   2379  2.942 0.587     0.129     0.041       12     1.7  parahippocampal
 2912   1823   4560  2.336 0.455     0.125     0.045       35     5.8  paracentral
 3475   2367   6522  2.474 0.395     0.133     0.046       55     6.5  parsopercularis
 1400    950   3211  2.645 0.622     0.188     0.086       47     4.5  parsorbitalis
 3276   2220   6186  2.388 0.520     0.146     0.053       63     6.6  parstriangularis
 2260   1544   2143  1.494 0.320     0.156     0.063       31     5.8  pericalcarine
 6873   4419   9459  1.919 0.622     0.125     0.042       88    12.3  postcentral
 2288   1569   4287  2.440 0.809     0.169     0.065       58     6.3  posteriorcingulate
 9038   5721  15299  2.452 0.483     0.122     0.056       99    26.7  precentral
 7451   4973  12470  2.380 0.469     0.138     0.050      115    13.8  precuneus
 1597   1057   3475  2.710 0.528     0.142     0.058       38     3.6  rostralanteriorcingulate
10541   7217  19853  2.382 0.539     0.175     0.099      403    33.1  rostralmiddlefrontal
12639   8537  26379  2.675 0.558     0.144     0.048      194    23.7  superiorfrontal
10631   6954  16075  2.115 0.396     0.130     0.041      147    17.5  superiorparietal
 6297   4245  14153  2.856 0.657     0.138     0.054      111    14.5  superiortemporal
 6728   4451  12177  2.443 0.494     0.137     0.046      109    12.5  supramarginal
  481    319   1027  2.335 0.601     0.204     0.102       22     1.7  frontalpole
  527    401   1932  3.618 0.759     0.203     0.103       16     1.9  temporalpole
  676    430    993  2.142 0.459     0.145     0.054       10     1.4  transversetemporal
 3748   2466   7690  2.880 0.851     0.138     0.071       72    10.8  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Thu Aug  8 22:56:10 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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...
20 labels changed using aseg
relabeling using gibbs priors...
000:  11252 changed, 159726 examined...
001:   2787 changed, 43437 examined...
002:    904 changed, 14416 examined...
003:    421 changed, 5075 examined...
004:    199 changed, 2262 examined...
005:     94 changed, 1109 examined...
006:     56 changed, 507 examined...
007:     22 changed, 284 examined...
008:     14 changed, 116 examined...
009:     10 changed, 80 examined...
010:     10 changed, 58 examined...
011:      5 changed, 51 examined...
012:      3 changed, 31 examined...
013:      1 changed, 18 examined...
014:      1 changed, 7 examined...
015:      1 changed, 7 examined...
016:      0 changed, 7 examined...
10 labels changed using aseg
000: 342 total segments, 256 labels (3703 vertices) changed
001: 117 total segments, 32 labels (234 vertices) changed
002: 88 total segments, 3 labels (22 vertices) changed
003: 85 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 181 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1215 vertices marked for relabeling...
1215 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 1 minutes and 25 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Thu Aug  8 22:57:35 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

 1089    718   1905  2.199 0.585     0.178     0.086       31     4.0  G_and_S_frontomargin
 1532   1035   2721  2.322 0.431     0.147     0.045       25     2.8  G_and_S_occipital_inf
 1508    888   2349  2.266 0.485     0.133     0.149       20    15.1  G_and_S_paracentral
 1760   1169   3324  2.579 0.473     0.150     0.055       30     4.0  G_and_S_subcentral
 1283    871   2491  2.224 0.528     0.190     0.088       50     4.2  G_and_S_transv_frontopol
 3430   2279   6392  2.523 0.477     0.137     0.049       64     6.8  G_and_S_cingul-Ant
 2187   1517   4475  2.715 0.531     0.138     0.040       31     3.4  G_and_S_cingul-Mid-Ant
 1691   1196   3366  2.624 0.590     0.147     0.056       33     4.2  G_and_S_cingul-Mid-Post
  817    545   1999  3.029 0.643     0.180     0.066       21     2.2  G_cingul-Post-dorsal
  390    251    881  2.898 0.719     0.175     0.071        9     1.1  G_cingul-Post-ventral
 2118   1404   2656  1.694 0.442     0.172     0.070       37     6.2  G_cuneus
 2481   1687   5246  2.574 0.381     0.151     0.061       58     6.2  G_front_inf-Opercular
  481    306   1226  2.905 0.365     0.185     0.094       18     1.5  G_front_inf-Orbital
 1889   1287   3820  2.401 0.504     0.165     0.066       44     4.6  G_front_inf-Triangul
 4290   2905  10090  2.690 0.503     0.184     0.125      240    14.8  G_front_middle
 8225   5466  18847  2.750 0.582     0.156     0.056      156    17.2  G_front_sup
  612    382   1398  3.174 0.720     0.138     0.103       19     2.5  G_Ins_lg_and_S_cent_ins
  608    403   2091  3.592 0.746     0.161     0.084       15     1.8  G_insular_short
 2423   1621   4717  2.388 0.464     0.170     0.081       65     7.7  G_occipital_middle
 2231   1422   3644  2.168 0.347     0.153     0.055       43     4.8  G_occipital_sup
 2233   1459   5090  2.720 0.457     0.162     0.078       57     5.5  G_oc-temp_lat-fusifor
 3215   2167   4918  1.953 0.585     0.195     0.094       79    12.2  G_oc-temp_med-Lingual
 1519   1021   4139  3.116 0.841     0.165     0.095       40     6.0  G_oc-temp_med-Parahip
 3017   2030   7523  2.812 0.672     0.190     0.095      100    11.4  G_orbital
 3650   2513   8384  2.595 0.539     0.165     0.060       88     8.8  G_pariet_inf-Angular
 3133   2047   6435  2.554 0.486     0.144     0.051       60     6.4  G_pariet_inf-Supramar
 3519   2273   6201  2.214 0.415     0.138     0.047       58     6.6  G_parietal_sup
 2380   1480   3567  1.944 0.557     0.139     0.060       44     6.0  G_postcentral
 3543   2097   7444  2.713 0.384     0.120     0.043       49     6.5  G_precentral
 3592   2349   6902  2.386 0.485     0.155     0.061       82     8.6  G_precuneus
  812    528   1739  2.334 0.654     0.197     0.134       47     4.5  G_rectus
  516    329   1079  2.802 0.919     0.097     0.042        8     0.6  G_subcallosal
  599    373    918  2.120 0.409     0.158     0.101       28     3.1  G_temp_sup-G_T_transv
 2144   1448   6428  3.222 0.597     0.173     0.078       53     6.7  G_temp_sup-Lateral
  687    477   2006  3.453 0.659     0.152     0.062       11     1.6  G_temp_sup-Plan_polar
 1008    676   1983  2.668 0.411     0.115     0.035       11     1.3  G_temp_sup-Plan_tempo
 3068   2120   7027  2.457 0.718     0.189     0.107      102    11.3  G_temporal_inf
 3587   2490   9985  2.954 0.576     0.167     0.076      101    12.2  G_temporal_middle
  486    319    644  2.185 0.355     0.096     0.023        2     0.4  Lat_Fis-ant-Horizont
  373    252    687  2.582 0.370     0.139     0.041        6     0.6  Lat_Fis-ant-Vertical
 1420    946   1775  2.177 0.507     0.120     0.042       13     2.2  Lat_Fis-post
 3676   2335   4646  1.831 0.401     0.168     0.087       80    14.3  Pole_occipital
 1845   1277   4874  2.828 0.819     0.169     0.081       43     5.6  Pole_temporal
 2810   2074   3555  1.899 0.640     0.162     0.065       54     6.5  S_calcarine
 3021   2013   3081  1.671 0.516     0.113     0.032       20     4.2  S_central
 1649   1105   2257  2.142 0.338     0.114     0.031       12     2.1  S_cingul-Marginalis
  746    503   1354  2.905 0.597     0.121     0.040        5     1.2  S_circular_insula_ant
 1300    881   2198  2.693 0.623     0.097     0.027        6     1.5  S_circular_insula_inf
 1931   1324   2829  2.342 0.437     0.117     0.035       13     3.0  S_circular_insula_sup
  844    604   1469  2.482 0.497     0.108     0.035        8     1.0  S_collat_transv_ant
  438    292    472  1.862 0.351     0.137     0.039        4     0.7  S_collat_transv_post
 3180   2155   5125  2.256 0.435     0.133     0.042       44     5.3  S_front_inf
 2533   1754   4325  2.294 0.483     0.164     0.084       68     6.6  S_front_middle
 3429   2375   5822  2.417 0.407     0.131     0.044       44     6.5  S_front_sup
  649    425    898  2.044 0.324     0.107     0.024        6     0.7  S_interm_prim-Jensen
 4462   2969   5822  2.064 0.392     0.115     0.031       41     5.4  S_intrapariet_and_P_trans
 1075    726   1259  1.849 0.394     0.155     0.048       13     2.1  S_oc_middle_and_Lunatus
 1758   1169   2396  2.159 0.330     0.140     0.039       20     3.0  S_oc_sup_and_transversal
  593    400    807  2.202 0.415     0.138     0.042        8     1.1  S_occipital_ant
 1320    899   2042  2.186 0.477     0.131     0.036       13     2.1  S_oc-temp_lat
 1906   1357   2953  2.419 0.550     0.116     0.030       12     2.3  S_oc-temp_med_and_Lingual
  632    429    785  1.907 0.387     0.147     0.046        7     1.2  S_orbital_lateral
  806    574   1396  2.304 0.807     0.119     0.034        7     1.0  S_orbital_med-olfact
 1553   1070   2744  2.532 0.501     0.154     0.060       24     3.8  S_orbital-H_Shaped
 2134   1448   3045  2.280 0.463     0.138     0.039       24     3.5  S_parieto_occipital
 2333   1482   2788  2.008 0.765     0.139     0.042       38     4.0  S_pericallosal
 3273   2158   3809  1.927 0.395     0.114     0.033       28     4.2  S_postcentral
 2151   1397   3258  2.343 0.389     0.110     0.031       20     2.8  S_precentral-inf-part
 1969   1285   2761  2.417 0.409     0.122     0.034       17     2.8  S_precentral-sup-part
  292    208    364  1.796 0.805     0.150     0.030        3     0.4  S_suborbital
 1722   1180   2679  2.379 0.482     0.121     0.036       15     2.5  S_subparietal
 1430    977   1791  2.047 0.529     0.128     0.033       12     2.0  S_temporal_inf
 7276   5009  12164  2.474 0.453     0.131     0.038       91    11.5  S_temporal_sup
  394    268    606  2.567 0.451     0.124     0.030        3     0.5  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Thu Aug  8 22:58:03 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub011 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...
1453 labels changed using aseg
relabeling using gibbs priors...
000:   3236 changed, 159726 examined...
001:    766 changed, 13731 examined...
002:    198 changed, 4170 examined...
003:     82 changed, 1154 examined...
004:     36 changed, 486 examined...
005:     22 changed, 219 examined...
006:      5 changed, 128 examined...
007:      3 changed, 34 examined...
008:      2 changed, 21 examined...
009:      2 changed, 16 examined...
010:      1 changed, 10 examined...
011:      2 changed, 5 examined...
012:      0 changed, 12 examined...
147 labels changed using aseg
000: 72 total segments, 39 labels (204 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 59 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1100 vertices marked for relabeling...
1100 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 1 minutes and 14 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Thu Aug  8 22:59:17 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 sub011 rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

 1775   1176   3484  2.559 0.638     0.138     0.032       31     2.4  caudalanteriorcingulate
 3758   2456   6760  2.475 0.470     0.130     0.038       52     6.1  caudalmiddlefrontal
 2863   1881   3767  1.857 0.438     0.171     0.066       51     7.7  cuneus
  566    416   1854  3.322 0.892     0.151     0.064        8     1.3  entorhinal
 4506   3053   8831  2.564 0.553     0.141     0.060       79     9.5  fusiform
 8837   6076  16423  2.417 0.500     0.151     0.055      164    19.4  inferiorparietal
 5751   3937  11827  2.404 0.680     0.166     0.081      140    16.6  inferiortemporal
 1888   1242   3287  2.398 0.847     0.154     0.056       33     4.3  isthmuscingulate
 8214   5347  12257  2.058 0.426     0.160     0.066      163    23.2  lateraloccipital
 4667   3157   9620  2.604 0.678     0.169     0.080      114    15.4  lateralorbitofrontal
 4699   3353   6875  1.937 0.535     0.180     0.079      106    14.8  lingual
 2361   1586   4687  2.349 0.782     0.165     0.083       82     7.8  medialorbitofrontal
 6800   4712  15334  2.709 0.616     0.148     0.057      135    16.9  middletemporal
 1001    679   2310  2.920 0.590     0.131     0.042       12     1.7  parahippocampal
 3035   1914   4699  2.321 0.461     0.125     0.044       35     6.0  paracentral
 3744   2548   7261  2.502 0.403     0.138     0.049       66     7.4  parsopercularis
 1507   1016   3232  2.635 0.507     0.161     0.066       38     3.6  parsorbitalis
 3684   2500   6779  2.342 0.499     0.150     0.056       71     8.0  parstriangularis
 2285   1559   2170  1.492 0.323     0.159     0.065       33     6.4  pericalcarine
 7596   4886  10385  1.932 0.620     0.127     0.044       98    13.8  postcentral
 2429   1671   4623  2.469 0.812     0.170     0.065       62     6.8  posteriorcingulate
 8753   5516  14882  2.447 0.488     0.122     0.056       98    26.4  precentral
 7548   5017  12810  2.388 0.459     0.139     0.052      125    14.6  precuneus
 1752   1159   3663  2.697 0.520     0.141     0.056       39     3.9  rostralanteriorcingulate
 6692   4601  12924  2.457 0.546     0.171     0.105      283    19.9  rostralmiddlefrontal
16079  10898  32236  2.582 0.564     0.150     0.056      296    34.2  superiorfrontal
 9332   6119  14292  2.132 0.395     0.127     0.039      120    14.4  superiorparietal
 8176   5542  18499  2.875 0.693     0.145     0.061      161    21.0  superiortemporal
 6287   4171  11145  2.405 0.484     0.134     0.044       98    11.0  supramarginal
  660    418    967  2.138 0.463     0.146     0.055       10     1.4  transversetemporal
 3431   2265   7001  2.842 0.831     0.128     0.058       50     7.9  insula
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR Thu Aug  8 22:59:45 CEST 2013

 bbregister --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta --init-fsl --T2 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat.log
Thu Aug  8 22:59:45 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux snake6 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/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998102, -0.0611237, 0.00753358)
j_ras = (-0.0606425, 0.996759, 0.0528636)
k_ras = (0.0107404, -0.0523064, 0.998573)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii...
fslregister --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fslregister.log

Thu Aug  8 22:59:51 CEST 2013
--s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
snake6
Linux snake6 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/sub011/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.31549e-08, 0)
j_ras = (0, -1.11759e-08, -1)
k_ras = (5.47152e-09, 1, -3.72529e-09)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998102, -0.0611237, 0.00753358)
j_ras = (-0.0606425, 0.996759, 0.0528636)
k_ras = (0.0107404, -0.0523064, 0.998573)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311072
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/reg0.22957.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat0 --s sub011 --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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/reg0.22957.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/sub011/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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 0.998   0.061  -0.008   0.000;
 0.011  -0.052   0.999  -0.000;
 0.061  -0.997  -0.053  -0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.998   0.061  -0.008   0.000;
 0.011  -0.052   0.999  -0.000;
 0.061  -0.997  -0.053  -0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub011
RegMat ---------------------------
 0.998   0.061  -0.008   0.000;
 0.011  -0.052   0.999  -0.000;
 0.061  -0.997  -0.053  -0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311072, ref det = -1
Thu Aug  8 22:59:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat0
Thu Aug  8 23:04:29 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.998   0.056  -0.006   25.361;
-0.003  -0.054  -0.999   262.100;
-0.057   0.997  -0.053   11.865;
 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/sub011/mri/transforms/tmp.bbregister.22917/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/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/sub011/mri/transforms/tmp.bbregister.22917/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI 
fsl2TkReg: mov det = -0.311072, ref det = -1
---- Input registration matrix (computed) --------
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 0.000   0.000   0.000   1.000;
Determinant 0.999999
subject = sub011
RegMat ---------------------------
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 22:59:51 CEST 2013 
Ended   at Thu Aug  8 23:10:51 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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 snake6
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat
subject sub011
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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 1376360729
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 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   1.057876
 1  -25.0 -25.0  25.0   0.998681
 2  -25.0  25.0 -25.0   1.013842
 3  -25.0  25.0  25.0   1.042111
 4   25.0 -25.0 -25.0   0.997035
 5   25.0 -25.0  25.0   1.048967
 6   25.0  25.0 -25.0   1.009851
 7   25.0  25.0  25.0   1.018001
REL:  8  0.203528    8.186364  1.023295 rel = 0.198894 
Initial costs ----------------
Number of surface hits 2995
WM  Intensity    56.5723 +/-   9.2411
Ctx Intensity    70.8426 +/-  10.0568
Pct Contrast     22.4807 +/-  17.0063
Cost   0.2035
RelCost   0.1989

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9896   0.9896  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9788   0.9788  0.0
     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      0.9485   0.9485  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8611   0.8611  0.0
    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.8176   0.8176  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.6454   0.6454  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.2035   0.2035  0.0
Brute Force --------------------------
Min cost was 0.203528
Number of iterations   729
Search time 2.491000 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  0.130  0.000  0.000  0.000  0.000  0.000   0.2034642916
   8  0.074  0.000  0.000  0.000  0.000  0.000   0.2031443284
  10  0.085  0.000  0.000  0.000  0.000  0.000   0.2031342843
  14  0.086  0.000  0.000  0.000  0.000  0.000   0.2031340495
  22  0.086 -0.189  0.000  0.000  0.000  0.000   0.1983937281
  24  0.086 -0.149  0.000  0.000  0.000  0.000   0.1980860239
  28  0.086 -0.144  0.000  0.000  0.000  0.000   0.1980705380
  32  0.086 -0.144  1.000  0.000  0.000  0.000   0.1577640908
  36  0.086 -0.144  0.618  0.000  0.000  0.000   0.1438398302
  37  0.086 -0.144  0.644  0.000  0.000  0.000   0.1426996156
  38  0.086 -0.144  0.728  0.000  0.000  0.000   0.1407010084
  42  0.086 -0.144  0.724  0.000  0.000  0.000   0.1406850420
  44  0.086 -0.144  0.722  0.000  0.000  0.000   0.1406820771
  45  0.086 -0.144  0.721  0.000  0.000  0.000   0.1406815801
  53  0.086 -0.144  0.721 -0.152  0.000  0.000   0.1373417461
  58  0.086 -0.144  0.721 -0.155  0.000  0.000   0.1373175690
  59  0.086 -0.144  0.721 -0.158  0.000  0.000   0.1373110666
  70  0.086 -0.144  0.721 -0.158 -0.014  0.000   0.1372380844
  74  0.086 -0.144  0.721 -0.158 -0.018  0.000   0.1372318346
  85  0.086 -0.144  0.721 -0.158 -0.018  0.011   0.1371067201
  86  0.086 -0.144  0.721 -0.158 -0.018  0.014   0.1371022266
  95  0.119 -0.199  0.997 -0.218 -0.025  0.019   0.1347986883
  96  0.109 -0.181  0.908 -0.199 -0.023  0.018   0.1327542424
  97  0.106 -0.177  0.884 -0.194 -0.022  0.017   0.1321923342
  99  0.103 -0.172  0.861 -0.189 -0.022  0.017   0.1319468574
 100  0.103 -0.172  0.859 -0.188 -0.022  0.017   0.1319444511
 109  0.011 -0.172  0.859 -0.188 -0.022  0.017   0.1317341795
 110  0.048 -0.172  0.859 -0.188 -0.022  0.017   0.1313706473
 112  0.038 -0.172  0.859 -0.188 -0.022  0.017   0.1312968957
 114  0.037 -0.172  0.859 -0.188 -0.022  0.017   0.1312965202
 122  0.037 -0.138  0.859 -0.188 -0.022  0.017   0.1305159360
 124  0.037 -0.132  0.859 -0.188 -0.022  0.017   0.1304955314
 134  0.037 -0.132  0.859 -0.188 -0.022  0.000   0.1303771844
 135  0.037 -0.132  0.859 -0.188 -0.022 -0.005   0.1303738252
 136  0.037 -0.132  0.859 -0.188 -0.022 -0.004   0.1303726948
 137  0.037 -0.132  0.859 -0.188 -0.022 -0.003   0.1303725804
 147  0.037 -0.132  0.859 -0.182 -0.022 -0.003   0.1303205523
 148  0.037 -0.132  0.859 -0.180 -0.022 -0.003   0.1303156177
 149  0.037 -0.132  0.859 -0.179 -0.022 -0.003   0.1303153989
 157  0.037 -0.132  0.859 -0.179 -0.095 -0.003   0.1287691551
 160  0.037 -0.132  0.859 -0.179 -0.103 -0.003   0.1287197687
 162  0.037 -0.132  0.859 -0.179 -0.107 -0.003   0.1287177795
 172  0.046 -0.146  0.932 -0.195 -0.108 -0.001   0.1276837702
 174  0.044 -0.142  0.912 -0.190 -0.108 -0.001   0.1275393465
 175  0.044 -0.143  0.913 -0.191 -0.108 -0.001   0.1275355191
 177  0.044 -0.143  0.914 -0.191 -0.108 -0.001   0.1275350705
 187  0.032 -0.143  0.914 -0.191 -0.108 -0.001   0.1274689031
 188  0.034 -0.143  0.914 -0.191 -0.108 -0.001   0.1274682212
 198  0.034 -0.125  0.914 -0.191 -0.108 -0.001   0.1274375066
 199  0.034 -0.133  0.914 -0.191 -0.108 -0.001   0.1273856814
 200  0.034 -0.132  0.914 -0.191 -0.108 -0.001   0.1273855168
 210  0.034 -0.132  0.914 -0.191 -0.108  0.005   0.1273372907
 211  0.034 -0.132  0.914 -0.191 -0.108  0.007   0.1273334255
 212  0.034 -0.132  0.914 -0.191 -0.108  0.006   0.1273333726
 222  0.034 -0.132  0.914 -0.197 -0.108  0.006   0.1273089560
 223  0.034 -0.132  0.914 -0.196 -0.108  0.006   0.1273074994
 224  0.034 -0.132  0.914 -0.195 -0.108  0.006   0.1273073781
 234  0.034 -0.132  0.914 -0.195 -0.087  0.006   0.1272798768
 235  0.034 -0.132  0.914 -0.195 -0.097  0.006   0.1272034896
 246  0.034 -0.132  0.915 -0.195 -0.097  0.006   0.1272033727
 277  0.034 -0.132  0.915 -0.195 -0.097  0.008   0.1272005113
 278  0.034 -0.132  0.915 -0.195 -0.097  0.009   0.1271987565
 289  0.034 -0.132  0.915 -0.198 -0.097  0.009   0.1271953611
 291  0.034 -0.132  0.915 -0.197 -0.097  0.009   0.1271936604
 300  0.034 -0.132  0.915 -0.197 -0.095  0.009   0.1271935051
Powell done niters = 3
Computing relative cost
 0  -25.0 -25.0 -25.0   1.037065
 1  -25.0 -25.0  25.0   0.998962
 2  -25.0  25.0 -25.0   1.011347
 3  -25.0  25.0  25.0   1.042337
 4   25.0 -25.0 -25.0   0.994005
 5   25.0 -25.0  25.0   1.033060
 6   25.0  25.0 -25.0   0.990798
 7   25.0  25.0  25.0   1.017536
REL:  8  0.127194    8.125111  1.015639 rel = 0.125235 
Number of iterations     3
Min cost was 0.127194
Number of FunctionCalls   312
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.987000 sec
Parameters at optimum (transmm)  0.03368 -0.13187  0.91475
Parameters at optimum (rotdeg) -0.19683 -0.09497  0.00918 
Final costs ----------------
Number of surface hits 2995
WM  Intensity    56.3299 +/-   8.8332
Ctx Intensity    70.5509 +/-   9.3439
Pct Contrast     22.5565 +/-  15.1786
Cost   0.1272
RelCost   0.1989
Reg at min cost was 
 0.998   0.058  -0.003  -0.359;
 0.006  -0.057   0.998  -1.018;
 0.058  -0.997  -0.057   0.168;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat, type = 14 
Original Reg 
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000  -0.002   0.000  -0.035;
-0.000   0.003   0.000   0.135;
-0.002  -0.000   0.003  -0.917;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.752483
Computing change in rh position
Surface RMS Diff (mm) 0.794010 1.036774
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat
subject sub011
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1376192635
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.998   0.058  -0.003  -0.359;
 0.006  -0.057   0.998  -1.018;
 0.058  -0.997  -0.057   0.168;
 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   1.018187
 1  -25.0 -25.0  25.0   0.995931
 2  -25.0  25.0 -25.0   1.003818
 3  -25.0  25.0  25.0   1.024126
 4   25.0 -25.0 -25.0   1.007993
 5   25.0 -25.0  25.0   1.014129
 6   25.0  25.0 -25.0   1.009329
 7   25.0  25.0  25.0   1.009792
REL:  8  0.139924    8.083305  1.010413 rel = 0.138482 
Initial costs ----------------
Number of surface hits 299567
WM  Intensity    56.3035 +/-   8.8680
Ctx Intensity    70.8888 +/-   9.3725
Pct Contrast     23.0747 +/-  15.5948
Cost   0.1399
RelCost   0.1385

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.1456   0.1456  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.1405   0.1405  0.0
     6  -0.1000  -0.1000  -0.1000  -0.1000   0.1000  -0.1000      0.1399   0.1399  0.0
     9  -0.1000  -0.1000  -0.1000   0.0000  -0.1000  -0.1000      0.1398   0.1398  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.1367   0.1367  0.0
    21  -0.1000  -0.1000  -0.1000   0.1000   0.0000  -0.1000      0.1366   0.1366  0.0
    30  -0.1000  -0.1000   0.0000  -0.1000   0.0000  -0.1000      0.1360   0.1360  0.0
    36  -0.1000  -0.1000   0.0000   0.0000  -0.1000  -0.1000      0.1350   0.1350  0.0
    39  -0.1000  -0.1000   0.0000   0.0000   0.0000  -0.1000      0.1325   0.1325  0.0
   120  -0.1000   0.0000   0.0000   0.0000   0.0000  -0.1000      0.1295   0.1295  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.1272   0.1272  0.0
Brute Force --------------------------
Min cost was 0.127194
Number of iterations   729
Search time 2.437000 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
   8  0.003  0.000  0.000  0.000  0.000  0.000   0.1399238739
   9  0.002  0.000  0.000  0.000  0.000  0.000   0.1399237850
  18  0.001 -0.011  0.000  0.000  0.000  0.000   0.1399164532
  19  0.001 -0.008  0.000  0.000  0.000  0.000   0.1399159395
  28  0.001 -0.008 -0.025  0.000  0.000  0.000   0.1398514145
  29  0.001 -0.008 -0.024  0.000  0.000  0.000   0.1398509487
  30  0.001 -0.008 -0.023  0.000  0.000  0.000   0.1398503664
  34  0.001 -0.008 -0.022  0.000  0.000  0.000   0.1398503202
  42  0.001 -0.008 -0.022 -0.012  0.000  0.000   0.1398157908
  43  0.001 -0.008 -0.022 -0.013  0.000  0.000   0.1398155572
  51  0.001 -0.008 -0.022 -0.013  0.048  0.000   0.1396358289
  54  0.001 -0.008 -0.022 -0.013  0.049  0.000   0.1396356576
  62  0.001 -0.008 -0.022 -0.013  0.049 -0.043   0.1396089500
  63  0.001 -0.008 -0.022 -0.013  0.049 -0.025   0.1395775731
  64  0.001 -0.008 -0.022 -0.013  0.049 -0.026   0.1395773433
  65  0.001 -0.008 -0.022 -0.013  0.049 -0.027   0.1395772903
  76  0.004 -0.008 -0.022 -0.013  0.049 -0.027   0.1395741771
  77  0.007 -0.008 -0.022 -0.013  0.049 -0.027   0.1395736245
  87  0.007 -0.006 -0.022 -0.013  0.049 -0.027   0.1395723785
  97  0.007 -0.006 -0.021 -0.013  0.049 -0.027   0.1395723097
 106  0.007 -0.006 -0.021 -0.014  0.049 -0.027   0.1395709356
 107  0.007 -0.006 -0.021 -0.016  0.049 -0.027   0.1395702076
 117  0.007 -0.006 -0.021 -0.016  0.052 -0.027   0.1395691506
 118  0.007 -0.006 -0.021 -0.016  0.051 -0.027   0.1395690480
 126  0.007 -0.006 -0.021 -0.016  0.051 -0.019   0.1395681076
 127  0.007 -0.006 -0.021 -0.016  0.051 -0.022   0.1395668976
 130  0.012 -0.003 -0.020 -0.019  0.053 -0.018   0.1395662622
 149  0.009 -0.007 -0.021 -0.016  0.051 -0.022   0.1395658813
 158  0.009 -0.007 -0.018 -0.016  0.051 -0.022   0.1395655102
 168  0.009 -0.007 -0.018 -0.017  0.051 -0.022   0.1395648956
 169  0.009 -0.007 -0.018 -0.018  0.051 -0.022   0.1395645236
 190  0.009 -0.007 -0.018 -0.018  0.051 -0.020   0.1395640269
 192  0.012 -0.008 -0.016 -0.020  0.051 -0.019   0.1395621190
 195  0.016 -0.010 -0.012 -0.023  0.051 -0.016   0.1395602555
 199  0.017 -0.010 -0.011 -0.024  0.051 -0.015   0.1395601198
 218  0.018 -0.010 -0.011 -0.024  0.051 -0.015   0.1395600548
 229  0.018 -0.009 -0.011 -0.024  0.051 -0.015   0.1395600195
 237  0.018 -0.009 -0.008 -0.024  0.051 -0.015   0.1395597334
 248  0.018 -0.009 -0.008 -0.024  0.051 -0.016   0.1395596285
 265  0.019 -0.010 -0.007 -0.025  0.051 -0.015   0.1395595386
 266  0.019 -0.010 -0.007 -0.025  0.051 -0.015   0.1395595061
 267  0.019 -0.009 -0.008 -0.025  0.051 -0.015   0.1395594792
 313  0.018 -0.009 -0.008 -0.025  0.051 -0.016   0.1395594687
 331  0.018 -0.010 -0.007 -0.025  0.051 -0.016   0.1395594184
 334  0.018 -0.010 -0.007 -0.025  0.051 -0.016   0.1395594180
 363  0.018 -0.010 -0.006 -0.025  0.051 -0.016   0.1395593736
 402  0.018 -0.010 -0.006 -0.025  0.051 -0.016   0.1395593565
 465  0.018 -0.010 -0.006 -0.025  0.051 -0.016   0.1395593556
Powell done niters = 6
Computing relative cost
 0  -25.0 -25.0 -25.0   1.018320
 1  -25.0 -25.0  25.0   0.995785
 2  -25.0  25.0 -25.0   1.004295
 3  -25.0  25.0  25.0   1.023517
 4   25.0 -25.0 -25.0   1.007522
 5   25.0 -25.0  25.0   1.014657
 6   25.0  25.0 -25.0   1.009360
 7   25.0  25.0  25.0   1.009739
REL:  8  0.139559    8.083193  1.010399 rel = 0.138123 
Number of iterations     6
Min cost was 0.139559
Number of FunctionCalls   468
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 167.267000 sec
Parameters at optimum (transmm)  0.01814 -0.00967 -0.00607
Parameters at optimum (rotdeg) -0.02500  0.05113 -0.01611 
Final costs ----------------
Number of surface hits 299567
WM  Intensity    56.3029 +/-   8.8562
Ctx Intensity    70.8842 +/-   9.3684
Pct Contrast     23.0685 +/-  15.5751
Cost   0.1396
RelCost   0.1385
Reg at min cost was 
 0.998   0.057  -0.003  -0.341;
 0.006  -0.057   0.998  -1.028;
 0.057  -0.997  -0.057   0.163;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.998   0.058  -0.003  -0.359;
 0.006  -0.057   0.998  -1.018;
 0.058  -0.997  -0.057   0.168;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000   0.001  -0.000  -0.018;
 0.000   0.000   0.000   0.009;
 0.001   0.000   0.000   0.005;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.064368
Computing change in rh position
Surface RMS Diff (mm) 0.071316 0.123242
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
 0.998   0.057  -0.003  -0.341;
 0.006  -0.057   0.998  -1.028;
 0.057  -0.997  -0.057   0.163;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 0.998   0.057  -0.003  -0.341;
 0.006  -0.057   0.998  -1.028;
 0.057  -0.997  -0.057   0.163;
 0.000   0.000   0.000   1.000;
Determinant 0.999999
subject = sub011
RegMat ---------------------------
 0.998   0.057  -0.003  -0.341;
 0.006  -0.057   0.998  -1.028;
 0.057  -0.997  -0.057   0.163;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000   0.004  -0.005   0.079;
-0.004   1.000  -0.005  -0.004;
 0.005   0.005   1.000   0.861;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.699   0.038  -0.004   25.386;
-0.002  -0.038  -0.666   262.359;
-0.040   0.664  -0.038   13.360;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 22:59:45 CEST 2013 
Ended   at Thu Aug  8 23:15:42 CEST 2013
BBR-Run-Time-Sec 956
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat --surf
 

 mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/T2.mgz 

mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998102, -0.0611237, 0.00753358)
j_ras = (-0.0606425, 0.996759, 0.0528636)
k_ras = (0.0107404, -0.0523064, 0.998573)
INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
reading extra input line subject sub011
reading extra input line fscale 0.150000
reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig.mgz...
INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
 1.000   0.004  -0.005   0.079;
-0.004   1.000  -0.005  -0.004;
 0.005   0.005   1.000   0.861;
 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/sub011/mri/T2.mgz...

 mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/T2.mgz...
computing distance transform
computing distance transform
computing nonmaximum suppression
18829 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/sub011/mri/T2.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub011 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/sub011/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
19648 bright wm thresholded.
948 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.orig...
computing class statistics...
border white:    292650 voxels (1.74%)
border gray      329335 voxels (1.96%)
WM (92.0): 93.5 +- 9.7 [70.0 --> 110.0]
GM (76.0) : 74.2 +- 13.1 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.9 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 33.8 (was 40)
setting MAX_GRAY to 94.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.6 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104,    GM=60
mean inside = 93.0, mean outside = 69.3
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/sub011/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.25 (0.04-->4.35) (max @ vno 120419 --> 121336)
face area 0.34 +- 0.16 (0.00-->2.85)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 3 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 16 points - only 0.00% unknown
deleting segment 6 with 811 points - only 0.00% unknown
deleting segment 8 with 31 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 6 points - only 0.00% unknown
deleting segment 14 with 8 points - only 0.00% unknown
deleting segment 15 with 5 points - only 0.00% unknown
deleting segment 16 with 47 points - only 0.00% unknown
deleting segment 17 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 18 with 1 points - only 0.00% unknown
tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.25 (0.06-->4.08) (max @ vno 76660 --> 75430)
face area 0.34 +- 0.16 (0.00-->2.85)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5097399.5, rms=0.00
rms = 1.34, time step reduction 1 of 3 to 0.250...
rms = 0.35, 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=5097399.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
deleting segment 4 with 16 points - only 0.00% unknown
deleting segment 5 with 811 points - only 0.00% unknown
deleting segment 6 with 31 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
deleting segment 14 with 47 points - only 0.00% unknown
deleting segment 15 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 16 with 1 points - only 0.00% unknown
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.06-->4.08) (max @ vno 76660 --> 75430)
face area 0.34 +- 0.16 (0.00-->2.85)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5097399.5, rms=0.00
rms = 1.34, time step reduction 1 of 3 to 0.250...
rms = 0.35, 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=5097399.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
deleting segment 4 with 16 points - only 0.00% unknown
deleting segment 5 with 811 points - only 0.00% unknown
deleting segment 6 with 31 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
deleting segment 14 with 47 points - only 0.00% unknown
deleting segment 15 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 16 with 1 points - only 0.00% unknown
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.06-->4.08) (max @ vno 76660 --> 75430)
face area 0.34 +- 0.16 (0.00-->2.85)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5097399.5, rms=0.00
rms = 1.34, time step reduction 1 of 3 to 0.250...
rms = 0.35, 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=5097399.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 0 with 3 points - only 0.00% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
deleting segment 4 with 16 points - only 0.00% unknown
deleting segment 5 with 811 points - only 0.00% unknown
deleting segment 6 with 31 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
deleting segment 9 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
deleting segment 14 with 47 points - only 0.00% unknown
deleting segment 15 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 16 with 1 points - only 0.00% unknown
tol=1.0e-04, sigma=0.2, host=snake, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5097399.5, rms=0.00
rms = 1.34, time step reduction 1 of 3 to 0.250...
rms = 0.35, 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=5097399.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
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 [96.00 222.00], gm=159.00+-21.00, and vertices in regions > 148.5
33588 surface locations found to contain inconsistent values (4191 in, 29397 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=579143.0, rms=0.22
001: dt: 0.5000, sse=543734.5, rms=0.215 (0.000%)
002: dt: 0.5000, sse=522328.2, rms=0.203 (0.000%)
003: dt: 0.5000, sse=508482.0, rms=0.194 (0.000%)
004: dt: 0.5000, sse=498241.7, rms=0.187 (0.000%)
005: dt: 0.5000, sse=490733.8, rms=0.180 (0.000%)
006: dt: 0.5000, sse=485137.5, rms=0.174 (0.000%)
007: dt: 0.5000, sse=481224.1, rms=0.169 (0.000%)
008: dt: 0.5000, sse=478117.3, rms=0.164 (0.000%)
009: dt: 0.5000, sse=475359.8, rms=0.161 (0.000%)
010: dt: 0.5000, sse=473671.0, rms=0.157 (0.000%)
011: dt: 0.5000, sse=471807.7, rms=0.155 (0.000%)
012: dt: 0.5000, sse=469805.4, rms=0.153 (0.000%)
013: dt: 0.5000, sse=467931.1, rms=0.151 (0.000%)
014: dt: 0.5000, sse=465915.2, rms=0.149 (0.000%)
015: dt: 0.5000, sse=464230.7, rms=0.148 (0.000%)
016: dt: 0.5000, sse=462990.1, rms=0.147 (0.000%)
017: dt: 0.5000, sse=461627.8, rms=0.146 (0.000%)
018: dt: 0.5000, sse=460109.9, rms=0.146 (0.000%)
019: dt: 0.5000, sse=458580.4, rms=0.145 (0.000%)
020: dt: 0.5000, sse=457147.6, rms=0.145 (0.000%)
021: dt: 0.5000, sse=455719.2, rms=0.145 (0.000%)
022: dt: 0.5000, sse=454223.4, rms=0.144 (0.000%)
023: dt: 0.5000, sse=453087.3, rms=0.145 (0.000%)
024: dt: 0.5000, sse=451466.9, rms=0.145 (0.000%)
025: dt: 0.5000, sse=450565.6, rms=0.145 (0.000%)
026: dt: 0.5000, sse=449091.8, rms=0.145 (0.000%)
027: dt: 0.5000, sse=447970.5, rms=0.145 (0.000%)
028: dt: 0.5000, sse=446655.2, rms=0.145 (0.000%)
029: dt: 0.5000, sse=445560.3, rms=0.146 (0.000%)
030: dt: 0.5000, sse=444394.9, rms=0.146 (0.000%)
positioning took 4.2 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [92.60 223.40], gm=158.00+-21.80, and vertices in regions > 147.1
26694 surface locations found to contain inconsistent values (1107 in, 25587 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=46144.3, rms=0.12
031: dt: 0.5000, sse=45886.8, rms=0.119 (0.000%)
032: dt: 0.5000, sse=46832.3, rms=0.109 (0.000%)
033: dt: 0.5000, sse=47972.2, rms=0.101 (0.000%)
034: dt: 0.5000, sse=48957.8, rms=0.096 (0.000%)
035: dt: 0.5000, sse=49832.3, rms=0.091 (0.000%)
036: dt: 0.5000, sse=50665.0, rms=0.087 (0.000%)
037: dt: 0.5000, sse=51462.3, rms=0.082 (0.000%)
038: dt: 0.5000, sse=52260.4, rms=0.078 (0.000%)
039: dt: 0.5000, sse=53058.8, rms=0.075 (0.000%)
040: dt: 0.5000, sse=53835.5, rms=0.071 (0.000%)
041: dt: 0.5000, sse=54601.3, rms=0.068 (0.000%)
042: dt: 0.5000, sse=55297.1, rms=0.065 (0.000%)
043: dt: 0.5000, sse=55947.0, rms=0.063 (0.000%)
044: dt: 0.5000, sse=56574.3, rms=0.060 (0.000%)
045: dt: 0.5000, sse=57183.2, rms=0.058 (0.000%)
046: dt: 0.5000, sse=57735.0, rms=0.056 (0.000%)
047: dt: 0.5000, sse=58241.3, rms=0.054 (0.000%)
048: dt: 0.5000, sse=58708.5, rms=0.052 (0.000%)
049: dt: 0.5000, sse=59163.7, rms=0.051 (0.000%)
050: dt: 0.5000, sse=59584.9, rms=0.049 (0.000%)
051: dt: 0.5000, sse=59956.4, rms=0.048 (0.000%)
052: dt: 0.5000, sse=60316.7, rms=0.047 (0.000%)
053: dt: 0.5000, sse=60633.4, rms=0.046 (0.000%)
054: dt: 0.5000, sse=60933.5, rms=0.045 (0.000%)
055: dt: 0.5000, sse=61227.5, rms=0.044 (0.000%)
056: dt: 0.5000, sse=61479.4, rms=0.043 (0.000%)
057: dt: 0.5000, sse=61720.0, rms=0.042 (0.000%)
058: dt: 0.5000, sse=61936.4, rms=0.041 (0.000%)
059: dt: 0.5000, sse=62120.2, rms=0.041 (0.000%)
060: dt: 0.5000, sse=62331.4, rms=0.040 (0.000%)
positioning took 4.2 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [92.00 224.00], gm=158.00+-22.00, and vertices in regions > 147.0
25567 surface locations found to contain inconsistent values (247 in, 25320 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=6599.8, rms=0.05
061: dt: 0.5000, sse=6588.7, rms=0.048 (0.000%)
062: dt: 0.5000, sse=6661.1, rms=0.044 (0.000%)
063: dt: 0.5000, sse=6721.1, rms=0.041 (0.000%)
064: dt: 0.5000, sse=6770.9, rms=0.038 (0.000%)
065: dt: 0.5000, sse=6804.1, rms=0.037 (0.000%)
066: dt: 0.5000, sse=6822.4, rms=0.035 (0.000%)
067: dt: 0.5000, sse=6832.7, rms=0.034 (0.000%)
068: dt: 0.5000, sse=6839.2, rms=0.033 (0.000%)
069: dt: 0.5000, sse=6844.1, rms=0.032 (0.000%)
070: dt: 0.5000, sse=6849.5, rms=0.031 (0.000%)
071: dt: 0.5000, sse=6854.8, rms=0.030 (0.000%)
072: dt: 0.5000, sse=6860.6, rms=0.029 (0.000%)
073: dt: 0.5000, sse=6869.8, rms=0.028 (0.000%)
074: dt: 0.5000, sse=6877.9, rms=0.028 (0.000%)
075: dt: 0.5000, sse=6883.4, rms=0.027 (0.000%)
076: dt: 0.5000, sse=6885.9, rms=0.026 (0.000%)
077: dt: 0.5000, sse=6889.6, rms=0.026 (0.000%)
078: dt: 0.5000, sse=6894.8, rms=0.025 (0.000%)
079: dt: 0.5000, sse=6898.4, rms=0.025 (0.000%)
080: dt: 0.5000, sse=6904.9, rms=0.024 (0.000%)
081: dt: 0.5000, sse=6908.6, rms=0.024 (0.000%)
082: dt: 0.5000, sse=6912.8, rms=0.024 (0.000%)
083: dt: 0.5000, sse=6917.1, rms=0.023 (0.000%)
084: dt: 0.5000, sse=6920.4, rms=0.023 (0.000%)
085: dt: 0.5000, sse=6925.6, rms=0.023 (0.000%)
086: dt: 0.5000, sse=6927.1, rms=0.023 (0.000%)
087: dt: 0.5000, sse=6930.3, rms=0.022 (0.000%)
088: dt: 0.5000, sse=6932.2, rms=0.022 (0.000%)
089: dt: 0.5000, sse=6934.7, rms=0.022 (0.000%)
090: dt: 0.5000, sse=6938.1, rms=0.022 (0.000%)
positioning took 4.2 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [92.00 224.00], gm=158.00+-22.00, and vertices in regions > 147.0
25331 surface locations found to contain inconsistent values (61 in, 25270 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/sub011/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=807.6, rms=0.03
091: dt: 0.5000, sse=806.8, rms=0.028 (0.000%)
092: dt: 0.5000, sse=798.8, rms=0.027 (0.000%)
093: dt: 0.5000, sse=792.7, rms=0.026 (0.000%)
094: dt: 0.5000, sse=787.4, rms=0.025 (0.000%)
095: dt: 0.5000, sse=782.6, rms=0.025 (0.000%)
096: dt: 0.5000, sse=778.9, rms=0.024 (0.000%)
097: dt: 0.5000, sse=776.2, rms=0.024 (0.000%)
098: dt: 0.5000, sse=774.1, rms=0.024 (0.000%)
099: dt: 0.5000, sse=772.4, rms=0.023 (0.000%)
100: dt: 0.5000, sse=770.2, rms=0.023 (0.000%)
101: dt: 0.5000, sse=769.0, rms=0.023 (0.000%)
102: dt: 0.5000, sse=766.5, rms=0.022 (0.000%)
103: dt: 0.5000, sse=764.3, rms=0.022 (0.000%)
104: dt: 0.5000, sse=762.4, rms=0.022 (0.000%)
105: dt: 0.5000, sse=760.7, rms=0.022 (0.000%)
106: dt: 0.5000, sse=759.3, rms=0.021 (0.000%)
107: dt: 0.5000, sse=758.7, rms=0.021 (0.000%)
108: dt: 0.5000, sse=757.9, rms=0.021 (0.000%)
109: dt: 0.5000, sse=757.2, rms=0.021 (0.000%)
110: dt: 0.5000, sse=756.8, rms=0.021 (0.000%)
111: dt: 0.5000, sse=756.1, rms=0.021 (0.000%)
112: dt: 0.5000, sse=755.2, rms=0.021 (0.000%)
113: dt: 0.5000, sse=754.5, rms=0.020 (0.000%)
114: dt: 0.5000, sse=753.9, rms=0.020 (0.000%)
115: dt: 0.5000, sse=753.4, rms=0.020 (0.000%)
116: dt: 0.5000, sse=753.6, rms=0.020 (0.000%)
117: dt: 0.5000, sse=753.3, rms=0.020 (0.000%)
118: dt: 0.5000, sse=753.2, rms=0.020 (0.000%)
119: dt: 0.5000, sse=752.8, rms=0.020 (0.000%)
120: dt: 0.5000, sse=752.6, rms=0.020 (0.000%)
positioning took 4.1 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.area.pial
vertex spacing 1.02 +- 0.43 (0.03-->8.04) (max @ vno 111042 --> 112201)
face area 0.41 +- 0.31 (0.00-->6.37)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 158499 vertices processed
25000 of 158499 vertices processed
50000 of 158499 vertices processed
75000 of 158499 vertices processed
100000 of 158499 vertices processed
125000 of 158499 vertices processed
150000 of 158499 vertices processed
0 of 158499 vertices processed
25000 of 158499 vertices processed
50000 of 158499 vertices processed
75000 of 158499 vertices processed
100000 of 158499 vertices processed
125000 of 158499 vertices processed
150000 of 158499 vertices processed
thickness calculation complete, 350:737 truncations.
34686 vertices at 0 distance
110927 vertices at 1 distance
101233 vertices at 2 distance
40584 vertices at 3 distance
11335 vertices at 4 distance
3143 vertices at 5 distance
996 vertices at 6 distance
328 vertices at 7 distance
124 vertices at 8 distance
54 vertices at 9 distance
31 vertices at 10 distance
14 vertices at 11 distance
13 vertices at 12 distance
7 vertices at 13 distance
10 vertices at 14 distance
7 vertices at 15 distance
5 vertices at 16 distance
4 vertices at 17 distance
0 vertices at 18 distance
4 vertices at 19 distance
9 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.thickness
positioning took 20.6 minutes
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub011 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/sub011/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
20244 bright wm thresholded.
947 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.orig...
computing class statistics...
border white:    292650 voxels (1.74%)
border gray      329335 voxels (1.96%)
WM (92.0): 93.5 +- 10.0 [70.0 --> 110.0]
GM (76.0) : 74.1 +- 12.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.1 (was 70)
setting MAX_BORDER_WHITE to 115.0 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.2 (was 40)
setting MAX_GRAY to 95.0 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.4 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 93.3, mean outside = 69.4
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/sub011/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.26 (0.04-->5.62) (max @ vno 159481 --> 159523)
face area 0.33 +- 0.16 (0.00-->9.01)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 8 with 533 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
deleting segment 13 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 with 1 points - only 0.00% unknown
deleting segment 16 with 7 points - only 0.00% unknown
deleting segment 17 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 18 with 2 points - only 0.00% unknown
deleting segment 19 with 16 points - only 0.00% unknown
tol=1.0e-04, sigma=2.0, host=snake, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.25 (0.05-->5.62) (max @ vno 159481 --> 159523)
face area 0.33 +- 0.16 (0.00-->9.01)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5228024.0, rms=0.00
rms = 1.17, 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=5228024.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
deleting segment 4 with 533 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
deleting segment 7 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 16 points - only 0.00% unknown
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.05-->5.62) (max @ vno 159481 --> 159523)
face area 0.33 +- 0.16 (0.00-->9.01)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5228024.0, rms=0.00
rms = 1.17, 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=5228024.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
deleting segment 4 with 533 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
deleting segment 7 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 16 points - only 0.00% unknown
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.05-->5.62) (max @ vno 159481 --> 159523)
face area 0.33 +- 0.16 (0.00-->9.01)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5228024.0, rms=0.00
rms = 1.17, 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=5228024.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
deleting segment 4 with 533 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
deleting segment 7 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 16 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=5228024.0, rms=0.00
rms = 1.17, 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=5228024.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
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 [98.40 219.60], gm=159.00+-20.20, and vertices in regions > 148.9
37368 surface locations found to contain inconsistent values (6251 in, 31117 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=593587.2, rms=0.23
001: dt: 0.5000, sse=556116.8, rms=0.219 (0.000%)
002: dt: 0.5000, sse=534006.2, rms=0.206 (0.000%)
003: dt: 0.5000, sse=520517.3, rms=0.197 (0.000%)
004: dt: 0.5000, sse=510310.8, rms=0.189 (0.000%)
005: dt: 0.5000, sse=503439.6, rms=0.182 (0.000%)
006: dt: 0.5000, sse=498120.3, rms=0.176 (0.000%)
007: dt: 0.5000, sse=493928.0, rms=0.170 (0.000%)
008: dt: 0.5000, sse=490564.3, rms=0.166 (0.000%)
009: dt: 0.5000, sse=487583.5, rms=0.162 (0.000%)
010: dt: 0.5000, sse=485813.7, rms=0.158 (0.000%)
011: dt: 0.5000, sse=483978.0, rms=0.156 (0.000%)
012: dt: 0.5000, sse=482284.1, rms=0.153 (0.000%)
013: dt: 0.5000, sse=480515.2, rms=0.151 (0.000%)
014: dt: 0.5000, sse=479003.7, rms=0.150 (0.000%)
015: dt: 0.5000, sse=477497.9, rms=0.148 (0.000%)
016: dt: 0.5000, sse=476095.7, rms=0.147 (0.000%)
017: dt: 0.5000, sse=474579.2, rms=0.146 (0.000%)
018: dt: 0.5000, sse=473293.8, rms=0.145 (0.000%)
019: dt: 0.5000, sse=472160.0, rms=0.145 (0.000%)
020: dt: 0.5000, sse=470798.0, rms=0.144 (0.000%)
021: dt: 0.5000, sse=469630.6, rms=0.144 (0.000%)
022: dt: 0.5000, sse=468210.7, rms=0.144 (0.000%)
023: dt: 0.5000, sse=467027.4, rms=0.144 (0.000%)
024: dt: 0.5000, sse=465823.0, rms=0.144 (0.000%)
025: dt: 0.5000, sse=464833.6, rms=0.144 (0.000%)
026: dt: 0.5000, sse=463456.4, rms=0.144 (0.000%)
027: dt: 0.5000, sse=462114.9, rms=0.144 (0.000%)
028: dt: 0.5000, sse=461239.4, rms=0.144 (0.000%)
029: dt: 0.5000, sse=460058.2, rms=0.144 (0.000%)
030: dt: 0.5000, sse=459035.3, rms=0.145 (0.000%)
positioning took 4.2 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [91.20 226.80], gm=159.00+-22.60, and vertices in regions > 147.7
28298 surface locations found to contain inconsistent values (845 in, 27453 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=47563.4, rms=0.12
031: dt: 0.5000, sse=47229.2, rms=0.117 (0.000%)
032: dt: 0.5000, sse=47999.2, rms=0.106 (0.000%)
033: dt: 0.5000, sse=49027.1, rms=0.099 (0.000%)
034: dt: 0.5000, sse=49949.0, rms=0.094 (0.000%)
035: dt: 0.5000, sse=50843.3, rms=0.089 (0.000%)
036: dt: 0.5000, sse=51689.9, rms=0.084 (0.000%)
037: dt: 0.5000, sse=52478.7, rms=0.080 (0.000%)
038: dt: 0.5000, sse=53272.0, rms=0.077 (0.000%)
039: dt: 0.5000, sse=54032.8, rms=0.073 (0.000%)
040: dt: 0.5000, sse=54793.0, rms=0.070 (0.000%)
041: dt: 0.5000, sse=55538.6, rms=0.067 (0.000%)
042: dt: 0.5000, sse=56232.8, rms=0.064 (0.000%)
043: dt: 0.5000, sse=56866.3, rms=0.061 (0.000%)
044: dt: 0.5000, sse=57474.3, rms=0.059 (0.000%)
045: dt: 0.5000, sse=58067.8, rms=0.056 (0.000%)
046: dt: 0.5000, sse=58601.0, rms=0.054 (0.000%)
047: dt: 0.5000, sse=59124.8, rms=0.052 (0.000%)
048: dt: 0.5000, sse=59599.1, rms=0.051 (0.000%)
049: dt: 0.5000, sse=60038.2, rms=0.049 (0.000%)
050: dt: 0.5000, sse=60433.9, rms=0.048 (0.000%)
051: dt: 0.5000, sse=60813.8, rms=0.046 (0.000%)
052: dt: 0.5000, sse=61167.3, rms=0.045 (0.000%)
053: dt: 0.5000, sse=61489.9, rms=0.044 (0.000%)
054: dt: 0.5000, sse=61770.3, rms=0.043 (0.000%)
055: dt: 0.5000, sse=62065.0, rms=0.042 (0.000%)
056: dt: 0.5000, sse=62325.3, rms=0.041 (0.000%)
057: dt: 0.5000, sse=62550.1, rms=0.040 (0.000%)
058: dt: 0.5000, sse=62766.7, rms=0.039 (0.000%)
059: dt: 0.5000, sse=62975.3, rms=0.039 (0.000%)
060: dt: 0.5000, sse=63176.6, rms=0.038 (0.000%)
positioning took 4.1 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [93.00 231.00], gm=162.00+-23.00, and vertices in regions > 150.5
26978 surface locations found to contain inconsistent values (357 in, 26621 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=6931.5, rms=0.06
061: dt: 0.5000, sse=6866.3, rms=0.060 (0.000%)
062: dt: 0.5000, sse=6944.6, rms=0.052 (0.000%)
063: dt: 0.5000, sse=7049.0, rms=0.047 (0.000%)
064: dt: 0.5000, sse=7143.1, rms=0.044 (0.000%)
065: dt: 0.5000, sse=7214.7, rms=0.041 (0.000%)
066: dt: 0.5000, sse=7259.7, rms=0.039 (0.000%)
067: dt: 0.5000, sse=7291.5, rms=0.038 (0.000%)
068: dt: 0.5000, sse=7321.6, rms=0.036 (0.000%)
069: dt: 0.5000, sse=7350.6, rms=0.035 (0.000%)
070: dt: 0.5000, sse=7376.5, rms=0.034 (0.000%)
071: dt: 0.5000, sse=7400.0, rms=0.033 (0.000%)
072: dt: 0.5000, sse=7421.6, rms=0.032 (0.000%)
073: dt: 0.5000, sse=7441.7, rms=0.031 (0.000%)
074: dt: 0.5000, sse=7459.0, rms=0.030 (0.000%)
075: dt: 0.5000, sse=7473.4, rms=0.029 (0.000%)
076: dt: 0.5000, sse=7486.1, rms=0.028 (0.000%)
077: dt: 0.5000, sse=7497.7, rms=0.028 (0.000%)
078: dt: 0.5000, sse=7508.1, rms=0.027 (0.000%)
079: dt: 0.5000, sse=7517.2, rms=0.027 (0.000%)
080: dt: 0.5000, sse=7526.8, rms=0.026 (0.000%)
081: dt: 0.5000, sse=7535.2, rms=0.026 (0.000%)
082: dt: 0.5000, sse=7543.5, rms=0.025 (0.000%)
083: dt: 0.5000, sse=7550.9, rms=0.025 (0.000%)
084: dt: 0.5000, sse=7557.1, rms=0.025 (0.000%)
085: dt: 0.5000, sse=7563.5, rms=0.024 (0.000%)
086: dt: 0.5000, sse=7568.0, rms=0.024 (0.000%)
087: dt: 0.5000, sse=7571.8, rms=0.024 (0.000%)
088: dt: 0.5000, sse=7575.8, rms=0.024 (0.000%)
089: dt: 0.5000, sse=7579.0, rms=0.024 (0.000%)
090: dt: 0.5000, sse=7581.7, rms=0.023 (0.000%)
positioning took 4.0 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [93.00 231.00], gm=162.00+-23.00, and vertices in regions > 150.5
26384 surface locations found to contain inconsistent values (73 in, 26311 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/sub011/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=861.3, rms=0.03
091: dt: 0.5000, sse=859.3, rms=0.027 (0.000%)
092: dt: 0.5000, sse=853.7, rms=0.026 (0.000%)
093: dt: 0.5000, sse=850.3, rms=0.025 (0.000%)
094: dt: 0.5000, sse=847.2, rms=0.025 (0.000%)
095: dt: 0.5000, sse=845.0, rms=0.024 (0.000%)
096: dt: 0.5000, sse=843.1, rms=0.024 (0.000%)
097: dt: 0.5000, sse=841.6, rms=0.024 (0.000%)
098: dt: 0.5000, sse=840.1, rms=0.023 (0.000%)
099: dt: 0.5000, sse=839.1, rms=0.023 (0.000%)
100: dt: 0.5000, sse=837.7, rms=0.023 (0.000%)
101: dt: 0.5000, sse=836.6, rms=0.023 (0.000%)
102: dt: 0.5000, sse=835.3, rms=0.023 (0.000%)
103: dt: 0.5000, sse=834.2, rms=0.022 (0.000%)
104: dt: 0.5000, sse=833.2, rms=0.022 (0.000%)
105: dt: 0.5000, sse=832.6, rms=0.022 (0.000%)
106: dt: 0.5000, sse=831.5, rms=0.022 (0.000%)
107: dt: 0.5000, sse=830.8, rms=0.022 (0.000%)
108: dt: 0.5000, sse=829.9, rms=0.022 (0.000%)
109: dt: 0.5000, sse=829.2, rms=0.022 (0.000%)
110: dt: 0.5000, sse=828.5, rms=0.022 (0.000%)
111: dt: 0.5000, sse=828.0, rms=0.022 (0.000%)
112: dt: 0.5000, sse=827.8, rms=0.021 (0.000%)
113: dt: 0.5000, sse=827.3, rms=0.021 (0.000%)
114: dt: 0.5000, sse=826.7, rms=0.021 (0.000%)
115: dt: 0.5000, sse=826.2, rms=0.021 (0.000%)
116: dt: 0.5000, sse=825.8, rms=0.021 (0.000%)
117: dt: 0.5000, sse=825.5, rms=0.021 (0.000%)
118: dt: 0.5000, sse=825.2, rms=0.021 (0.000%)
119: dt: 0.5000, sse=824.8, rms=0.021 (0.000%)
120: dt: 0.5000, sse=824.6, rms=0.021 (0.000%)
positioning took 4.1 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.area.pial
vertex spacing 1.02 +- 0.43 (0.02-->8.86) (max @ vno 111253 --> 109961)
face area 0.41 +- 0.31 (0.00-->14.30)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 159726 vertices processed
25000 of 159726 vertices processed
50000 of 159726 vertices processed
75000 of 159726 vertices processed
100000 of 159726 vertices processed
125000 of 159726 vertices processed
150000 of 159726 vertices processed
0 of 159726 vertices processed
25000 of 159726 vertices processed
50000 of 159726 vertices processed
75000 of 159726 vertices processed
100000 of 159726 vertices processed
125000 of 159726 vertices processed
150000 of 159726 vertices processed
thickness calculation complete, 408:849 truncations.
36239 vertices at 0 distance
111631 vertices at 1 distance
102370 vertices at 2 distance
40094 vertices at 3 distance
11130 vertices at 4 distance
2880 vertices at 5 distance
827 vertices at 6 distance
284 vertices at 7 distance
115 vertices at 8 distance
74 vertices at 9 distance
33 vertices at 10 distance
20 vertices at 11 distance
9 vertices at 12 distance
15 vertices at 13 distance
14 vertices at 14 distance
11 vertices at 15 distance
12 vertices at 16 distance
8 vertices at 17 distance
11 vertices at 18 distance
7 vertices at 19 distance
4 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.thickness
positioning took 20.4 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 23:58:42 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf

 mris_calc -o lh.area.mid lh.area add lh.area.pial 

Saving result to 'lh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]

 mris_calc -o lh.area.mid lh.area.mid div 2 

Saving result to 'lh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]

 mris_calc -o lh.volume lh.area.mid mul lh.thickness 

Saving result to 'lh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#--------------------------------------------
#@# Surf Volume rh Thu Aug  8 23:58:42 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf

 mris_calc -o rh.area.mid rh.area add rh.area.pial 

Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]

 mris_calc -o rh.area.mid rh.area.mid div 2 

Saving result to 'rh.area.mid' (type = MRI_CURV_FILE)                       [ ok ]

 mris_calc -o rh.volume rh.area.mid mul rh.thickness 

Saving result to 'rh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#--------------------------------------------
#@# Cortical ribbon mask Thu Aug  8 23:58:43 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub011 

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 = 15
writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/ribbon.mgz
 writing ribbon files
#--------------------------------------------
#@# ASeg Stats Fri Aug  9 00:22:06 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011

 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 sub011 


$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 sub011 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1370643 mm^3    (det: 1.421308 )
Computing euler number
orig.nofix lheno =  -36, rheno = -30
orig.nofix lhholes =   19, rhholes = 16
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 277278.946 276423.000  diff=  855.9  pctdiff= 0.309
rhCtxGM: 280858.011 279721.000  diff= 1137.0  pctdiff= 0.405
lhCtxWM: 269869.337 269453.000  diff=  416.3  pctdiff= 0.154
rhCtxWM: 269533.409 269763.000  diff= -229.6  pctdiff=-0.085
SubCortGMVol  70375.000
SupraTentVol  1195183.703 (1191979.000) diff=3204.703 pctdiff=0.268
SupraTentVolNotVent  1169136.703 (1165932.000) diff=3204.703 pctdiff=0.274
BrainSegVol  1329620.000 (1325983.000) diff=3637.000 pctdiff=0.274
BrainSegVolNotVent  1298971.000 (1300821.703) diff=-1850.703 pctdiff=-0.142
BrainSegVolNotVent  1298971.000
CerebellumVol 132710.000
VentChorVol   26047.000
3rd4th5thCSF   4602.000
CSFVol   992.000, OptChiasmVol   302.000
MaskVol 1907947.000
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   13402   13402.228
  4     5                  Left-Inf-Lat-Vent     557     556.833
  5     7       Left-Cerebellum-White-Matter   16888   16887.748
  6     8             Left-Cerebellum-Cortex   51200   51199.930
  7    10               Left-Thalamus-Proper    8908    8907.775
  8    11                       Left-Caudate    4195    4195.446
  9    12                       Left-Putamen    6838    6837.960
 10    13                      Left-Pallidum    2472    2472.189
 11    14                      3rd-Ventricle    1050    1050.020
 12    15                      4th-Ventricle    2785    2784.907
 13    16                         Brain-Stem   26255   26255.059
 14    17                   Left-Hippocampus    3823    3823.231
 15    18                      Left-Amygdala    1957    1957.385
 16    24                                CSF     995     995.296
 17    26                Left-Accumbens-area     985     985.015
 18    28                     Left-VentralDC    4880    4880.312
 19    30                        Left-vessel      89      89.321
 20    31                Left-choroid-plexus    1319    1319.028
 23    43            Right-Lateral-Ventricle    8247    8246.752
 24    44                 Right-Inf-Lat-Vent     621     621.314
 25    46      Right-Cerebellum-White-Matter   16640   16639.832
 26    47            Right-Cerebellum-Cortex   50786   50786.008
 27    49              Right-Thalamus-Proper    8448    8447.721
 28    50                      Right-Caudate    4647    4646.635
 29    51                      Right-Putamen    6611    6611.235
 30    52                     Right-Pallidum    2692    2692.193
 31    53                  Right-Hippocampus    4395    4394.645
 32    54                     Right-Amygdala    1787    1787.437
 33    58               Right-Accumbens-area     842     842.284
 34    60                    Right-VentralDC    4547    4546.748
 35    62                       Right-vessel      93      93.224
 36    63               Right-choroid-plexus    1749    1749.249
 37    72                      5th-Ventricle       0       0.000
 38    77                 WM-hypointensities    1693    1693.373
 39    78            Left-WM-hypointensities       0       0.000
 40    79           Right-WM-hypointensities       0       0.000
 41    80             non-WM-hypointensities      23      22.659
 42    81        Left-non-WM-hypointensities       0       0.000
 43    82       Right-non-WM-hypointensities       0       0.000
 44    85                       Optic-Chiasm     309     309.220
 45   251                       CC_Posterior    1230    1230.396
 46   252                   CC_Mid_Posterior     596     595.513
 47   253                         CC_Central     557     557.162
 48   254                    CC_Mid_Anterior     552     552.144
 49   255                        CC_Anterior    1264    1263.762

Reporting on  45 segmentations
mri_segstats done
#-----------------------------------------
#@# AParc-to-ASeg Fri Aug  9 00:25:20 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011

 mri_aparc2aseg --s sub011 --volmask 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub011
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/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/sub011/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 = 553178
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc+aseg.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011

 mri_aparc2aseg --s sub011 --volmask --a2009s 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub011
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/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/sub011/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 = 553178
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Fri Aug  9 00:30:33 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011

 mri_aparc2aseg --s sub011 --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 sub011
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/sub011/mri/aparc+aseg.mgz

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/ribbon.mgz
Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 9608 vertices from left hemi
Ripped 9050 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/sub011/mri/aseg.mgz
Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 = 1090974
Used brute-force search on 421 voxels
Fixing Parahip LH WM
  Found 7 clusters
     0 k 11.000000
     1 k 3.000000
     2 k 2.000000
     3 k 1.000000
     4 k 1.000000
     5 k 1557.000000
     6 k 2.000000
Fixing Parahip RH WM
  Found 5 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1745.000000
Writing output aseg to mri/wmparc.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011

 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 sub011 --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 sub011 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1370643 mm^3    (det: 1.421308 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 277278.946 276423.000  diff=  855.9  pctdiff= 0.309
rhCtxGM: 280858.011 279721.000  diff= 1137.0  pctdiff= 0.405
lhCtxWM: 269869.337 269453.000  diff=  416.3  pctdiff= 0.154
rhCtxWM: 269533.409 269763.000  diff= -229.6  pctdiff=-0.085
SubCortGMVol  70375.000
SupraTentVol  1195183.703 (1191979.000) diff=3204.703 pctdiff=0.268
SupraTentVolNotVent  1169136.703 (1165932.000) diff=3204.703 pctdiff=0.274
BrainSegVol  1329620.000 (1325983.000) diff=3637.000 pctdiff=0.274
BrainSegVolNotVent  1298971.000 (1300821.703) diff=-1850.703 pctdiff=-0.142
BrainSegVolNotVent  1298971.000
CerebellumVol 132710.000
VentChorVol   26047.000
3rd4th5thCSF   4602.000
CSFVol   992.000, OptChiasmVol   302.000
MaskVol 1907947.000
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    3645    3644.832
  2   3002      wm-lh-caudalanteriorcingulate    3672    3671.576
  3   3003          wm-lh-caudalmiddlefrontal    7879    7878.777
  4   3004               wm-lh-corpuscallosum       0       0.000
  5   3005                       wm-lh-cuneus    2393    2392.712
  6   3006                   wm-lh-entorhinal     965     964.953
  7   3007                     wm-lh-fusiform    8100    8100.317
  8   3008             wm-lh-inferiorparietal   12255   12254.634
  9   3009             wm-lh-inferiortemporal    7852    7852.207
 10   3010             wm-lh-isthmuscingulate    4515    4515.104
 11   3011             wm-lh-lateraloccipital   11248   11247.744
 12   3012         wm-lh-lateralorbitofrontal    7404    7403.953
 13   3013                      wm-lh-lingual    5579    5579.343
 14   3014          wm-lh-medialorbitofrontal    3285    3284.814
 15   3015               wm-lh-middletemporal    6625    6624.548
 16   3016              wm-lh-parahippocampal    1634    1633.566
 17   3017                  wm-lh-paracentral    3996    3996.251
 18   3018              wm-lh-parsopercularis    4093    4093.467
 19   3019                wm-lh-parsorbitalis    1129    1128.731
 20   3020             wm-lh-parstriangularis    3488    3488.130
 21   3021                wm-lh-pericalcarine    2795    2794.539
 22   3022                  wm-lh-postcentral    9876    9875.706
 23   3023           wm-lh-posteriorcingulate    5082    5081.741
 24   3024                   wm-lh-precentral   15693   15693.481
 25   3025                    wm-lh-precuneus   11155   11155.121
 26   3026     wm-lh-rostralanteriorcingulate    2905    2905.290
 27   3027         wm-lh-rostralmiddlefrontal   15253   15252.552
 28   3028              wm-lh-superiorfrontal   21260   21260.111
 29   3029             wm-lh-superiorparietal   15877   15876.854
 30   3030             wm-lh-superiortemporal    7807    7806.925
 31   3031                wm-lh-supramarginal    9209    9209.423
 32   3032                  wm-lh-frontalpole     267     267.368
 33   3033                 wm-lh-temporalpole     570     569.530
 34   3034           wm-lh-transversetemporal     738     738.356
 35   3035                       wm-lh-insula    9239    9238.698
 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    3179    3179.003
120   4002      wm-rh-caudalanteriorcingulate    4736    4735.516
121   4003          wm-rh-caudalmiddlefrontal    6257    6257.334
122   4004               wm-rh-corpuscallosum       0       0.000
123   4005                       wm-rh-cuneus    2379    2378.581
124   4006                   wm-rh-entorhinal     943     943.463
125   4007                     wm-rh-fusiform    7227    7226.715
126   4008             wm-rh-inferiorparietal   13632   13631.592
127   4009             wm-rh-inferiortemporal    7156    7156.098
128   4010             wm-rh-isthmuscingulate    4491    4490.825
129   4011             wm-rh-lateraloccipital    9463    9462.910
130   4012         wm-rh-lateralorbitofrontal    6939    6939.206
131   4013                      wm-rh-lingual    6059    6058.833
132   4014          wm-rh-medialorbitofrontal    4376    4375.835
133   4015               wm-rh-middletemporal    7106    7106.391
134   4016              wm-rh-parahippocampal    1818    1817.799
135   4017                  wm-rh-paracentral    5608    5608.405
136   4018              wm-rh-parsopercularis    5339    5338.899
137   4019                wm-rh-parsorbitalis    1471    1470.843
138   4020             wm-rh-parstriangularis    4540    4539.630
139   4021                wm-rh-pericalcarine    3282    3281.974
140   4022                  wm-rh-postcentral    8250    8250.193
141   4023           wm-rh-posteriorcingulate    5564    5564.180
142   4024                   wm-rh-precentral   15888   15888.439
143   4025                    wm-rh-precuneus   11886   11886.087
144   4026     wm-rh-rostralanteriorcingulate    2360    2359.758
145   4027         wm-rh-rostralmiddlefrontal   15533   15533.347
146   4028              wm-rh-superiorfrontal   19765   19765.396
147   4029             wm-rh-superiorparietal   14394   14394.141
148   4030             wm-rh-superiortemporal    8042    8042.229
149   4031                wm-rh-supramarginal   10316   10315.623
150   4032                  wm-rh-frontalpole     314     314.393
151   4033                 wm-rh-temporalpole     654     653.988
152   4034           wm-rh-transversetemporal     707     707.230
153   4035                       wm-rh-insula    9834    9833.537
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   41087   41086.664
237   5002       Right-UnsegmentedWhiteMatter   40709   40708.680
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/sub011/label
#--------------------------------------------
#@# BA Labels lh Fri Aug  9 00:42:06 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 697
Checking for and removing duplicates
Writing label file ./lh.BA1.label 4826
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 1518
Checking for and removing duplicates
Writing label file ./lh.BA2.label 9427
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 234
Checking for and removing duplicates
Writing label file ./lh.BA3a.label 4311
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 506
Checking for and removing duplicates
Writing label file ./lh.BA3b.label 6489
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 694
Checking for and removing duplicates
Writing label file ./lh.BA4a.label 6478
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 403
Checking for and removing duplicates
Writing label file ./lh.BA4p.label 4473
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 2804
Checking for and removing duplicates
Writing label file ./lh.BA6.label 16393
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 587
Checking for and removing duplicates
Writing label file ./lh.BA44.label 4768
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 1465
Checking for and removing duplicates
Writing label file ./lh.BA45.label 4887
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 1722
Checking for and removing duplicates
Writing label file ./lh.V1.label 6363
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 3462
Checking for and removing duplicates
Writing label file ./lh.V2.label 11576
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 912
Checking for and removing duplicates
Writing label file ./lh.MT.label 2930
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 99
Checking for and removing duplicates
Writing label file ./lh.perirhinal.label 1298
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 153
Checking for and removing duplicates
Writing label file ./lh.BA1.thresh.label 1167
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 624
Checking for and removing duplicates
Writing label file ./lh.BA2.thresh.label 2716
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 69
Checking for and removing duplicates
Writing label file ./lh.BA3a.thresh.label 1573
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 207
Checking for and removing duplicates
Writing label file ./lh.BA3b.thresh.label 2203
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 392
Checking for and removing duplicates
Writing label file ./lh.BA4a.thresh.label 2711
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 104
Checking for and removing duplicates
Writing label file ./lh.BA4p.thresh.label 1653
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 1046
Checking for and removing duplicates
Writing label file ./lh.BA6.thresh.label 8081
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 280
Checking for and removing duplicates
Writing label file ./lh.BA44.thresh.label 2192
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 528
Checking for and removing duplicates
Writing label file ./lh.BA45.thresh.label 1679
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 1285
Checking for and removing duplicates
Writing label file ./lh.V1.thresh.label 4690
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 1485
Checking for and removing duplicates
Writing label file ./lh.V2.thresh.label 4819
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 158499
Number of reverse mapping hits = 272
Checking for and removing duplicates
Writing label file ./lh.MT.thresh.label 785
mri_label2label: Done


 mris_label2annot --s sub011 --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/sub011/label
cmdline mris_label2annot --s sub011 --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 snake6
machine  x86_64
user     fkaule

subject sub011
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/sub011/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 109048 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.BA.annot

 mris_label2annot --s sub011 --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/sub011/label
cmdline mris_label2annot --s sub011 --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 snake6
machine  x86_64
user     fkaule

subject sub011
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/sub011/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 130961 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/lh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub011 lh white 

computing statistics for each annotation in ./lh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

 1385    876   2516  2.162 0.511     0.157     0.060       29     3.5  BA1
 5659   3795   8768  2.169 0.554     0.132     0.039       67     8.8  BA2
 1015    670    861  1.705 0.392     0.149     0.047       10     2.0  BA3a
 2670   1784   3363  1.673 0.542     0.134     0.051       44     5.0  BA3b
 1882   1100   3676  2.744 0.455     0.123     0.045       28     3.9  BA4a
 1500   1025   2181  2.189 0.520     0.117     0.038       11     2.4  BA4p
12072   8156  26146  2.686 0.583     0.132     0.037      159    17.9  BA6
 2778   1904   5938  2.697 0.500     0.141     0.044       52     5.0  BA44
 3970   2705   7547  2.380 0.563     0.149     0.051       72     7.8  BA45
 3890   2550   4493  1.713 0.424     0.166     0.078       76    11.6  V1
 8987   5928  12659  1.992 0.466     0.163     0.067      165    21.9  V2
 2733   1780   4007  2.136 0.467     0.135     0.046       35     4.8  MT
  910    650   2695  3.351 0.884     0.147     0.051       11     1.8  perirhinal

 mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub011 lh white 

computing statistics for each annotation in ./lh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

  821    491   1520  2.243 0.481     0.166     0.065       19     2.2  BA1
 2398   1624   3805  2.090 0.537     0.126     0.034       26     3.3  BA2
  884    578    678  1.648 0.353     0.156     0.052       10     1.9  BA3a
 1660   1145   1848  1.446 0.378     0.118     0.032       17     2.2  BA3b
 1928   1130   3670  2.667 0.489     0.116     0.044       28     3.8  BA4a
 1146    824   1625  2.137 0.542     0.121     0.037        7     1.9  BA4p
 6192   4186  13915  2.714 0.590     0.135     0.038       85     9.5  BA6
 1751   1195   3875  2.755 0.434     0.149     0.049       38     3.7  BA44
 1520   1054   3354  2.555 0.499     0.165     0.064       38     3.4  BA45
 4131   2718   4876  1.717 0.418     0.166     0.078       81    12.5  V1
 4348   2915   5878  1.899 0.436     0.171     0.081       87    11.7  V2
  759    488    996  1.952 0.407     0.135     0.043        8     1.6  MT
#--------------------------------------------
#@# BA Labels rh Fri Aug  9 00:47:03 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 415
Checking for and removing duplicates
Writing label file ./rh.BA1.label 4377
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 795
Checking for and removing duplicates
Writing label file ./rh.BA2.label 7482
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 152
Checking for and removing duplicates
Writing label file ./rh.BA3a.label 4132
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 330
Checking for and removing duplicates
Writing label file ./rh.BA3b.label 4852
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 722
Checking for and removing duplicates
Writing label file ./rh.BA4a.label 6469
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 285
Checking for and removing duplicates
Writing label file ./rh.BA4p.label 4758
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 2177
Checking for and removing duplicates
Writing label file ./rh.BA6.label 14433
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 3004
Checking for and removing duplicates
Writing label file ./rh.BA44.label 9916
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 3364
Checking for and removing duplicates
Writing label file ./rh.BA45.label 8719
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 2066
Checking for and removing duplicates
Writing label file ./rh.V1.label 6793
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 3411
Checking for and removing duplicates
Writing label file ./rh.V2.label 11427
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 404
Checking for and removing duplicates
Writing label file ./rh.MT.label 2336
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 68
Checking for and removing duplicates
Writing label file ./rh.perirhinal.label 820
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 88
Checking for and removing duplicates
Writing label file ./rh.BA1.thresh.label 964
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 283
Checking for and removing duplicates
Writing label file ./rh.BA2.thresh.label 2971
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 45
Checking for and removing duplicates
Writing label file ./rh.BA3a.thresh.label 1743
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 197
Checking for and removing duplicates
Writing label file ./rh.BA3b.thresh.label 2380
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 119
Checking for and removing duplicates
Writing label file ./rh.BA4a.thresh.label 1507
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 81
Checking for and removing duplicates
Writing label file ./rh.BA4p.thresh.label 1570
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 1396
Checking for and removing duplicates
Writing label file ./rh.BA6.thresh.label 8355
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 783
Checking for and removing duplicates
Writing label file ./rh.BA44.thresh.label 1795
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 772
Checking for and removing duplicates
Writing label file ./rh.BA45.thresh.label 1950
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 1379
Checking for and removing duplicates
Writing label file ./rh.V1.thresh.label 4611
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 1507
Checking for and removing duplicates
Writing label file ./rh.V2.thresh.label 4944
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub011 --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 = sub011
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/sub011/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 159726
Number of reverse mapping hits = 27
Checking for and removing duplicates
Writing label file ./rh.MT.thresh.label 295
mri_label2label: Done


 mris_label2annot --s sub011 --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/sub011/label
cmdline mris_label2annot --s sub011 --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 snake6
machine  x86_64
user     fkaule

subject sub011
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/sub011/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 109967 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.BA.annot

 mris_label2annot --s sub011 --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/sub011/label
cmdline mris_label2annot --s sub011 --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 snake6
machine  x86_64
user     fkaule

subject sub011
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/sub011/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 132713 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label/rh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub011 rh white 

computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

  982    585   1686  2.119 0.494     0.149     0.075       23     2.9  BA1
 4065   2680   5956  2.111 0.452     0.119     0.036       42     6.4  BA2
  979    634    898  1.743 0.455     0.140     0.047       10     1.9  BA3a
 2098   1344   2504  1.604 0.538     0.118     0.035       24     3.0  BA3b
 1740   1016   3091  2.613 0.444     0.107     0.118       13    13.9  BA4a
 1245    817   1915  2.378 0.414     0.114     0.035        9     1.9  BA4p
10534   6864  23281  2.771 0.544     0.134     0.044      143    18.5  BA6
 5399   3613  10416  2.553 0.427     0.123     0.039       72     8.8  BA44
 6744   4539  13515  2.486 0.508     0.156     0.059      145    15.5  BA45
 4438   3024   4935  1.626 0.407     0.174     0.093       91    17.8  V1
 8903   5977  12445  1.974 0.476     0.175     0.072      193    25.6  V2
 1989   1378   3268  2.248 0.468     0.156     0.057       37     4.6  MT
  643    462   2166  3.363 0.654     0.150     0.062       10     1.5  perirhinal

 mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub011 rh white 

computing statistics for each annotation in ./rh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

  670    376    946  1.899 0.482     0.150     0.079       18     2.4  BA1
 2123   1407   3089  2.011 0.474     0.112     0.032       19     3.1  BA2
  862    547    703  1.695 0.364     0.136     0.044        7     1.6  BA3a
 1716   1123   1816  1.453 0.424     0.105     0.032       14     1.9  BA3b
 1019    544   1941  2.759 0.499     0.113     0.181        9    13.1  BA4a
  999    675   1499  2.359 0.398     0.117     0.038        7     1.6  BA4p
 6955   4494  15037  2.739 0.526     0.133     0.047       95    12.8  BA6
 1759   1195   3785  2.641 0.377     0.132     0.046       30     3.4  BA44
 1886   1305   3972  2.472 0.474     0.157     0.059       42     4.4  BA45
 4196   2887   4668  1.621 0.400     0.172     0.090       85    16.4  V1
 4600   3131   6091  1.859 0.480     0.192     0.089      116    16.0  V2
  228    161    443  2.359 0.343     0.156     0.067        4     0.6  MT
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label lh Fri Aug  9 00:52:09 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub011 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

painting output onto subject sub011.
processing subject lh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 890 points to lh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub011 lh white 

limiting computations to label ./lh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

  311    209   1068  3.180 0.748     0.138     0.057        5     0.8  ./lh.entorhinal_exvivo.label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label rh Fri Aug  9 00:52:26 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub011 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 

painting output onto subject sub011.
processing subject rh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 801 points to rh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub011 rh white 

limiting computations to label ./rh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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

  306    202   1337  3.840 0.502     0.159     0.074        6     1.0  ./rh.entorhinal_exvivo.label

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

Started at Thu Aug 8 10:54:16 CEST 2013 
Ended   at Fri Aug 9 00:52:42 CEST 2013
#@#%# recon-all-run-time-hours 13.974
recon-all -s sub011 finished without error at Fri Aug  9 00:52:42 CEST 2013