cortical-surfaces-freesurfer/sub-18/scripts/recon-all.log

Thu Aug  8 10:53:55 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018
/opt/freesurfer/5.3.0/bin/recon-all
-i /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/other/t2w001.nii.gz -T2pial -subjid sub018 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subjid sub018
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 snake5 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   96471788    2729904          0     177872   94401932
-/+ buffers/cache:    1891984   97309708
Swap:     25165780       3620   25162160

########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $

ProgramName: mri_robust_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: snake5  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/sub018

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/001.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/anatomy/highres001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998519, 0.0146261, 0.052401)
j_ras = (0.020019, 0.994384, 0.103917)
k_ras = (0.0505869, -0.104812, 0.993205)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Thu Aug  8 10:54:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub018/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/anatomy/other/t2w001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998519, 0.0146261, 0.052401)
j_ras = (0.020019, 0.994384, 0.103917)
k_ras = (0.0505869, -0.104812, 0.993205)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Thu Aug  8 10:54:32 CEST 2013
Found 1 runs
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz 

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz --conform --cw256 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998519, 0.0146261, 0.052401)
j_ras = (0.020019, 0.994384, 0.103917)
k_ras = (0.0505869, -0.104812, 0.993205)
Original Data has (0.699936, 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/sub018/mri/orig.mgz...

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Aug  8 10:55:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 10:58:37 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7211, pval=0.4932 >= threshold=0.0050)

 awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/talairach_avi.log 


 tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/talairach_avi.log 

TalAviQA: 0.96888
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Thu Aug  8 10:58:37 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/sub018/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 snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
Thu Aug  8 10:58:37 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.14649
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14649/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14649/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, -1.86265e-09, 0)
j_ras = (0, 2.23517e-08, -1)
k_ras = (-9.31323e-10, 1, 7.45058e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.14649/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Thu Aug  8 10:58:43 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.14649/nu0.mnc ./tmp.mri_nu_correct.mni.14649/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14649/0/
[fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/] [2013-08-08 10:58:43] 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.14649/0/ ./tmp.mri_nu_correct.mni.14649/nu0.mnc ./tmp.mri_nu_correct.mni.14649/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00113831
[fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/] [2013-08-08 11:00:07] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14649/nu0.mnc ./tmp.mri_nu_correct.mni.14649/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Thu Aug  8 11:00:13 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.14649/nu1.mnc ./tmp.mri_nu_correct.mni.14649/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.14649/1/
[fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/] [2013-08-08 11:00:13] 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.14649/1/ ./tmp.mri_nu_correct.mni.14649/nu1.mnc ./tmp.mri_nu_correct.mni.14649/nu2.imp

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Number of iterations: 50 
CV of field change: 0.000991634
[fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/] [2013-08-08 11:01:19] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14649/nu1.mnc ./tmp.mri_nu_correct.mni.14649/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.14649/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14649/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/sub018/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14649/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14649/ones.mgz 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule

input      ./tmp.mri_nu_correct.mni.14649/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.14649/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.14649/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14649/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.14649/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14649/input.mean.dat 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.14649/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.14649/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14649/ones.mgz --i ./tmp.mri_nu_correct.mni.14649/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14649/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.14649/ones.mgz --i ./tmp.mri_nu_correct.mni.14649/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14649/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14649/output.mean.dat 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.14649/ones.mgz
Loading ./tmp.mri_nu_correct.mni.14649/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.14649/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.14649/nu2.mnc ./tmp.mri_nu_correct.mni.14649/nu2.mnc mul .87816104870743779040
Saving result to './tmp.mri_nu_correct.mni.14649/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.14649/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.14649/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.14649/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.86265e-09, 0)
j_ras = (0, 2.23517e-08, -1)
k_ras = (-9.31323e-10, 1, 7.45058e-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 (13, 161) to ( 3, 110)
 
 
Thu Aug  8 11:02:18 CEST 2013
mri_nu_correct.mni done

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Aug  8 11:02:20 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri

 mri_normalize -g 1 nu.mgz T1.mgz 

using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
 1.184  -0.017  -0.054   4.517;
 0.038   1.079   0.328  -41.092;
 0.050  -0.405   1.164  -1.179;
 0.000   0.000   0.000   1.000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 17
Starting OpenSpline(): npoints = 17
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 108
gm peak at 54 (54), valley at 37 (37)
csf peak at 27, setting threshold to 45
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 52 (52), valley at 39 (39)
csf peak at 26, setting threshold to 43
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 3 minutes and 19 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Aug  8 11:05:39 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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=9.0
skull bounding box = (51, 10, 16) --> (201, 255, 204)
using (101, 92, 110) as brain centroid...
mean wm in atlas = 126, using box (83,62,87) --> (119, 122,133) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 108, scaling input intensities by 1.167
scaling channel 0 by 1.16667
initial log_p = -4.9
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.569289 @ (-9.091, 27.273, -9.091)
max log p =    -4.460065 @ (13.636, -4.545, -4.545)
max log p =    -4.410065 @ (-6.818, -2.273, 2.273)
max log p =    -4.391715 @ (3.409, 3.409, 1.136)
max log p =    -4.386332 @ (-2.841, -1.705, -0.568)
max log p =    -4.386332 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, 22.2, -10.8): log p = -4.386
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.4 (thresh=-4.4)
 1.236   0.000   0.000  -31.818;
 0.000   1.142   0.473  -39.679;
 0.000  -0.473   1.142   26.911;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.236   0.000   0.000  -31.818;
 0.000   1.284   0.344  -39.157;
 0.000  -0.296   1.105   6.558;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.236   0.000   0.000  -31.818;
 0.000   1.284   0.344  -39.157;
 0.000  -0.296   1.105   6.558;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
 1.167  -0.046   0.026  -19.806;
 0.045   1.331   0.355  -52.556;
-0.040  -0.299   1.125   11.331;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.188  -0.047   0.026  -22.536;
 0.045   1.331   0.355  -52.556;
-0.040  -0.304   1.146   9.555;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.190  -0.052   0.045  -23.508;
 0.045   1.336   0.357  -53.167;
-0.060  -0.303   1.146   11.994;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.190  -0.052   0.045  -23.508;
 0.045   1.336   0.357  -53.167;
-0.060  -0.303   1.146   11.994;
 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
 1.19036  -0.05200   0.04499  -23.50809;
 0.04517   1.33590   0.35668  -53.16697;
-0.05976  -0.30345   1.14592   11.99424;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.19036  -0.05200   0.04499  -23.50809;
 0.04517   1.33590   0.35668  -53.16697;
-0.05976  -0.30345   1.14592   11.99424;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.190  -0.052   0.045  -23.508;
 0.045   1.336   0.357  -53.167;
-0.060  -0.303   1.146   11.994;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.9)
transform before final EM align:
 1.190  -0.052   0.045  -23.508;
 0.045   1.336   0.357  -53.167;
-0.060  -0.303   1.146   11.994;
 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
 1.19036  -0.05200   0.04499  -23.50809;
 0.04517   1.33590   0.35668  -53.16697;
-0.05976  -0.30345   1.14592   11.99424;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.19036  -0.05200   0.04499  -23.50809;
 0.04517   1.33590   0.35668  -53.16697;
-0.05976  -0.30345   1.14592   11.99424;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =    4.4  tol 0.000000
final transform:
 1.190  -0.052   0.045  -23.508;
 0.045   1.336   0.357  -53.167;
-0.060  -0.303   1.146   11.994;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 35 minutes and 23 seconds.

 mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


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

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

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=125 y=83 z=117 r=94
      first estimation of the main basin volume: 3567053 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        12 found in the rest of the brain 
      global maximum in x=108, y=81, z=85, 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=15872698844 voxels, voxel volume =1.000 
                     = 15872698844 mmm3 = 15872698.368 cm3
done.
PostAnalyze...Basin Prior
 64 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=96, z=110, r=10261 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45532
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=11 , nb = -1032548792
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=10 , nb = 1100101065
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1075437826
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1081450114
    OTHER      CSF_MIN=0, CSF_intensity=9, CSF_MAX=19 , nb = 1072930794
 (2) Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    4,      6,        32,   50
  after  analyzing :    4,      23,        32,   29
   RIGHT_CER   
  before analyzing :    11,      16,        30,   50
  after  analyzing :    11,      25,        30,   31
   LEFT_CER    
  before analyzing :    10,      14,        30,   56
  after  analyzing :    10,      24,        30,   32
  RIGHT_BRAIN  
  before analyzing :    4,      6,        30,   50
  after  analyzing :    4,      22,        30,   29
  LEFT_BRAIN   
  before analyzing :    4,      6,        30,   50
  after  analyzing :    4,      22,        30,   29
     OTHER     
  before analyzing :    19,      48,        93,   108
  after  analyzing :    19,      78,        93,   85
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...70 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.012
curvature mean = 69.413, std = 7.854

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 1.67, sigma = 2.86
      after  rotation: sse = 1.67, sigma = 2.86
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  1.71, its var is  2.52   
      before Erosion-Dilatation  0.07% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...39 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1660037 voxels, voxel volume = 1.000 mm3
           = 1660037 mmm3 = 1660.037 cm3


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

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Thu Aug  8 11:41:31 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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=23.0
skull bounding box = (60, 41, 38) --> (191, 173, 199)
using (104, 85, 119) as brain centroid...
mean wm in atlas = 107, using box (88,69,99) --> (120, 101,138) to find MRI wm
before smoothing, mri peak at 106
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.5
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.098838 @ (-9.091, 27.273, -9.091)
max log p =    -3.886874 @ (4.545, -4.545, -4.545)
max log p =    -3.871808 @ (2.273, 2.273, -2.273)
max log p =    -3.835258 @ (1.136, -3.409, 3.409)
max log p =    -3.815219 @ (0.568, -0.568, -1.705)
max log p =    -3.815219 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, 21.0, -14.2): log p = -3.815
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.8 (thresh=-3.8)
 1.150   0.000   0.000  -19.675;
 0.000   1.111   0.298  -17.897;
 0.000  -0.236   0.883   30.466;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6)
 1.055  -0.134  -0.036   8.983;
 0.150   1.101   0.295  -35.847;
 0.000  -0.272   1.015   19.236;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.6)
 1.065   0.011   0.003  -10.203;
 0.011   1.109   0.297  -19.144;
 0.000  -0.272   1.015   19.236;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5)
 1.065   0.011   0.003  -10.203;
 0.011   1.109   0.297  -19.144;
 0.000  -0.272   1.015   19.236;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.5 (thresh=-3.5)
 1.104  -0.035   0.020  -12.843;
 0.045   1.129   0.304  -28.083;
-0.032  -0.262   0.996   24.176;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
 1.104  -0.035   0.020  -12.843;
 0.045   1.129   0.304  -28.083;
-0.032  -0.262   0.996   24.176;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
 1.103  -0.074   0.018  -8.708;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 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
 1.10000  -0.07384   0.01772  -8.39068;
 0.08076   1.11928   0.31996  -34.30147;
-0.04177  -0.27917   0.98873   27.43496;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2772
Quasinewton: input matrix
 1.10000  -0.07384   0.01772  -8.39068;
 0.08076   1.11928   0.31996  -34.30147;
-0.04177  -0.27917   0.98873   27.43496;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.3 (old=-4.5)
transform before final EM align:
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 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
 1.10000  -0.07384   0.01772  -8.39068;
 0.08076   1.11928   0.31996  -34.30147;
-0.04177  -0.27917   0.98873   27.43496;
 0.00000   0.00000   0.00000   1.00000;
nsamples 312841
Quasinewton: input matrix
 1.10000  -0.07384   0.01772  -8.39068;
 0.08076   1.11928   0.31996  -34.30147;
-0.04177  -0.27917   0.98873   27.43496;
 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: 013: -log(p) =    3.8  tol 0.000000
final transform:
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 35 minutes and 46 seconds.
#--------------------------------------
#@# CA Normalize Thu Aug  8 12:17:17 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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=23.0
skull bounding box = (60, 41, 38) --> (191, 173, 200)
using (104, 85, 119) as brain centroid...
mean wm in atlas = 107, using box (88,69,99) --> (120, 101,138) to find MRI wm
before smoothing, mri peak at 106
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
using 244171 sample points...
INFO: compute sample coordinates transform
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 0.000   0.000   0.000   1.000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (126, 38, 39) --> (188, 141, 196)
Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 160.0
0 of 17 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 39, 37) --> (127, 137, 197)
Right_Cerebral_White_Matter: limiting intensities to 106.0 --> 160.0
1 of 8 (12.5%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 117, 68) --> (176, 154, 118)
Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 160.0
0 of 16 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (89, 117, 64) --> (130, 157, 119)
Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 160.0
1 of 7 (14.3%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (114, 106, 99) --> (144, 166, 128)
Brain_Stem: limiting intensities to 77.0 --> 160.0
0 of 7 (0.0%) samples deleted
using 55 total control points for intensity normalization...
bias field = 0.924 +- 0.069
0 of 53 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (126, 38, 39) --> (188, 141, 196)
Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 143.0
0 of 103 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 39, 37) --> (127, 137, 197)
Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 143.0
0 of 99 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 117, 68) --> (176, 154, 118)
Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 143.0
0 of 19 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (89, 117, 64) --> (130, 157, 119)
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (114, 106, 99) --> (144, 166, 128)
Brain_Stem: limiting intensities to 85.0 --> 143.0
30 of 63 (47.6%) samples deleted
using 284 total control points for intensity normalization...
bias field = 1.000 +- 0.061
0 of 254 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (126, 38, 39) --> (188, 141, 196)
Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 136.0
0 of 201 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 39, 37) --> (127, 137, 197)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 136.0
0 of 196 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 117, 68) --> (176, 154, 118)
Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 136.0
0 of 8 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (89, 117, 64) --> (130, 157, 119)
Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 136.0
1 of 12 (8.3%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (114, 106, 99) --> (144, 166, 128)
Brain_Stem: limiting intensities to 67.0 --> 136.0
0 of 70 (0.0%) samples deleted
using 487 total control points for intensity normalization...
bias field = 1.025 +- 0.062
0 of 486 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 2 minutes and 7 seconds.
#--------------------------------------
#@# CA Reg Thu Aug  8 12:19:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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) = 1.32 (predicted orig area = 6.0)
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=0.820, neg=0, invalid=96777
0001: dt=129.472000, rms=0.774 (5.632%), neg=0, invalid=96777
0002: dt=129.472000, rms=0.764 (1.319%), neg=0, invalid=96777
0003: dt=221.952000, rms=0.755 (1.188%), neg=0, invalid=96777
0004: dt=129.472000, rms=0.750 (0.682%), neg=0, invalid=96777
0005: dt=129.472000, rms=0.746 (0.442%), neg=0, invalid=96777
0006: dt=129.472000, rms=0.743 (0.489%), neg=0, invalid=96777
0007: dt=129.472000, rms=0.741 (0.291%), neg=0, invalid=96777
0008: dt=129.472000, rms=0.738 (0.398%), neg=0, invalid=96777
0009: dt=129.472000, rms=0.736 (0.244%), neg=0, invalid=96777
0010: dt=129.472000, rms=0.734 (0.292%), neg=0, invalid=96777
0011: dt=129.472000, rms=0.730 (0.448%), neg=0, invalid=96777
0012: dt=129.472000, rms=0.727 (0.480%), neg=0, invalid=96777
0013: dt=129.472000, rms=0.722 (0.600%), neg=0, invalid=96777
0014: dt=129.472000, rms=0.718 (0.587%), neg=0, invalid=96777
0015: dt=129.472000, rms=0.715 (0.500%), neg=0, invalid=96777
0016: dt=129.472000, rms=0.712 (0.407%), neg=0, invalid=96777
0017: dt=129.472000, rms=0.709 (0.451%), neg=0, invalid=96777
0018: dt=129.472000, rms=0.706 (0.398%), neg=0, invalid=96777
0019: dt=129.472000, rms=0.703 (0.328%), neg=0, invalid=96777
0020: dt=129.472000, rms=0.701 (0.278%), neg=0, invalid=96777
0021: dt=129.472000, rms=0.700 (0.267%), neg=0, invalid=96777
0022: dt=129.472000, rms=0.698 (0.242%), neg=0, invalid=96777
0023: dt=129.472000, rms=0.696 (0.250%), neg=0, invalid=96777
0024: dt=129.472000, rms=0.695 (0.213%), neg=0, invalid=96777
0025: dt=129.472000, rms=0.693 (0.236%), neg=0, invalid=96777
0026: dt=129.472000, rms=0.691 (0.226%), neg=0, invalid=96777
0027: dt=129.472000, rms=0.690 (0.240%), neg=0, invalid=96777
0028: dt=129.472000, rms=0.688 (0.211%), neg=0, invalid=96777
0029: dt=129.472000, rms=0.687 (0.205%), neg=0, invalid=96777
0030: dt=129.472000, rms=0.686 (0.184%), neg=0, invalid=96777
0031: dt=129.472000, rms=0.684 (0.188%), neg=0, invalid=96777
0032: dt=129.472000, rms=0.683 (0.149%), neg=0, invalid=96777
0033: dt=129.472000, rms=0.682 (0.128%), neg=0, invalid=96777
0034: dt=129.472000, rms=0.682 (0.125%), neg=0, invalid=96777
0035: dt=129.472000, rms=0.681 (0.130%), neg=0, invalid=96777
0036: dt=129.472000, rms=0.680 (0.111%), neg=0, invalid=96777
0037: dt=129.472000, rms=0.679 (0.096%), neg=0, invalid=96777
0038: dt=443.904000, rms=0.679 (0.056%), neg=0, invalid=96777
0039: dt=443.904000, rms=0.679 (-1.585%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.679, neg=0, invalid=96777
0040: dt=32.368000, rms=0.679 (0.041%), neg=0, invalid=96777
0041: dt=92.480000, rms=0.678 (0.043%), neg=0, invalid=96777
0042: dt=443.904000, rms=0.677 (0.201%), neg=0, invalid=96777
0043: dt=23.120000, rms=0.677 (-0.002%), neg=0, invalid=96777
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.684, neg=0, invalid=96777
0044: dt=103.680000, rms=0.678 (0.909%), neg=0, invalid=96777
0045: dt=36.288000, rms=0.672 (0.804%), neg=0, invalid=96777
0046: dt=25.920000, rms=0.671 (0.214%), neg=0, invalid=96777
0047: dt=25.920000, rms=0.669 (0.318%), neg=0, invalid=96777
0048: dt=25.920000, rms=0.666 (0.471%), neg=0, invalid=96777
0049: dt=25.920000, rms=0.662 (0.592%), neg=0, invalid=96777
0050: dt=25.920000, rms=0.658 (0.646%), neg=0, invalid=96777
0051: dt=25.920000, rms=0.653 (0.698%), neg=0, invalid=96777
0052: dt=25.920000, rms=0.648 (0.721%), neg=0, invalid=96777
0053: dt=25.920000, rms=0.644 (0.663%), neg=0, invalid=96777
0054: dt=25.920000, rms=0.640 (0.599%), neg=0, invalid=96777
0055: dt=25.920000, rms=0.637 (0.536%), neg=0, invalid=96777
0056: dt=25.920000, rms=0.634 (0.490%), neg=0, invalid=96777
0057: dt=25.920000, rms=0.631 (0.455%), neg=0, invalid=96777
0058: dt=25.920000, rms=0.628 (0.424%), neg=0, invalid=96777
0059: dt=25.920000, rms=0.626 (0.369%), neg=0, invalid=96777
0060: dt=25.920000, rms=0.624 (0.335%), neg=0, invalid=96777
0061: dt=25.920000, rms=0.622 (0.295%), neg=0, invalid=96777
0062: dt=25.920000, rms=0.620 (0.278%), neg=0, invalid=96777
0063: dt=25.920000, rms=0.618 (0.257%), neg=0, invalid=96777
0064: dt=25.920000, rms=0.617 (0.225%), neg=0, invalid=96777
0065: dt=25.920000, rms=0.616 (0.192%), neg=0, invalid=96777
0066: dt=25.920000, rms=0.615 (0.154%), neg=0, invalid=96777
0067: dt=25.920000, rms=0.614 (0.138%), neg=0, invalid=96777
0068: dt=25.920000, rms=0.613 (0.136%), neg=0, invalid=96777
0069: dt=25.920000, rms=0.612 (0.116%), neg=0, invalid=96777
0070: dt=25.920000, rms=0.612 (0.092%), neg=0, invalid=96777
0071: dt=103.680000, rms=0.612 (0.032%), neg=0, invalid=96777
0072: dt=103.680000, rms=0.611 (0.113%), neg=0, invalid=96777
0073: dt=103.680000, rms=0.611 (-1.233%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.611, neg=0, invalid=96777
0074: dt=9.072000, rms=0.611 (0.066%), neg=0, invalid=96777
0075: dt=9.072000, rms=0.610 (0.035%), neg=0, invalid=96777
0076: dt=9.072000, rms=0.610 (0.020%), neg=0, invalid=96777
0077: dt=9.072000, rms=0.610 (0.010%), neg=0, invalid=96777
0078: dt=9.072000, rms=0.610 (0.002%), neg=0, invalid=96777
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.636, neg=0, invalid=96777
0079: dt=6.372881, rms=0.636 (0.086%), neg=0, invalid=96777
0080: dt=1.200000, rms=0.636 (0.003%), neg=0, invalid=96777
0081: dt=1.200000, rms=0.636 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.636, neg=0, invalid=96777
0082: dt=0.500000, rms=0.636 (0.000%), neg=0, invalid=96777
0083: dt=0.125000, rms=0.636 (0.000%), neg=0, invalid=96777
0084: dt=0.125000, rms=0.636 (0.000%), neg=0, invalid=96777
0085: dt=0.125000, rms=0.636 (-0.000%), neg=0, invalid=96777
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.705, neg=0, invalid=96777
0086: dt=5.310924, rms=0.686 (2.764%), neg=0, invalid=96777
0087: dt=2.880000, rms=0.685 (0.141%), neg=0, invalid=96777
0088: dt=2.880000, rms=0.685 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.685, neg=0, invalid=96777
0089: dt=0.000000, rms=0.685 (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=0.750, neg=0, invalid=96777
0090: dt=1.024000, rms=0.746 (0.510%), neg=0, invalid=96777
0091: dt=2.056180, rms=0.740 (0.796%), neg=0, invalid=96777
0092: dt=0.488095, rms=0.739 (0.084%), neg=0, invalid=96777
0093: dt=0.488095, rms=0.739 (0.065%), neg=0, invalid=96777
0094: dt=0.488095, rms=0.738 (0.072%), neg=0, invalid=96777
0095: dt=0.488095, rms=0.738 (0.046%), neg=0, invalid=96777
0096: dt=0.488095, rms=0.738 (-0.026%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.738, neg=0, invalid=96777
0097: dt=1.792000, rms=0.736 (0.296%), neg=0, invalid=96777
0098: dt=0.000000, rms=0.736 (-0.001%), neg=0, invalid=96777
0099: dt=0.100000, rms=0.736 (-0.007%), 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=0.699, neg=0, invalid=96777
0100: dt=0.448000, rms=0.679 (2.883%), neg=0, invalid=96777
0101: dt=0.000000, rms=0.679 (0.006%), neg=0, invalid=96777
0102: dt=0.050000, rms=0.679 (-0.503%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.679, neg=0, invalid=96777
0103: dt=0.000000, rms=0.679 (0.000%), neg=0, invalid=96777
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.11725 (24)
mri peak = 0.15967 ( 9)
Left_Lateral_Ventricle (4): linear fit = 0.22 x + 0.0 (762 voxels, overlap=0.005)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (762 voxels, peak =  5), gca=9.6
gca peak = 0.14022 (22)
mri peak = 0.20958 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (565 voxels, overlap=0.005)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (565 voxels, peak =  6), gca=8.8
gca peak = 0.24234 (100)
mri peak = 0.11045 (83)
Right_Pallidum (52): linear fit = 0.83 x + 0.0 (381 voxels, overlap=0.049)
Right_Pallidum (52): linear fit = 0.83 x + 0.0 (381 voxels, peak = 84), gca=83.5
gca peak = 0.19192 (97)
mri peak = 0.10127 (79)
Left_Pallidum (13): linear fit = 0.83 x + 0.0 (265 voxels, overlap=0.061)
Left_Pallidum (13): linear fit = 0.83 x + 0.0 (265 voxels, peak = 81), gca=81.0
gca peak = 0.24007 (63)
mri peak = 0.07595 (56)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (408 voxels, overlap=0.301)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (408 voxels, peak = 55), gca=55.1
gca peak = 0.29892 (64)
mri peak = 0.08306 (56)
Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (614 voxels, overlap=0.449)
Left_Hippocampus (17): linear fit = 0.85 x + 0.0 (614 voxels, peak = 54), gca=54.1
gca peak = 0.12541 (104)
mri peak = 0.06587 (107)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (60604 voxels, overlap=0.859)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (60604 voxels, peak = 107), gca=106.6
gca peak = 0.13686 (104)
mri peak = 0.07229 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (62492 voxels, overlap=0.824)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (62492 voxels, peak = 107), gca=106.6
gca peak = 0.11691 (63)
mri peak = 0.06072 (51)
Left_Cerebral_Cortex (3): linear fit = 0.81 x + 0.0 (15397 voxels, overlap=0.274)
Left_Cerebral_Cortex (3): linear fit = 0.81 x + 0.0 (15397 voxels, peak = 51), gca=51.3
gca peak = 0.13270 (63)
mri peak = 0.05634 (51)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (15467 voxels, overlap=0.270)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (15467 voxels, peak = 52), gca=52.0
gca peak = 0.15182 (70)
mri peak = 0.11664 (63)
Right_Caudate (50): linear fit = 0.86 x + 0.0 (430 voxels, overlap=0.015)
Right_Caudate (50): linear fit = 0.86 x + 0.0 (430 voxels, peak = 60), gca=59.9
gca peak = 0.14251 (76)
mri peak = 0.08069 (64)
Left_Caudate (11): linear fit = 0.85 x + 0.0 (596 voxels, overlap=0.168)
Left_Caudate (11): linear fit = 0.85 x + 0.0 (596 voxels, peak = 64), gca=64.2
gca peak = 0.12116 (60)
mri peak = 0.04818 (56)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (8260 voxels, overlap=0.979)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (8260 voxels, peak = 56), gca=56.1
gca peak = 0.12723 (61)
mri peak = 0.04496 (55)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (10207 voxels, overlap=0.839)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (10207 voxels, peak = 57), gca=57.0
gca peak = 0.22684 (88)
mri peak = 0.05895 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5012 voxels, overlap=0.904)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (5012 voxels, peak = 89), gca=89.3
gca peak = 0.21067 (87)
mri peak = 0.05106 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4542 voxels, overlap=0.965)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (4542 voxels, peak = 90), gca=90.0
gca peak = 0.25455 (62)
mri peak = 0.10453 (55)
Left_Amygdala (18): linear fit = 0.86 x + 0.0 (316 voxels, overlap=0.404)
Left_Amygdala (18): linear fit = 0.86 x + 0.0 (316 voxels, peak = 53), gca=53.0
gca peak = 0.39668 (62)
mri peak = 0.12132 (58)
Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, overlap=0.244)
Right_Amygdala (54): linear fit = 0.85 x + 0.0 (308 voxels, peak = 52), gca=52.4
gca peak = 0.10129 (93)
mri peak = 0.05714 (83)
Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4717 voxels, overlap=0.756)
Left_Thalamus_Proper (10): linear fit = 0.92 x + 0.0 (4717 voxels, peak = 85), gca=85.1
gca peak = 0.12071 (89)
mri peak = 0.07686 (80)
Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3821 voxels, overlap=0.565)
Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (3821 voxels, peak = 83), gca=83.2
gca peak = 0.13716 (82)
mri peak = 0.05967 (71)
Left_Putamen (12): linear fit = 0.88 x + 0.0 (1644 voxels, overlap=0.415)
Left_Putamen (12): linear fit = 0.88 x + 0.0 (1644 voxels, peak = 73), gca=72.6
gca peak = 0.15214 (84)
mri peak = 0.06344 (70)
Right_Putamen (51): linear fit = 0.83 x + 0.0 (1899 voxels, overlap=0.159)
Right_Putamen (51): linear fit = 0.83 x + 0.0 (1899 voxels, peak = 70), gca=70.1
gca peak = 0.08983 (85)
mri peak = 0.08139 (82)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (8892 voxels, overlap=0.777)
Brain_Stem (16): linear fit = 1.02 x + 0.0 (8892 voxels, peak = 87), gca=87.1
gca peak = 0.11809 (92)
mri peak = 0.06918 (89)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (684 voxels, overlap=0.675)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (684 voxels, peak = 89), gca=88.8
gca peak = 0.12914 (94)
mri peak = 0.08774 (88)
Left_VentralDC (28): linear fit = 0.94 x + 0.0 (952 voxels, overlap=0.652)
Left_VentralDC (28): linear fit = 0.94 x + 0.0 (952 voxels, peak = 89), gca=88.8
gca peak = 0.21100 (36)
mri peak = 0.27273 (51)
gca peak = 0.13542 (27)
mri peak = 0.19745 ( 6)
Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (366 voxels, overlap=0.024)
Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (366 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 0.84 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.40 x + 0.0
saving intensity scales to 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=0.697, neg=0, invalid=96777
0104: dt=129.472000, rms=0.692 (0.715%), neg=0, invalid=96777
0105: dt=221.952000, rms=0.689 (0.488%), neg=0, invalid=96777
0106: dt=92.480000, rms=0.687 (0.228%), neg=0, invalid=96777
0107: dt=295.936000, rms=0.686 (0.240%), neg=0, invalid=96777
0108: dt=92.480000, rms=0.684 (0.199%), neg=0, invalid=96777
0109: dt=129.472000, rms=0.684 (0.091%), neg=0, invalid=96777
0110: dt=129.472000, rms=0.683 (0.107%), neg=0, invalid=96777
0111: dt=92.480000, rms=0.683 (0.057%), neg=0, invalid=96777
0112: dt=295.936000, rms=0.682 (0.137%), neg=0, invalid=96777
0113: dt=32.368000, rms=0.681 (0.084%), neg=0, invalid=96777
0114: dt=73.984000, rms=0.681 (0.032%), neg=0, invalid=96777
0115: dt=73.984000, rms=0.681 (0.042%), neg=0, invalid=96777
0116: dt=73.984000, rms=0.680 (0.078%), neg=0, invalid=96777
0117: dt=73.984000, rms=0.680 (0.095%), neg=0, invalid=96777
0118: dt=73.984000, rms=0.679 (0.099%), neg=0, invalid=96777
0119: dt=73.984000, rms=0.678 (0.119%), neg=0, invalid=96777
0120: dt=73.984000, rms=0.677 (0.120%), neg=0, invalid=96777
0121: dt=73.984000, rms=0.676 (0.120%), neg=0, invalid=96777
0122: dt=73.984000, rms=0.676 (0.117%), neg=0, invalid=96777
0123: dt=73.984000, rms=0.675 (0.117%), neg=0, invalid=96777
0124: dt=73.984000, rms=0.674 (0.118%), neg=0, invalid=96777
0125: dt=73.984000, rms=0.673 (0.098%), neg=0, invalid=96777
0126: dt=73.984000, rms=0.673 (0.075%), neg=0, invalid=96777
0127: dt=73.984000, rms=0.673 (0.057%), neg=0, invalid=96777
0128: dt=73.984000, rms=0.672 (0.057%), neg=0, invalid=96777
0129: dt=73.984000, rms=0.672 (0.071%), neg=0, invalid=96777
0130: dt=73.984000, rms=0.671 (0.072%), neg=0, invalid=96777
0131: dt=73.984000, rms=0.671 (0.069%), neg=0, invalid=96777
0132: dt=73.984000, rms=0.670 (0.053%), neg=0, invalid=96777
0133: dt=73.984000, rms=0.670 (0.047%), neg=0, invalid=96777
0134: dt=73.984000, rms=0.670 (0.052%), neg=0, invalid=96777
0135: dt=73.984000, rms=0.669 (0.053%), neg=0, invalid=96777
0136: dt=73.984000, rms=0.669 (0.063%), neg=0, invalid=96777
0137: dt=73.984000, rms=0.668 (0.065%), neg=0, invalid=96777
0138: dt=73.984000, rms=0.668 (0.059%), neg=0, invalid=96777
0139: dt=73.984000, rms=0.668 (0.055%), neg=0, invalid=96777
0140: dt=73.984000, rms=0.667 (0.042%), neg=0, invalid=96777
0141: dt=73.984000, rms=0.667 (0.039%), neg=0, invalid=96777
0142: dt=73.984000, rms=0.667 (0.042%), neg=0, invalid=96777
0143: dt=73.984000, rms=0.667 (0.045%), neg=0, invalid=96777
0144: dt=73.984000, rms=0.666 (0.046%), neg=0, invalid=96777
0145: dt=73.984000, rms=0.666 (0.046%), neg=0, invalid=96777
0146: dt=73.984000, rms=0.666 (0.038%), neg=0, invalid=96777
0147: dt=73.984000, rms=0.665 (0.037%), neg=0, invalid=96777
0148: dt=73.984000, rms=0.665 (0.032%), neg=0, invalid=96777
0149: dt=73.984000, rms=0.665 (0.034%), neg=0, invalid=96777
0150: dt=73.984000, rms=0.665 (0.039%), neg=0, invalid=96777
0151: dt=73.984000, rms=0.665 (0.045%), neg=0, invalid=96777
0152: dt=73.984000, rms=0.664 (0.042%), neg=0, invalid=96777
0153: dt=73.984000, rms=0.664 (0.037%), neg=0, invalid=96777
0154: dt=73.984000, rms=0.664 (0.028%), neg=0, invalid=96777
0155: dt=73.984000, rms=0.664 (0.019%), neg=0, invalid=96777
0156: dt=73.984000, rms=0.664 (0.023%), neg=0, invalid=96777
0157: dt=73.984000, rms=0.663 (0.033%), neg=0, invalid=96777
0158: dt=73.984000, rms=0.663 (0.036%), neg=0, invalid=96777
0159: dt=73.984000, rms=0.663 (0.039%), neg=0, invalid=96777
0160: dt=73.984000, rms=0.663 (0.027%), neg=0, invalid=96777
0161: dt=73.984000, rms=0.662 (0.018%), neg=0, invalid=96777
0162: dt=73.984000, rms=0.662 (0.017%), neg=0, invalid=96777
0163: dt=369.920000, rms=0.662 (0.014%), neg=0, invalid=96777
0164: dt=369.920000, rms=0.662 (-0.127%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.662, neg=0, invalid=96777
0165: dt=369.920000, rms=0.661 (0.243%), neg=0, invalid=96777
0166: dt=92.480000, rms=0.660 (0.059%), neg=0, invalid=96777
0167: dt=443.904000, rms=0.660 (0.068%), neg=0, invalid=96777
0168: dt=129.472000, rms=0.659 (0.057%), neg=0, invalid=96777
0169: dt=129.472000, rms=0.659 (0.028%), neg=0, invalid=96777
0170: dt=129.472000, rms=0.659 (0.007%), neg=0, invalid=96777
0171: dt=129.472000, rms=0.659 (0.043%), neg=0, invalid=96777
0172: dt=129.472000, rms=0.659 (0.053%), neg=0, invalid=96777
0173: dt=129.472000, rms=0.658 (0.041%), neg=0, invalid=96777
0174: dt=129.472000, rms=0.658 (0.042%), neg=0, invalid=96777
0175: dt=129.472000, rms=0.658 (0.051%), neg=0, invalid=96777
0176: dt=129.472000, rms=0.657 (0.050%), neg=0, invalid=96777
0177: dt=129.472000, rms=0.657 (0.038%), neg=0, invalid=96777
0178: dt=129.472000, rms=0.657 (0.041%), neg=0, invalid=96777
0179: dt=129.472000, rms=0.657 (0.042%), neg=0, invalid=96777
0180: dt=129.472000, rms=0.656 (0.027%), neg=0, invalid=96777
0181: dt=129.472000, rms=0.656 (0.023%), neg=0, invalid=96777
0182: dt=129.472000, rms=0.656 (0.039%), neg=0, invalid=96777
0183: dt=129.472000, rms=0.656 (0.040%), neg=0, invalid=96777
0184: dt=129.472000, rms=0.656 (0.029%), neg=0, invalid=96777
0185: dt=129.472000, rms=0.655 (0.019%), neg=0, invalid=96777
0186: dt=129.472000, rms=0.655 (0.016%), neg=0, invalid=96777
0187: dt=110.976000, rms=0.655 (0.004%), neg=0, invalid=96777
0188: dt=110.976000, rms=0.655 (0.003%), neg=0, invalid=96777
0189: dt=110.976000, rms=0.655 (0.001%), neg=0, invalid=96777
0190: dt=110.976000, rms=0.655 (0.006%), neg=0, invalid=96777
0191: dt=110.976000, rms=0.655 (0.013%), neg=0, invalid=96777
0192: dt=110.976000, rms=0.655 (0.017%), neg=0, invalid=96777
0193: dt=110.976000, rms=0.655 (0.012%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.656, neg=0, invalid=96777
0194: dt=145.152000, rms=0.650 (0.849%), neg=0, invalid=96777
0195: dt=124.416000, rms=0.645 (0.731%), neg=0, invalid=96777
0196: dt=36.288000, rms=0.642 (0.511%), neg=0, invalid=96777
0197: dt=62.208000, rms=0.641 (0.218%), neg=0, invalid=96777
0198: dt=36.288000, rms=0.639 (0.246%), neg=0, invalid=96777
0199: dt=36.288000, rms=0.638 (0.146%), neg=0, invalid=96777
0200: dt=36.288000, rms=0.637 (0.211%), neg=0, invalid=96777
0201: dt=62.208000, rms=0.636 (0.180%), neg=0, invalid=96777
0202: dt=36.288000, rms=0.634 (0.219%), neg=0, invalid=96777
0203: dt=36.288000, rms=0.633 (0.117%), neg=0, invalid=96777
0204: dt=36.288000, rms=0.632 (0.189%), neg=0, invalid=96777
0205: dt=36.288000, rms=0.632 (0.114%), neg=0, invalid=96777
0206: dt=145.152000, rms=0.629 (0.362%), neg=0, invalid=96777
0207: dt=20.736000, rms=0.628 (0.212%), neg=0, invalid=96777
0208: dt=414.720000, rms=0.623 (0.728%), neg=0, invalid=96777
0209: dt=17.968883, rms=0.621 (0.427%), neg=0, invalid=96777
0210: dt=25.920000, rms=0.620 (0.070%), neg=0, invalid=96777
0211: dt=248.832000, rms=0.618 (0.370%), neg=0, invalid=96777
0212: dt=20.736000, rms=0.617 (0.168%), neg=0, invalid=96777
0213: dt=145.152000, rms=0.615 (0.252%), neg=0, invalid=96777
0214: dt=36.288000, rms=0.615 (0.101%), neg=0, invalid=96777
0215: dt=62.208000, rms=0.614 (0.106%), neg=0, invalid=96777
0216: dt=31.104000, rms=0.614 (0.057%), neg=0, invalid=96777
0217: dt=82.944000, rms=0.613 (0.123%), neg=0, invalid=96777
0218: dt=25.920000, rms=0.613 (0.058%), neg=0, invalid=96777
0219: dt=331.776000, rms=0.610 (0.357%), neg=0, invalid=96777
0220: dt=15.552000, rms=0.610 (0.155%), neg=0, invalid=96777
0221: dt=25.920000, rms=0.609 (0.045%), neg=0, invalid=96777
0222: dt=25.920000, rms=0.609 (0.051%), neg=0, invalid=96777
0223: dt=25.920000, rms=0.608 (0.071%), neg=0, invalid=96777
0224: dt=25.920000, rms=0.608 (0.084%), neg=0, invalid=96777
0225: dt=25.920000, rms=0.607 (0.098%), neg=0, invalid=96777
0226: dt=25.920000, rms=0.607 (0.134%), neg=0, invalid=96777
0227: dt=25.920000, rms=0.606 (0.159%), neg=0, invalid=96777
0228: dt=25.920000, rms=0.605 (0.160%), neg=0, invalid=96777
0229: dt=25.920000, rms=0.604 (0.165%), neg=0, invalid=96777
0230: dt=25.920000, rms=0.603 (0.158%), neg=0, invalid=96777
0231: dt=25.920000, rms=0.602 (0.163%), neg=0, invalid=96777
0232: dt=25.920000, rms=0.601 (0.181%), neg=0, invalid=96777
0233: dt=25.920000, rms=0.599 (0.190%), neg=0, invalid=96777
0234: dt=25.920000, rms=0.598 (0.164%), neg=0, invalid=96777
0235: dt=25.920000, rms=0.598 (0.148%), neg=0, invalid=96777
0236: dt=25.920000, rms=0.597 (0.163%), neg=0, invalid=96777
0237: dt=25.920000, rms=0.596 (0.176%), neg=0, invalid=96777
0238: dt=25.920000, rms=0.595 (0.164%), neg=0, invalid=96777
0239: dt=25.920000, rms=0.594 (0.130%), neg=0, invalid=96777
0240: dt=25.920000, rms=0.594 (0.003%), neg=0, invalid=96777
0241: dt=25.920000, rms=0.594 (0.020%), neg=0, invalid=96777
0242: dt=25.920000, rms=0.593 (0.034%), neg=0, invalid=96777
0243: dt=25.920000, rms=0.593 (0.050%), neg=0, invalid=96777
0244: dt=25.920000, rms=0.593 (0.053%), neg=0, invalid=96777
0245: dt=25.920000, rms=0.593 (0.053%), neg=0, invalid=96777
0246: dt=25.920000, rms=0.592 (0.050%), neg=0, invalid=96777
0247: dt=25.920000, rms=0.592 (0.060%), neg=0, invalid=96777
0248: dt=25.920000, rms=0.591 (0.088%), neg=0, invalid=96777
0249: dt=25.920000, rms=0.591 (0.081%), neg=0, invalid=96777
0250: dt=25.920000, rms=0.590 (0.075%), neg=0, invalid=96777
0251: dt=25.920000, rms=0.590 (0.077%), neg=0, invalid=96777
0252: dt=25.920000, rms=0.590 (0.077%), neg=0, invalid=96777
0253: dt=25.920000, rms=0.589 (0.084%), neg=0, invalid=96777
0254: dt=25.920000, rms=0.589 (0.090%), neg=0, invalid=96777
0255: dt=25.920000, rms=0.588 (0.085%), neg=0, invalid=96777
0256: dt=25.920000, rms=0.588 (0.067%), neg=0, invalid=96777
0257: dt=25.920000, rms=0.587 (0.060%), neg=0, invalid=96777
0258: dt=25.920000, rms=0.587 (0.076%), neg=0, invalid=96777
0259: dt=25.920000, rms=0.586 (0.091%), neg=0, invalid=96777
0260: dt=25.920000, rms=0.586 (0.081%), neg=0, invalid=96777
0261: dt=25.920000, rms=0.585 (0.076%), neg=0, invalid=96777
0262: dt=25.920000, rms=0.585 (0.071%), neg=0, invalid=96777
0263: dt=25.920000, rms=0.584 (0.091%), neg=0, invalid=96777
0264: dt=25.920000, rms=0.584 (0.070%), neg=0, invalid=96777
0265: dt=25.920000, rms=0.584 (0.031%), neg=0, invalid=96777
0266: dt=25.920000, rms=0.584 (0.048%), neg=0, invalid=96777
0267: dt=25.920000, rms=0.583 (0.066%), neg=0, invalid=96777
0268: dt=25.920000, rms=0.583 (0.074%), neg=0, invalid=96777
0269: dt=25.920000, rms=0.582 (0.064%), neg=0, invalid=96777
0270: dt=25.920000, rms=0.582 (0.054%), neg=0, invalid=96777
0271: dt=25.920000, rms=0.582 (0.045%), neg=0, invalid=96777
0272: dt=25.920000, rms=0.582 (0.048%), neg=0, invalid=96777
0273: dt=25.920000, rms=0.581 (0.046%), neg=0, invalid=96777
0274: dt=25.920000, rms=0.581 (0.057%), neg=0, invalid=96777
0275: dt=25.920000, rms=0.581 (0.041%), neg=0, invalid=96777
0276: dt=25.920000, rms=0.581 (0.030%), neg=0, invalid=96777
0277: dt=25.920000, rms=0.580 (0.040%), neg=0, invalid=96777
0278: dt=25.920000, rms=0.580 (0.050%), neg=0, invalid=96777
0279: dt=25.920000, rms=0.580 (0.057%), neg=0, invalid=96777
0280: dt=25.920000, rms=0.579 (0.047%), neg=0, invalid=96777
0281: dt=25.920000, rms=0.579 (0.037%), neg=0, invalid=96777
0282: dt=25.920000, rms=0.579 (0.043%), neg=0, invalid=96777
0283: dt=25.920000, rms=0.579 (0.045%), neg=0, invalid=96777
0284: dt=25.920000, rms=0.578 (0.048%), neg=0, invalid=96777
0285: dt=25.920000, rms=0.578 (0.040%), neg=0, invalid=96777
0286: dt=25.920000, rms=0.578 (0.035%), neg=0, invalid=96777
0287: dt=25.920000, rms=0.578 (0.038%), neg=0, invalid=96777
0288: dt=25.920000, rms=0.578 (0.035%), neg=0, invalid=96777
0289: dt=25.920000, rms=0.577 (0.040%), neg=0, invalid=96777
0290: dt=25.920000, rms=0.577 (0.028%), neg=0, invalid=96777
0291: dt=25.920000, rms=0.577 (0.036%), neg=0, invalid=96777
0292: dt=25.920000, rms=0.577 (0.030%), neg=0, invalid=96777
0293: dt=25.920000, rms=0.577 (0.026%), neg=0, invalid=96777
0294: dt=25.920000, rms=0.576 (0.027%), neg=0, invalid=96777
0295: dt=25.920000, rms=0.576 (0.032%), neg=0, invalid=96777
0296: dt=25.920000, rms=0.576 (0.041%), neg=0, invalid=96777
0297: dt=25.920000, rms=0.576 (0.040%), neg=0, invalid=96777
0298: dt=25.920000, rms=0.576 (0.028%), neg=0, invalid=96777
0299: dt=25.920000, rms=0.576 (0.021%), neg=0, invalid=96777
0300: dt=25.920000, rms=0.575 (0.025%), neg=0, invalid=96777
0301: dt=25.920000, rms=0.575 (0.032%), neg=0, invalid=96777
0302: dt=25.920000, rms=0.575 (0.030%), neg=0, invalid=96777
0303: dt=25.920000, rms=0.575 (0.024%), neg=0, invalid=96777
0304: dt=25.920000, rms=0.575 (0.036%), neg=0, invalid=96777
0305: dt=25.920000, rms=0.574 (0.034%), neg=0, invalid=96777
0306: dt=25.920000, rms=0.574 (0.015%), neg=0, invalid=96777
0307: dt=25.920000, rms=0.574 (-0.002%), neg=0, invalid=96777
0308: dt=9.072000, rms=0.574 (0.000%), neg=0, invalid=96777
0309: dt=36.288000, rms=0.574 (0.002%), neg=0, invalid=96777
0310: dt=20.736000, rms=0.574 (0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.574, neg=0, invalid=96777
0311: dt=145.152000, rms=0.572 (0.413%), neg=0, invalid=96777
0312: dt=36.288000, rms=0.571 (0.108%), neg=0, invalid=96777
0313: dt=82.944000, rms=0.571 (0.050%), neg=0, invalid=96777
0314: dt=82.944000, rms=0.571 (0.066%), neg=0, invalid=96777
0315: dt=20.736000, rms=0.570 (0.063%), neg=0, invalid=96777
0316: dt=20.736000, rms=0.570 (0.039%), neg=0, invalid=96777
0317: dt=20.736000, rms=0.570 (0.040%), neg=0, invalid=96777
0318: dt=20.736000, rms=0.570 (0.040%), neg=0, invalid=96777
0319: dt=20.736000, rms=0.569 (0.039%), neg=0, invalid=96777
0320: dt=20.736000, rms=0.569 (0.040%), neg=0, invalid=96777
0321: dt=20.736000, rms=0.569 (0.061%), neg=0, invalid=96777
0322: dt=20.736000, rms=0.569 (0.056%), neg=0, invalid=96777
0323: dt=20.736000, rms=0.568 (0.066%), neg=0, invalid=96777
0324: dt=20.736000, rms=0.568 (0.050%), neg=0, invalid=96777
0325: dt=20.736000, rms=0.568 (0.035%), neg=0, invalid=96777
0326: dt=20.736000, rms=0.567 (0.040%), neg=0, invalid=96777
0327: dt=20.736000, rms=0.567 (0.041%), neg=0, invalid=96777
0328: dt=20.736000, rms=0.567 (0.052%), neg=0, invalid=96777
0329: dt=20.736000, rms=0.567 (0.036%), neg=0, invalid=96777
0330: dt=20.736000, rms=0.567 (0.028%), neg=0, invalid=96777
0331: dt=20.736000, rms=0.566 (0.025%), neg=0, invalid=96777
0332: dt=20.736000, rms=0.566 (0.028%), neg=0, invalid=96777
0333: dt=20.736000, rms=0.566 (0.039%), neg=0, invalid=96777
0334: dt=20.736000, rms=0.566 (0.046%), neg=0, invalid=96777
0335: dt=20.736000, rms=0.566 (0.032%), neg=0, invalid=96777
0336: dt=20.736000, rms=0.565 (0.023%), neg=0, invalid=96777
0337: dt=20.736000, rms=0.565 (0.021%), neg=0, invalid=96777
0338: dt=145.152000, rms=0.565 (0.052%), neg=0, invalid=96777
0339: dt=6.480000, rms=0.565 (0.002%), neg=0, invalid=96777
0340: dt=6.480000, rms=0.565 (-0.001%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.573, neg=0, invalid=96777
0341: dt=2.800000, rms=0.573 (0.071%), neg=0, invalid=96777
0342: dt=2.800000, rms=0.572 (0.072%), neg=0, invalid=96777
0343: dt=11.200000, rms=0.571 (0.223%), neg=0, invalid=96777
0344: dt=44.800000, rms=0.568 (0.519%), neg=0, invalid=96777
0345: dt=11.200000, rms=0.567 (0.167%), neg=0, invalid=96777
0346: dt=38.400000, rms=0.564 (0.500%), neg=0, invalid=96777
0347: dt=5.757322, rms=0.563 (0.141%), neg=0, invalid=96777
0348: dt=32.000000, rms=0.562 (0.252%), neg=0, invalid=96777
0349: dt=11.200000, rms=0.560 (0.307%), neg=0, invalid=96777
0350: dt=11.200000, rms=0.560 (0.059%), neg=0, invalid=96777
0351: dt=32.000000, rms=0.558 (0.313%), neg=0, invalid=96777
0352: dt=3.523810, rms=0.558 (0.084%), neg=0, invalid=96777
0353: dt=8.000000, rms=0.557 (0.064%), neg=0, invalid=96777
0354: dt=44.800000, rms=0.555 (0.402%), neg=0, invalid=96777
0355: dt=4.800000, rms=0.555 (0.073%), neg=0, invalid=96777
0356: dt=11.200000, rms=0.554 (0.084%), neg=0, invalid=96777
0357: dt=44.800000, rms=0.552 (0.390%), neg=0, invalid=96777
0358: dt=2.800000, rms=0.552 (0.019%), neg=0, invalid=96777
0359: dt=2.800000, rms=0.552 (0.021%), neg=0, invalid=96777
0360: dt=2.800000, rms=0.552 (0.016%), neg=0, invalid=96777
0361: dt=2.800000, rms=0.552 (0.040%), neg=0, invalid=96777
0362: dt=2.800000, rms=0.551 (0.065%), neg=0, invalid=96777
0363: dt=2.800000, rms=0.551 (0.099%), neg=0, invalid=96777
0364: dt=2.800000, rms=0.550 (0.103%), neg=0, invalid=96777
0365: dt=2.800000, rms=0.549 (0.115%), neg=0, invalid=96777
0366: dt=2.800000, rms=0.549 (0.114%), neg=0, invalid=96777
0367: dt=2.800000, rms=0.548 (0.111%), neg=0, invalid=96777
0368: dt=2.800000, rms=0.548 (0.113%), neg=0, invalid=96777
0369: dt=2.800000, rms=0.547 (0.106%), neg=0, invalid=96777
0370: dt=2.800000, rms=0.546 (0.112%), neg=0, invalid=96777
0371: dt=2.800000, rms=0.546 (0.123%), neg=0, invalid=96777
0372: dt=2.800000, rms=0.545 (0.128%), neg=0, invalid=96777
0373: dt=2.800000, rms=0.544 (0.126%), neg=0, invalid=96777
0374: dt=2.800000, rms=0.544 (0.127%), neg=0, invalid=96777
0375: dt=2.800000, rms=0.543 (0.121%), neg=0, invalid=96777
0376: dt=2.800000, rms=0.542 (0.110%), neg=0, invalid=96777
0377: dt=2.800000, rms=0.542 (0.110%), neg=0, invalid=96777
0378: dt=2.800000, rms=0.541 (0.107%), neg=0, invalid=96777
0379: dt=2.800000, rms=0.541 (0.108%), neg=0, invalid=96777
0380: dt=2.800000, rms=0.540 (0.110%), neg=0, invalid=96777
0381: dt=2.800000, rms=0.539 (0.111%), neg=0, invalid=96777
0382: dt=2.800000, rms=0.539 (0.114%), neg=0, invalid=96777
0383: dt=2.800000, rms=0.538 (0.101%), neg=0, invalid=96777
0384: dt=2.800000, rms=0.538 (0.095%), neg=0, invalid=96777
0385: dt=2.800000, rms=0.537 (0.092%), neg=0, invalid=96777
0386: dt=2.800000, rms=0.537 (0.087%), neg=0, invalid=96777
0387: dt=2.800000, rms=0.536 (0.081%), neg=0, invalid=96777
0388: dt=2.800000, rms=0.536 (0.082%), neg=0, invalid=96777
0389: dt=2.800000, rms=0.535 (0.081%), neg=0, invalid=96777
0390: dt=2.800000, rms=0.535 (0.073%), neg=0, invalid=96777
0391: dt=2.800000, rms=0.535 (0.075%), neg=0, invalid=96777
0392: dt=2.800000, rms=0.534 (0.076%), neg=0, invalid=96777
0393: dt=2.800000, rms=0.534 (0.066%), neg=0, invalid=96777
0394: dt=2.800000, rms=0.534 (0.064%), neg=0, invalid=96777
0395: dt=2.800000, rms=0.533 (0.064%), neg=0, invalid=96777
0396: dt=2.800000, rms=0.533 (0.069%), neg=0, invalid=96777
0397: dt=2.800000, rms=0.533 (0.062%), neg=0, invalid=96777
0398: dt=2.800000, rms=0.532 (0.060%), neg=0, invalid=96777
0399: dt=2.800000, rms=0.532 (0.063%), neg=0, invalid=96777
0400: dt=2.800000, rms=0.532 (0.057%), neg=0, invalid=96777
0401: dt=2.800000, rms=0.531 (0.055%), neg=0, invalid=96777
0402: dt=2.800000, rms=0.531 (0.049%), neg=0, invalid=96777
0403: dt=2.800000, rms=0.531 (0.052%), neg=0, invalid=96777
0404: dt=2.800000, rms=0.530 (0.047%), neg=0, invalid=96777
0405: dt=2.800000, rms=0.530 (0.047%), neg=0, invalid=96777
0406: dt=2.800000, rms=0.530 (0.040%), neg=0, invalid=96777
0407: dt=2.800000, rms=0.530 (0.042%), neg=0, invalid=96777
0408: dt=2.800000, rms=0.530 (0.036%), neg=0, invalid=96777
0409: dt=2.800000, rms=0.529 (0.042%), neg=0, invalid=96777
0410: dt=2.800000, rms=0.529 (0.040%), neg=0, invalid=96777
0411: dt=2.800000, rms=0.529 (0.037%), neg=0, invalid=96777
0412: dt=2.800000, rms=0.529 (0.039%), neg=0, invalid=96777
0413: dt=2.800000, rms=0.529 (0.036%), neg=0, invalid=96777
0414: dt=2.800000, rms=0.528 (0.036%), neg=0, invalid=96777
0415: dt=2.800000, rms=0.528 (0.034%), neg=0, invalid=96777
0416: dt=2.800000, rms=0.528 (0.030%), neg=0, invalid=96777
0417: dt=2.800000, rms=0.528 (0.033%), neg=0, invalid=96777
0418: dt=2.800000, rms=0.528 (0.030%), neg=0, invalid=96777
0419: dt=2.800000, rms=0.528 (0.033%), neg=0, invalid=96777
0420: dt=2.800000, rms=0.527 (0.029%), neg=0, invalid=96777
0421: dt=2.800000, rms=0.527 (0.030%), neg=0, invalid=96777
0422: dt=2.800000, rms=0.527 (0.028%), neg=0, invalid=96777
0423: dt=2.800000, rms=0.527 (0.030%), neg=0, invalid=96777
0424: dt=2.800000, rms=0.527 (0.026%), neg=0, invalid=96777
0425: dt=2.800000, rms=0.527 (0.029%), neg=0, invalid=96777
0426: dt=2.800000, rms=0.527 (0.022%), neg=0, invalid=96777
0427: dt=2.800000, rms=0.526 (0.022%), neg=0, invalid=96777
0428: dt=44.800000, rms=0.526 (0.040%), neg=0, invalid=96777
0429: dt=2.400000, rms=0.526 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.526, neg=0, invalid=96777
0430: dt=32.000000, rms=0.524 (0.387%), neg=0, invalid=96777
0431: dt=11.200000, rms=0.523 (0.205%), neg=0, invalid=96777
0432: dt=6.400000, rms=0.523 (0.032%), neg=0, invalid=96777
0433: dt=6.400000, rms=0.523 (0.047%), neg=0, invalid=96777
0434: dt=6.400000, rms=0.522 (0.058%), neg=0, invalid=96777
0435: dt=6.400000, rms=0.522 (0.068%), neg=0, invalid=96777
0436: dt=6.400000, rms=0.522 (0.071%), neg=0, invalid=96777
0437: dt=6.400000, rms=0.521 (0.067%), neg=0, invalid=96777
0438: dt=6.400000, rms=0.521 (0.055%), neg=0, invalid=96777
0439: dt=6.400000, rms=0.521 (0.039%), neg=0, invalid=96777
0440: dt=6.400000, rms=0.521 (0.027%), neg=0, invalid=96777
0441: dt=6.400000, rms=0.521 (0.020%), neg=0, invalid=96777
0442: dt=6.400000, rms=0.520 (0.034%), neg=0, invalid=96777
0443: dt=6.400000, rms=0.520 (0.036%), neg=0, invalid=96777
0444: dt=6.400000, rms=0.520 (0.035%), neg=0, invalid=96777
0445: dt=6.400000, rms=0.520 (0.038%), neg=0, invalid=96777
0446: dt=6.400000, rms=0.520 (0.038%), neg=0, invalid=96777
0447: dt=6.400000, rms=0.519 (0.047%), neg=0, invalid=96777
0448: dt=6.400000, rms=0.519 (0.050%), neg=0, invalid=96777
0449: dt=6.400000, rms=0.519 (0.047%), neg=0, invalid=96777
0450: dt=6.400000, rms=0.519 (0.060%), neg=0, invalid=96777
0451: dt=6.400000, rms=0.518 (0.061%), neg=0, invalid=96777
0452: dt=6.400000, rms=0.518 (0.050%), neg=0, invalid=96777
0453: dt=6.400000, rms=0.518 (0.055%), neg=0, invalid=96777
0454: dt=6.400000, rms=0.517 (0.056%), neg=0, invalid=96777
0455: dt=6.400000, rms=0.517 (0.051%), neg=0, invalid=96777
0456: dt=6.400000, rms=0.517 (0.048%), neg=0, invalid=96777
0457: dt=6.400000, rms=0.517 (0.039%), neg=0, invalid=96777
0458: dt=6.400000, rms=0.517 (0.025%), neg=0, invalid=96777
0459: dt=6.400000, rms=0.516 (0.031%), neg=0, invalid=96777
0460: dt=6.400000, rms=0.516 (0.050%), neg=0, invalid=96777
0461: dt=6.400000, rms=0.516 (0.047%), neg=0, invalid=96777
0462: dt=6.400000, rms=0.516 (0.047%), neg=0, invalid=96777
0463: dt=6.400000, rms=0.516 (0.031%), neg=0, invalid=96777
0464: dt=6.400000, rms=0.515 (0.044%), neg=0, invalid=96777
0465: dt=6.400000, rms=0.515 (0.040%), neg=0, invalid=96777
0466: dt=6.400000, rms=0.515 (0.038%), neg=0, invalid=96777
0467: dt=6.400000, rms=0.515 (0.023%), neg=0, invalid=96777
0468: dt=6.400000, rms=0.515 (0.036%), neg=0, invalid=96777
0469: dt=6.400000, rms=0.514 (0.042%), neg=0, invalid=96777
0470: dt=6.400000, rms=0.514 (0.033%), neg=0, invalid=96777
0471: dt=6.400000, rms=0.514 (0.040%), neg=0, invalid=96777
0472: dt=6.400000, rms=0.514 (0.036%), neg=0, invalid=96777
0473: dt=6.400000, rms=0.514 (0.025%), neg=0, invalid=96777
0474: dt=6.400000, rms=0.514 (0.025%), neg=0, invalid=96777
0475: dt=6.400000, rms=0.513 (0.030%), neg=0, invalid=96777
0476: dt=6.400000, rms=0.513 (0.034%), neg=0, invalid=96777
0477: dt=6.400000, rms=0.513 (0.030%), neg=0, invalid=96777
0478: dt=6.400000, rms=0.513 (0.030%), neg=0, invalid=96777
0479: dt=6.400000, rms=0.513 (0.024%), neg=0, invalid=96777
0480: dt=6.400000, rms=0.513 (0.020%), neg=0, invalid=96777
0481: dt=11.200000, rms=0.513 (0.015%), neg=0, invalid=96777
0482: dt=11.200000, rms=0.513 (-0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.531, neg=0, invalid=96777
0483: dt=0.000000, rms=0.531 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.531, neg=0, invalid=96777
0484: dt=0.000000, rms=0.531 (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=0.567, neg=0, invalid=96777
0485: dt=0.555556, rms=0.566 (0.177%), neg=0, invalid=96777
0486: dt=0.112000, rms=0.566 (0.009%), neg=0, invalid=96777
0487: dt=0.112000, rms=0.566 (0.001%), neg=0, invalid=96777
0488: dt=0.112000, rms=0.566 (-0.022%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.566, neg=0, invalid=96777
0489: dt=0.384000, rms=0.566 (0.035%), neg=0, invalid=96777
0490: dt=0.028000, rms=0.566 (0.001%), neg=0, invalid=96777
0491: dt=0.028000, rms=0.566 (0.001%), neg=0, invalid=96777
0492: dt=0.028000, rms=0.566 (-0.002%), 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=0.517, neg=0, invalid=96777
0493: dt=0.169643, rms=0.509 (1.367%), neg=0, invalid=96777
0494: dt=0.140625, rms=0.506 (0.752%), neg=0, invalid=96777
0495: dt=0.122863, rms=0.503 (0.491%), neg=0, invalid=96777
0496: dt=0.384000, rms=0.497 (1.179%), neg=0, invalid=96777
0497: dt=0.028000, rms=0.497 (0.031%), neg=0, invalid=96777
0498: dt=0.028000, rms=0.497 (0.030%), neg=0, invalid=96777
0499: dt=0.028000, rms=0.497 (0.055%), neg=0, invalid=96777
0500: dt=0.028000, rms=0.496 (0.080%), neg=0, invalid=96777
0501: dt=0.028000, rms=0.496 (0.097%), neg=0, invalid=96777
0502: dt=0.028000, rms=0.495 (0.108%), neg=0, invalid=96777
0503: dt=0.028000, rms=0.495 (0.115%), neg=0, invalid=96777
0504: dt=0.028000, rms=0.495 (0.012%), neg=0, invalid=96777
0505: dt=0.028000, rms=0.494 (0.033%), neg=0, invalid=96777
0506: dt=0.028000, rms=0.494 (0.040%), neg=0, invalid=96777
0507: dt=0.028000, rms=0.494 (0.051%), neg=0, invalid=96777
0508: dt=0.028000, rms=0.494 (0.057%), neg=0, invalid=96777
0509: dt=0.028000, rms=0.493 (0.060%), neg=0, invalid=96777
0510: dt=0.028000, rms=0.493 (0.066%), neg=0, invalid=96777
0511: dt=0.028000, rms=0.493 (0.066%), neg=0, invalid=96777
0512: dt=0.028000, rms=0.492 (0.071%), neg=0, invalid=96777
0513: dt=0.028000, rms=0.492 (0.065%), neg=0, invalid=96777
0514: dt=0.028000, rms=0.492 (0.064%), neg=0, invalid=96777
0515: dt=0.028000, rms=0.491 (0.064%), neg=0, invalid=96777
0516: dt=0.028000, rms=0.491 (0.056%), neg=0, invalid=96777
0517: dt=0.028000, rms=0.491 (0.047%), neg=0, invalid=96777
0518: dt=0.028000, rms=0.491 (0.045%), neg=0, invalid=96777
0519: dt=0.028000, rms=0.490 (0.045%), neg=0, invalid=96777
0520: dt=0.028000, rms=0.490 (0.034%), neg=0, invalid=96777
0521: dt=0.028000, rms=0.490 (0.030%), neg=0, invalid=96777
0522: dt=0.028000, rms=0.490 (0.030%), neg=0, invalid=96777
0523: dt=0.028000, rms=0.490 (0.027%), neg=0, invalid=96777
0524: dt=0.028000, rms=0.490 (0.019%), neg=0, invalid=96777
0525: dt=0.028000, rms=0.490 (0.017%), neg=0, invalid=96777
0526: dt=0.000000, rms=0.490 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.490, neg=0, invalid=96777
0527: dt=0.320000, rms=0.485 (0.895%), neg=0, invalid=96777
0528: dt=0.112000, rms=0.485 (0.087%), neg=0, invalid=96777
0529: dt=0.028000, rms=0.485 (0.015%), neg=0, invalid=96777
0530: dt=0.028000, rms=0.485 (0.016%), neg=0, invalid=96777
0531: dt=0.028000, rms=0.485 (0.028%), neg=0, invalid=96777
0532: dt=0.028000, rms=0.484 (0.038%), neg=0, invalid=96777
0533: dt=0.028000, rms=0.484 (0.044%), neg=0, invalid=96777
0534: dt=0.028000, rms=0.484 (0.044%), neg=0, invalid=96777
0535: dt=0.028000, rms=0.484 (0.046%), neg=0, invalid=96777
0536: dt=0.028000, rms=0.484 (0.001%), neg=0, invalid=96777
0537: dt=0.028000, rms=0.484 (0.003%), neg=0, invalid=96777
0538: dt=0.028000, rms=0.484 (0.007%), neg=0, invalid=96777
0539: dt=0.028000, rms=0.484 (0.003%), neg=0, invalid=96777
0540: dt=0.384000, rms=0.484 (0.007%), neg=0, invalid=96777
0541: dt=0.001250, rms=0.484 (-0.001%), neg=0, invalid=96777
label assignment complete, 0 changed (0.00%)
*********************************************************************************************
*********************************************************************************************
*********************************************************************************************
********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
*********************************************************************************************
*********************************************************************************************
*********************************************************************************************
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.482, neg=0, invalid=96777
0542: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.482, neg=0, invalid=96777
0543: dt=129.472000, rms=0.482 (0.014%), neg=0, invalid=96777
0544: dt=517.888000, rms=0.482 (0.043%), neg=0, invalid=96777
0545: dt=32.368000, rms=0.482 (0.000%), neg=0, invalid=96777
0546: dt=32.368000, rms=0.481 (0.002%), neg=0, invalid=96777
0547: dt=32.368000, rms=0.481 (0.001%), neg=0, invalid=96777
0548: dt=32.368000, rms=0.481 (0.003%), neg=0, invalid=96777
0549: dt=32.368000, rms=0.481 (0.006%), neg=0, invalid=96777
0550: dt=32.368000, rms=0.481 (0.011%), neg=0, invalid=96777
0551: dt=32.368000, rms=0.481 (0.008%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.481, neg=0, invalid=96777
0552: dt=20.736000, rms=0.481 (0.027%), neg=0, invalid=96777
0553: dt=2.268000, rms=0.481 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.481, neg=0, invalid=96777
0554: dt=145.152000, rms=0.480 (0.274%), neg=0, invalid=96777
0555: dt=31.104000, rms=0.480 (0.077%), neg=0, invalid=96777
0556: dt=31.104000, rms=0.479 (0.022%), neg=0, invalid=96777
0557: dt=31.104000, rms=0.479 (0.063%), neg=0, invalid=96777
0558: dt=31.104000, rms=0.479 (0.092%), neg=0, invalid=96777
0559: dt=31.104000, rms=0.478 (0.072%), neg=0, invalid=96777
0560: dt=31.104000, rms=0.478 (0.052%), neg=0, invalid=96777
0561: dt=36.288000, rms=0.478 (0.037%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.478, neg=0, invalid=96777
iter 0, gcam->neg = 4
after 6 iterations, nbhd size=1, neg = 0
0562: dt=32.000000, rms=0.476 (0.348%), neg=0, invalid=96777
0563: dt=19.200000, rms=0.476 (0.193%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0564: dt=19.200000, rms=0.476 (-0.129%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.476, neg=0, invalid=96777
0565: dt=11.200000, rms=0.474 (0.306%), neg=0, invalid=96777
0566: dt=11.200000, rms=0.473 (0.304%), neg=0, invalid=96777
0567: dt=9.600000, rms=0.472 (0.150%), neg=0, invalid=96777
0568: dt=9.600000, rms=0.471 (0.187%), neg=0, invalid=96777
0569: dt=9.600000, rms=0.470 (0.227%), neg=0, invalid=96777
0570: dt=9.600000, rms=0.469 (0.258%), neg=0, invalid=96777
0571: dt=9.600000, rms=0.468 (0.240%), neg=0, invalid=96777
0572: dt=9.600000, rms=0.466 (0.330%), neg=0, invalid=96777
0573: dt=9.600000, rms=0.465 (0.260%), neg=0, invalid=96777
0574: dt=9.600000, rms=0.464 (0.233%), neg=0, invalid=96777
0575: dt=9.600000, rms=0.463 (0.168%), neg=0, invalid=96777
0576: dt=9.600000, rms=0.462 (0.238%), neg=0, invalid=96777
0577: dt=9.600000, rms=0.461 (0.193%), neg=0, invalid=96777
0578: dt=9.600000, rms=0.460 (0.140%), neg=0, invalid=96777
0579: dt=9.600000, rms=0.460 (0.100%), neg=0, invalid=96777
0580: dt=9.600000, rms=0.459 (0.158%), neg=0, invalid=96777
0581: dt=9.600000, rms=0.459 (0.136%), neg=0, invalid=96777
0582: dt=9.600000, rms=0.458 (0.109%), neg=0, invalid=96777
0583: dt=9.600000, rms=0.458 (0.074%), neg=0, invalid=96777
0584: dt=11.200000, rms=0.457 (0.053%), neg=0, invalid=96777
0585: dt=11.200000, rms=0.457 (-0.003%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.461, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0586: dt=5.076923, rms=0.460 (0.152%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0587: dt=5.000000, rms=0.460 (0.104%), neg=0, invalid=96777
iter 0, gcam->neg = 5
after 7 iterations, nbhd size=1, neg = 0
0588: dt=5.000000, rms=0.460 (0.005%), neg=0, invalid=96777
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0589: dt=5.000000, rms=0.459 (-0.010%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.459, neg=0, invalid=96777
iter 0, gcam->neg = 33
after 4 iterations, nbhd size=0, neg = 0
0590: dt=7.721393, rms=0.458 (0.267%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 5 iterations, nbhd size=1, neg = 0
0591: dt=2.880000, rms=0.458 (0.047%), neg=0, invalid=96777
0592: dt=2.880000, rms=0.458 (0.105%), neg=0, invalid=96777
iter 0, gcam->neg = 6
after 0 iterations, nbhd size=0, neg = 0
0593: dt=2.880000, rms=0.457 (0.145%), neg=0, invalid=96777
iter 0, gcam->neg = 5
after 6 iterations, nbhd size=1, neg = 0
0594: dt=2.880000, rms=0.456 (0.156%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0595: dt=2.880000, rms=0.456 (0.147%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 1 iterations, nbhd size=0, neg = 0
0596: dt=2.880000, rms=0.455 (0.149%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 8 iterations, nbhd size=1, neg = 0
0597: dt=2.880000, rms=0.454 (0.169%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 6 iterations, nbhd size=1, neg = 0
0598: dt=2.880000, rms=0.453 (0.193%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0599: dt=2.880000, rms=0.452 (0.237%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 6 iterations, nbhd size=1, neg = 0
0600: dt=2.880000, rms=0.451 (0.266%), neg=0, invalid=96777
0601: dt=2.880000, rms=0.450 (0.287%), neg=0, invalid=96777
iter 0, gcam->neg = 6
after 6 iterations, nbhd size=1, neg = 0
0602: dt=2.880000, rms=0.449 (0.236%), neg=0, invalid=96777
iter 0, gcam->neg = 8
after 7 iterations, nbhd size=1, neg = 0
0603: dt=2.880000, rms=0.448 (0.210%), neg=0, invalid=96777
iter 0, gcam->neg = 9
after 1 iterations, nbhd size=0, neg = 0
0604: dt=2.880000, rms=0.447 (0.187%), neg=0, invalid=96777
iter 0, gcam->neg = 12
after 2 iterations, nbhd size=0, neg = 0
0605: dt=2.880000, rms=0.446 (0.157%), neg=0, invalid=96777
iter 0, gcam->neg = 14
after 1 iterations, nbhd size=0, neg = 0
0606: dt=2.880000, rms=0.446 (0.099%), neg=0, invalid=96777
iter 0, gcam->neg = 7
after 2 iterations, nbhd size=0, neg = 0
0607: dt=2.880000, rms=0.445 (0.070%), neg=0, invalid=96777
0608: dt=0.000176, rms=0.445 (-0.006%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.450, neg=0, invalid=96777
0609: dt=0.000000, rms=0.450 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.450, neg=0, invalid=96777
0610: dt=0.000000, rms=0.450 (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=0.442, neg=0, invalid=96777
iter 0, gcam->neg = 560
after 50 iterations, nbhd size=2, neg = 0
0611: dt=1.894243, rms=0.404 (8.672%), neg=0, invalid=96777
0612: dt=0.000027, rms=0.404 (0.001%), neg=0, invalid=96777
0613: dt=0.000027, rms=0.404 (0.000%), neg=0, invalid=96777
0614: dt=0.000027, rms=0.404 (0.000%), neg=0, invalid=96777
0615: dt=0.000027, rms=0.404 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.404, neg=0, invalid=96777
0616: dt=0.000313, rms=0.404 (0.000%), neg=0, invalid=96777
0617: dt=0.000000, rms=0.404 (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=0.389, neg=0, invalid=96777
0618: dt=8.092000, rms=0.390 (-0.351%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.390, neg=0, invalid=96777
0619: dt=18.496000, rms=0.390 (0.003%), neg=0, invalid=96777
0620: dt=0.003387, rms=0.390 (0.000%), neg=0, invalid=96777
0621: dt=0.003387, rms=0.390 (-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=0.390, neg=0, invalid=96777
0622: dt=5.184000, rms=0.390 (0.004%), neg=0, invalid=96777
0623: dt=0.567000, rms=0.390 (0.000%), neg=0, invalid=96777
0624: dt=0.567000, rms=0.390 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.390, neg=0, invalid=96777
0625: dt=15.552000, rms=0.390 (0.008%), neg=0, invalid=96777
0626: dt=9.072000, rms=0.390 (0.001%), neg=0, invalid=96777
0627: dt=9.072000, rms=0.390 (0.000%), neg=0, invalid=96777
0628: dt=9.072000, rms=0.390 (-0.003%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.391, neg=0, invalid=96777
iter 0, gcam->neg = 2
after 200 iterations, nbhd size=4, neg = 1
starting rms=0.005, neg=1, removing folds in lattice....
iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.005 (0.000%)
---------- unfolding failed - restoring original position --------------------
0629: dt=6.400000, rms=0.391 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.391, neg=0, invalid=96777
iter 0, gcam->neg = 13
after 200 iterations, nbhd size=1, neg = 2
starting rms=0.006, neg=2, removing folds in lattice....
iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (32.252%)
iter 2, dt=0.000143: new neg 0, old_neg 2, delta 2, rms=0.002 (39.247%)
0630: dt=32.000000, rms=0.391 (0.060%), neg=0, invalid=96777
iter 0, gcam->neg = 26
after 200 iterations, nbhd size=1, neg = 4
starting rms=0.009, neg=4, removing folds in lattice....
iter 1, dt=0.000023: new neg 2, old_neg 4, delta 2, rms=0.005 (51.144%)
iter 2, dt=0.000143: new neg 0, old_neg 2, delta 2, rms=0.003 (38.835%)
0631: dt=44.800000, rms=0.390 (0.160%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 200 iterations, nbhd size=4, neg = 1
starting rms=0.005, neg=1, removing folds in lattice....
iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (49.100%)
0632: dt=19.200000, rms=0.390 (0.041%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 200 iterations, nbhd size=3, neg = 3
starting rms=0.009, neg=3, removing folds in lattice....
iter 1, dt=0.000023: new neg 3, old_neg 3, delta 0, rms=0.004 (53.953%)
iter 2, dt=0.000143: new neg 0, old_neg 3, delta 3, rms=0.002 (44.184%)
0633: dt=19.200000, rms=0.389 (0.062%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 200 iterations, nbhd size=3, neg = 3
starting rms=0.010, neg=3, removing folds in lattice....
iter 1, dt=0.000023: new neg 3, old_neg 3, delta 0, rms=0.004 (56.157%)
iter 2, dt=0.000143: new neg 0, old_neg 3, delta 3, rms=0.002 (45.372%)
0634: dt=19.200000, rms=0.389 (0.047%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 200 iterations, nbhd size=3, neg = 3
starting rms=0.010, neg=3, removing folds in lattice....
iter 1, dt=0.000023: new neg 3, old_neg 3, delta 0, rms=0.004 (58.553%)
iter 2, dt=0.000146: new neg 0, old_neg 3, delta 3, rms=0.002 (45.065%)
0635: dt=19.200000, rms=0.389 (0.040%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.392, neg=0, invalid=96777
iter 0, gcam->neg = 26
after 200 iterations, nbhd size=1, neg = 4
starting rms=0.010, neg=4, removing folds in lattice....
iter 1, dt=0.000023: new neg 3, old_neg 4, delta 1, rms=0.004 (60.159%)
iter 2, dt=0.000163: new neg 0, old_neg 3, delta 3, rms=0.002 (53.533%)
0636: dt=6.142857, rms=0.391 (0.135%), neg=0, invalid=96777
iter 0, gcam->neg = 10
after 200 iterations, nbhd size=3, neg = 2
starting rms=0.005, neg=2, removing folds in lattice....
iter 1, dt=0.000100: new neg 0, old_neg 2, delta 2, rms=0.002 (64.348%)
0637: dt=4.032000, rms=0.391 (0.043%), neg=0, invalid=96777
iter 0, gcam->neg = 8
after 200 iterations, nbhd size=2, neg = 3
starting rms=0.010, neg=3, removing folds in lattice....
iter 1, dt=0.000023: new neg 3, old_neg 3, delta 0, rms=0.004 (58.277%)
iter 2, dt=0.000159: new neg 0, old_neg 3, delta 3, rms=0.002 (52.635%)
0638: dt=4.032000, rms=0.391 (0.036%), neg=0, invalid=96777
iter 0, gcam->neg = 8
after 200 iterations, nbhd size=2, neg = 1
starting rms=0.005, neg=1, removing folds in lattice....
iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.002 (57.822%)
0639: dt=4.032000, rms=0.391 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.391, neg=0, invalid=96777
iter 0, gcam->neg = 66
after 200 iterations, nbhd size=1, neg = 3
starting rms=0.008, neg=3, removing folds in lattice....
iter 1, dt=0.000023: new neg 2, old_neg 3, delta 1, rms=0.004 (50.445%)
iter 2, dt=0.000156: new neg 0, old_neg 2, delta 2, rms=0.002 (51.943%)
0640: dt=13.824000, rms=0.389 (0.429%), neg=0, invalid=96777
iter 0, gcam->neg = 6
after 200 iterations, nbhd size=3, neg = 2
starting rms=0.007, neg=2, removing folds in lattice....
iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (50.357%)
iter 2, dt=0.000162: new neg 0, old_neg 2, delta 2, rms=0.001 (58.636%)
0641: dt=4.032000, rms=0.389 (0.042%), neg=0, invalid=96777
iter 0, gcam->neg = 7
after 200 iterations, nbhd size=3, neg = 2
starting rms=0.007, neg=2, removing folds in lattice....
iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (50.420%)
iter 2, dt=0.000163: new neg 0, old_neg 2, delta 2, rms=0.001 (58.869%)
0642: dt=4.032000, rms=0.389 (0.084%), neg=0, invalid=96777
iter 0, gcam->neg = 7
after 200 iterations, nbhd size=4, neg = 2
starting rms=0.007, neg=2, removing folds in lattice....
iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.003 (49.979%)
iter 2, dt=0.000159: new neg 0, old_neg 2, delta 2, rms=0.001 (58.237%)
0643: dt=4.032000, rms=0.388 (0.064%), neg=0, invalid=96777
iter 0, gcam->neg = 7
after 200 iterations, nbhd size=3, neg = 2
starting rms=0.007, neg=2, removing folds in lattice....
iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (49.903%)
iter 2, dt=0.000155: new neg 0, old_neg 2, delta 2, rms=0.002 (56.725%)
0644: dt=4.032000, rms=0.388 (0.050%), neg=0, invalid=96777
iter 0, gcam->neg = 7
after 200 iterations, nbhd size=3, neg = 2
starting rms=0.007, neg=2, removing folds in lattice....
iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (50.161%)
iter 2, dt=0.000160: new neg 0, old_neg 2, delta 2, rms=0.001 (57.942%)
0645: dt=4.032000, rms=0.388 (0.034%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.393, neg=0, invalid=96777
0646: dt=0.000000, rms=0.393 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.393, neg=0, invalid=96777
0647: dt=0.000000, rms=0.393 (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=0.384, neg=0, invalid=96777
iter 0, gcam->neg = 500
after 32 iterations, nbhd size=3, neg = 0
0648: dt=1.020921, rms=0.370 (3.680%), neg=0, invalid=96777
0649: dt=0.000109, rms=0.370 (0.003%), neg=0, invalid=96777
0650: dt=0.000109, rms=0.370 (0.000%), neg=0, invalid=96777
0651: dt=0.000109, rms=0.370 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.370, neg=0, invalid=96777
0652: dt=0.000375, rms=0.370 (0.000%), neg=0, invalid=96777
0653: dt=0.000000, rms=0.370 (0.000%), neg=0, invalid=96777
writing output transformation to transforms/talairach.m3z...
GCAMwrite
registration took 5 hours, 3 minutes and 31 seconds.
#--------------------------------------
#@# CA Reg Inv Thu Aug  8 17:22:55 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 17:24:29 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...
11336786 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 1 minutes and 35 seconds.
#--------------------------------------
#@# SkullLTA Thu Aug  8 17:26:04 CEST 2013

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



 ======= NUMBER OF OPENMP THREADS = 1 ======= 
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach_with_skull_2.log
reading '/opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca'...
average std = 23.1   using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu_noneck.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7 
total sample mean = 92.0 (1443 zeros)
************************************************
spacing=8, using 3481 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=9.0
skull bounding box = (47, 10, 15) --> (206, 201, 197)
using (100, 74, 106) as brain centroid...
mean wm in atlas = 126, using box (80,50,84) --> (119, 97,128) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 108, scaling input intensities by 1.167
scaling channel 0 by 1.16667
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.039  -0.258   0.915   33.330;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.278   0.983   27.877;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.278   0.983   27.877;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
 1.081  -0.039   0.031  -10.858;
 0.047   1.111   0.351  -34.627;
-0.042  -0.320   0.990   31.306;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.081  -0.039   0.031  -10.858;
 0.047   1.111   0.351  -34.627;
-0.042  -0.320   0.990   31.306;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.078  -0.054   0.017  -7.838;
 0.065   1.111   0.351  -36.800;
-0.033  -0.319   0.988   29.866;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.078  -0.054   0.017  -7.838;
 0.065   1.111   0.351  -36.800;
-0.033  -0.319   0.988   29.866;
 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
 1.07751  -0.05390   0.01694  -7.83754;
 0.06476   1.11064   0.35119  -36.80036;
-0.03333  -0.31928   0.98830   29.86566;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.07751  -0.05390   0.01694  -7.83754;
 0.06476   1.11064   0.35119  -36.80036;
-0.03333  -0.31928   0.98830   29.86566;
 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:
 1.078  -0.054   0.017  -7.838;
 0.065   1.111   0.351  -36.800;
-0.033  -0.319   0.988   29.866;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.1)
transform before final EM align:
 1.078  -0.054   0.017  -7.838;
 0.065   1.111   0.351  -36.800;
-0.033  -0.319   0.988   29.866;
 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
 1.07751  -0.05390   0.01694  -7.83754;
 0.06476   1.11064   0.35119  -36.80036;
-0.03333  -0.31928   0.98830   29.86566;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.07751  -0.05390   0.01694  -7.83754;
 0.06476   1.11064   0.35119  -36.80036;
-0.03333  -0.31928   0.98830   29.86566;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 009: -log(p) = 4.4
after pass:transform: ( 1.08, -0.05, 0.02, -7.84)
                      ( 0.06, 1.11, 0.35, -36.80)
                      ( -0.03, -0.32, 0.99, 29.87)
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization...
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =    4.4  tol 0.000000
final transform:
 1.078  -0.054   0.017  -7.838;
 0.065   1.111   0.351  -36.800;
-0.033  -0.319   0.988   29.866;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull_2.lta...
registration took 40 minutes and 25 seconds.
#--------------------------------------
#@# SubCort Seg Thu Aug  8 18:06:29 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 snake5
machine  x86_64

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 0.13981 ( 8)
Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1031 voxels, overlap=0.007)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1031 voxels, peak =  7), gca=10.8
gca peak = 0.14982 (20)
mri peak = 0.15612 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (686 voxels, overlap=0.007)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (686 voxels, peak =  6), gca=8.0
gca peak = 0.28003 (97)
mri peak = 0.11525 (85)
Right_Pallidum (52): linear fit = 0.87 x + 0.0 (300 voxels, overlap=0.049)
Right_Pallidum (52): linear fit = 0.87 x + 0.0 (300 voxels, peak = 84), gca=83.9
gca peak = 0.18160 (96)
mri peak = 0.08915 (86)
Left_Pallidum (13): linear fit = 0.85 x + 0.0 (272 voxels, overlap=0.058)
Left_Pallidum (13): linear fit = 0.85 x + 0.0 (272 voxels, peak = 81), gca=81.1
gca peak = 0.27536 (62)
mri peak = 0.08966 (56)
Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (435 voxels, overlap=0.478)
Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (435 voxels, peak = 52), gca=51.8
gca peak = 0.32745 (63)
mri peak = 0.09177 (54)
Left_Hippocampus (17): linear fit = 0.83 x + 0.0 (575 voxels, overlap=0.506)
Left_Hippocampus (17): linear fit = 0.83 x + 0.0 (575 voxels, peak = 53), gca=52.6
gca peak = 0.08597 (105)
mri peak = 0.06693 (107)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (36446 voxels, overlap=0.786)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (36446 voxels, peak = 108), gca=107.6
gca peak = 0.09209 (106)
mri peak = 0.07390 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (37210 voxels, overlap=0.750)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (37210 voxels, peak = 110), gca=109.7
gca peak = 0.07826 (63)
mri peak = 0.06130 (53)
Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14531 voxels, overlap=0.307)
Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14531 voxels, peak = 52), gca=52.0
gca peak = 0.08598 (64)
mri peak = 0.05382 (50)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (13475 voxels, overlap=0.343)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (13475 voxels, peak = 53), gca=52.8
gca peak = 0.24164 (71)
mri peak = 0.11916 (64)
Right_Caudate (50): linear fit = 0.88 x + 0.0 (621 voxels, overlap=0.022)
Right_Caudate (50): linear fit = 0.88 x + 0.0 (621 voxels, peak = 62), gca=62.1
gca peak = 0.18227 (75)
mri peak = 0.10624 (64)
Left_Caudate (11): linear fit = 0.83 x + 0.0 (753 voxels, overlap=0.033)
Left_Caudate (11): linear fit = 0.83 x + 0.0 (753 voxels, peak = 63), gca=62.6
gca peak = 0.10629 (62)
mri peak = 0.05693 (56)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (7455 voxels, overlap=0.995)
Left_Cerebellum_Cortex (8): linear fit = 0.96 x + 0.0 (7455 voxels, peak = 60), gca=59.8
gca peak = 0.11668 (59)
mri peak = 0.05915 (55)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (7984 voxels, overlap=0.959)
Right_Cerebellum_Cortex (47): linear fit = 0.94 x + 0.0 (7984 voxels, peak = 55), gca=55.2
gca peak = 0.17849 (88)
mri peak = 0.07214 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4066 voxels, overlap=0.980)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4066 voxels, peak = 88), gca=87.6
gca peak = 0.16819 (86)
mri peak = 0.06366 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3816 voxels, overlap=0.973)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (3816 voxels, peak = 91), gca=90.7
gca peak = 0.41688 (64)
mri peak = 0.10417 (56)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (353 voxels, overlap=0.347)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (353 voxels, peak = 56), gca=56.0
gca peak = 0.42394 (62)
mri peak = 0.08871 (53)
Right_Amygdala (54): linear fit = 0.83 x + 0.0 (285 voxels, overlap=0.626)
Right_Amygdala (54): linear fit = 0.83 x + 0.0 (285 voxels, peak = 52), gca=51.8
gca peak = 0.10041 (96)
mri peak = 0.07617 (83)
Left_Thalamus_Proper (10): linear fit = 0.89 x + 0.0 (3455 voxels, overlap=0.341)
Left_Thalamus_Proper (10): linear fit = 0.89 x + 0.0 (3455 voxels, peak = 86), gca=85.9
gca peak = 0.13978 (88)
mri peak = 0.08348 (80)
Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3666 voxels, overlap=0.485)
Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3666 voxels, peak = 81), gca=81.4
gca peak = 0.08514 (81)
mri peak = 0.07058 (71)
Left_Putamen (12): linear fit = 0.87 x + 0.0 (1815 voxels, overlap=0.463)
Left_Putamen (12): linear fit = 0.87 x + 0.0 (1815 voxels, peak = 70), gca=70.1
gca peak = 0.09624 (82)
mri peak = 0.07984 (70)
Right_Putamen (51): linear fit = 0.85 x + 0.0 (1569 voxels, overlap=0.264)
Right_Putamen (51): linear fit = 0.85 x + 0.0 (1569 voxels, peak = 69), gca=69.3
gca peak = 0.07543 (88)
mri peak = 0.08096 (82)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (8414 voxels, overlap=0.764)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (8414 voxels, peak = 88), gca=87.6
gca peak = 0.12757 (95)
mri peak = 0.08039 (86)
Right_VentralDC (60): linear fit = 0.94 x + 0.0 (835 voxels, overlap=0.549)
Right_VentralDC (60): linear fit = 0.94 x + 0.0 (835 voxels, peak = 89), gca=88.8
gca peak = 0.17004 (92)
mri peak = 0.08398 (88)
Left_VentralDC (28): linear fit = 0.94 x + 0.0 (958 voxels, overlap=0.646)
Left_VentralDC (28): linear fit = 0.94 x + 0.0 (958 voxels, peak = 87), gca=86.9
gca peak = 0.21361 (36)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.26069 (23)
mri peak = 0.11343 ( 9)
Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (334 voxels, overlap=0.027)
Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (334 voxels, peak =  8), gca=8.2
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 0.84 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.40 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.31600 (11)
mri peak = 0.13981 ( 8)
Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (1031 voxels, overlap=0.781)
Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (1031 voxels, peak =  7), gca=6.8
gca peak = 0.29325 ( 9)
mri peak = 0.15612 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.75 x + 0.0 (686 voxels, overlap=0.829)
Right_Lateral_Ventricle (43): linear fit = 0.75 x + 0.0 (686 voxels, peak =  7), gca=6.7
gca peak = 0.26182 (84)
mri peak = 0.11525 (85)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (300 voxels, overlap=1.021)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (300 voxels, peak = 84), gca=84.0
gca peak = 0.22767 (81)
mri peak = 0.08915 (86)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (272 voxels, overlap=1.008)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (272 voxels, peak = 81), gca=81.0
gca peak = 0.32299 (52)
mri peak = 0.08966 (56)
Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (435 voxels, overlap=1.007)
Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (435 voxels, peak = 53), gca=52.8
gca peak = 0.28448 (53)
mri peak = 0.09177 (54)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (575 voxels, overlap=1.007)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (575 voxels, peak = 55), gca=55.4
gca peak = 0.08344 (108)
mri peak = 0.06693 (107)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36446 voxels, overlap=0.861)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36446 voxels, peak = 108), gca=108.0
gca peak = 0.08545 (110)
mri peak = 0.07390 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37210 voxels, overlap=0.823)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37210 voxels, peak = 109), gca=109.4
gca peak = 0.09526 (52)
mri peak = 0.06130 (53)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (14531 voxels, overlap=0.974)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (14531 voxels, peak = 52), gca=52.0
gca peak = 0.10572 (53)
mri peak = 0.05382 (50)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (13475 voxels, overlap=0.992)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (13475 voxels, peak = 52), gca=52.2
gca peak = 0.24214 (64)
mri peak = 0.11916 (64)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (621 voxels, overlap=1.001)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (621 voxels, peak = 63), gca=63.0
gca peak = 0.17636 (62)
mri peak = 0.10624 (64)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (753 voxels, overlap=0.983)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (753 voxels, peak = 62), gca=62.0
gca peak = 0.10995 (60)
mri peak = 0.05693 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7455 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (7455 voxels, peak = 62), gca=61.5
gca peak = 0.13104 (56)
mri peak = 0.05915 (55)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7984 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (7984 voxels, peak = 55), gca=55.2
gca peak = 0.18448 (87)
mri peak = 0.07214 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4066 voxels, overlap=0.977)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (4066 voxels, peak = 88), gca=88.3
gca peak = 0.16436 (91)
mri peak = 0.06366 (91)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (3816 voxels, overlap=1.000)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (3816 voxels, peak = 90), gca=89.6
gca peak = 0.54115 (56)
mri peak = 0.10417 (56)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (353 voxels, overlap=1.023)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (353 voxels, peak = 56), gca=56.0
gca peak = 0.63626 (52)
mri peak = 0.08871 (53)
Right_Amygdala (54): linear fit = 1.11 x + 0.0 (285 voxels, overlap=1.018)
Right_Amygdala (54): linear fit = 1.11 x + 0.0 (285 voxels, peak = 57), gca=57.5
gca peak = 0.11392 (86)
mri peak = 0.07617 (83)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3455 voxels, overlap=0.983)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3455 voxels, peak = 85), gca=84.7
gca peak = 0.11701 (81)
mri peak = 0.08348 (80)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3666 voxels, overlap=0.950)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3666 voxels, peak = 81), gca=80.6
gca peak = 0.09481 (74)
mri peak = 0.07058 (71)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1815 voxels, overlap=1.000)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1815 voxels, peak = 73), gca=72.9
gca peak = 0.12360 (64)
mri peak = 0.07984 (70)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1569 voxels, overlap=0.999)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1569 voxels, peak = 64), gca=64.0
gca peak = 0.07838 (85)
mri peak = 0.08096 (82)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (8414 voxels, overlap=0.757)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (8414 voxels, peak = 85), gca=84.6
gca peak = 0.11836 (85)
mri peak = 0.08039 (86)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (835 voxels, overlap=0.817)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (835 voxels, peak = 85), gca=84.6
gca peak = 0.15844 (87)
mri peak = 0.08398 (88)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (958 voxels, overlap=0.930)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (958 voxels, peak = 87), gca=86.6
gca peak = 0.35640 (14)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.33827 ( 9)
mri peak = 0.11343 ( 9)
Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (334 voxels, overlap=0.870)
Fourth_Ventricle (15): linear fit = 0.88 x + 0.0 (334 voxels, peak =  8), gca=8.0
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.24968 (29)
gca peak Third_Ventricle = 0.35640 (14)
gca peak CSF = 0.30128 (18)
gca peak Left_Accumbens_area = 0.44849 (58)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.44155 (61)
gca peak Left_choroid_plexus = 0.09164 (48)
gca peak Right_Inf_Lat_Vent = 0.30433 (27)
gca peak Right_Accumbens_area = 0.31145 (63)
gca peak Right_vessel = 0.57697 (60)
gca peak Right_choroid_plexus = 0.10280 (48)
gca peak Fifth_Ventricle = 0.45329 (19)
gca peak WM_hypointensities = 0.17626 (84)
gca peak non_WM_hypointensities = 0.08624 (54)
gca peak Optic_Chiasm = 0.34843 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.02 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.75 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
11056 gm and wm labels changed (%12 to gray, %88 to white out of all changed labels)
273 hippocampal voxels changed.
2 amygdala voxels changed.
pass 1: 84602 changed. image ll: -2.194, PF=1.000
pass 2: 15160 changed. image ll: -2.192, PF=1.000
pass 3: 5407 changed.
pass 4: 2374 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
auto-labeling took 19 minutes and 49 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/cc_up.lta sub018 

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/sub018/mri/transforms/cc_up.lta
reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.auto_noCCseg.mgz
reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/norm.mgz
26739 voxels in left wm, 23098 in right wm, xrange [123, 130]
searching rotation angles z=[-5  9], y=[-6  8]

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  
searching scale 1 Z rot 5.0  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.5  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.0  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.5  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.0  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.5  
searching scale 1 Z rot 7.8  
searching scale 1 Z rot 8.0  
searching scale 1 Z rot 8.3  
searching scale 1 Z rot 8.5  global minimum found at slice 126.0, rotations (1.24, 1.77)
final transformation (x=126.0, yr=1.237, zr=1.773):
 0.999  -0.031   0.022   2.395;
 0.031   1.000   0.001   43.073;
-0.022   0.000   1.000   28.744;
 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 128 151 118
eigenvectors:
-0.001   0.005   1.000;
-0.197  -0.980   0.005;
 0.980  -0.197   0.002;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.auto.mgz...
corpus callosum matter segmentation took 0.7 minutes
#--------------------------------------
#@# Merge ASeg Thu Aug  8 18:26:59 CEST 2013

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Thu Aug  8 18:26:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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...
4822 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 29 (29)
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 57 (57), valley at 30 (30)
csf peak at 28, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 4 minutes and 35 seconds.
#--------------------------------------------
#@# Mask BFS Thu Aug  8 18:31:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1492386 voxels in mask (pct=  8.90)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Thu Aug  8 18:31:38 CEST 2013

 mri_segment brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (107.0): 107.1 +- 5.1 [80.0 --> 125.0]
GM (67.0) : 66.2 +- 9.5 [30.0 --> 96.0]
setting bottom of white matter range to 75.6
setting top of gray matter range to 85.1
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...
6666 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5586 filled
304 bright non-wm voxels segmented.
4272 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 0.71 minutes
reading wm segmentation from wm.seg.mgz...
85 voxels added to wm to prevent paths from MTL structures to cortex
989 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 48610 voxels turned on, 33564 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+):  19 found -  19 modified     |    TOTAL:  19
pass   2 (xy+):   0 found -  19 modified     |    TOTAL:  19
pass   1 (xy-):  14 found -  14 modified     |    TOTAL:  33
pass   2 (xy-):   0 found -  14 modified     |    TOTAL:  33
pass   1 (yz+):  30 found -  30 modified     |    TOTAL:  63
pass   2 (yz+):   0 found -  30 modified     |    TOTAL:  63
pass   1 (yz-):  22 found -  22 modified     |    TOTAL:  85
pass   2 (yz-):   0 found -  22 modified     |    TOTAL:  85
pass   1 (xz+):  19 found -  19 modified     |    TOTAL: 104
pass   2 (xz+):   0 found -  19 modified     |    TOTAL: 104
pass   1 (xz-):  15 found -  15 modified     |    TOTAL: 119
pass   2 (xz-):   0 found -  15 modified     |    TOTAL: 119
Iteration Number : 1
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  10
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  10
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  22
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  22
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  28
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  28
pass   1 (+++):  13 found -  13 modified     |    TOTAL:  41
pass   2 (+++):   0 found -  13 modified     |    TOTAL:  41
Iteration Number : 1
pass   1 (++): 246 found - 246 modified     |    TOTAL: 246
pass   2 (++):   0 found - 246 modified     |    TOTAL: 246
pass   1 (+-): 259 found - 259 modified     |    TOTAL: 505
pass   2 (+-):   0 found - 259 modified     |    TOTAL: 505
pass   1 (--): 249 found - 249 modified     |    TOTAL: 754
pass   2 (--):   0 found - 249 modified     |    TOTAL: 754
pass   1 (-+): 187 found - 187 modified     |    TOTAL: 941
pass   2 (-+):   0 found - 187 modified     |    TOTAL: 941
Iteration Number : 2
pass   1 (xy+):   7 found -   7 modified     |    TOTAL:   7
pass   2 (xy+):   0 found -   7 modified     |    TOTAL:   7
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:  11
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:  11
pass   1 (yz+):   6 found -   6 modified     |    TOTAL:  17
pass   2 (yz+):   0 found -   6 modified     |    TOTAL:  17
pass   1 (yz-):   5 found -   5 modified     |    TOTAL:  22
pass   2 (yz-):   0 found -   5 modified     |    TOTAL:  22
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  24
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  24
pass   1 (xz-):   7 found -   7 modified     |    TOTAL:  31
pass   2 (xz-):   0 found -   7 modified     |    TOTAL:  31
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 (+++):   0 found -   0 modified     |    TOTAL:   2
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 (--):   3 found -   3 modified     |    TOTAL:   6
pass   2 (--):   0 found -   3 modified     |    TOTAL:   6
pass   1 (-+):   3 found -   3 modified     |    TOTAL:   9
pass   2 (-+):   0 found -   3 modified     |    TOTAL:   9
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-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 1145 (out of 524771: 0.218190)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Thu Aug  8 18:34:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 1.100  -0.074   0.018  -8.391;
 0.081   1.119   0.320  -34.301;
-0.042  -0.279   0.989   27.435;
 0.000   0.000   0.000   1.000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1467 (min = 350, max = 1400), aspect = 0.48 (min = 0.10, max = 0.75)
need search nearby
using seed (125, 116, 88), TAL = (3.0, -40.0, 12.0)
talairach voxel to voxel transform
 0.904   0.051  -0.033   10.252;
-0.070   0.823  -0.265   34.898;
 0.018   0.234   0.935  -17.461;
 0.000   0.000   0.000   1.000;
segmentation indicates cc at (125,  116,  88) --> (3.0, -40.0, 12.0)
done.
writing output to filled.mgz...
filling took 1.0 minutes
talairach cc position changed to (3.00, -40.00, 12.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(21.00, -40.00, 12.00) SRC: (110.06, 99.47, 93.99)
search lh wm seed point around talairach space (-15.00, -40.00, 12.00), SRC: (142.61, 96.94, 94.65)
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 18:35:12 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   5
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   5
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   6
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 11 (out of 252305: 0.004360)
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 40: 369 vertices, 442 faces
slice 50: 5096 vertices, 5342 faces
slice 60: 14713 vertices, 15113 faces
slice 70: 25609 vertices, 25991 faces
slice 80: 36637 vertices, 37045 faces
slice 90: 47909 vertices, 48274 faces
slice 100: 59689 vertices, 60118 faces
slice 110: 71655 vertices, 72016 faces
slice 120: 82662 vertices, 83062 faces
slice 130: 93039 vertices, 93456 faces
slice 140: 103686 vertices, 104077 faces
slice 150: 113884 vertices, 114206 faces
slice 160: 122538 vertices, 122871 faces
slice 170: 129522 vertices, 129746 faces
slice 180: 135300 vertices, 135518 faces
slice 190: 139566 vertices, 139717 faces
slice 200: 140950 vertices, 140968 faces
slice 210: 140950 vertices, 140968 faces
slice 220: 140950 vertices, 140968 faces
slice 230: 140950 vertices, 140968 faces
slice 240: 140950 vertices, 140968 faces
slice 250: 140950 vertices, 140968 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...
   140950 voxel in cpt #1: X=-18 [v=140950,e=422904,f=281936] located at (-25.064953, -17.840284, 40.186329)
For the whole surface: X=-18 [v=140950,e=422904,f=281936]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Thu Aug  8 18:35:21 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 18:35:25 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
avg radius = 46.9 mm, total surface area = 73518 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.6 minutes
Not saving sulc

step 000: RMS=0.101 (target=0.015)   
step 005: RMS=0.074 (target=0.015)   
step 010: RMS=0.052 (target=0.015)   
step 015: RMS=0.042 (target=0.015)   
step 020: RMS=0.036 (target=0.015)   
step 025: RMS=0.031 (target=0.015)   
step 030: RMS=0.027 (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=0.022 (target=0.015)   
step 055: RMS=0.021 (target=0.015)   
step 060: RMS=0.020 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Thu Aug  8 18:36:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 0.97 +- 0.57 (0.00-->6.20) (max @ vno 57771 --> 57772)
face area 0.03 +- 0.03 (-0.08-->0.61)
scaling brain by 0.315...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.193, avgs=0
005/300: dt: 0.9000, rms radial error=175.934, avgs=0
010/300: dt: 0.9000, rms radial error=175.377, avgs=0
015/300: dt: 0.9000, rms radial error=174.646, avgs=0
020/300: dt: 0.9000, rms radial error=173.815, avgs=0
025/300: dt: 0.9000, rms radial error=172.927, avgs=0
030/300: dt: 0.9000, rms radial error=172.011, avgs=0
035/300: dt: 0.9000, rms radial error=171.078, avgs=0
040/300: dt: 0.9000, rms radial error=170.137, avgs=0
045/300: dt: 0.9000, rms radial error=169.193, avgs=0
050/300: dt: 0.9000, rms radial error=168.250, avgs=0
055/300: dt: 0.9000, rms radial error=167.310, avgs=0
060/300: dt: 0.9000, rms radial error=166.373, avgs=0
065/300: dt: 0.9000, rms radial error=165.440, avgs=0
070/300: dt: 0.9000, rms radial error=164.512, avgs=0
075/300: dt: 0.9000, rms radial error=163.588, avgs=0
080/300: dt: 0.9000, rms radial error=162.669, avgs=0
085/300: dt: 0.9000, rms radial error=161.755, avgs=0
090/300: dt: 0.9000, rms radial error=160.846, avgs=0
095/300: dt: 0.9000, rms radial error=159.942, avgs=0
100/300: dt: 0.9000, rms radial error=159.043, avgs=0
105/300: dt: 0.9000, rms radial error=158.148, avgs=0
110/300: dt: 0.9000, rms radial error=157.258, avgs=0
115/300: dt: 0.9000, rms radial error=156.373, avgs=0
120/300: dt: 0.9000, rms radial error=155.494, avgs=0
125/300: dt: 0.9000, rms radial error=154.618, avgs=0
130/300: dt: 0.9000, rms radial error=153.748, avgs=0
135/300: dt: 0.9000, rms radial error=152.882, avgs=0
140/300: dt: 0.9000, rms radial error=152.021, avgs=0
145/300: dt: 0.9000, rms radial error=151.165, avgs=0
150/300: dt: 0.9000, rms radial error=150.314, avgs=0
155/300: dt: 0.9000, rms radial error=149.467, avgs=0
160/300: dt: 0.9000, rms radial error=148.624, avgs=0
165/300: dt: 0.9000, rms radial error=147.787, avgs=0
170/300: dt: 0.9000, rms radial error=146.954, avgs=0
175/300: dt: 0.9000, rms radial error=146.126, avgs=0
180/300: dt: 0.9000, rms radial error=145.302, avgs=0
185/300: dt: 0.9000, rms radial error=144.484, avgs=0
190/300: dt: 0.9000, rms radial error=143.673, avgs=0
195/300: dt: 0.9000, rms radial error=142.865, avgs=0
200/300: dt: 0.9000, rms radial error=142.062, avgs=0
205/300: dt: 0.9000, rms radial error=141.264, avgs=0
210/300: dt: 0.9000, rms radial error=140.470, avgs=0
215/300: dt: 0.9000, rms radial error=139.680, avgs=0
220/300: dt: 0.9000, rms radial error=138.895, avgs=0
225/300: dt: 0.9000, rms radial error=138.114, avgs=0
230/300: dt: 0.9000, rms radial error=137.337, avgs=0
235/300: dt: 0.9000, rms radial error=136.565, avgs=0
240/300: dt: 0.9000, rms radial error=135.797, avgs=0
245/300: dt: 0.9000, rms radial error=135.033, avgs=0
250/300: dt: 0.9000, rms radial error=134.273, avgs=0
255/300: dt: 0.9000, rms radial error=133.518, avgs=0
260/300: dt: 0.9000, rms radial error=132.767, avgs=0
265/300: dt: 0.9000, rms radial error=132.019, avgs=0
270/300: dt: 0.9000, rms radial error=131.276, avgs=0
275/300: dt: 0.9000, rms radial error=130.538, avgs=0
280/300: dt: 0.9000, rms radial error=129.803, avgs=0
285/300: dt: 0.9000, rms radial error=129.072, avgs=0
290/300: dt: 0.9000, rms radial error=128.345, avgs=0
295/300: dt: 0.9000, rms radial error=127.623, avgs=0
300/300: dt: 0.9000, rms radial error=126.904, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 16464.00
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
epoch 2 (K=40.0), pass 1, starting sse = 2748.27
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 3 (K=160.0), pass 1, starting sse = 270.71
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/12 = 0.00934
epoch 4 (K=640.0), pass 1, starting sse = 12.09
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.12/13 = 0.00952
final writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology lh Thu Aug  8 18:41:03 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/sub018/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub018 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=-18 (nv=140950, nf=281936, ne=422904, g=10)
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 10 iterations
marking ambiguous vertices...
1221 ambiguous faces found in tessellation
segmenting defects...
18 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
18 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7732  (-4.8866)
      -vertex     loglikelihood: -6.6526  (-3.3263)
      -normal dot loglikelihood: -3.6298  (-3.6298)
      -quad curv  loglikelihood: -6.5572  (-3.2786)
      Total Loglikelihood : -26.6128

CORRECTING DEFECT 0 (vertices=69, convex hull=33)
After retessellation of defect 0, euler #=-15 (140193,420265,280057) : difference with theory (-15) = 0 

CORRECTING DEFECT 1 (vertices=100, convex hull=112)
After retessellation of defect 1, euler #=-14 (140237,420445,280194) : difference with theory (-14) = 0 

CORRECTING DEFECT 2 (vertices=66, convex hull=82)
After retessellation of defect 2, euler #=-13 (140256,420539,280270) : difference with theory (-13) = 0 

CORRECTING DEFECT 3 (vertices=39, convex hull=58)
After retessellation of defect 3, euler #=-12 (140281,420637,280344) : difference with theory (-12) = 0 

CORRECTING DEFECT 4 (vertices=82, convex hull=30)
After retessellation of defect 4, euler #=-11 (140290,420675,280374) : difference with theory (-11) = 0 

CORRECTING DEFECT 5 (vertices=21, convex hull=49)
After retessellation of defect 5, euler #=-10 (140303,420729,280416) : difference with theory (-10) = 0 

CORRECTING DEFECT 6 (vertices=25, convex hull=42)
After retessellation of defect 6, euler #=-9 (140312,420774,280453) : difference with theory (-9) = 0 

CORRECTING DEFECT 7 (vertices=64, convex hull=38)
After retessellation of defect 7, euler #=-8 (140317,420806,280481) : difference with theory (-8) = 0 

CORRECTING DEFECT 8 (vertices=18, convex hull=37)
After retessellation of defect 8, euler #=-7 (140328,420850,280515) : difference with theory (-7) = 0 

CORRECTING DEFECT 9 (vertices=68, convex hull=53)
After retessellation of defect 9, euler #=-6 (140335,420896,280555) : difference with theory (-6) = 0 

CORRECTING DEFECT 10 (vertices=28, convex hull=34)
After retessellation of defect 10, euler #=-5 (140335,420907,280567) : difference with theory (-5) = 0 

CORRECTING DEFECT 11 (vertices=41, convex hull=58)
After retessellation of defect 11, euler #=-4 (140356,420992,280632) : difference with theory (-4) = 0 

CORRECTING DEFECT 12 (vertices=47, convex hull=26)
After retessellation of defect 12, euler #=-3 (140361,421013,280649) : difference with theory (-3) = 0 

CORRECTING DEFECT 13 (vertices=6, convex hull=24)
After retessellation of defect 13, euler #=-2 (140362,421022,280658) : difference with theory (-2) = 0 

CORRECTING DEFECT 14 (vertices=24, convex hull=30)
After retessellation of defect 14, euler #=-1 (140365,421039,280673) : difference with theory (-1) = 0 

CORRECTING DEFECT 15 (vertices=35, convex hull=57)
After retessellation of defect 15, euler #=0 (140381,421107,280726) : difference with theory (0) = 0 

CORRECTING DEFECT 16 (vertices=8, convex hull=26)
After retessellation of defect 16, euler #=1 (140382,421116,280735) : difference with theory (1) = 0 

CORRECTING DEFECT 17 (vertices=22, convex hull=61)
After retessellation of defect 17, euler #=2 (140393,421173,280782) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.21 (0.12-->5.92) (max @ vno 116747 --> 119326)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.21 (0.12-->5.92) (max @ vno 116747 --> 119326)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
58 mutations (34.3%), 111 crossovers (65.7%), 15 vertices were eliminated
building final representation...
557 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=140393, nf=280782, ne=421173, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 11.0 minutes
0 defective edges
removing intersecting faces
000: 72 intersecting
001: 6 intersecting

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 140393 - 421173 + 280782 = 2 --> 0 holes
      F =2V-4:          280782 = 280786-4 (0)
      2E=3F:            842346 = 842346 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

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

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

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make White Surf lh Thu Aug  8 18:52:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub018 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/sub018/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
18104 bright wm thresholded.
357 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.orig...
computing class statistics...
border white:    252064 voxels (1.50%)
border gray      291583 voxels (1.74%)
WM (92.0): 92.8 +- 10.4 [70.0 --> 110.0]
GM (74.0) : 73.1 +- 12.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.4 (was 70)
setting MAX_BORDER_WHITE to 115.4 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.9 (was 40)
setting MAX_GRAY to 94.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.02-->2.38) (max @ vno 106072 --> 140333)
face area 0.28 +- 0.12 (0.00-->1.59)
mean absolute distance = 0.68 +- 0.81
3584 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 = 92.7, mean outside = 68.4
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 2 vertex label from ripped group
mean border=72.3, 46 (46) missing vertices, mean dist 0.4 [0.5 (%31.0)->0.8 (%69.0))]
%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 (0.09-->3.87) (max @ vno 106917 --> 107997)
face area 0.28 +- 0.13 (0.00-->2.22)
mean absolute distance = 0.31 +- 0.45
2784 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7593535.0, rms=13.69
001: dt: 0.5000, sse=7623433.5, rms=9.925 (0.000%)
002: dt: 0.5000, sse=7783613.5, rms=7.737 (0.000%)
003: dt: 0.5000, sse=7928952.5, rms=6.320 (0.000%)
004: dt: 0.5000, sse=8101897.0, rms=5.481 (0.000%)
005: dt: 0.5000, sse=8220709.5, rms=4.985 (0.000%)
006: dt: 0.5000, sse=8272811.5, rms=4.733 (0.000%)
007: dt: 0.5000, sse=8306699.5, rms=4.565 (0.000%)
008: dt: 0.5000, sse=8310262.5, rms=4.482 (0.000%)
009: dt: 0.5000, sse=8284134.0, rms=4.398 (0.000%)
rms = 4.36, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=8276810.5, rms=4.365 (0.000%)
011: dt: 0.2500, sse=5265968.0, rms=3.045 (0.000%)
012: dt: 0.2500, sse=4850102.0, rms=2.615 (0.000%)
013: dt: 0.2500, sse=4584692.5, rms=2.513 (0.000%)
014: dt: 0.2500, sse=4506709.5, rms=2.420 (0.000%)
rms = 2.38, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4401575.5, rms=2.383 (0.000%)
016: dt: 0.1250, sse=4179055.0, rms=2.151 (0.000%)
rms = 2.12, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4133489.2, rms=2.118 (0.000%)
positioning took 2.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=77.1, 29 (1) missing vertices, mean dist -0.2 [0.3 (%79.3)->0.2 (%20.7))]
%83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.12-->3.57) (max @ vno 104764 --> 104766)
face area 0.35 +- 0.16 (0.00-->2.88)
mean absolute distance = 0.21 +- 0.28
2447 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5193968.0, rms=6.31
018: dt: 0.5000, sse=5327800.5, rms=4.178 (0.000%)
rms = 4.51, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=4858880.0, rms=3.036 (0.000%)
020: dt: 0.2500, sse=4654450.5, rms=2.406 (0.000%)
021: dt: 0.2500, sse=4601864.0, rms=1.993 (0.000%)
022: dt: 0.2500, sse=4568304.5, rms=1.942 (0.000%)
023: dt: 0.2500, sse=4511403.0, rms=1.852 (0.000%)
rms = 1.86, time step reduction 2 of 3 to 0.125...
024: dt: 0.1250, sse=4453722.5, rms=1.774 (0.000%)
025: dt: 0.1250, sse=4370604.0, rms=1.668 (0.000%)
rms = 1.66, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=4327520.5, rms=1.663 (0.000%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=80.4, 30 (0) missing vertices, mean dist -0.1 [0.2 (%76.6)->0.2 (%23.4))]
%90 local maxima, % 4 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-->3.64) (max @ vno 140247 --> 57770)
face area 0.34 +- 0.16 (0.00-->2.83)
mean absolute distance = 0.16 +- 0.24
2791 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4728897.5, rms=4.32
027: dt: 0.5000, sse=5132050.0, rms=4.118 (0.000%)
rms = 4.33, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=4651926.5, rms=2.591 (0.000%)
029: dt: 0.2500, sse=4517009.5, rms=2.128 (0.000%)
030: dt: 0.2500, sse=4575766.5, rms=1.791 (0.000%)
rms = 1.84, time step reduction 2 of 3 to 0.125...
031: dt: 0.1250, sse=4509472.5, rms=1.655 (0.000%)
032: dt: 0.1250, sse=4419950.0, rms=1.467 (0.000%)
rms = 1.45, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=4382431.0, rms=1.448 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=81.4, 27 (0) missing vertices, mean dist -0.0 [0.2 (%58.3)->0.2 (%41.7))]
%92 local maxima, % 3 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/sub018/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=4408231.0, rms=1.82
rms = 2.75, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=4506050.0, rms=1.205 (0.000%)
035: dt: 0.2500, sse=4678282.5, rms=1.078 (0.000%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
rms = 1.07, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=4681872.0, rms=1.067 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
12 non-cortical segments detected
only using segment with 1853 vertices
erasing segment 1 (vno[0] = 80872)
erasing segment 2 (vno[0] = 85194)
erasing segment 3 (vno[0] = 85231)
erasing segment 4 (vno[0] = 96348)
erasing segment 5 (vno[0] = 98385)
erasing segment 6 (vno[0] = 98405)
erasing segment 7 (vno[0] = 99451)
erasing segment 8 (vno[0] = 100513)
erasing segment 9 (vno[0] = 107997)
erasing segment 10 (vno[0] = 108015)
erasing segment 11 (vno[0] = 108027)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.area
vertex spacing 0.90 +- 0.25 (0.06-->3.87) (max @ vno 107997 --> 106917)
face area 0.34 +- 0.16 (0.00-->2.82)
refinement took 7.7 minutes
#--------------------------------------------
#@# Smooth2 lh Thu Aug  8 18:59:52 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 18:59:57 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

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

avg radius = 47.0 mm, total surface area = 85951 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.118 (target=0.015)   
step 005: RMS=0.082 (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=0.027 (target=0.015)   
step 035: RMS=0.022 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.018 (target=0.015)   
step 050: RMS=0.017 (target=0.015)   
step 055: RMS=0.015 (target=0.015)   
inflation complete.
inflation took 0.7 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
160 vertices thresholded to be in k1 ~ [-0.49 0.42], k2 ~ [-0.31 0.06]
total integrated curvature = 0.616*4pi (7.743) --> 0 handles
ICI = 1.6, FI = 10.8, variation=180.166
134 vertices thresholded to be in [-0.04 0.02]
writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
120 vertices thresholded to be in [-0.17 0.19]
done.
writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024
done.

#-----------------------------------------
#@# Curvature Stats lh Thu Aug  8 19:02:33 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub018 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       [ sub018/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                      [ 284 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.503964
WARN:    S explicit min:                          0.000000	vertex = 37
#--------------------------------------------
#@# Sphere lh Thu Aug  8 19:02:38 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 0.291...
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 %20.26
pass 1: epoch 2 of 3 starting distance error %20.22
unfolding complete - removing small folds...
starting distance error %20.12
removing remaining folds...
final distance error %20.14
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.10 hours
#--------------------------------------------
#@# Surf Reg lh Thu Aug  8 20:08:53 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 0.575
curvature mean = 0.028, std = 0.935
curvature mean = 0.025, std = 0.848
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, 0.00) sse = 258895.9, tmin=2.6441
  d=16.00 min @ (4.00, 4.00, -4.00) sse = 223271.4, tmin=4.0141
  d=8.00 min @ (0.00, -2.00, 0.00) sse = 221178.8, tmin=5.4640
  d=4.00 min @ (0.00, 1.00, 1.00) sse = 218526.3, tmin=6.9095
  d=2.00 min @ (-0.50, 0.00, 0.00) sse = 218236.0, tmin=8.4010
  d=1.00 min @ (0.00, -0.25, 0.00) sse = 218099.9, tmin=9.8591
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  11.29 min
curvature mean = 0.017, std = 0.946
curvature mean = 0.013, std = 0.934
curvature mean = 0.017, std = 0.958
curvature mean = 0.006, std = 0.970
curvature mean = 0.016, std = 0.960
curvature mean = 0.002, std = 0.987
2 Reading smoothwm
curvature mean = -0.024, std = 0.311
curvature mean = 0.004, std = 0.067
curvature mean = 0.073, std = 0.312
curvature mean = 0.004, std = 0.079
curvature mean = 0.035, std = 0.506
curvature mean = 0.004, std = 0.085
curvature mean = 0.020, std = 0.646
curvature mean = 0.005, std = 0.087
curvature mean = 0.007, std = 0.757
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white lh Thu Aug  8 20:40:56 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 20:40:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 20:41:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
1406 labels changed using aseg
relabeling using gibbs priors...
000:   3202 changed, 140393 examined...
001:    746 changed, 13633 examined...
002:    172 changed, 4130 examined...
003:     50 changed, 1030 examined...
004:     26 changed, 303 examined...
005:     14 changed, 142 examined...
006:      8 changed, 70 examined...
007:      5 changed, 50 examined...
008:      4 changed, 26 examined...
009:      2 changed, 25 examined...
010:      1 changed, 12 examined...
011:      0 changed, 8 examined...
214 labels changed using aseg
000: 141 total segments, 99 labels (244 vertices) changed
001: 44 total segments, 4 labels (19 vertices) changed
002: 40 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 58 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1613 vertices marked for relabeling...
1613 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 1 minutes and 5 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Thu Aug  8 20:42:06 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub018 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/sub018/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
18104 bright wm thresholded.
357 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.orig...
computing class statistics...
border white:    252064 voxels (1.50%)
border gray      291583 voxels (1.74%)
WM (92.0): 92.8 +- 10.4 [70.0 --> 110.0]
GM (74.0) : 73.1 +- 12.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.4 (was 70)
setting MAX_BORDER_WHITE to 115.4 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.9 (was 40)
setting MAX_GRAY to 94.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 92.7, mean outside = 68.4
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/sub018/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.02-->2.38) (max @ vno 106072 --> 140333)
face area 0.28 +- 0.12 (0.00-->1.59)
mean absolute distance = 0.68 +- 0.81
3711 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 18 points - only 5.56% unknown
deleting segment 1 with 6 points - only 0.00% unknown
deleting segment 2 with 8 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
deleting segment 8 with 936 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 12 with 17 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
mean border=72.3, 46 (46) missing vertices, mean dist 0.4 [0.5 (%31.0)->0.8 (%69.0))]
%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 (0.08-->3.87) (max @ vno 106917 --> 107997)
face area 0.28 +- 0.13 (0.00-->2.22)
mean absolute distance = 0.31 +- 0.46
2879 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7621995.5, rms=13.66
001: dt: 0.5000, sse=7660257.0, rms=9.906 (0.000%)
002: dt: 0.5000, sse=7828697.5, rms=7.722 (0.000%)
003: dt: 0.5000, sse=7974345.0, rms=6.309 (0.000%)
004: dt: 0.5000, sse=8155546.5, rms=5.472 (0.000%)
005: dt: 0.5000, sse=8276563.0, rms=4.977 (0.000%)
006: dt: 0.5000, sse=8335153.0, rms=4.727 (0.000%)
007: dt: 0.5000, sse=8362605.0, rms=4.559 (0.000%)
008: dt: 0.5000, sse=8378905.5, rms=4.476 (0.000%)
009: dt: 0.5000, sse=8346949.0, rms=4.393 (0.000%)
rms = 4.36, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=8344572.5, rms=4.360 (0.000%)
011: dt: 0.2500, sse=5306193.5, rms=3.044 (0.000%)
012: dt: 0.2500, sse=4887464.0, rms=2.615 (0.000%)
013: dt: 0.2500, sse=4619242.5, rms=2.514 (0.000%)
014: dt: 0.2500, sse=4542062.0, rms=2.422 (0.000%)
rms = 2.38, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4437022.5, rms=2.385 (0.000%)
016: dt: 0.1250, sse=4214991.5, rms=2.155 (0.000%)
rms = 2.12, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4168743.5, rms=2.122 (0.000%)
positioning took 2.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 27 points - only 3.70% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 760 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
deleting segment 12 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 16 with 22 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 17 with 2 points - only 0.00% unknown
mean border=77.0, 34 (0) missing vertices, mean dist -0.2 [0.3 (%79.3)->0.2 (%20.7))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.07-->3.44) (max @ vno 140247 --> 57770)
face area 0.35 +- 0.16 (0.00-->2.88)
mean absolute distance = 0.21 +- 0.29
2578 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5235586.5, rms=6.30
018: dt: 0.5000, sse=5374121.5, rms=4.174 (0.000%)
rms = 4.50, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=4902543.0, rms=3.036 (0.000%)
020: dt: 0.2500, sse=4698838.5, rms=2.409 (0.000%)
021: dt: 0.2500, sse=4646128.5, rms=2.000 (0.000%)
022: dt: 0.2500, sse=4612254.0, rms=1.948 (0.000%)
023: dt: 0.2500, sse=4555632.5, rms=1.859 (0.000%)
rms = 1.87, time step reduction 2 of 3 to 0.125...
024: dt: 0.1250, sse=4497848.0, rms=1.781 (0.000%)
025: dt: 0.1250, sse=4415576.0, rms=1.676 (0.000%)
rms = 1.67, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=4373170.0, rms=1.671 (0.000%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 25 points - only 4.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 8 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
deleting segment 6 with 844 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
deleting segment 10 with 24 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
mean border=80.4, 26 (0) missing vertices, mean dist -0.1 [0.2 (%76.5)->0.2 (%23.5))]
%91 local maxima, % 4 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-->3.64) (max @ vno 140247 --> 57770)
face area 0.34 +- 0.16 (0.00-->2.83)
mean absolute distance = 0.16 +- 0.24
2917 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4775664.0, rms=4.31
027: dt: 0.5000, sse=5184141.0, rms=4.113 (0.000%)
rms = 4.32, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=4703077.0, rms=2.593 (0.000%)
029: dt: 0.2500, sse=4569690.5, rms=2.130 (0.000%)
030: dt: 0.2500, sse=4627375.5, rms=1.796 (0.000%)
rms = 1.85, time step reduction 2 of 3 to 0.125...
031: dt: 0.1250, sse=4561258.0, rms=1.662 (0.000%)
032: dt: 0.1250, sse=4472172.5, rms=1.475 (0.000%)
rms = 1.46, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=4434970.0, rms=1.457 (0.000%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 25 points - only 4.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 2 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 8 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
deleting segment 6 with 832 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
deleting segment 9 with 24 points - only 0.00% unknown
deleting segment 10 with 9 points - only 0.00% unknown
mean border=81.4, 23 (0) missing vertices, mean dist -0.0 [0.2 (%58.2)->0.2 (%41.8))]
%92 local maxima, % 3 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=4460609.5, rms=1.82
rms = 2.74, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=4564330.0, rms=1.211 (0.000%)
035: dt: 0.2500, sse=4743142.5, rms=1.085 (0.000%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
rms = 1.08, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=4746944.0, rms=1.075 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
smoothing surface for 5 iterations...
mean border=48.9, 43 (43) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.4 (%100.0))]
%16 local maxima, %53 large gradients and %26 min vals, 1454 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=30063754.0, rms=31.85
001: dt: 0.5000, sse=21528794.0, rms=26.341 (0.000%)
002: dt: 0.5000, sse=15669557.0, rms=21.799 (0.000%)
003: dt: 0.5000, sse=11786185.0, rms=18.150 (0.000%)
004: dt: 0.5000, sse=9423024.0, rms=15.280 (0.000%)
005: dt: 0.5000, sse=8114454.5, rms=13.092 (0.000%)
006: dt: 0.5000, sse=7403228.5, rms=11.445 (0.000%)
007: dt: 0.5000, sse=6982222.5, rms=10.046 (0.000%)
008: dt: 0.5000, sse=6682913.5, rms=8.755 (0.000%)
009: dt: 0.5000, sse=6516733.0, rms=7.576 (0.000%)
010: dt: 0.5000, sse=6528485.0, rms=6.573 (0.000%)
011: dt: 0.5000, sse=6626331.5, rms=5.815 (0.000%)
012: dt: 0.5000, sse=6805241.5, rms=5.283 (0.000%)
013: dt: 0.5000, sse=6982417.5, rms=4.950 (0.000%)
014: dt: 0.5000, sse=7075462.5, rms=4.699 (0.000%)
015: dt: 0.5000, sse=7209154.5, rms=4.537 (0.000%)
016: dt: 0.5000, sse=7271487.0, rms=4.371 (0.000%)
017: dt: 0.5000, sse=7277579.0, rms=4.296 (0.000%)
018: dt: 0.5000, sse=7301311.0, rms=4.199 (0.000%)
rms = 4.17, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=7313636.5, rms=4.174 (0.000%)
020: dt: 0.2500, sse=5187138.0, rms=3.420 (0.000%)
021: dt: 0.2500, sse=4989134.5, rms=3.199 (0.000%)
rms = 3.17, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=4851979.0, rms=3.174 (0.000%)
023: dt: 0.1250, sse=4606620.5, rms=3.027 (0.000%)
rms = 3.01, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=4567122.0, rms=3.008 (0.000%)
positioning took 3.0 minutes
mean border=46.5, 1028 (1) missing vertices, mean dist 0.2 [0.2 (%45.8)->0.5 (%54.2))]
%33 local maxima, %41 large gradients and %21 min vals, 517 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=5220012.5, rms=4.93
025: dt: 0.5000, sse=5544372.5, rms=4.330 (0.000%)
rms = 4.29, time step reduction 1 of 3 to 0.250...
026: dt: 0.5000, sse=7141533.5, rms=4.293 (0.000%)
027: dt: 0.2500, sse=5351392.5, rms=3.401 (0.000%)
028: dt: 0.2500, sse=5407391.5, rms=3.143 (0.000%)
rms = 3.12, time step reduction 2 of 3 to 0.125...
029: dt: 0.2500, sse=5262638.5, rms=3.121 (0.000%)
030: dt: 0.1250, sse=5051425.5, rms=2.909 (0.000%)
rms = 2.87, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=5028570.5, rms=2.873 (0.000%)
positioning took 0.9 minutes
mean border=44.1, 1171 (1) missing vertices, mean dist 0.1 [0.2 (%36.6)->0.4 (%63.4))]
%52 local maxima, %22 large gradients and %21 min vals, 595 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=5322592.5, rms=4.29
rms = 4.25, time step reduction 1 of 3 to 0.250...
032: dt: 0.5000, sse=5611925.5, rms=4.246 (0.000%)
033: dt: 0.2500, sse=5443074.0, rms=3.199 (0.000%)
034: dt: 0.2500, sse=5500722.5, rms=2.993 (0.000%)
rms = 3.00, time step reduction 2 of 3 to 0.125...
035: dt: 0.1250, sse=5383388.0, rms=2.896 (0.000%)
036: dt: 0.1250, sse=5211532.0, rms=2.756 (0.000%)
rms = 2.73, time step reduction 3 of 3 to 0.062...
037: dt: 0.1250, sse=5181308.5, rms=2.726 (0.000%)
positioning took 0.9 minutes
mean border=43.0, 2334 (1) missing vertices, mean dist 0.0 [0.2 (%45.2)->0.3 (%54.8))]
%54 local maxima, %19 large gradients and %21 min vals, 456 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/sub018/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=5233645.0, rms=3.08
rms = 3.95, time step reduction 1 of 3 to 0.250...
038: dt: 0.2500, sse=5105996.5, rms=2.796 (0.000%)
039: dt: 0.2500, sse=5307478.5, rms=2.738 (0.000%)
rms = 2.74, time step reduction 2 of 3 to 0.125...
040: dt: 0.2500, sse=5357674.5, rms=2.738 (0.000%)
041: dt: 0.1250, sse=5252671.5, rms=2.598 (0.000%)
rms = 2.58, time step reduction 3 of 3 to 0.062...
042: dt: 0.1250, sse=5265458.5, rms=2.577 (0.000%)
positioning took 0.8 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.area.pial
vertex spacing 1.02 +- 0.43 (0.08-->8.77) (max @ vno 105864 --> 105855)
face area 0.41 +- 0.30 (0.00-->6.11)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 140393 vertices processed
25000 of 140393 vertices processed
50000 of 140393 vertices processed
75000 of 140393 vertices processed
100000 of 140393 vertices processed
125000 of 140393 vertices processed
0 of 140393 vertices processed
25000 of 140393 vertices processed
50000 of 140393 vertices processed
75000 of 140393 vertices processed
100000 of 140393 vertices processed
125000 of 140393 vertices processed
thickness calculation complete, 531:971 truncations.
29027 vertices at 0 distance
91199 vertices at 1 distance
91889 vertices at 2 distance
38639 vertices at 3 distance
11593 vertices at 4 distance
3553 vertices at 5 distance
1201 vertices at 6 distance
426 vertices at 7 distance
168 vertices at 8 distance
81 vertices at 9 distance
58 vertices at 10 distance
32 vertices at 11 distance
24 vertices at 12 distance
21 vertices at 13 distance
22 vertices at 14 distance
22 vertices at 15 distance
15 vertices at 16 distance
6 vertices at 17 distance
7 vertices at 18 distance
3 vertices at 19 distance
12 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.thickness
positioning took 14.7 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 20:56:47 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 20:56:48 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 pctsurfcon --s sub018 --lh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts/pctsurfcon.log
Thu Aug  8 20:56:48 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake5 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/sub018/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.wm.mgh --regheader sub018 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 108892
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.wm.mgh
Dim: 140393 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.gm.mgh --projfrac 0.3 --regheader sub018 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 124928
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.gm.mgh
Dim: 140393 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.5580/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/lh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.w-g.pct.mgh --annot sub018 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/lh.w-g.pct.mgh --annot sub018 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname snake5
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/sub018/surf/lh.w-g.pct.mgh
Vertex Area is 0.67026 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   1000                            unknown       0       0.000
  1   1001                           bankssts    1852    1259.917
  2   1002            caudalanteriorcingulate    1196     780.580
  3   1003                caudalmiddlefrontal    3440    2289.014
  4   1004                     corpuscallosum       0       0.000
  5   1005                             cuneus    1824    1238.933
  6   1006                         entorhinal     678     499.968
  7   1007                           fusiform    5745    3862.256
  8   1008                   inferiorparietal    7495    5033.733
  9   1009                   inferiortemporal    5631    3831.789
 10   1010                   isthmuscingulate    1580    1052.516
 11   1011                   lateraloccipital    7198    4698.103
 12   1012               lateralorbitofrontal    3274    2189.129
 13   1013                            lingual    3909    2703.998
 14   1014                medialorbitofrontal    2719    1797.822
 15   1015                     middletemporal    5284    3650.135
 16   1016                    parahippocampal    1033     713.050
 17   1017                        paracentral    2203    1451.589
 18   1018                    parsopercularis    2306    1618.291
 19   1019                      parsorbitalis     870     560.306
 20   1020                   parstriangularis    1903    1282.946
 21   1021                      pericalcarine    1774    1193.827
 22   1022                        postcentral    7175    4734.376
 23   1023                 posteriorcingulate    2231    1461.519
 24   1024                         precentral    7197    4745.302
 25   1025                          precuneus    5474    3707.295
 26   1026           rostralanteriorcingulate    1415     926.042
 27   1027               rostralmiddlefrontal    9507    6529.832
 28   1028                    superiorfrontal   11324    7799.412
 29   1029                   superiorparietal    8021    5314.134
 30   1030                   superiortemporal    6471    4277.174
 31   1031                      supramarginal    5690    3868.281
 32   1032                        frontalpole     436     279.005
 33   1033                       temporalpole     793     537.071
 34   1034                 transversetemporal     776     496.099
 35   1035                             insula    3379    2195.280

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats lh Thu Aug  8 20:57:02 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

 1852   1260   3420  2.848 0.437     0.136     0.038       23     3.1  bankssts
 1196    781   2418  2.825 0.763     0.158     0.049       26     2.5  caudalanteriorcingulate
 3440   2289   6238  2.523 0.381     0.123     0.039       37     5.1  caudalmiddlefrontal
 1824   1239   2715  2.012 0.407     0.179     0.076       40     5.8  cuneus
  678    500   2301  3.466 0.777     0.155     0.057       14     1.6  entorhinal
 5745   3862  12326  2.773 0.513     0.159     0.069      133    15.1  fusiform
 7495   5034  13974  2.471 0.418     0.142     0.052      211    15.9  inferiorparietal
 5631   3832  12344  2.830 0.627     0.159     0.078      143    15.3  inferiortemporal
 1580   1053   2810  2.415 0.795     0.170     0.071       33     4.4  isthmuscingulate
 7198   4698  11769  2.212 0.418     0.167     0.127      346    50.7  lateraloccipital
 3274   2189   6927  2.742 0.731     0.163     0.080       83    10.3  lateralorbitofrontal
 3909   2704   6263  2.106 0.506     0.176     0.084       95    12.5  lingual
 2719   1798   5068  2.395 0.772     0.152     0.074       80     8.0  medialorbitofrontal
 5284   3650  12540  2.838 0.555     0.166     0.062      124    13.2  middletemporal
 1033    713   2681  3.126 0.837     0.172     0.075       35     3.2  parahippocampal
 2203   1452   3996  2.372 0.471     0.126     0.038       26     3.3  paracentral
 2306   1618   4788  2.567 0.407     0.146     0.048       43     4.3  parsopercularis
  870    560   2060  2.883 0.604     0.169     0.067       21     2.6  parsorbitalis
 1903   1283   3803  2.554 0.441     0.135     0.043       32     3.5  parstriangularis
 1774   1194   1960  1.747 0.409     0.160     0.104      161     4.7  pericalcarine
 7175   4734  11311  2.118 0.529     0.133     0.041      102    12.0  postcentral
 2231   1462   3632  2.253 0.704     0.153     0.055       51     5.0  posteriorcingulate
 7197   4745  13464  2.599 0.483     0.125     0.040       87    12.1  precentral
 5474   3707   9773  2.441 0.495     0.143     0.053      107    12.1  precuneus
 1415    926   3093  2.824 0.616     0.146     0.055       31     3.1  rostralanteriorcingulate
 9507   6530  17771  2.383 0.477     0.161     0.069      225    26.4  rostralmiddlefrontal
11324   7799  22717  2.554 0.517     0.140     0.049      188    22.0  superiorfrontal
 8021   5314  13208  2.241 0.392     0.141     0.051      148    14.8  superiorparietal
 6471   4277  13766  2.779 0.607     0.129     0.041       89    11.1  superiortemporal
 5690   3868  11055  2.582 0.480     0.141     0.047       92    10.6  supramarginal
  436    279    930  2.393 0.527     0.190     0.112       17     2.1  frontalpole
  793    537   2610  3.720 0.554     0.150     0.060       13     2.1  temporalpole
  776    496   1233  2.333 0.328     0.152     0.056       13     1.7  transversetemporal
 3379   2195   7645  3.220 0.850     0.131     0.134      291    15.2  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Thu Aug  8 20:57:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
42 labels changed using aseg
relabeling using gibbs priors...
000:   9776 changed, 140393 examined...
001:   2378 changed, 37338 examined...
002:    744 changed, 12271 examined...
003:    329 changed, 4211 examined...
004:    161 changed, 1868 examined...
005:     92 changed, 919 examined...
006:     66 changed, 511 examined...
007:     28 changed, 358 examined...
008:     19 changed, 170 examined...
009:      5 changed, 96 examined...
010:      4 changed, 27 examined...
011:      2 changed, 26 examined...
012:      4 changed, 14 examined...
013:      1 changed, 20 examined...
014:      1 changed, 7 examined...
015:      2 changed, 6 examined...
016:      1 changed, 14 examined...
017:      3 changed, 7 examined...
018:      4 changed, 17 examined...
019:      0 changed, 14 examined...
1 labels changed using aseg
000: 299 total segments, 213 labels (2941 vertices) changed
001: 106 total segments, 20 labels (56 vertices) changed
002: 88 total segments, 2 labels (2 vertices) changed
003: 86 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 158 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
892 vertices marked for relabeling...
892 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 1 minutes and 13 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Thu Aug  8 20:58:34 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

 1425    996   2706  2.534 0.597     0.183     0.093       38     5.7  G_and_S_frontomargin
 1770   1176   3109  2.329 0.385     0.169     0.289      161    36.2  G_and_S_occipital_inf
 1774   1125   3438  2.430 0.513     0.131     0.044       25     2.9  G_and_S_paracentral
 1451    961   2967  2.663 0.437     0.154     0.056       26     3.1  G_and_S_subcentral
  770    539   1597  2.319 0.464     0.195     0.098       25     2.9  G_and_S_transv_frontopol
 2761   1820   5144  2.493 0.577     0.134     0.048       48     5.7  G_and_S_cingul-Ant
 1455    987   2814  2.677 0.626     0.140     0.047       22     2.8  G_and_S_cingul-Mid-Ant
 1841   1251   3198  2.389 0.546     0.144     0.048       30     3.7  G_and_S_cingul-Mid-Post
  509    340   1263  2.743 0.540     0.193     0.078       14     1.6  G_cingul-Post-dorsal
  282    176    501  2.469 0.856     0.181     0.084        7     0.9  G_cingul-Post-ventral
 1690   1133   2665  2.013 0.463     0.193     0.089       46     6.2  G_cuneus
 1460   1016   3421  2.697 0.446     0.175     0.072       39     4.1  G_front_inf-Opercular
  363    222    883  3.113 0.373     0.185     0.083       10     1.2  G_front_inf-Orbital
 1122    736   2551  2.681 0.365     0.141     0.048       23     2.3  G_front_inf-Triangul
 5123   3456  10918  2.484 0.405     0.165     0.074      140    15.2  G_front_middle
 7360   5054  16642  2.681 0.494     0.152     0.058      154    16.7  G_front_sup
  563    345   1419  3.373 0.851     0.134     0.133       39     1.9  G_Ins_lg_and_S_cent_ins
  713    455   2445  3.726 0.729     0.133     0.136       36     4.3  G_insular_short
 2459   1595   5190  2.495 0.388     0.180     0.089      183     8.8  G_occipital_middle
 1589   1020   3074  2.381 0.463     0.164     0.067       35     3.9  G_occipital_sup
 2121   1381   4936  2.787 0.481     0.176     0.082       70     6.5  G_oc-temp_lat-fusifor
 2444   1675   4320  2.138 0.486     0.205     0.116       81    10.4  G_oc-temp_med-Lingual
 1307    919   4239  3.413 0.713     0.174     0.079       42     4.3  G_oc-temp_med-Parahip
 2342   1533   6393  2.998 0.706     0.191     0.102       81     9.9  G_orbital
 2511   1695   5759  2.620 0.438     0.161     0.065       61     6.1  G_pariet_inf-Angular
 3129   2093   6863  2.700 0.455     0.150     0.054       62     6.4  G_pariet_inf-Supramar
 2981   1980   5370  2.242 0.373     0.144     0.048       57     5.7  G_parietal_sup
 2944   1894   5335  2.278 0.477     0.142     0.045       53     5.5  G_postcentral
 2434   1601   5626  2.677 0.400     0.135     0.049       45     5.1  G_precentral
 2408   1614   5043  2.561 0.522     0.151     0.055       51     5.3  G_precuneus
 1032    675   2352  2.449 0.672     0.197     0.107       53     4.6  G_rectus
  290    196    758  3.623 0.694     0.141     0.060        7     0.6  G_subcallosal
  575    352   1043  2.391 0.403     0.152     0.059       11     1.3  G_temp_sup-G_T_transv
 2376   1567   6403  2.989 0.477     0.161     0.055       53     5.5  G_temp_sup-Lateral
  901    598   2402  3.653 0.682     0.105     0.039        6     1.3  G_temp_sup-Plan_polar
 1095    748   2218  2.609 0.469     0.122     0.035       12     1.4  G_temp_sup-Plan_tempo
 3300   2243   8481  2.919 0.660     0.180     0.099      111    11.5  G_temporal_inf
 3541   2457   9221  2.873 0.566     0.178     0.068       96    10.1  G_temporal_middle
  301    211    523  2.410 0.349     0.114     0.025        3     0.3  Lat_Fis-ant-Horizont
  202    147    387  2.545 0.331     0.104     0.025        1     0.2  Lat_Fis-ant-Vertical
 1232    843   1643  2.409 0.569     0.134     0.042       12     2.1  Lat_Fis-post
 1863   1198   2857  2.119 0.409     0.178     0.098       89     5.5  Pole_occipital
 2068   1389   6178  3.329 0.639     0.170     0.080       48     6.5  Pole_temporal
 2189   1508   2770  1.931 0.615     0.156     0.088      163     5.2  S_calcarine
 3325   2243   4062  1.990 0.548     0.108     0.028       20     4.0  S_central
 1153    777   1764  2.323 0.531     0.123     0.035       13     1.7  S_cingul-Marginalis
  658    434   1159  3.105 0.660     0.120     0.051       11     1.7  S_circular_insula_ant
 1323    882   2320  2.902 0.726     0.088     0.022        6     1.2  S_circular_insula_inf
 1840   1210   2777  2.640 0.539     0.125     0.126      201     7.0  S_circular_insula_sup
 1436   1023   2620  2.739 0.524     0.117     0.031       10     1.9  S_collat_transv_ant
  416    272    500  2.332 0.363     0.157     0.058        6     0.9  S_collat_transv_post
 2133   1487   3388  2.333 0.343     0.121     0.030       19     2.8  S_front_inf
 2110   1411   2958  2.127 0.412     0.127     0.044       24     3.2  S_front_middle
 3069   2145   5145  2.362 0.403     0.125     0.037       37     4.6  S_front_sup
   85     58    105  2.214 0.411     0.128     0.035        1     0.2  S_interm_prim-Jensen
 2900   1986   4194  2.167 0.335     0.119     0.039       40     3.8  S_intrapariet_and_P_trans
 1447    965   1785  1.951 0.306     0.144     0.047       20     3.0  S_oc_middle_and_Lunatus
 1262    844   1688  2.131 0.296     0.134     0.037       14     2.0  S_oc_sup_and_transversal
  928    615   1327  2.267 0.399     0.120     0.033        7     1.4  S_occipital_ant
 1313    868   2077  2.650 0.417     0.135     0.046       16     2.3  S_oc-temp_lat
 2062   1449   3335  2.422 0.578     0.136     0.041       27     3.5  S_oc-temp_med_and_Lingual
  491    324    634  2.277 0.452     0.120     0.031        3     0.7  S_orbital_lateral
  805    531   1323  2.512 0.975     0.129     0.061       17     1.8  S_orbital_med-olfact
  986    687   1624  2.315 0.479     0.145     0.059       18     1.8  S_orbital-H_Shaped
 1888   1285   2633  2.231 0.446     0.131     0.037       19     3.0  S_parieto_occipital
 1698   1067   1935  2.073 0.961     0.141     0.042       26     3.0  S_pericallosal
 3474   2341   4903  2.206 0.445     0.132     0.044       43     5.7  S_postcentral
 1573   1067   2455  2.478 0.404     0.117     0.030       14     2.0  S_precentral-inf-part
 1122    730   1650  2.567 0.415     0.114     0.028        8     1.3  S_precentral-sup-part
  518    354    761  2.049 0.447     0.154     0.081       12     1.5  S_suborbital
 1430    959   2510  2.472 0.369     0.155     0.076       51     4.7  S_subparietal
 1102    762   1869  2.718 0.614     0.138     0.066       22     2.2  S_temporal_inf
 6687   4534  11334  2.585 0.463     0.128     0.038       81    10.5  S_temporal_sup
  503    348    710  2.357 0.355     0.113     0.028        3     0.7  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Thu Aug  8 20:58:56 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
1069 labels changed using aseg
relabeling using gibbs priors...
000:   2877 changed, 140393 examined...
001:    703 changed, 12283 examined...
002:    172 changed, 3678 examined...
003:     67 changed, 1030 examined...
004:     31 changed, 412 examined...
005:     13 changed, 196 examined...
006:      9 changed, 84 examined...
007:      6 changed, 53 examined...
008:      6 changed, 44 examined...
009:      2 changed, 33 examined...
010:      1 changed, 13 examined...
011:      1 changed, 7 examined...
012:      0 changed, 7 examined...
111 labels changed using aseg
000: 66 total segments, 33 labels (344 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 39 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
599 vertices marked for relabeling...
599 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas40.annot...
classification took 1 minutes and 5 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Thu Aug  8 21:00:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

 2015   1320   3918  2.750 0.670     0.143     0.043       34     3.6  caudalanteriorcingulate
 3524   2361   6444  2.525 0.381     0.124     0.039       38     5.3  caudalmiddlefrontal
 2619   1770   3994  2.053 0.415     0.163     0.067       48     7.0  cuneus
  645    485   2166  3.392 0.764     0.153     0.057       13     1.5  entorhinal
 5088   3432  10500  2.736 0.494     0.156     0.063      112    12.5  fusiform
 6971   4701  12889  2.454 0.423     0.141     0.052      201    14.7  inferiorparietal
 5743   3883  13245  2.897 0.644     0.165     0.086      158    17.2  inferiortemporal
 1583   1052   2828  2.418 0.799     0.169     0.070       33     4.4  isthmuscingulate
 7551   4921  12394  2.222 0.424     0.167     0.124      353    51.5  lateraloccipital
 3578   2414   7876  2.790 0.782     0.173     0.096      106    14.0  lateralorbitofrontal
 3879   2678   6213  2.105 0.505     0.177     0.084       95    12.5  lingual
 2285   1513   4414  2.379 0.767     0.163     0.083       78     7.8  medialorbitofrontal
 7103   4872  15934  2.808 0.540     0.159     0.057      149    16.6  middletemporal
 1051    727   2729  3.120 0.836     0.173     0.075       35     3.2  parahippocampal
 2518   1649   4445  2.375 0.470     0.127     0.038       29     3.7  paracentral
 2116   1492   4348  2.566 0.411     0.147     0.048       40     4.1  parsopercularis
 1087    690   2379  2.956 0.540     0.153     0.059       21     2.7  parsorbitalis
 2368   1579   4408  2.491 0.407     0.132     0.041       36     4.0  parstriangularis
 1760   1188   1957  1.750 0.407     0.160     0.104      161     4.6  pericalcarine
 7913   5220  12357  2.128 0.534     0.134     0.042      116    13.2  postcentral
 2387   1573   3831  2.265 0.688     0.153     0.054       52     5.3  posteriorcingulate
 7128   4696  13263  2.595 0.487     0.125     0.040       85    12.1  precentral
 5444   3667   9847  2.454 0.484     0.145     0.054      110    12.2  precuneus
 1810   1187   3850  2.760 0.650     0.143     0.052       35     3.8  rostralanteriorcingulate
 6603   4540  12618  2.380 0.470     0.157     0.064      151    16.8  rostralmiddlefrontal
12690   8746  25302  2.503 0.514     0.148     0.056      248    28.2  superiorfrontal
 6317   4215  10485  2.259 0.382     0.141     0.051      120    11.6  superiorparietal
 8764   5845  19245  2.869 0.655     0.133     0.047      149    16.1  superiortemporal
 5688   3849  10937  2.571 0.486     0.142     0.048       92    10.9  supramarginal
  721    460   1143  2.323 0.330     0.151     0.057       12     1.6  transversetemporal
 2854   1852   6651  3.246 0.794     0.120     0.125      246    12.6  insula
#--------------------------------------------
#@# Tessellate rh Thu Aug  8 21:00:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

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


Iteration Number : 1
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz+):   3 found -   3 modified     |    TOTAL:   7
pass   2 (yz+):   0 found -   3 modified     |    TOTAL:   7
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  10
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  12
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  12
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  14
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  14
Iteration Number : 1
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 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   3 found -   3 modified     |    TOTAL:   4
pass   2 (--):   0 found -   3 modified     |    TOTAL:   4
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   6
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   6
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-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
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 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 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

Total Number of Modified Voxels = 26 (out of 253765: 0.010246)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 40: 331 vertices, 371 faces
slice 50: 5078 vertices, 5341 faces
slice 60: 14015 vertices, 14396 faces
slice 70: 25467 vertices, 25875 faces
slice 80: 36908 vertices, 37355 faces
slice 90: 48626 vertices, 49004 faces
slice 100: 60756 vertices, 61146 faces
slice 110: 72130 vertices, 72516 faces
slice 120: 83319 vertices, 83720 faces
slice 130: 94132 vertices, 94519 faces
slice 140: 104736 vertices, 105132 faces
slice 150: 114706 vertices, 115067 faces
slice 160: 123354 vertices, 123680 faces
slice 170: 130307 vertices, 130553 faces
slice 180: 135997 vertices, 136219 faces
slice 190: 140127 vertices, 140268 faces
slice 200: 141786 vertices, 141818 faces
slice 210: 141786 vertices, 141818 faces
slice 220: 141786 vertices, 141818 faces
slice 230: 141786 vertices, 141818 faces
slice 240: 141786 vertices, 141818 faces
slice 250: 141786 vertices, 141818 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...
   141786 voxel in cpt #1: X=-32 [v=141786,e=425454,f=283636] located at (28.757198, -17.942865, 38.571156)
For the whole surface: X=-32 [v=141786,e=425454,f=283636]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 rh Thu Aug  8 21:00:33 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 21:00:38 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
avg radius = 46.8 mm, total surface area = 73891 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.6 minutes
Not saving sulc

step 000: RMS=0.103 (target=0.015)   
step 005: RMS=0.075 (target=0.015)   
step 010: RMS=0.054 (target=0.015)   
step 015: RMS=0.045 (target=0.015)   
step 020: RMS=0.040 (target=0.015)   
step 025: RMS=0.034 (target=0.015)   
step 030: RMS=0.030 (target=0.015)   
step 035: RMS=0.028 (target=0.015)   
step 040: RMS=0.026 (target=0.015)   
step 045: RMS=0.025 (target=0.015)   
step 050: RMS=0.023 (target=0.015)   
step 055: RMS=0.024 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Thu Aug  8 21:01:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.97 +- 0.56 (0.00-->6.33) (max @ vno 107641 --> 108659)
face area 0.03 +- 0.03 (-0.07-->0.62)
scaling brain by 0.315...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.101, avgs=0
005/300: dt: 0.9000, rms radial error=175.844, avgs=0
010/300: dt: 0.9000, rms radial error=175.293, avgs=0
015/300: dt: 0.9000, rms radial error=174.567, avgs=0
020/300: dt: 0.9000, rms radial error=173.741, avgs=0
025/300: dt: 0.9000, rms radial error=172.857, avgs=0
030/300: dt: 0.9000, rms radial error=171.941, avgs=0
035/300: dt: 0.9000, rms radial error=171.008, avgs=0
040/300: dt: 0.9000, rms radial error=170.068, avgs=0
045/300: dt: 0.9000, rms radial error=169.126, avgs=0
050/300: dt: 0.9000, rms radial error=168.185, avgs=0
055/300: dt: 0.9000, rms radial error=167.246, avgs=0
060/300: dt: 0.9000, rms radial error=166.311, avgs=0
065/300: dt: 0.9000, rms radial error=165.381, avgs=0
070/300: dt: 0.9000, rms radial error=164.455, avgs=0
075/300: dt: 0.9000, rms radial error=163.533, avgs=0
080/300: dt: 0.9000, rms radial error=162.617, avgs=0
085/300: dt: 0.9000, rms radial error=161.705, avgs=0
090/300: dt: 0.9000, rms radial error=160.799, avgs=0
095/300: dt: 0.9000, rms radial error=159.898, avgs=0
100/300: dt: 0.9000, rms radial error=159.001, avgs=0
105/300: dt: 0.9000, rms radial error=158.109, avgs=0
110/300: dt: 0.9000, rms radial error=157.222, avgs=0
115/300: dt: 0.9000, rms radial error=156.340, avgs=0
120/300: dt: 0.9000, rms radial error=155.463, avgs=0
125/300: dt: 0.9000, rms radial error=154.590, avgs=0
130/300: dt: 0.9000, rms radial error=153.722, avgs=0
135/300: dt: 0.9000, rms radial error=152.859, avgs=0
140/300: dt: 0.9000, rms radial error=152.001, avgs=0
145/300: dt: 0.9000, rms radial error=151.148, avgs=0
150/300: dt: 0.9000, rms radial error=150.299, avgs=0
155/300: dt: 0.9000, rms radial error=149.455, avgs=0
160/300: dt: 0.9000, rms radial error=148.615, avgs=0
165/300: dt: 0.9000, rms radial error=147.781, avgs=0
170/300: dt: 0.9000, rms radial error=146.951, avgs=0
175/300: dt: 0.9000, rms radial error=146.125, avgs=0
180/300: dt: 0.9000, rms radial error=145.304, avgs=0
185/300: dt: 0.9000, rms radial error=144.488, avgs=0
190/300: dt: 0.9000, rms radial error=143.676, avgs=0
195/300: dt: 0.9000, rms radial error=142.869, avgs=0
200/300: dt: 0.9000, rms radial error=142.066, avgs=0
205/300: dt: 0.9000, rms radial error=141.267, avgs=0
210/300: dt: 0.9000, rms radial error=140.473, avgs=0
215/300: dt: 0.9000, rms radial error=139.684, avgs=0
220/300: dt: 0.9000, rms radial error=138.898, avgs=0
225/300: dt: 0.9000, rms radial error=138.117, avgs=0
230/300: dt: 0.9000, rms radial error=137.340, avgs=0
235/300: dt: 0.9000, rms radial error=136.568, avgs=0
240/300: dt: 0.9000, rms radial error=135.799, avgs=0
245/300: dt: 0.9000, rms radial error=135.035, avgs=0
250/300: dt: 0.9000, rms radial error=134.276, avgs=0
255/300: dt: 0.9000, rms radial error=133.520, avgs=0
260/300: dt: 0.9000, rms radial error=132.769, avgs=0
265/300: dt: 0.9000, rms radial error=132.022, avgs=0
270/300: dt: 0.9000, rms radial error=131.279, avgs=0
275/300: dt: 0.9000, rms radial error=130.540, avgs=0
280/300: dt: 0.9000, rms radial error=129.805, avgs=0
285/300: dt: 0.9000, rms radial error=129.074, avgs=0
290/300: dt: 0.9000, rms radial error=128.348, avgs=0
295/300: dt: 0.9000, rms radial error=127.625, avgs=0
300/300: dt: 0.9000, rms radial error=126.906, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 16544.76
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 2751.23
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
epoch 3 (K=160.0), pass 1, starting sse = 277.17
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/12 = 0.00932
epoch 4 (K=640.0), pass 1, starting sse = 14.00
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/13 = 0.00601
final writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology rh Thu Aug  8 21:06:10 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/sub018/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub018 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=-32 (nv=141786, nf=283636, ne=425454, g=17)
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 7 iterations
marking ambiguous vertices...
2360 ambiguous faces found in tessellation
segmenting defects...
29 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
29 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8497  (-4.9249)
      -vertex     loglikelihood: -6.7026  (-3.3513)
      -normal dot loglikelihood: -3.6949  (-3.6949)
      -quad curv  loglikelihood: -6.4290  (-3.2145)
      Total Loglikelihood : -26.6762

CORRECTING DEFECT 0 (vertices=46, convex hull=88)
After retessellation of defect 0, euler #=-26 (140321,420356,280009) : difference with theory (-26) = 0 

CORRECTING DEFECT 1 (vertices=44, convex hull=81)
After retessellation of defect 1, euler #=-25 (140339,420441,280077) : difference with theory (-25) = 0 

CORRECTING DEFECT 2 (vertices=18, convex hull=59)
After retessellation of defect 2, euler #=-24 (140347,420484,280113) : difference with theory (-24) = 0 

CORRECTING DEFECT 3 (vertices=58, convex hull=47)
After retessellation of defect 3, euler #=-23 (140360,420540,280157) : difference with theory (-23) = 0 

CORRECTING DEFECT 4 (vertices=39, convex hull=80)
After retessellation of defect 4, euler #=-22 (140385,420648,280241) : difference with theory (-22) = 0 

CORRECTING DEFECT 5 (vertices=35, convex hull=66)
After retessellation of defect 5, euler #=-21 (140407,420739,280311) : difference with theory (-21) = 0 

CORRECTING DEFECT 6 (vertices=37, convex hull=52)
After retessellation of defect 6, euler #=-20 (140425,420813,280368) : difference with theory (-20) = 0 

CORRECTING DEFECT 7 (vertices=24, convex hull=56)
After retessellation of defect 7, euler #=-19 (140437,420870,280414) : difference with theory (-19) = 0 

CORRECTING DEFECT 8 (vertices=29, convex hull=29)
After retessellation of defect 8, euler #=-18 (140442,420898,280438) : difference with theory (-18) = 0 

CORRECTING DEFECT 9 (vertices=30, convex hull=24)
After retessellation of defect 9, euler #=-17 (140447,420921,280457) : difference with theory (-17) = 0 

CORRECTING DEFECT 10 (vertices=7, convex hull=18)
After retessellation of defect 10, euler #=-16 (140449,420933,280468) : difference with theory (-16) = 0 

CORRECTING DEFECT 11 (vertices=13, convex hull=27)
After retessellation of defect 11, euler #=-15 (140450,420946,280481) : difference with theory (-15) = 0 

CORRECTING DEFECT 12 (vertices=17, convex hull=18)
After retessellation of defect 12, euler #=-14 (140451,420957,280492) : difference with theory (-14) = 0 

CORRECTING DEFECT 13 (vertices=45, convex hull=81)
After retessellation of defect 13, euler #=-13 (140471,421051,280567) : difference with theory (-13) = 0 

CORRECTING DEFECT 14 (vertices=98, convex hull=57)
After retessellation of defect 14, euler #=-12 (140486,421117,280619) : difference with theory (-12) = 0 

CORRECTING DEFECT 15 (vertices=41, convex hull=25)
After retessellation of defect 15, euler #=-11 (140492,421141,280638) : difference with theory (-11) = 0 

CORRECTING DEFECT 16 (vertices=64, convex hull=94)
After retessellation of defect 16, euler #=-10 (140505,421217,280702) : difference with theory (-10) = 0 

CORRECTING DEFECT 17 (vertices=357, convex hull=73)
After retessellation of defect 17, euler #=-9 (140519,421291,280763) : difference with theory (-9) = 0 

CORRECTING DEFECT 18 (vertices=6, convex hull=26)
After retessellation of defect 18, euler #=-8 (140522,421307,280777) : difference with theory (-8) = 0 

CORRECTING DEFECT 19 (vertices=20, convex hull=49)
After retessellation of defect 19, euler #=-7 (140532,421356,280817) : difference with theory (-7) = 0 

CORRECTING DEFECT 20 (vertices=103, convex hull=89)
After retessellation of defect 20, euler #=-6 (140549,421453,280898) : difference with theory (-6) = 0 

CORRECTING DEFECT 21 (vertices=93, convex hull=51)
After retessellation of defect 21, euler #=-5 (140566,421523,280952) : difference with theory (-5) = 0 

CORRECTING DEFECT 22 (vertices=25, convex hull=65)
After retessellation of defect 22, euler #=-4 (140578,421581,280999) : difference with theory (-4) = 0 

CORRECTING DEFECT 23 (vertices=54, convex hull=61)
After retessellation of defect 23, euler #=-3 (140605,421686,281078) : difference with theory (-3) = 0 

CORRECTING DEFECT 24 (vertices=42, convex hull=85)
After retessellation of defect 24, euler #=-2 (140630,421799,281167) : difference with theory (-2) = 0 

CORRECTING DEFECT 25 (vertices=11, convex hull=25)
After retessellation of defect 25, euler #=-1 (140634,421818,281183) : difference with theory (-1) = 0 

CORRECTING DEFECT 26 (vertices=56, convex hull=82)
After retessellation of defect 26, euler #=0 (140655,421917,281262) : difference with theory (0) = 0 

CORRECTING DEFECT 27 (vertices=5, convex hull=16)
After retessellation of defect 27, euler #=1 (140655,421923,281269) : difference with theory (1) = 0 

CORRECTING DEFECT 28 (vertices=58, convex hull=95)
After retessellation of defect 28, euler #=2 (140674,422016,281344) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.04-->8.60) (max @ vno 104127 --> 112533)
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 (0.04-->8.60) (max @ vno 104127 --> 112533)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
91 mutations (32.5%), 189 crossovers (67.5%), 81 vertices were eliminated
building final representation...
1112 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=140674, nf=281344, ne=422016, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 16.9 minutes
0 defective edges
removing intersecting faces
000: 118 intersecting

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 140674 - 422016 + 281344 = 2 --> 0 holes
      F =2V-4:          281344 = 281348-4 (0)
      2E=3F:            844032 = 844032 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 4 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Thu Aug  8 21:23:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub018 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/sub018/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
18329 bright wm thresholded.
358 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.orig...
computing class statistics...
border white:    252064 voxels (1.50%)
border gray      291583 voxels (1.74%)
WM (92.0): 92.8 +- 10.3 [70.0 --> 110.0]
GM (75.0) : 73.1 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.2 (was 70)
setting MAX_BORDER_WHITE to 115.3 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.3 (was 40)
setting MAX_GRAY to 94.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.5 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.03-->3.39) (max @ vno 112533 --> 112541)
face area 0.28 +- 0.12 (0.00-->1.58)
mean absolute distance = 0.67 +- 0.80
3416 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 = 92.3, mean outside = 68.0
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
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=72.1, 17 (17) missing vertices, mean dist 0.4 [0.5 (%31.1)->0.8 (%68.9))]
%69 local maxima, %26 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 (0.06-->3.76) (max @ vno 112533 --> 112541)
face area 0.28 +- 0.13 (0.00-->2.08)
mean absolute distance = 0.30 +- 0.45
2693 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7638578.5, rms=13.66
001: dt: 0.5000, sse=7735224.0, rms=9.914 (0.000%)
002: dt: 0.5000, sse=7946793.0, rms=7.765 (0.000%)
003: dt: 0.5000, sse=8078725.0, rms=6.376 (0.000%)
004: dt: 0.5000, sse=8303485.0, rms=5.534 (0.000%)
005: dt: 0.5000, sse=8364559.5, rms=5.026 (0.000%)
006: dt: 0.5000, sse=8479828.0, rms=4.769 (0.000%)
007: dt: 0.5000, sse=8483572.0, rms=4.601 (0.000%)
008: dt: 0.5000, sse=8509081.0, rms=4.524 (0.000%)
009: dt: 0.5000, sse=8453526.0, rms=4.444 (0.000%)
rms = 4.41, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=8477690.0, rms=4.412 (0.000%)
011: dt: 0.2500, sse=5390386.5, rms=3.088 (0.000%)
012: dt: 0.2500, sse=4957025.5, rms=2.644 (0.000%)
013: dt: 0.2500, sse=4668622.5, rms=2.543 (0.000%)
014: dt: 0.2500, sse=4598623.5, rms=2.448 (0.000%)
rms = 2.42, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4492008.5, rms=2.416 (0.000%)
016: dt: 0.1250, sse=4263743.5, rms=2.179 (0.000%)
rms = 2.15, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4217011.5, rms=2.147 (0.000%)
positioning took 2.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=76.7, 42 (0) missing vertices, mean dist -0.2 [0.3 (%78.9)->0.2 (%21.1))]
%83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.09-->3.79) (max @ vno 109649 --> 108789)
face area 0.35 +- 0.17 (0.00-->2.94)
mean absolute distance = 0.21 +- 0.28
2483 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5232417.5, rms=6.11
018: dt: 0.5000, sse=5443994.5, rms=4.119 (0.000%)
rms = 4.51, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=4946836.5, rms=2.960 (0.000%)
020: dt: 0.2500, sse=4758923.0, rms=2.385 (0.000%)
021: dt: 0.2500, sse=4709420.0, rms=2.017 (0.000%)
rms = 1.98, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=4680545.0, rms=1.983 (0.000%)
023: dt: 0.1250, sse=4513012.0, rms=1.752 (0.000%)
rms = 1.72, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=4461856.0, rms=1.718 (0.000%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=80.1, 38 (0) missing vertices, mean dist -0.1 [0.2 (%76.5)->0.2 (%23.5))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.11-->3.97) (max @ vno 105781 --> 105775)
face area 0.34 +- 0.16 (0.00-->2.97)
mean absolute distance = 0.16 +- 0.23
2695 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4872873.5, rms=4.37
025: dt: 0.5000, sse=5245514.0, rms=4.128 (0.000%)
rms = 4.38, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=4759571.5, rms=2.605 (0.000%)
027: dt: 0.2500, sse=4629446.5, rms=2.143 (0.000%)
028: dt: 0.2500, sse=4698822.5, rms=1.812 (0.000%)
rms = 1.87, time step reduction 2 of 3 to 0.125...
029: dt: 0.1250, sse=4629751.5, rms=1.678 (0.000%)
030: dt: 0.1250, sse=4536684.0, rms=1.494 (0.000%)
rms = 1.48, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=4498084.5, rms=1.477 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=81.1, 43 (0) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
%92 local maxima, % 3 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/sub018/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=4525111.0, rms=1.87
rms = 2.83, time step reduction 1 of 3 to 0.250...
032: dt: 0.2500, sse=4622103.5, rms=1.231 (0.000%)
033: dt: 0.2500, sse=4792168.0, rms=1.095 (0.000%)
rms = 1.10, time step reduction 2 of 3 to 0.125...
rms = 1.08, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=4794696.5, rms=1.083 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
generating cortex label...
21 non-cortical segments detected
only using segment with 1862 vertices
erasing segment 1 (vno[0] = 85895)
erasing segment 2 (vno[0] = 90215)
erasing segment 3 (vno[0] = 91287)
erasing segment 4 (vno[0] = 92317)
erasing segment 5 (vno[0] = 93344)
erasing segment 6 (vno[0] = 98491)
erasing segment 7 (vno[0] = 101512)
erasing segment 8 (vno[0] = 102484)
erasing segment 9 (vno[0] = 103653)
erasing segment 10 (vno[0] = 103691)
erasing segment 11 (vno[0] = 103760)
erasing segment 12 (vno[0] = 104760)
erasing segment 13 (vno[0] = 104772)
erasing segment 14 (vno[0] = 104776)
erasing segment 15 (vno[0] = 108752)
erasing segment 16 (vno[0] = 110467)
erasing segment 17 (vno[0] = 113223)
erasing segment 18 (vno[0] = 114132)
erasing segment 19 (vno[0] = 114135)
erasing segment 20 (vno[0] = 114967)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.area
vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 105775 --> 105781)
face area 0.34 +- 0.16 (0.00-->2.90)
refinement took 7.2 minutes
#--------------------------------------------
#@# Smooth2 rh Thu Aug  8 21:30:26 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 21:30:31 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

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

avg radius = 47.0 mm, total surface area = 86269 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.119 (target=0.015)   
step 005: RMS=0.082 (target=0.015)   
step 010: RMS=0.058 (target=0.015)   
step 015: RMS=0.048 (target=0.015)   
step 020: RMS=0.040 (target=0.015)   
step 025: RMS=0.033 (target=0.015)   
step 030: RMS=0.027 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.017 (target=0.015)   
step 050: RMS=0.015 (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
194 vertices thresholded to be in k1 ~ [-0.45 0.28], k2 ~ [-0.13 0.09]
total integrated curvature = 0.497*4pi (6.245) --> 1 handles
ICI = 1.6, FI = 12.1, variation=197.838
124 vertices thresholded to be in [-0.01 0.03]
writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
148 vertices thresholded to be in [-0.20 0.15]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025
done.

#-----------------------------------------
#@# Curvature Stats rh Thu Aug  8 21:32:56 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub018 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       [ sub018/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                      [ 290 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.858727
WARN:    S explicit min:                          0.000000	vertex = 57
#--------------------------------------------
#@# Sphere rh Thu Aug  8 21:33:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 0.291...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %19.39
pass 1: epoch 2 of 3 starting distance error %19.36
unfolding complete - removing small folds...
starting distance error %19.25
removing remaining folds...
final distance error %19.28
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.92 hours
#--------------------------------------------
#@# Surf Reg rh Thu Aug  8 22:28:10 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 0.571
curvature mean = 0.025, std = 0.941
curvature mean = 0.024, std = 0.846
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (8.00, 0.00, 0.00) sse = 330420.8, tmin=2.3634
  d=16.00 min @ (-4.00, -4.00, -4.00) sse = 290384.7, tmin=3.5345
  d=8.00 min @ (2.00, 0.00, 2.00) sse = 283195.0, tmin=4.8137
  d=4.00 min @ (0.00, -1.00, 0.00) sse = 281545.2, tmin=6.1740
  d=1.00 min @ (0.00, 0.25, -0.25) sse = 281422.7, tmin=8.8672
  d=0.50 min @ (-0.12, -0.12, 0.00) sse = 281390.3, tmin=10.1250
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  10.13 min
curvature mean = 0.009, std = 0.945
curvature mean = 0.012, std = 0.933
curvature mean = 0.005, std = 0.953
curvature mean = 0.006, std = 0.969
curvature mean = 0.004, std = 0.952
curvature mean = 0.002, std = 0.987
2 Reading smoothwm
curvature mean = -0.026, std = 0.309
curvature mean = 0.005, std = 0.070
curvature mean = 0.074, std = 0.321
curvature mean = 0.006, std = 0.083
curvature mean = 0.037, std = 0.512
curvature mean = 0.006, std = 0.089
curvature mean = 0.020, std = 0.655
curvature mean = 0.006, std = 0.092
curvature mean = 0.007, std = 0.771
MRISregister() return, current seed 0
writing registered surface to ../surf/rh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white rh Thu Aug  8 22:58:53 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 22:58:56 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 22:58:58 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
1248 labels changed using aseg
relabeling using gibbs priors...
000:   3001 changed, 140674 examined...
001:    700 changed, 12875 examined...
002:    154 changed, 3895 examined...
003:     54 changed, 949 examined...
004:     22 changed, 332 examined...
005:     11 changed, 142 examined...
006:     11 changed, 63 examined...
007:      4 changed, 52 examined...
008:      1 changed, 22 examined...
009:      0 changed, 7 examined...
204 labels changed using aseg
000: 115 total segments, 78 labels (379 vertices) changed
001: 42 total segments, 5 labels (21 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 56 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1633 vertices marked for relabeling...
1633 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 1 minutes and 6 seconds.
#--------------------------------------------
#@# Make Pial Surf rh Thu Aug  8 23:00:04 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub018 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/sub018/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
18329 bright wm thresholded.
358 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.orig...
computing class statistics...
border white:    252064 voxels (1.50%)
border gray      291583 voxels (1.74%)
WM (92.0): 92.8 +- 10.3 [70.0 --> 110.0]
GM (75.0) : 73.1 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.2 (was 70)
setting MAX_BORDER_WHITE to 115.3 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.3 (was 40)
setting MAX_GRAY to 94.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.5 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 92.3, mean outside = 68.0
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/sub018/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.03-->3.39) (max @ vno 112533 --> 112541)
face area 0.28 +- 0.12 (0.00-->1.58)
mean absolute distance = 0.68 +- 0.81
3552 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 554 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
deleting segment 10 with 11 points - only 0.00% unknown
mean border=72.1, 27 (27) missing vertices, mean dist 0.4 [0.5 (%31.1)->0.8 (%68.9))]
%70 local maxima, %26 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 (0.06-->3.76) (max @ vno 112533 --> 112541)
face area 0.28 +- 0.13 (0.00-->1.65)
mean absolute distance = 0.31 +- 0.46
2809 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7659028.0, rms=13.64
001: dt: 0.5000, sse=7760990.0, rms=9.904 (0.000%)
002: dt: 0.5000, sse=7975447.5, rms=7.757 (0.000%)
003: dt: 0.5000, sse=8111912.0, rms=6.371 (0.000%)
004: dt: 0.5000, sse=8339576.0, rms=5.532 (0.000%)
005: dt: 0.5000, sse=8403690.0, rms=5.024 (0.000%)
006: dt: 0.5000, sse=8516842.0, rms=4.767 (0.000%)
007: dt: 0.5000, sse=8522448.0, rms=4.599 (0.000%)
008: dt: 0.5000, sse=8553356.0, rms=4.523 (0.000%)
009: dt: 0.5000, sse=8496498.0, rms=4.443 (0.000%)
rms = 4.41, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=8521070.0, rms=4.411 (0.000%)
011: dt: 0.2500, sse=5420795.0, rms=3.090 (0.000%)
012: dt: 0.2500, sse=4984787.5, rms=2.647 (0.000%)
013: dt: 0.2500, sse=4696399.0, rms=2.547 (0.000%)
014: dt: 0.2500, sse=4625884.0, rms=2.452 (0.000%)
rms = 2.42, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4521661.0, rms=2.420 (0.000%)
016: dt: 0.1250, sse=4292207.0, rms=2.185 (0.000%)
rms = 2.15, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4244613.5, rms=2.153 (0.000%)
positioning took 2.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 19 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 380 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
deleting segment 13 with 13 points - only 0.00% unknown
mean border=76.7, 47 (0) missing vertices, mean dist -0.2 [0.3 (%78.8)->0.2 (%21.2))]
%83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.09-->3.79) (max @ vno 109649 --> 108789)
face area 0.35 +- 0.16 (0.00-->2.26)
mean absolute distance = 0.21 +- 0.29
2620 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5262403.0, rms=6.11
018: dt: 0.5000, sse=5477437.5, rms=4.119 (0.000%)
rms = 4.51, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=4979068.5, rms=2.963 (0.000%)
020: dt: 0.2500, sse=4792263.5, rms=2.392 (0.000%)
021: dt: 0.2500, sse=4739906.5, rms=2.026 (0.000%)
rms = 1.99, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=4714875.0, rms=1.991 (0.000%)
023: dt: 0.1250, sse=4547834.5, rms=1.762 (0.000%)
rms = 1.73, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=4497464.5, rms=1.728 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 406 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 14 points - only 0.00% unknown
mean border=80.1, 50 (0) missing vertices, mean dist -0.1 [0.2 (%76.3)->0.2 (%23.7))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.11-->3.90) (max @ vno 109649 --> 108789)
face area 0.34 +- 0.16 (0.00-->2.21)
mean absolute distance = 0.16 +- 0.24
2854 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4909105.0, rms=4.37
025: dt: 0.5000, sse=5282792.5, rms=4.123 (0.000%)
rms = 4.38, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=4797796.0, rms=2.606 (0.000%)
027: dt: 0.2500, sse=4671445.5, rms=2.146 (0.000%)
028: dt: 0.2500, sse=4740144.0, rms=1.818 (0.000%)
rms = 1.87, time step reduction 2 of 3 to 0.125...
029: dt: 0.1250, sse=4671353.0, rms=1.685 (0.000%)
030: dt: 0.1250, sse=4579445.0, rms=1.503 (0.000%)
rms = 1.49, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=4541135.5, rms=1.486 (0.000%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 23 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 404 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
deleting segment 9 with 18 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 15 points - only 0.00% unknown
mean border=81.1, 62 (0) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
%92 local maxima, % 3 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=4569562.0, rms=1.88
rms = 2.83, time step reduction 1 of 3 to 0.250...
032: dt: 0.2500, sse=4669610.5, rms=1.244 (0.000%)
033: dt: 0.2500, sse=4848851.5, rms=1.105 (0.000%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
rms = 1.09, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=4850852.5, rms=1.093 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
smoothing surface for 5 iterations...
mean border=48.7, 46 (46) missing vertices, mean dist 1.7 [1.8 (%0.0)->2.3 (%100.0))]
%15 local maxima, %55 large gradients and %25 min vals, 1642 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=30324244.0, rms=31.89
001: dt: 0.5000, sse=21799216.0, rms=26.441 (0.000%)
002: dt: 0.5000, sse=15906418.0, rms=21.922 (0.000%)
003: dt: 0.5000, sse=11987753.0, rms=18.262 (0.000%)
004: dt: 0.5000, sse=9634395.0, rms=15.373 (0.000%)
005: dt: 0.5000, sse=8367373.0, rms=13.175 (0.000%)
006: dt: 0.5000, sse=7643142.5, rms=11.511 (0.000%)
007: dt: 0.5000, sse=7218855.0, rms=10.131 (0.000%)
008: dt: 0.5000, sse=6936126.5, rms=8.862 (0.000%)
009: dt: 0.5000, sse=6762184.0, rms=7.687 (0.000%)
010: dt: 0.5000, sse=6701401.0, rms=6.633 (0.000%)
011: dt: 0.5000, sse=6778396.5, rms=5.817 (0.000%)
012: dt: 0.5000, sse=6853216.0, rms=5.210 (0.000%)
013: dt: 0.5000, sse=7049942.0, rms=4.811 (0.000%)
014: dt: 0.5000, sse=7157293.0, rms=4.558 (0.000%)
015: dt: 0.5000, sse=7281402.0, rms=4.409 (0.000%)
016: dt: 0.5000, sse=7318152.5, rms=4.275 (0.000%)
017: dt: 0.5000, sse=7368391.0, rms=4.210 (0.000%)
018: dt: 0.5000, sse=7383507.0, rms=4.136 (0.000%)
rms = 4.12, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=7414520.5, rms=4.120 (0.000%)
020: dt: 0.2500, sse=5230792.5, rms=3.345 (0.000%)
021: dt: 0.2500, sse=5021916.5, rms=3.133 (0.000%)
rms = 3.11, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=4890396.0, rms=3.109 (0.000%)
023: dt: 0.1250, sse=4647630.0, rms=2.942 (0.000%)
rms = 2.92, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=4612350.0, rms=2.923 (0.000%)
positioning took 3.0 minutes
mean border=46.3, 908 (3) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.5 (%52.2))]
%33 local maxima, %42 large gradients and %21 min vals, 536 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=5263673.0, rms=4.84
025: dt: 0.5000, sse=5619839.5, rms=4.202 (0.000%)
rms = 4.20, time step reduction 1 of 3 to 0.250...
026: dt: 0.5000, sse=7308819.5, rms=4.198 (0.000%)
027: dt: 0.2500, sse=5476913.5, rms=3.310 (0.000%)
028: dt: 0.2500, sse=5516556.5, rms=3.060 (0.000%)
rms = 3.05, time step reduction 2 of 3 to 0.125...
029: dt: 0.2500, sse=5368743.0, rms=3.050 (0.000%)
030: dt: 0.1250, sse=5169254.5, rms=2.832 (0.000%)
rms = 2.80, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=5149804.0, rms=2.799 (0.000%)
positioning took 0.9 minutes
mean border=43.9, 1070 (2) missing vertices, mean dist 0.1 [0.2 (%37.8)->0.4 (%62.2))]
%52 local maxima, %23 large gradients and %21 min vals, 668 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=5445441.0, rms=4.23
rms = 4.24, time step reduction 1 of 3 to 0.250...
032: dt: 0.2500, sse=5194419.5, rms=3.559 (0.000%)
033: dt: 0.2500, sse=5128623.0, rms=3.096 (0.000%)
034: dt: 0.2500, sse=5406338.0, rms=2.976 (0.000%)
rms = 2.96, time step reduction 2 of 3 to 0.125...
035: dt: 0.2500, sse=5458813.0, rms=2.963 (0.000%)
036: dt: 0.1250, sse=5262790.0, rms=2.783 (0.000%)
rms = 2.75, time step reduction 3 of 3 to 0.062...
037: dt: 0.1250, sse=5265726.0, rms=2.750 (0.000%)
positioning took 0.8 minutes
mean border=42.8, 2160 (1) missing vertices, mean dist 0.0 [0.2 (%46.2)->0.3 (%53.8))]
%54 local maxima, %19 large gradients and %21 min vals, 522 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/sub018/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=5320184.0, rms=3.11
rms = 3.95, time step reduction 1 of 3 to 0.250...
038: dt: 0.2500, sse=5198895.0, rms=2.829 (0.000%)
039: dt: 0.2500, sse=5420553.5, rms=2.766 (0.000%)
rms = 2.76, time step reduction 2 of 3 to 0.125...
040: dt: 0.2500, sse=5492392.5, rms=2.756 (0.000%)
041: dt: 0.1250, sse=5391824.0, rms=2.619 (0.000%)
rms = 2.60, time step reduction 3 of 3 to 0.062...
042: dt: 0.1250, sse=5402777.0, rms=2.598 (0.000%)
positioning took 0.7 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.area.pial
vertex spacing 1.02 +- 0.43 (0.07-->7.56) (max @ vno 95616 --> 94572)
face area 0.41 +- 0.30 (0.00-->4.80)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 140674 vertices processed
25000 of 140674 vertices processed
50000 of 140674 vertices processed
75000 of 140674 vertices processed
100000 of 140674 vertices processed
125000 of 140674 vertices processed
0 of 140674 vertices processed
25000 of 140674 vertices processed
50000 of 140674 vertices processed
75000 of 140674 vertices processed
100000 of 140674 vertices processed
125000 of 140674 vertices processed
thickness calculation complete, 430:749 truncations.
30437 vertices at 0 distance
92836 vertices at 1 distance
92683 vertices at 2 distance
38465 vertices at 3 distance
10644 vertices at 4 distance
2743 vertices at 5 distance
834 vertices at 6 distance
292 vertices at 7 distance
129 vertices at 8 distance
71 vertices at 9 distance
37 vertices at 10 distance
30 vertices at 11 distance
27 vertices at 12 distance
30 vertices at 13 distance
19 vertices at 14 distance
16 vertices at 15 distance
18 vertices at 16 distance
21 vertices at 17 distance
15 vertices at 18 distance
9 vertices at 19 distance
10 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.thickness
positioning took 14.4 minutes
#--------------------------------------------
#@# Surf Volume rh Thu Aug  8 23:14:27 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 23:14:33 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 pctsurfcon --s sub018 --rh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts/pctsurfcon.log
Thu Aug  8 23:14:35 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake5 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/sub018/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.wm.mgh --regheader sub018 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 109099
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.wm.mgh
Dim: 140674 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.gm.mgh --projfrac 0.3 --regheader sub018 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 125400
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.gm.mgh
Dim: 140674 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/tmp.pctsurfcon.17811/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.w-g.pct.mgh --annot sub018 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.w-g.pct.mgh --annot sub018 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname snake5
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/sub018/surf/rh.w-g.pct.mgh
Vertex Area is 0.671661 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   2000                            unknown       0       0.000
  1   2001                           bankssts    1434    1010.913
  2   2002            caudalanteriorcingulate    1126     779.239
  3   2003                caudalmiddlefrontal    2468    1663.740
  4   2004                     corpuscallosum       0       0.000
  5   2005                             cuneus    2184    1480.223
  6   2006                         entorhinal     543     417.656
  7   2007                           fusiform    5301    3632.559
  8   2008                   inferiorparietal    8787    5906.465
  9   2009                   inferiortemporal    5251    3472.157
 10   2010                   isthmuscingulate    1300     849.411
 11   2011                   lateraloccipital    6951    4616.411
 12   2012               lateralorbitofrontal    4082    2812.683
 13   2013                            lingual    3755    2601.209
 14   2014                medialorbitofrontal    2900    1936.270
 15   2015                     middletemporal    5356    3735.882
 16   2016                    parahippocampal    1018     700.393
 17   2017                        paracentral    2628    1761.580
 18   2018                    parsopercularis    1907    1300.100
 19   2019                      parsorbitalis    1415     959.741
 20   2020                   parstriangularis    2410    1635.932
 21   2021                      pericalcarine    1888    1307.391
 22   2022                        postcentral    6371    4168.021
 23   2023                 posteriorcingulate    1993    1311.019
 24   2024                         precentral    7540    4920.251
 25   2025                          precuneus    5646    3797.060
 26   2026           rostralanteriorcingulate    1100     729.041
 27   2027               rostralmiddlefrontal    8852    6071.164
 28   2028                    superiorfrontal   11828    8067.851
 29   2029                   superiorparietal    8476    5627.131
 30   2030                   superiortemporal    6446    4263.047
 31   2031                      supramarginal    6581    4451.633
 32   2032                        frontalpole     499     338.852
 33   2033                       temporalpole     670     442.973
 34   2034                 transversetemporal     590     365.158
 35   2035                             insula    3241    2161.131

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats rh Thu Aug  8 23:14:54 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

 1434   1011   2845  2.668 0.433     0.129     0.034       15     2.1  bankssts
 1126    779   2237  2.516 0.836     0.158     0.044       21     2.0  caudalanteriorcingulate
 2468   1664   4367  2.449 0.398     0.125     0.036       28     3.8  caudalmiddlefrontal
 2184   1480   3241  1.953 0.389     0.178     0.077       56     6.4  cuneus
  543    418   1858  3.013 0.881     0.172     0.065       10     1.5  entorhinal
 5301   3633  11180  2.664 0.546     0.158     0.065      105    14.4  fusiform
 8787   5906  16518  2.452 0.502     0.149     0.061      186    20.5  inferiorparietal
 5251   3472   9976  2.377 0.720     0.163     0.105      175    19.8  inferiortemporal
 1300    849   2238  2.409 0.792     0.165     0.066       29     3.3  isthmuscingulate
 6951   4616  11391  2.190 0.444     0.169     0.079      165    20.4  lateraloccipital
 4082   2813   8628  2.760 0.665     0.159     0.092       94    11.0  lateralorbitofrontal
 3755   2601   6116  2.062 0.500     0.171     0.116      280    19.6  lingual
 2900   1936   5426  2.458 0.630     0.152     0.080       75     6.8  medialorbitofrontal
 5356   3736  12540  2.704 0.665     0.154     0.057      118    12.8  middletemporal
 1018    700   2257  2.903 0.797     0.155     0.070       19     2.6  parahippocampal
 2628   1762   4585  2.304 0.445     0.131     0.044       55     5.6  paracentral
 1907   1300   3925  2.646 0.450     0.143     0.054       33     3.7  parsopercularis
 1415    960   3519  2.886 0.553     0.186     0.097       45     4.8  parsorbitalis
 2410   1636   4844  2.559 0.436     0.150     0.057       45     5.4  parstriangularis
 1888   1307   2317  1.788 0.387     0.162     0.091       49     5.3  pericalcarine
 6371   4168   9711  2.044 0.543     0.126     0.038       82    10.1  postcentral
 1993   1311   3544  2.420 0.831     0.166     0.070       47     5.3  posteriorcingulate
 7540   4920  13968  2.575 0.465     0.123     0.046      133    14.8  precentral
 5646   3797   9941  2.451 0.506     0.141     0.048       92    11.0  precuneus
 1100    729   2659  3.092 0.603     0.162     0.075       25     3.3  rostralanteriorcingulate
 8852   6071  17140  2.445 0.501     0.169     0.082      237    25.0  rostralmiddlefrontal
11828   8068  23629  2.591 0.483     0.143     0.049      198    22.8  superiorfrontal
 8476   5627  13056  2.125 0.395     0.144     0.049      152    17.3  superiorparietal
 6446   4263  13607  2.763 0.568     0.139     0.051      102    12.4  superiortemporal
 6581   4452  12030  2.352 0.477     0.138     0.044       96    11.1  supramarginal
  499    339   1213  2.732 0.452     0.231     0.124       25     2.3  frontalpole
  670    443   2046  3.472 0.763     0.172     0.108       22     2.9  temporalpole
  590    365   1014  2.417 0.387     0.153     0.065       10     1.6  transversetemporal
 3241   2161   7378  3.120 0.884     0.149     0.109      112    14.2  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Thu Aug  8 23:15:17 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
13 labels changed using aseg
relabeling using gibbs priors...
000:  10136 changed, 140674 examined...
001:   2434 changed, 38479 examined...
002:    752 changed, 12552 examined...
003:    333 changed, 4263 examined...
004:    171 changed, 1808 examined...
005:     85 changed, 943 examined...
006:     52 changed, 510 examined...
007:     25 changed, 289 examined...
008:     14 changed, 147 examined...
009:      8 changed, 86 examined...
010:      6 changed, 45 examined...
011:      3 changed, 36 examined...
012:      0 changed, 10 examined...
12 labels changed using aseg
000: 307 total segments, 220 labels (2856 vertices) changed
001: 115 total segments, 29 labels (186 vertices) changed
002: 90 total segments, 4 labels (6 vertices) changed
003: 86 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 129 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1024 vertices marked for relabeling...
1024 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 1 minutes and 18 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Thu Aug  8 23:16:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

 1041    764   2222  2.506 0.573     0.206     0.092       36     3.4  G_and_S_frontomargin
 1312    897   2297  2.260 0.629     0.155     0.063       27     3.4  G_and_S_occipital_inf
 1518    968   2882  2.390 0.499     0.125     0.050       45     3.6  G_and_S_paracentral
 1262    849   2529  2.496 0.467     0.144     0.045       20     2.3  G_and_S_subcentral
 1103    741   2359  2.466 0.397     0.189     0.102       38     3.7  G_and_S_transv_frontopol
 2971   2003   6127  2.745 0.500     0.152     0.067       62     7.5  G_and_S_cingul-Ant
 1658   1132   3451  2.805 0.503     0.140     0.045       24     3.0  G_and_S_cingul-Mid-Ant
 1453   1007   2730  2.531 0.601     0.148     0.056       25     3.1  G_and_S_cingul-Mid-Post
  559    349   1396  2.999 0.623     0.210     0.109       23     2.3  G_cingul-Post-dorsal
  204    129    495  3.164 0.832     0.183     0.092        5     0.6  G_cingul-Post-ventral
 2090   1412   3116  1.924 0.405     0.186     0.091       61     7.1  G_cuneus
 1200    835   3079  2.838 0.416     0.159     0.071       28     2.8  G_front_inf-Opercular
  369    238    952  2.894 0.362     0.170     0.069        9     1.0  G_front_inf-Orbital
 1092    732   2736  2.740 0.390     0.174     0.074       30     3.2  G_front_inf-Triangul
 4265   2910   9680  2.581 0.458     0.176     0.096      146    13.8  G_front_middle
 7826   5283  17102  2.634 0.496     0.151     0.054      157    16.6  G_front_sup
  547    360   1477  3.374 0.800     0.159     0.257       58     6.6  G_Ins_lg_and_S_cent_ins
  727    480   2511  3.709 0.695     0.186     0.145       30     3.4  G_insular_short
 2896   1929   5865  2.436 0.451     0.178     0.079       85     9.0  G_occipital_middle
 1636   1074   2826  2.217 0.337     0.167     0.057       37     3.7  G_occipital_sup
 2234   1486   5268  2.805 0.491     0.182     0.083       65     7.8  G_oc-temp_lat-fusifor
 2277   1554   4210  2.189 0.493     0.199     0.159      262    16.1  G_oc-temp_med-Lingual
 1682   1167   5005  3.229 0.874     0.178     0.150       47     5.8  G_oc-temp_med-Parahip
 3212   2167   8377  2.984 0.615     0.186     0.094      104    11.4  G_orbital
 2393   1609   5839  2.770 0.512     0.180     0.087       72     7.5  G_pariet_inf-Angular
 3652   2471   7604  2.442 0.478     0.143     0.042       60     6.3  G_pariet_inf-Supramar
 2961   1953   5272  2.234 0.439     0.156     0.053       61     6.4  G_parietal_sup
 2413   1532   4290  2.172 0.457     0.139     0.045       39     4.7  G_postcentral
 2819   1815   6443  2.732 0.438     0.139     0.059       78     6.3  G_precentral
 2480   1689   5164  2.472 0.474     0.169     0.071       74     7.2  G_precuneus
  687    484   1522  2.451 0.645     0.186     0.125       28     2.3  G_rectus
  497    294    883  2.666 0.795     0.092     0.091        6     0.7  G_subcallosal
  531    312    954  2.485 0.362     0.155     0.066       11     1.4  G_temp_sup-G_T_transv
 2219   1449   5994  2.973 0.478     0.162     0.070       56     5.8  G_temp_sup-Lateral
  854    556   2152  3.202 0.792     0.138     0.064       12     2.4  G_temp_sup-Plan_polar
  897    619   1761  2.549 0.458     0.131     0.034       11     1.1  G_temp_sup-Plan_tempo
 2894   1881   6090  2.394 0.810     0.189     0.157      147    15.8  G_temporal_inf
 3138   2214   8748  2.891 0.624     0.174     0.072       93     9.5  G_temporal_middle
  411    275    583  2.378 0.383     0.100     0.026        2     0.4  Lat_Fis-ant-Horizont
  248    176    460  2.474 0.417     0.138     0.031        2     0.4  Lat_Fis-ant-Vertical
 1420    938   1956  2.278 0.438     0.120     0.044       12     2.1  Lat_Fis-post
 2963   1947   4540  2.066 0.414     0.179     0.104       83    10.6  Pole_occipital
 1816   1217   5130  3.037 0.701     0.174     0.091       56     6.7  Pole_temporal
 2135   1476   2697  1.911 0.637     0.152     0.075       47     4.9  S_calcarine
 3254   2154   3911  2.004 0.612     0.110     0.041       43     6.6  S_central
 1624   1105   2435  2.198 0.448     0.126     0.042       21     2.9  S_cingul-Marginalis
  687    471   1162  2.665 0.535     0.133     0.043        5     1.2  S_circular_insula_ant
 1251    853   2012  2.600 0.733     0.101     0.031        8     1.6  S_circular_insula_inf
 1355    922   2080  2.599 0.445     0.119     0.034        9     2.1  S_circular_insula_sup
 1220    871   2124  2.455 0.483     0.114     0.028        8     1.5  S_collat_transv_ant
  443    318    570  1.902 0.370     0.128     0.039        3     0.7  S_collat_transv_post
 2061   1376   2986  2.234 0.420     0.132     0.041       24     3.3  S_front_inf
 1949   1330   3123  2.395 0.500     0.146     0.049       27     3.7  S_front_middle
 2826   2003   4733  2.368 0.422     0.133     0.039       32     4.6  S_front_sup
  829    564   1113  2.061 0.410     0.136     0.042        9     1.4  S_interm_prim-Jensen
 3068   2059   4090  2.075 0.341     0.124     0.035       32     4.7  S_intrapariet_and_P_trans
 1192    810   1627  2.047 0.354     0.130     0.045       16     2.0  S_oc_middle_and_Lunatus
 1743   1151   2301  2.079 0.332     0.119     0.032       18     2.3  S_oc_sup_and_transversal
  825    558   1533  2.461 0.339     0.158     0.071       15     2.9  S_occipital_ant
 1279    832   1698  2.287 0.372     0.122     0.037       11     2.0  S_oc-temp_lat
 1762   1258   2795  2.349 0.474     0.130     0.038       19     2.9  S_oc-temp_med_and_Lingual
  576    405    989  2.452 0.463     0.171     0.081       13     1.7  S_orbital_lateral
  777    562   1254  2.266 0.742     0.117     0.036        7     1.2  S_orbital_med-olfact
 1372    972   2425  2.582 0.662     0.149     0.049       19     2.9  S_orbital-H_Shaped
 2211   1481   3066  2.244 0.463     0.134     0.038       25     3.5  S_parieto_occipital
 1784   1148   2017  2.027 0.877     0.143     0.039       26     2.8  S_pericallosal
 2732   1818   3332  2.003 0.385     0.115     0.038       25     4.6  S_postcentral
 1192    800   1809  2.448 0.425     0.097     0.022        6     1.1  S_precentral-inf-part
 1695   1112   2426  2.366 0.369     0.112     0.032       16     2.2  S_precentral-sup-part
  449    298    654  2.260 0.666     0.124     0.035        5     0.6  S_suborbital
  977    668   1573  2.509 0.375     0.132     0.038       10     1.5  S_subparietal
 1254    856   1558  2.143 0.571     0.128     0.033       10     1.8  S_temporal_inf
 7172   4887  12111  2.503 0.470     0.130     0.042       98    11.5  S_temporal_sup
  416    281    656  2.441 0.365     0.123     0.032        3     0.6  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Thu Aug  8 23:16:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub018 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...
1124 labels changed using aseg
relabeling using gibbs priors...
000:   2895 changed, 140674 examined...
001:    653 changed, 12295 examined...
002:    168 changed, 3484 examined...
003:     53 changed, 989 examined...
004:     21 changed, 332 examined...
005:      9 changed, 118 examined...
006:      6 changed, 57 examined...
007:      6 changed, 32 examined...
008:      6 changed, 37 examined...
009:      7 changed, 30 examined...
010:      6 changed, 35 examined...
011:      2 changed, 28 examined...
012:      1 changed, 12 examined...
013:      0 changed, 7 examined...
139 labels changed using aseg
000: 74 total segments, 41 labels (163 vertices) changed
001: 35 total segments, 2 labels (4 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 48 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
962 vertices marked for relabeling...
962 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 1 minutes and 3 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Thu Aug  8 23:18:03 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 sub018 rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

 1128    783   2268  2.540 0.832     0.159     0.045       21     2.0  caudalanteriorcingulate
 2596   1755   4571  2.455 0.402     0.126     0.036       30     4.0  caudalmiddlefrontal
 2775   1865   4100  1.974 0.394     0.173     0.070       67     7.6  cuneus
  568    447   1975  3.045 0.869     0.170     0.062       10     1.5  entorhinal
 4625   3178   9767  2.668 0.549     0.158     0.064       91    12.4  fusiform
 8162   5472  15093  2.436 0.497     0.151     0.062      174    19.4  inferiorparietal
 5883   3875  11234  2.400 0.701     0.163     0.103      190    21.8  inferiortemporal
 1374    900   2322  2.393 0.791     0.162     0.064       29     3.3  isthmuscingulate
 7341   4888  12159  2.202 0.445     0.170     0.077      174    21.3  lateraloccipital
 4438   3077   9736  2.776 0.666     0.171     0.100      123    13.3  lateralorbitofrontal
 3782   2614   6148  2.063 0.502     0.170     0.114      280    19.6  lingual
 2331   1570   4435  2.405 0.695     0.150     0.088       59     5.5  medialorbitofrontal
 6278   4394  14194  2.678 0.633     0.148     0.052      124    13.8  middletemporal
  992    681   2205  2.911 0.804     0.155     0.072       19     2.6  parahippocampal
 2745   1840   4727  2.296 0.440     0.131     0.045       58     5.8  paracentral
 1952   1328   4000  2.638 0.451     0.144     0.053       35     3.8  parsopercularis
 1394    946   3285  2.830 0.528     0.164     0.079       32     4.0  parsorbitalis
 2539   1716   4855  2.526 0.443     0.153     0.059       47     5.8  parstriangularis
 1880   1304   2319  1.785 0.384     0.163     0.096       51     5.3  pericalcarine
 7018   4599  10623  2.060 0.538     0.128     0.040       98    11.9  postcentral
 2150   1407   3902  2.457 0.806     0.165     0.068       51     5.7  posteriorcingulate
 7137   4651  13353  2.581 0.473     0.122     0.047      128    14.0  precentral
 5678   3833  10067  2.443 0.506     0.142     0.048       95    11.1  precuneus
 1087    736   2616  3.089 0.575     0.167     0.071       25     3.3  rostralanteriorcingulate
 6110   4151  12012  2.474 0.527     0.171     0.083      177    18.3  rostralmiddlefrontal
15075  10266  29872  2.567 0.472     0.148     0.055      281    31.3  superiorfrontal
 7145   4728  11129  2.136 0.395     0.140     0.047      120    14.1  superiorparietal
 8369   5556  18190  2.829 0.642     0.142     0.055      143    18.1  superiortemporal
 6348   4314  11766  2.359 0.496     0.138     0.045       93    11.0  supramarginal
  583    361   1009  2.423 0.389     0.153     0.066       10     1.6  transversetemporal
 3054   2058   7007  3.066 0.849     0.143     0.105      103    12.9  insula
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR Thu Aug  8 23:18:22 CEST 2013

 bbregister --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta --init-fsl --T2 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat.log
Thu Aug  8 23:18:22 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux snake5 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/sub018/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998519, 0.0146261, 0.052401)
j_ras = (0.020019, 0.994384, 0.103917)
k_ras = (0.0505869, -0.104812, 0.993205)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii...
fslregister --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fslregister.log

Thu Aug  8 23:18:28 CEST 2013
--s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
snake5
Linux snake5 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/sub018/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.86265e-09, 0)
j_ras = (0, 2.23517e-08, -1)
k_ras = (-9.31323e-10, 1, 7.45058e-09)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/transforms/tmp.bbregister.18743/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998519, 0.0146261, 0.052401)
j_ras = (0.020019, 0.994384, 0.103917)
k_ras = (0.0505869, -0.104812, 0.993205)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311083
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/reg0.18809.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fsl.mat0 --s sub018 --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/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/reg0.18809.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/sub018/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/sub018/mri/transforms/tmp.bbregister.18743/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.891;
 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) --------
 0.999  -0.015  -0.052   0.000;
 0.051  -0.105   0.993  -0.000;
-0.020  -0.994  -0.104  -0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999  -0.015  -0.052   0.000;
 0.051  -0.105   0.993  -0.000;
-0.020  -0.994  -0.104  -0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub018
RegMat ---------------------------
 0.999  -0.015  -0.052   0.000;
 0.051  -0.105   0.993  -0.000;
-0.020  -0.994  -0.104  -0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311083, ref det = -1
Thu Aug  8 23:18:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/transforms/tmp.bbregister.18743/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fsl.mat0
Thu Aug  8 23:23:10 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub018 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.999  -0.010  -0.036   38.367;
-0.037  -0.079  -0.996   271.929;
 0.007   0.997  -0.080   7.702;
 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/sub018/mri/transforms/tmp.bbregister.18743/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/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/sub018/mri/transforms/tmp.bbregister.18743/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.891;
 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 = -0.311083, ref det = -1
---- Input registration matrix (computed) --------
 0.999  -0.007  -0.037   0.114;
 0.036  -0.080   0.996   2.546;
-0.010  -0.997  -0.079  -2.406;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999  -0.007  -0.037   0.114;
 0.036  -0.080   0.996   2.546;
-0.010  -0.997  -0.079  -2.406;
 0.000   0.000   0.000   1.000;
Determinant 0.999999
subject = sub018
RegMat ---------------------------
 0.999  -0.007  -0.037   0.114;
 0.036  -0.080   0.996   2.546;
-0.010  -0.997  -0.079  -2.406;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 23:18:28 CEST 2013 
Ended   at Thu Aug  8 23:28:56 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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 snake5
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.init.dat
subject sub018
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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 1376242799
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.007  -0.037   0.114;
 0.036  -0.080   0.996   2.546;
-0.010  -0.997  -0.079  -2.406;
 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   1.041746
 1  -25.0 -25.0  25.0   0.984698
 2  -25.0  25.0 -25.0   1.011810
 3  -25.0  25.0  25.0   1.025865
 4   25.0 -25.0 -25.0   1.055057
 5   25.0 -25.0  25.0   1.039686
 6   25.0  25.0 -25.0   1.030573
 7   25.0  25.0  25.0   0.991700
REL:  8  0.588958    8.181136  1.022642 rel = 0.575918 
Initial costs ----------------
Number of surface hits 2640
WM  Intensity    67.8500 +/-  11.4675
Ctx Intensity    77.5842 +/-  18.1108
Pct Contrast     12.0347 +/-  24.6941
Cost   0.5890
RelCost   0.5759

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9661   0.9661  0.0
     4  -4.0000  -4.0000  -4.0000  -4.0000   0.0000   0.0000      0.9622   0.9622  0.0
     9  -4.0000  -4.0000  -4.0000   0.0000  -4.0000  -4.0000      0.9606   0.9606  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.9344   0.9344  0.0
    18  -4.0000  -4.0000  -4.0000   4.0000  -4.0000  -4.0000      0.9141   0.9141  0.0
    21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.8603   0.8603  0.0
    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.8092   0.8092  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.7879   0.7879  0.0
   265   0.0000  -4.0000  -4.0000   4.0000   0.0000   0.0000      0.7760   0.7760  0.0
   283   0.0000  -4.0000   0.0000   0.0000   0.0000   0.0000      0.6998   0.6998  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.5890   0.5890  0.0
Brute Force --------------------------
Min cost was 0.588958
Number of iterations   729
Search time 2.197000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
   6  0.382  0.000  0.000  0.000  0.000  0.000   0.5879920980
   7  0.224  0.000  0.000  0.000  0.000  0.000   0.5867100454
  10  0.247  0.000  0.000  0.000  0.000  0.000   0.5860232764
  11  0.254  0.000  0.000  0.000  0.000  0.000   0.5858303350
  12  0.266  0.000  0.000  0.000  0.000  0.000   0.5857333842
  13  0.264  0.000  0.000  0.000  0.000  0.000   0.5857094534
  14  0.262  0.000  0.000  0.000  0.000  0.000   0.5857073857
  18  0.262 -1.618  0.000  0.000  0.000  0.000   0.4161117247
  23  0.262 -1.686  0.000  0.000  0.000  0.000   0.4141458505
  26  0.262 -1.692  0.000  0.000  0.000  0.000   0.4140394165
  28  0.262 -1.702  0.000  0.000  0.000  0.000   0.4139065104
  30  0.262 -1.704  0.000  0.000  0.000  0.000   0.4138997323
  34  0.262 -1.704  1.000  0.000  0.000  0.000   0.2384291117
  37  0.262 -1.704  1.618  0.000  0.000  0.000   0.2093884544
  39  0.262 -1.704  1.669  0.000  0.000  0.000   0.2077620808
  40  0.262 -1.704  1.749  0.000  0.000  0.000   0.2068155934
  41  0.262 -1.704  1.748  0.000  0.000  0.000   0.2068002212
  43  0.262 -1.704  1.739  0.000  0.000  0.000   0.2067601614
  44  0.262 -1.704  1.741  0.000  0.000  0.000   0.2067571153
  52  0.262 -1.704  1.741 -0.209  0.000  0.000   0.2048846490
  53  0.262 -1.704  1.741 -0.144  0.000  0.000   0.2039094829
  61  0.262 -1.704  1.741 -0.144 -0.618  0.000   0.1966389266
  63  0.262 -1.704  1.741 -0.144 -0.375  0.000   0.1945087313
  64  0.262 -1.704  1.741 -0.144 -0.416  0.000   0.1942394525
  66  0.262 -1.704  1.741 -0.144 -0.406  0.000   0.1941748574
  76  0.262 -1.704  1.741 -0.144 -0.406  0.382   0.1682036035
  77  0.262 -1.704  1.741 -0.144 -0.406  0.455   0.1664617252
  79  0.262 -1.704  1.741 -0.144 -0.406  0.486   0.1663602688
  81  0.262 -1.704  1.741 -0.144 -0.406  0.499   0.1663421996
  86  0.262 -1.704  1.741 -0.144 -0.406  0.498   0.1663410348
  93  0.644 -1.704  1.741 -0.144 -0.406  0.498   0.1603594329
  94  0.551 -1.704  1.741 -0.144 -0.406  0.498   0.1591008981
  98  0.543 -1.704  1.741 -0.144 -0.406  0.498   0.1590989369
 100  0.546 -1.704  1.741 -0.144 -0.406  0.498   0.1590925179
 108  0.546 -1.322  1.741 -0.144 -0.406  0.498   0.1552985040
 109  0.546 -1.450  1.741 -0.144 -0.406  0.498   0.1523504292
 112  0.546 -1.439  1.741 -0.144 -0.406  0.498   0.1522467919
 114  0.546 -1.440  1.741 -0.144 -0.406  0.498   0.1522467704
 123  0.546 -1.440  1.754 -0.144 -0.406  0.498   0.1522174389
 124  0.546 -1.440  1.757 -0.144 -0.406  0.498   0.1522148949
 127  0.546 -1.440  1.758 -0.144 -0.406  0.498   0.1522134162
 129  0.546 -1.440  1.759 -0.144 -0.406  0.498   0.1522132120
 136  0.546 -1.440  1.759 -0.150 -0.406  0.498   0.1521746023
 139  0.546 -1.440  1.759 -0.151 -0.406  0.498   0.1521742852
 147  0.546 -1.440  1.759 -0.151 -0.382  0.498   0.1519943474
 150  0.546 -1.440  1.759 -0.151 -0.379  0.498   0.1519908503
 161  0.546 -1.440  1.759 -0.151 -0.379  0.474   0.1515666271
 163  0.546 -1.440  1.759 -0.151 -0.379  0.467   0.1515640098
 164  0.546 -1.440  1.759 -0.151 -0.379  0.470   0.1515627603
 176  0.557 -1.440  1.759 -0.151 -0.379  0.470   0.1513918774
 177  0.562 -1.440  1.759 -0.151 -0.379  0.470   0.1513736202
 188  0.562 -1.451  1.759 -0.151 -0.379  0.470   0.1513468517
 189  0.562 -1.448  1.759 -0.151 -0.379  0.470   0.1513354966
 201  0.562 -1.448  1.753 -0.151 -0.379  0.470   0.1513139863
 202  0.562 -1.448  1.754 -0.151 -0.379  0.470   0.1513122666
 210  0.562 -1.448  1.754 -0.157 -0.379  0.470   0.1512945001
 222  0.562 -1.448  1.754 -0.157 -0.382  0.470   0.1512942819
 224  0.562 -1.448  1.754 -0.157 -0.381  0.470   0.1512929437
 234  0.562 -1.448  1.754 -0.157 -0.381  0.476   0.1512685837
 248  0.561 -1.448  1.754 -0.157 -0.381  0.476   0.1512684864
 270  0.561 -1.448  1.755 -0.157 -0.381  0.476   0.1512676976
 278  0.561 -1.448  1.755 -0.158 -0.381  0.476   0.1512659353
 279  0.561 -1.448  1.755 -0.161 -0.381  0.476   0.1512644976
 285  0.561 -1.448  1.755 -0.166 -0.381  0.476   0.1512520652
 287  0.561 -1.448  1.755 -0.165 -0.381  0.476   0.1512518804
 308  0.561 -1.448  1.755 -0.165 -0.381  0.477   0.1512509105
 309  0.561 -1.448  1.755 -0.165 -0.381  0.478   0.1512503998
 311  0.561 -1.448  1.755 -0.165 -0.381  0.479   0.1512495714
 325  0.560 -1.448  1.755 -0.165 -0.381  0.479   0.1512493680
 337  0.560 -1.449  1.755 -0.165 -0.381  0.479   0.1512482459
 348  0.560 -1.449  1.754 -0.165 -0.381  0.479   0.1512479253
 358  0.560 -1.449  1.754 -0.166 -0.381  0.479   0.1512471210
Powell done niters = 4
Computing relative cost
 0  -25.0 -25.0 -25.0   1.042787
 1  -25.0 -25.0  25.0   1.011592
 2  -25.0  25.0 -25.0   0.995579
 3  -25.0  25.0  25.0   0.996637
 4   25.0 -25.0 -25.0   1.043201
 5   25.0 -25.0  25.0   1.036614
 6   25.0  25.0 -25.0   0.996732
 7   25.0  25.0  25.0   1.010675
REL:  8  0.151247    8.133818  1.016727 rel = 0.148759 
Number of iterations     4
Min cost was 0.151247
Number of FunctionCalls   382
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 1.311000 sec
Parameters at optimum (transmm)  0.55998 -1.44907  1.75383
Parameters at optimum (rotdeg) -0.16627 -0.38085  0.47888 
Final costs ----------------
Number of surface hits 2640
WM  Intensity    64.0135 +/-   8.6665
Ctx Intensity    77.1130 +/-   9.0735
Pct Contrast     18.6154 +/-  13.4914
Cost   0.1512
RelCost   0.5759
Reg at min cost was 
 0.999  -0.000  -0.045   0.669;
 0.045  -0.083   0.996   1.091;
-0.004  -0.997  -0.082  -0.659;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/bbr.pass1.dat, type = 14 
Original Reg 
 0.999  -0.007  -0.037   0.114;
 0.036  -0.080   0.996   2.546;
-0.010  -0.997  -0.079  -2.406;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000  -0.007   0.008  -0.555;
-0.008   0.003   0.001   1.455;
-0.007  -0.000   0.003  -1.747;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 2.219454
Computing change in rh position
Surface RMS Diff (mm) 2.208397 2.510514
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/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/sub018/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/tmp.bbregister.18743/bbr.pass1.dat
subject sub018
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 1376918144
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.000  -0.045   0.669;
 0.045  -0.083   0.996   1.091;
-0.004  -0.997  -0.082  -0.659;
 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   1.024493
 1  -25.0 -25.0  25.0   0.996708
 2  -25.0  25.0 -25.0   1.002013
 3  -25.0  25.0  25.0   1.014795
 4   25.0 -25.0 -25.0   1.035938
 5   25.0 -25.0  25.0   1.025038
 6   25.0  25.0 -25.0   1.014441
 7   25.0  25.0  25.0   1.030576
REL:  8  0.152406    8.144001  1.018000 rel = 0.149711 
Initial costs ----------------
Number of surface hits 264340
WM  Intensity    64.0253 +/-   8.8203
Ctx Intensity    77.0513 +/-   8.9915
Pct Contrast     18.5621 +/-  13.3074
Cost   0.1524
RelCost   0.1497

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.1700   0.1700  0.0
     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.1665   0.1665  0.0
     2  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.1000      0.1645   0.1645  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.1643   0.1643  0.0
     4  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.0000      0.1605   0.1605  0.0
     5  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.1000      0.1603   0.1603  0.0
     7  -0.1000  -0.1000  -0.1000  -0.1000   0.1000   0.0000      0.1591   0.1591  0.0
    11  -0.1000  -0.1000  -0.1000   0.0000  -0.1000   0.1000      0.1591   0.1591  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.1574   0.1574  0.0
    14  -0.1000  -0.1000  -0.1000   0.0000   0.0000   0.1000      0.1566   0.1566  0.0
    23  -0.1000  -0.1000  -0.1000   0.1000   0.0000   0.1000      0.1554   0.1554  0.0
    41  -0.1000  -0.1000   0.0000   0.0000   0.0000   0.1000      0.1545   0.1545  0.0
   115  -0.1000   0.0000   0.0000  -0.1000   0.1000   0.0000      0.1540   0.1540  0.0
   361   0.0000   0.0000   0.0000   0.0000  -0.1000   0.0000      0.1538   0.1538  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.1512   0.1512  0.0
Brute Force --------------------------
Min cost was 0.151247
Number of iterations   729
Search time 2.508000 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 -0.103  0.000  0.000  0.000  0.000  0.000   0.1514410443
   8 -0.098  0.000  0.000  0.000  0.000  0.000   0.1514376236
  10 -0.099  0.000  0.000  0.000  0.000  0.000   0.1514375714
  18 -0.099 -0.188  0.000  0.000  0.000  0.000   0.1474554874
  20 -0.099 -0.204  0.000  0.000  0.000  0.000   0.1474188042
  23 -0.099 -0.207  0.000  0.000  0.000  0.000   0.1474174539
  32 -0.099 -0.207  0.085  0.000  0.000  0.000   0.1470072030
  33 -0.099 -0.207  0.070  0.000  0.000  0.000   0.1469717651
  34 -0.099 -0.207  0.066  0.000  0.000  0.000   0.1469699249
  35 -0.099 -0.207  0.065  0.000  0.000  0.000   0.1469698799
  44 -0.099 -0.207  0.065  0.004  0.000  0.000   0.1469677710
  45 -0.099 -0.207  0.065  0.003  0.000  0.000   0.1469674959
  53 -0.099 -0.207  0.065  0.003 -0.045  0.000   0.1466450423
  55 -0.099 -0.207  0.065  0.003 -0.049  0.000   0.1466425446
  64 -0.099 -0.207  0.065  0.003 -0.049  0.078   0.1464056346
  65 -0.099 -0.207  0.065  0.003 -0.049  0.053   0.1463072446
  76 -0.026 -0.207  0.065  0.003 -0.049  0.053   0.1457893481
  77 -0.025 -0.207  0.065  0.003 -0.049  0.053   0.1457890903
  87 -0.025 -0.211  0.065  0.003 -0.049  0.053   0.1457842654
  88 -0.025 -0.212  0.065  0.003 -0.049  0.053   0.1457838702
  97 -0.025 -0.212  0.067  0.003 -0.049  0.053   0.1457826645
  98 -0.025 -0.212  0.069  0.003 -0.049  0.053   0.1457823566
 107 -0.025 -0.212  0.069  0.001 -0.049  0.053   0.1457796311
 108 -0.025 -0.212  0.069 -0.000 -0.049  0.053   0.1457794023
 116 -0.025 -0.212  0.069 -0.000 -0.058  0.053   0.1457480750
 117 -0.025 -0.212  0.069 -0.000 -0.069  0.053   0.1457342743
 126 -0.025 -0.212  0.069 -0.000 -0.069  0.122   0.1456523038
 127 -0.025 -0.212  0.069 -0.000 -0.069  0.093   0.1455206534
 128 -0.025 -0.212  0.069 -0.000 -0.069  0.091   0.1455204359
 130  0.048 -0.217  0.073 -0.003 -0.090  0.130   0.1452989735
 137  0.043 -0.217  0.072 -0.003 -0.088  0.127   0.1452987752
 138  0.045 -0.217  0.073 -0.003 -0.089  0.128   0.1452984860
 140  0.045 -0.217  0.072 -0.003 -0.089  0.128   0.1452984346
 154  0.045 -0.217  0.073 -0.003 -0.089  0.125   0.1452969859
 155  0.045 -0.217  0.073 -0.003 -0.089  0.124   0.1452969832
 165  0.045 -0.218  0.073 -0.003 -0.089  0.124   0.1452965334
 166  0.045 -0.219  0.073 -0.003 -0.089  0.124   0.1452964729
 175  0.045 -0.219  0.077 -0.003 -0.089  0.124   0.1452953222
 185  0.045 -0.219  0.076 -0.005 -0.089  0.124   0.1452950500
 187  0.045 -0.219  0.076 -0.004 -0.089  0.124   0.1452948291
 195  0.045 -0.219  0.076 -0.004 -0.080  0.124   0.1452900846
 197  0.045 -0.219  0.076 -0.004 -0.079  0.124   0.1452900215
 210  0.046 -0.219  0.076 -0.004 -0.080  0.125   0.1452899887
 211  0.046 -0.219  0.076 -0.004 -0.079  0.124   0.1452899581
 213  0.045 -0.219  0.076 -0.004 -0.079  0.124   0.1452899287
 216  0.045 -0.219  0.076 -0.004 -0.079  0.124   0.1452899224
 226  0.045 -0.219  0.076 -0.004 -0.079  0.127   0.1452891807
 246  0.045 -0.219  0.078 -0.004 -0.079  0.127   0.1452887423
 255  0.045 -0.219  0.078 -0.007 -0.079  0.127   0.1452878948
 257  0.045 -0.219  0.078 -0.008 -0.079  0.127   0.1452878558
 266  0.045 -0.219  0.078 -0.008 -0.078  0.127   0.1452875652
 274  0.043 -0.219  0.077 -0.008 -0.077  0.126   0.1452872541
 308  0.043 -0.219  0.080 -0.008 -0.077  0.126   0.1452869217
 318  0.043 -0.219  0.080 -0.009 -0.077  0.126   0.1452868518
 327  0.043 -0.219  0.080 -0.009 -0.076  0.126   0.1452868253
 338  0.043 -0.219  0.080 -0.009 -0.076  0.125   0.1452867932
 369  0.043 -0.219  0.081 -0.009 -0.076  0.125   0.1452867836
 397  0.042 -0.219  0.081 -0.009 -0.076  0.125   0.1452867634
 401  0.042 -0.219  0.081 -0.009 -0.076  0.125   0.1452867545
Powell done niters = 6
Computing relative cost
 0  -25.0 -25.0 -25.0   1.021529
 1  -25.0 -25.0  25.0   0.997812
 2  -25.0  25.0 -25.0   1.001644
 3  -25.0  25.0  25.0   1.014670
 4   25.0 -25.0 -25.0   1.037124
 5   25.0 -25.0  25.0   1.023458
 6   25.0  25.0 -25.0   1.013873
 7   25.0  25.0  25.0   1.028459
REL:  8  0.145287    8.138568  1.017321 rel = 0.142813 
Number of iterations     6
Min cost was 0.145287
Number of FunctionCalls   462
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 51.225000 sec
Parameters at optimum (transmm)  0.04247 -0.21886  0.08104
Parameters at optimum (rotdeg) -0.00864 -0.07592  0.12517 
Final costs ----------------
Number of surface hits 264340
WM  Intensity    63.9905 +/-   8.6991
Ctx Intensity    77.0184 +/-   8.9911
Pct Contrast     18.5599 +/-  13.1458
Cost   0.1453
RelCost   0.1497
Reg at min cost was 
 0.999   0.001  -0.047   0.710;
 0.047  -0.083   0.995   0.874;
-0.002  -0.997  -0.083  -0.577;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.999  -0.000  -0.045   0.669;
 0.045  -0.083   0.996   1.091;
-0.004  -0.997  -0.082  -0.659;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000  -0.002   0.002  -0.041;
-0.002   0.000   0.000   0.218;
-0.001  -0.000   0.000  -0.082;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.294693
Computing change in rh position
Surface RMS Diff (mm) 0.256290 0.360918
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 --------
 0.999   0.001  -0.047   0.710;
 0.047  -0.083   0.995   0.874;
-0.002  -0.997  -0.083  -0.577;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.891;
 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 --------
 0.999   0.001  -0.047   0.710;
 0.047  -0.083   0.995   0.874;
-0.002  -0.997  -0.083  -0.577;
 0.000   0.000   0.000   1.000;
Determinant 0.999999
subject = sub018
RegMat ---------------------------
 0.999   0.001  -0.047   0.710;
 0.047  -0.083   0.995   0.874;
-0.002  -0.997  -0.083  -0.577;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000  -0.017  -0.006  -0.343;
 0.017   1.000   0.021   0.018;
 0.005  -0.021   1.000  -0.206;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.699  -0.002  -0.031   39.264;
-0.033  -0.055  -0.664   271.374;
-0.001   0.664  -0.055   10.656;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 23:18:22 CEST 2013 
Ended   at Thu Aug  8 23:30:41 CEST 2013
BBR-Run-Time-Sec 739
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.dat --surf
 

 mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/T2.mgz 

mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998519, 0.0146261, 0.052401)
j_ras = (0.020019, 0.994384, 0.103917)
k_ras = (0.0505869, -0.104812, 0.993205)
INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
reading extra input line subject sub018
reading extra input line fscale 0.150000
reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/orig.mgz...
INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/transforms/T2raw.lta...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
 1.000  -0.017  -0.006  -0.343;
 0.017   1.000   0.021   0.018;
 0.005  -0.021   1.000  -0.206;
 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/sub018/mri/T2.mgz...

 mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/T2.mgz...
computing distance transform
computing distance transform
computing nonmaximum suppression
10518 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/sub018/mri/T2.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub018 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/sub018/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
18104 bright wm thresholded.
357 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.orig...
computing class statistics...
border white:    252064 voxels (1.50%)
border gray      291583 voxels (1.74%)
WM (92.0): 92.8 +- 10.4 [70.0 --> 110.0]
GM (74.0) : 73.1 +- 12.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.4 (was 70)
setting MAX_BORDER_WHITE to 115.4 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.9 (was 40)
setting MAX_GRAY to 94.6 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.3 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 92.7, mean outside = 68.4
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/sub018/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.26 (0.02-->3.87) (max @ vno 106917 --> 107997)
face area 0.34 +- 0.16 (0.00-->2.81)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 18 points - only 5.56% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 9 with 9 points - only 0.00% unknown
deleting segment 10 with 941 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
removing 3 vertex label from ripped group
deleting segment 13 with 3 points - only 0.00% unknown
deleting segment 16 with 17 points - only 0.00% unknown
deleting segment 17 with 16 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-->3.70) (max @ vno 140247 --> 57770)
face area 0.34 +- 0.16 (0.00-->2.81)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4681382.0, rms=0.00
rms = 1.19, time step reduction 1 of 3 to 0.250...
rms = 0.29, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
001: dt: 0.1250, sse=4681382.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 18 points - only 5.56% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 941 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
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 17 points - only 0.00% unknown
deleting segment 14 with 16 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 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-->3.70) (max @ vno 140247 --> 57770)
face area 0.34 +- 0.16 (0.00-->2.81)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4681382.0, rms=0.00
rms = 1.19, time step reduction 1 of 3 to 0.250...
rms = 0.29, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
002: dt: 0.1250, sse=4681382.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 18 points - only 5.56% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 941 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
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 17 points - only 0.00% unknown
deleting segment 14 with 16 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 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-->3.70) (max @ vno 140247 --> 57770)
face area 0.34 +- 0.16 (0.00-->2.81)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4681382.0, rms=0.00
rms = 1.19, time step reduction 1 of 3 to 0.250...
rms = 0.29, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
003: dt: 0.1250, sse=4681382.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 18 points - only 5.56% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 8 with 9 points - only 0.00% unknown
deleting segment 9 with 941 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
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 17 points - only 0.00% unknown
deleting segment 14 with 16 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 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=4681382.0, rms=0.00
rms = 1.19, time step reduction 1 of 3 to 0.250...
rms = 0.29, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
004: dt: 0.1250, sse=4681382.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from woT2.pial...
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [98.20 197.80], gm=148.00+-16.60, and vertices in regions > 139.7
48371 surface locations found to contain inconsistent values (7249 in, 41122 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=518552.8, rms=0.25
001: dt: 0.5000, sse=484730.8, rms=0.237 (0.000%)
002: dt: 0.5000, sse=463887.4, rms=0.223 (0.000%)
003: dt: 0.5000, sse=450499.2, rms=0.212 (0.000%)
004: dt: 0.5000, sse=439782.9, rms=0.203 (0.000%)
005: dt: 0.5000, sse=431609.1, rms=0.195 (0.000%)
006: dt: 0.5000, sse=425387.3, rms=0.188 (0.000%)
007: dt: 0.5000, sse=420621.0, rms=0.182 (0.000%)
008: dt: 0.5000, sse=416597.2, rms=0.177 (0.000%)
009: dt: 0.5000, sse=413149.0, rms=0.172 (0.000%)
010: dt: 0.5000, sse=410282.3, rms=0.168 (0.000%)
011: dt: 0.5000, sse=407744.1, rms=0.165 (0.000%)
012: dt: 0.5000, sse=405407.5, rms=0.162 (0.000%)
013: dt: 0.5000, sse=403395.5, rms=0.160 (0.000%)
014: dt: 0.5000, sse=401590.5, rms=0.158 (0.000%)
015: dt: 0.5000, sse=399903.2, rms=0.156 (0.000%)
016: dt: 0.5000, sse=398341.5, rms=0.154 (0.000%)
017: dt: 0.5000, sse=397009.2, rms=0.153 (0.000%)
018: dt: 0.5000, sse=395486.3, rms=0.152 (0.000%)
019: dt: 0.5000, sse=394187.9, rms=0.151 (0.000%)
020: dt: 0.5000, sse=392849.1, rms=0.150 (0.000%)
021: dt: 0.5000, sse=391597.4, rms=0.149 (0.000%)
022: dt: 0.5000, sse=390378.1, rms=0.149 (0.000%)
023: dt: 0.5000, sse=389127.1, rms=0.148 (0.000%)
024: dt: 0.5000, sse=388217.4, rms=0.148 (0.000%)
025: dt: 0.5000, sse=387028.1, rms=0.148 (0.000%)
026: dt: 0.5000, sse=385734.9, rms=0.148 (0.000%)
027: dt: 0.5000, sse=384735.2, rms=0.148 (0.000%)
028: dt: 0.5000, sse=383646.8, rms=0.147 (0.000%)
029: dt: 0.5000, sse=382348.2, rms=0.148 (0.000%)
030: dt: 0.5000, sse=381476.7, rms=0.148 (0.000%)
positioning took 3.8 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [91.90 204.10], gm=148.00+-18.70, and vertices in regions > 138.6
40560 surface locations found to contain inconsistent values (1380 in, 39180 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=40035.6, rms=0.13
031: dt: 0.5000, sse=39744.6, rms=0.129 (0.000%)
032: dt: 0.5000, sse=40575.2, rms=0.117 (0.000%)
033: dt: 0.5000, sse=41644.4, rms=0.108 (0.000%)
034: dt: 0.5000, sse=42539.4, rms=0.103 (0.000%)
035: dt: 0.5000, sse=43306.9, rms=0.098 (0.000%)
036: dt: 0.5000, sse=44077.8, rms=0.093 (0.000%)
037: dt: 0.5000, sse=44816.4, rms=0.089 (0.000%)
038: dt: 0.5000, sse=45517.9, rms=0.085 (0.000%)
039: dt: 0.5000, sse=46207.3, rms=0.081 (0.000%)
040: dt: 0.5000, sse=46861.9, rms=0.077 (0.000%)
041: dt: 0.5000, sse=47500.9, rms=0.074 (0.000%)
042: dt: 0.5000, sse=48092.5, rms=0.071 (0.000%)
043: dt: 0.5000, sse=48642.2, rms=0.068 (0.000%)
044: dt: 0.5000, sse=49177.7, rms=0.066 (0.000%)
045: dt: 0.5000, sse=49657.5, rms=0.064 (0.000%)
046: dt: 0.5000, sse=50124.4, rms=0.061 (0.000%)
047: dt: 0.5000, sse=50548.6, rms=0.059 (0.000%)
048: dt: 0.5000, sse=50948.0, rms=0.057 (0.000%)
049: dt: 0.5000, sse=51315.6, rms=0.056 (0.000%)
050: dt: 0.5000, sse=51667.8, rms=0.054 (0.000%)
051: dt: 0.5000, sse=52005.2, rms=0.053 (0.000%)
052: dt: 0.5000, sse=52307.1, rms=0.051 (0.000%)
053: dt: 0.5000, sse=52592.9, rms=0.050 (0.000%)
054: dt: 0.5000, sse=52862.3, rms=0.049 (0.000%)
055: dt: 0.5000, sse=53107.9, rms=0.047 (0.000%)
056: dt: 0.5000, sse=53321.7, rms=0.046 (0.000%)
057: dt: 0.5000, sse=53544.5, rms=0.045 (0.000%)
058: dt: 0.5000, sse=53733.9, rms=0.044 (0.000%)
059: dt: 0.5000, sse=53928.5, rms=0.044 (0.000%)
060: dt: 0.5000, sse=54086.1, rms=0.043 (0.000%)
positioning took 3.8 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [88.00 208.00], gm=148.00+-20.00, and vertices in regions > 138.0
39904 surface locations found to contain inconsistent values (196 in, 39708 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=5962.3, rms=0.06
061: dt: 0.5000, sse=5914.0, rms=0.062 (0.000%)
062: dt: 0.5000, sse=5976.0, rms=0.053 (0.000%)
063: dt: 0.5000, sse=6066.8, rms=0.048 (0.000%)
064: dt: 0.5000, sse=6144.3, rms=0.045 (0.000%)
065: dt: 0.5000, sse=6199.1, rms=0.043 (0.000%)
066: dt: 0.5000, sse=6231.9, rms=0.041 (0.000%)
067: dt: 0.5000, sse=6250.7, rms=0.040 (0.000%)
068: dt: 0.5000, sse=6266.9, rms=0.038 (0.000%)
069: dt: 0.5000, sse=6283.2, rms=0.037 (0.000%)
070: dt: 0.5000, sse=6297.0, rms=0.036 (0.000%)
071: dt: 0.5000, sse=6311.6, rms=0.035 (0.000%)
072: dt: 0.5000, sse=6323.0, rms=0.034 (0.000%)
073: dt: 0.5000, sse=6333.2, rms=0.033 (0.000%)
074: dt: 0.5000, sse=6342.9, rms=0.032 (0.000%)
075: dt: 0.5000, sse=6350.4, rms=0.031 (0.000%)
076: dt: 0.5000, sse=6357.1, rms=0.031 (0.000%)
077: dt: 0.5000, sse=6364.1, rms=0.030 (0.000%)
078: dt: 0.5000, sse=6368.8, rms=0.029 (0.000%)
079: dt: 0.5000, sse=6373.8, rms=0.029 (0.000%)
080: dt: 0.5000, sse=6378.7, rms=0.028 (0.000%)
081: dt: 0.5000, sse=6382.8, rms=0.028 (0.000%)
082: dt: 0.5000, sse=6387.8, rms=0.028 (0.000%)
083: dt: 0.5000, sse=6392.5, rms=0.027 (0.000%)
084: dt: 0.5000, sse=6395.8, rms=0.027 (0.000%)
085: dt: 0.5000, sse=6398.5, rms=0.027 (0.000%)
086: dt: 0.5000, sse=6401.3, rms=0.027 (0.000%)
087: dt: 0.5000, sse=6403.1, rms=0.026 (0.000%)
088: dt: 0.5000, sse=6405.5, rms=0.026 (0.000%)
089: dt: 0.5000, sse=6406.4, rms=0.026 (0.000%)
090: dt: 0.5000, sse=6408.0, rms=0.026 (0.000%)
positioning took 3.7 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [86.80 209.20], gm=148.00+-20.40, and vertices in regions > 137.8
39827 surface locations found to contain inconsistent values (57 in, 39770 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/sub018/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=817.3, rms=0.04
091: dt: 0.5000, sse=806.3, rms=0.036 (0.000%)
092: dt: 0.5000, sse=773.5, rms=0.031 (0.000%)
093: dt: 0.5000, sse=763.7, rms=0.030 (0.000%)
094: dt: 0.5000, sse=758.7, rms=0.029 (0.000%)
095: dt: 0.5000, sse=754.5, rms=0.028 (0.000%)
096: dt: 0.5000, sse=750.9, rms=0.027 (0.000%)
097: dt: 0.5000, sse=748.2, rms=0.027 (0.000%)
098: dt: 0.5000, sse=745.7, rms=0.026 (0.000%)
099: dt: 0.5000, sse=743.6, rms=0.026 (0.000%)
100: dt: 0.5000, sse=741.3, rms=0.026 (0.000%)
101: dt: 0.5000, sse=739.4, rms=0.025 (0.000%)
102: dt: 0.5000, sse=737.4, rms=0.025 (0.000%)
103: dt: 0.5000, sse=735.3, rms=0.025 (0.000%)
104: dt: 0.5000, sse=733.6, rms=0.024 (0.000%)
105: dt: 0.5000, sse=733.2, rms=0.024 (0.000%)
106: dt: 0.5000, sse=731.6, rms=0.024 (0.000%)
107: dt: 0.5000, sse=730.2, rms=0.024 (0.000%)
108: dt: 0.5000, sse=729.1, rms=0.024 (0.000%)
109: dt: 0.5000, sse=728.0, rms=0.023 (0.000%)
110: dt: 0.5000, sse=727.1, rms=0.023 (0.000%)
111: dt: 0.5000, sse=726.2, rms=0.023 (0.000%)
112: dt: 0.5000, sse=725.7, rms=0.023 (0.000%)
113: dt: 0.5000, sse=725.1, rms=0.023 (0.000%)
114: dt: 0.5000, sse=724.7, rms=0.023 (0.000%)
115: dt: 0.5000, sse=723.9, rms=0.023 (0.000%)
116: dt: 0.5000, sse=723.5, rms=0.022 (0.000%)
117: dt: 0.5000, sse=723.2, rms=0.022 (0.000%)
118: dt: 0.5000, sse=722.7, rms=0.022 (0.000%)
119: dt: 0.5000, sse=722.5, rms=0.022 (0.000%)
120: dt: 0.5000, sse=722.2, rms=0.022 (0.000%)
positioning took 3.6 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.area.pial
vertex spacing 1.03 +- 0.44 (0.05-->8.78) (max @ vno 105864 --> 105855)
face area 0.41 +- 0.32 (0.00-->6.08)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 140393 vertices processed
25000 of 140393 vertices processed
50000 of 140393 vertices processed
75000 of 140393 vertices processed
100000 of 140393 vertices processed
125000 of 140393 vertices processed
0 of 140393 vertices processed
25000 of 140393 vertices processed
50000 of 140393 vertices processed
75000 of 140393 vertices processed
100000 of 140393 vertices processed
125000 of 140393 vertices processed
thickness calculation complete, 504:1123 truncations.
28473 vertices at 0 distance
90269 vertices at 1 distance
91832 vertices at 2 distance
39562 vertices at 3 distance
12001 vertices at 4 distance
3696 vertices at 5 distance
1308 vertices at 6 distance
460 vertices at 7 distance
159 vertices at 8 distance
80 vertices at 9 distance
51 vertices at 10 distance
41 vertices at 11 distance
21 vertices at 12 distance
25 vertices at 13 distance
22 vertices at 14 distance
24 vertices at 15 distance
13 vertices at 16 distance
10 vertices at 17 distance
8 vertices at 18 distance
8 vertices at 19 distance
11 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.thickness
positioning took 18.6 minutes
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub018 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/sub018/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
18329 bright wm thresholded.
358 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.orig...
computing class statistics...
border white:    252064 voxels (1.50%)
border gray      291583 voxels (1.74%)
WM (92.0): 92.8 +- 10.3 [70.0 --> 110.0]
GM (75.0) : 73.1 +- 12.8 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 46.2 (was 70)
setting MAX_BORDER_WHITE to 115.3 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 33.3 (was 40)
setting MAX_GRAY to 94.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 20.5 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 92.3, mean outside = 68.0
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/sub018/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.25 (0.05-->3.94) (max @ vno 105775 --> 105781)
face area 0.34 +- 0.16 (0.00-->2.89)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 4 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 517 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 9 with 5 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 5 points - only 0.00% unknown
deleting segment 12 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 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 (0.07-->3.94) (max @ vno 105775 --> 105781)
face area 0.34 +- 0.16 (0.00-->2.89)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4786804.0, rms=0.00
rms = 1.12, 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=4786804.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 517 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 5 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 5 points - only 0.00% unknown
deleting segment 11 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 105775 --> 105781)
face area 0.34 +- 0.16 (0.00-->2.89)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4786804.0, rms=0.00
rms = 1.12, 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=4786804.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 517 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 5 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 5 points - only 0.00% unknown
deleting segment 11 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.07-->3.94) (max @ vno 105775 --> 105781)
face area 0.34 +- 0.16 (0.00-->2.89)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4786804.0, rms=0.00
rms = 1.12, 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=4786804.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 3 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 517 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 5 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 5 points - only 0.00% unknown
deleting segment 11 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 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=4786804.0, rms=0.00
rms = 1.12, 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=4786804.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from woT2.pial...
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [95.50 206.50], gm=151.00+-18.50, and vertices in regions > 141.7
44232 surface locations found to contain inconsistent values (4850 in, 39382 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=530450.2, rms=0.24
001: dt: 0.5000, sse=496390.7, rms=0.228 (0.000%)
002: dt: 0.5000, sse=475648.5, rms=0.214 (0.000%)
003: dt: 0.5000, sse=462108.0, rms=0.203 (0.000%)
004: dt: 0.5000, sse=451678.9, rms=0.193 (0.000%)
005: dt: 0.5000, sse=444022.7, rms=0.185 (0.000%)
006: dt: 0.5000, sse=438176.1, rms=0.178 (0.000%)
007: dt: 0.5000, sse=433698.3, rms=0.172 (0.000%)
008: dt: 0.5000, sse=430027.5, rms=0.167 (0.000%)
009: dt: 0.5000, sse=426949.0, rms=0.162 (0.000%)
010: dt: 0.5000, sse=424324.4, rms=0.158 (0.000%)
011: dt: 0.5000, sse=422159.2, rms=0.155 (0.000%)
012: dt: 0.5000, sse=420066.1, rms=0.153 (0.000%)
013: dt: 0.5000, sse=418046.2, rms=0.150 (0.000%)
014: dt: 0.5000, sse=416339.5, rms=0.149 (0.000%)
015: dt: 0.5000, sse=414964.9, rms=0.147 (0.000%)
016: dt: 0.5000, sse=413199.2, rms=0.146 (0.000%)
017: dt: 0.5000, sse=411796.6, rms=0.145 (0.000%)
018: dt: 0.5000, sse=410236.3, rms=0.144 (0.000%)
019: dt: 0.5000, sse=408883.5, rms=0.143 (0.000%)
020: dt: 0.5000, sse=407251.7, rms=0.143 (0.000%)
021: dt: 0.5000, sse=405678.5, rms=0.143 (0.000%)
022: dt: 0.5000, sse=404358.2, rms=0.142 (0.000%)
023: dt: 0.5000, sse=403124.8, rms=0.142 (0.000%)
024: dt: 0.5000, sse=402216.7, rms=0.142 (0.000%)
025: dt: 0.5000, sse=401032.8, rms=0.142 (0.000%)
026: dt: 0.5000, sse=399742.6, rms=0.142 (0.000%)
027: dt: 0.5000, sse=399105.4, rms=0.142 (0.000%)
028: dt: 0.5000, sse=397467.0, rms=0.142 (0.000%)
029: dt: 0.5000, sse=396512.8, rms=0.143 (0.000%)
030: dt: 0.5000, sse=395344.1, rms=0.143 (0.000%)
positioning took 3.8 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [95.00 209.00], gm=152.00+-19.00, and vertices in regions > 142.5
36893 surface locations found to contain inconsistent values (1674 in, 35219 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=41072.2, rms=0.12
031: dt: 0.5000, sse=40811.2, rms=0.119 (0.000%)
032: dt: 0.5000, sse=41752.4, rms=0.108 (0.000%)
033: dt: 0.5000, sse=42858.4, rms=0.100 (0.000%)
034: dt: 0.5000, sse=43748.3, rms=0.095 (0.000%)
035: dt: 0.5000, sse=44465.2, rms=0.090 (0.000%)
036: dt: 0.5000, sse=45185.7, rms=0.086 (0.000%)
037: dt: 0.5000, sse=45831.9, rms=0.082 (0.000%)
038: dt: 0.5000, sse=46480.4, rms=0.078 (0.000%)
039: dt: 0.5000, sse=47102.3, rms=0.074 (0.000%)
040: dt: 0.5000, sse=47684.6, rms=0.071 (0.000%)
041: dt: 0.5000, sse=48250.4, rms=0.068 (0.000%)
042: dt: 0.5000, sse=48767.7, rms=0.065 (0.000%)
043: dt: 0.5000, sse=49249.2, rms=0.063 (0.000%)
044: dt: 0.5000, sse=49677.4, rms=0.061 (0.000%)
045: dt: 0.5000, sse=50121.8, rms=0.058 (0.000%)
046: dt: 0.5000, sse=50552.3, rms=0.056 (0.000%)
047: dt: 0.5000, sse=50947.3, rms=0.055 (0.000%)
048: dt: 0.5000, sse=51327.3, rms=0.053 (0.000%)
049: dt: 0.5000, sse=51671.2, rms=0.051 (0.000%)
050: dt: 0.5000, sse=51978.6, rms=0.050 (0.000%)
051: dt: 0.5000, sse=52259.2, rms=0.049 (0.000%)
052: dt: 0.5000, sse=52553.6, rms=0.048 (0.000%)
053: dt: 0.5000, sse=52788.2, rms=0.046 (0.000%)
054: dt: 0.5000, sse=53029.3, rms=0.045 (0.000%)
055: dt: 0.5000, sse=53250.7, rms=0.044 (0.000%)
056: dt: 0.5000, sse=53457.5, rms=0.043 (0.000%)
057: dt: 0.5000, sse=53632.2, rms=0.043 (0.000%)
058: dt: 0.5000, sse=53805.5, rms=0.042 (0.000%)
059: dt: 0.5000, sse=53961.0, rms=0.041 (0.000%)
060: dt: 0.5000, sse=54098.8, rms=0.040 (0.000%)
positioning took 3.8 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [92.80 209.20], gm=151.00+-19.40, and vertices in regions > 141.3
33949 surface locations found to contain inconsistent values (300 in, 33649 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=5741.9, rms=0.05
061: dt: 0.5000, sse=5735.1, rms=0.049 (0.000%)
062: dt: 0.5000, sse=5759.6, rms=0.046 (0.000%)
063: dt: 0.5000, sse=5779.8, rms=0.043 (0.000%)
064: dt: 0.5000, sse=5800.0, rms=0.041 (0.000%)
065: dt: 0.5000, sse=5811.0, rms=0.039 (0.000%)
066: dt: 0.5000, sse=5818.1, rms=0.038 (0.000%)
067: dt: 0.5000, sse=5822.6, rms=0.036 (0.000%)
068: dt: 0.5000, sse=5824.8, rms=0.035 (0.000%)
069: dt: 0.5000, sse=5828.1, rms=0.034 (0.000%)
070: dt: 0.5000, sse=5832.3, rms=0.033 (0.000%)
071: dt: 0.5000, sse=5835.2, rms=0.033 (0.000%)
072: dt: 0.5000, sse=5840.0, rms=0.032 (0.000%)
073: dt: 0.5000, sse=5843.6, rms=0.031 (0.000%)
074: dt: 0.5000, sse=5846.3, rms=0.030 (0.000%)
075: dt: 0.5000, sse=5849.5, rms=0.029 (0.000%)
076: dt: 0.5000, sse=5850.6, rms=0.029 (0.000%)
077: dt: 0.5000, sse=5853.0, rms=0.028 (0.000%)
078: dt: 0.5000, sse=5855.4, rms=0.028 (0.000%)
079: dt: 0.5000, sse=5857.1, rms=0.027 (0.000%)
080: dt: 0.5000, sse=5859.6, rms=0.027 (0.000%)
081: dt: 0.5000, sse=5861.7, rms=0.026 (0.000%)
082: dt: 0.5000, sse=5863.9, rms=0.026 (0.000%)
083: dt: 0.5000, sse=5865.9, rms=0.025 (0.000%)
084: dt: 0.5000, sse=5868.4, rms=0.025 (0.000%)
085: dt: 0.5000, sse=5869.6, rms=0.025 (0.000%)
086: dt: 0.5000, sse=5870.3, rms=0.024 (0.000%)
087: dt: 0.5000, sse=5872.2, rms=0.024 (0.000%)
088: dt: 0.5000, sse=5874.2, rms=0.024 (0.000%)
089: dt: 0.5000, sse=5876.5, rms=0.024 (0.000%)
090: dt: 0.5000, sse=5877.6, rms=0.024 (0.000%)
positioning took 3.7 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [92.50 209.50], gm=151.00+-19.50, and vertices in regions > 141.2
34266 surface locations found to contain inconsistent values (62 in, 34204 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/sub018/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=699.2, rms=0.03
091: dt: 0.5000, sse=698.4, rms=0.030 (0.000%)
092: dt: 0.5000, sse=689.3, rms=0.028 (0.000%)
093: dt: 0.5000, sse=683.6, rms=0.027 (0.000%)
094: dt: 0.5000, sse=678.6, rms=0.026 (0.000%)
095: dt: 0.5000, sse=674.1, rms=0.026 (0.000%)
096: dt: 0.5000, sse=670.6, rms=0.025 (0.000%)
097: dt: 0.5000, sse=667.7, rms=0.025 (0.000%)
098: dt: 0.5000, sse=665.2, rms=0.024 (0.000%)
099: dt: 0.5000, sse=663.1, rms=0.024 (0.000%)
100: dt: 0.5000, sse=660.9, rms=0.024 (0.000%)
101: dt: 0.5000, sse=659.7, rms=0.023 (0.000%)
102: dt: 0.5000, sse=658.1, rms=0.023 (0.000%)
103: dt: 0.5000, sse=657.1, rms=0.023 (0.000%)
104: dt: 0.5000, sse=655.2, rms=0.023 (0.000%)
105: dt: 0.5000, sse=653.8, rms=0.022 (0.000%)
106: dt: 0.5000, sse=652.3, rms=0.022 (0.000%)
107: dt: 0.5000, sse=651.3, rms=0.022 (0.000%)
108: dt: 0.5000, sse=650.1, rms=0.022 (0.000%)
109: dt: 0.5000, sse=649.0, rms=0.021 (0.000%)
110: dt: 0.5000, sse=648.2, rms=0.021 (0.000%)
111: dt: 0.5000, sse=648.1, rms=0.021 (0.000%)
112: dt: 0.5000, sse=647.5, rms=0.021 (0.000%)
113: dt: 0.5000, sse=647.0, rms=0.021 (0.000%)
114: dt: 0.5000, sse=647.6, rms=0.021 (0.000%)
115: dt: 0.5000, sse=647.1, rms=0.021 (0.000%)
116: dt: 0.5000, sse=646.2, rms=0.021 (0.000%)
117: dt: 0.5000, sse=645.5, rms=0.021 (0.000%)
118: dt: 0.5000, sse=645.0, rms=0.021 (0.000%)
119: dt: 0.5000, sse=644.5, rms=0.021 (0.000%)
120: dt: 0.5000, sse=644.1, rms=0.021 (0.000%)
positioning took 3.6 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.area.pial
vertex spacing 1.03 +- 0.44 (0.09-->7.51) (max @ vno 95616 --> 94572)
face area 0.41 +- 0.31 (0.00-->4.80)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 140674 vertices processed
25000 of 140674 vertices processed
50000 of 140674 vertices processed
75000 of 140674 vertices processed
100000 of 140674 vertices processed
125000 of 140674 vertices processed
0 of 140674 vertices processed
25000 of 140674 vertices processed
50000 of 140674 vertices processed
75000 of 140674 vertices processed
100000 of 140674 vertices processed
125000 of 140674 vertices processed
thickness calculation complete, 475:801 truncations.
29524 vertices at 0 distance
92204 vertices at 1 distance
92773 vertices at 2 distance
39374 vertices at 3 distance
11163 vertices at 4 distance
2833 vertices at 5 distance
823 vertices at 6 distance
324 vertices at 7 distance
118 vertices at 8 distance
70 vertices at 9 distance
38 vertices at 10 distance
34 vertices at 11 distance
26 vertices at 12 distance
19 vertices at 13 distance
25 vertices at 14 distance
11 vertices at 15 distance
14 vertices at 16 distance
16 vertices at 17 distance
11 vertices at 18 distance
13 vertices at 19 distance
11 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.thickness
positioning took 18.5 minutes
#--------------------------------------------
#@# Surf Volume lh Fri Aug  9 00:09:30 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 Fri Aug  9 00:09:30 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 Fri Aug  9 00:09:31 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub018 

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 = 27
writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/ribbon.mgz
 writing ribbon files
#--------------------------------------------
#@# ASeg Stats Fri Aug  9 00:27:32 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018

 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 sub018 


$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 sub018 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1181492 mm^3    (det: 1.648852 )
Computing euler number
orig.nofix lheno =  -18, rheno = -32
orig.nofix lhholes =   10, rhholes = 17
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 262772.781 262088.000  diff=  684.8  pctdiff= 0.261
rhCtxGM: 259118.403 258515.000  diff=  603.4  pctdiff= 0.233
lhCtxWM: 216828.496 216683.000  diff=  145.5  pctdiff= 0.067
rhCtxWM: 218597.423 218508.000  diff=   89.4  pctdiff= 0.041
SubCortGMVol  63231.000
SupraTentVol  1038215.103 (1035985.000) diff=2230.103 pctdiff=0.215
SupraTentVolNotVent  1021603.103 (1019373.000) diff=2230.103 pctdiff=0.218
BrainSegVol  1156426.000 (1153227.000) diff=3199.000 pctdiff=0.277
BrainSegVolNotVent  1135637.000 (1136886.103) diff=-1249.103 pctdiff=-0.110
BrainSegVolNotVent  1135637.000
CerebellumVol 115990.000
VentChorVol   16612.000
3rd4th5thCSF   4177.000
CSFVol   997.000, OptChiasmVol   255.000
MaskVol 1567075.000
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    6794    6793.784
  4     5                  Left-Inf-Lat-Vent     648     647.810
  5     7       Left-Cerebellum-White-Matter   13292   13292.321
  6     8             Left-Cerebellum-Cortex   44830   44830.324
  7    10               Left-Thalamus-Proper    8046    8045.522
  8    11                       Left-Caudate    3815    3814.885
  9    12                       Left-Putamen    6339    6339.314
 10    13                      Left-Pallidum    1831    1830.605
 11    14                      3rd-Ventricle     814     814.475
 12    15                      4th-Ventricle    2579    2579.153
 13    16                         Brain-Stem   21153   21152.502
 14    17                   Left-Hippocampus    3717    3717.286
 15    18                      Left-Amygdala    1772    1771.706
 16    24                                CSF     988     988.454
 17    26                Left-Accumbens-area     680     680.352
 18    28                     Left-VentralDC    4406    4406.250
 19    30                        Left-vessel     137     137.068
 20    31                Left-choroid-plexus    1239    1239.441
 23    43            Right-Lateral-Ventricle    6025    6025.433
 24    44                 Right-Inf-Lat-Vent     317     317.407
 25    46      Right-Cerebellum-White-Matter   13968   13967.782
 26    47            Right-Cerebellum-Cortex   46835   46834.531
 27    49              Right-Thalamus-Proper    7796    7795.538
 28    50                      Right-Caudate    3946    3946.068
 29    51                      Right-Putamen    5839    5838.778
 30    52                     Right-Pallidum    2229    2228.593
 31    53                  Right-Hippocampus    3824    3823.980
 32    54                     Right-Amygdala    1798    1797.534
 33    58               Right-Accumbens-area     719     719.100
 34    60                    Right-VentralDC    4067    4067.275
 35    62                       Right-vessel     183     182.967
 36    63               Right-choroid-plexus    1566    1565.628
 37    72                      5th-Ventricle       0       0.000
 38    77                 WM-hypointensities    1449    1449.195
 39    78            Left-WM-hypointensities       0       0.000
 40    79           Right-WM-hypointensities       0       0.000
 41    80             non-WM-hypointensities      15      14.949
 42    81        Left-non-WM-hypointensities       0       0.000
 43    82       Right-non-WM-hypointensities       0       0.000
 44    85                       Optic-Chiasm     264     263.729
 45   251                       CC_Posterior     879     879.355
 46   252                   CC_Mid_Posterior     427     426.819
 47   253                         CC_Central     415     414.964
 48   254                    CC_Mid_Anterior     448     448.003
 49   255                        CC_Anterior     883     882.874

Reporting on  45 segmentations
mri_segstats done
#-----------------------------------------
#@# AParc-to-ASeg Fri Aug  9 00:31:05 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018

 mri_aparc2aseg --s sub018 --volmask 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub018
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/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/sub018/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 = 518587
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aparc+aseg.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018

 mri_aparc2aseg --s sub018 --volmask --a2009s 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub018
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/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/sub018/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 = 518587
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Fri Aug  9 00:36:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018

 mri_aparc2aseg --s sub018 --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 sub018
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/sub018/mri/aparc+aseg.mgz

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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/sub018/mri/ribbon.mgz
Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 8590 vertices from left hemi
Ripped 8137 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/sub018/mri/aseg.mgz
Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 = 952645
Used brute-force search on 13 voxels
Fixing Parahip LH WM
  Found 6 clusters
     0 k 1.000000
     1 k 3.000000
     2 k 1.000000
     3 k 14.000000
     4 k 1539.000000
     5 k 1.000000
Fixing Parahip RH WM
  Found 10 clusters
     0 k 1.000000
     1 k 6.000000
     2 k 1.000000
     3 k 2.000000
     4 k 2.000000
     5 k 1.000000
     6 k 1538.000000
     7 k 2.000000
     8 k 2.000000
     9 k 1.000000
Writing output aseg to mri/wmparc.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018

 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 sub018 --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 sub018 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1181492 mm^3    (det: 1.648852 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 262772.781 262088.000  diff=  684.8  pctdiff= 0.261
rhCtxGM: 259118.403 258515.000  diff=  603.4  pctdiff= 0.233
lhCtxWM: 216828.496 216683.000  diff=  145.5  pctdiff= 0.067
rhCtxWM: 218597.423 218508.000  diff=   89.4  pctdiff= 0.041
SubCortGMVol  63231.000
SupraTentVol  1038215.103 (1035985.000) diff=2230.103 pctdiff=0.215
SupraTentVolNotVent  1021603.103 (1019373.000) diff=2230.103 pctdiff=0.218
BrainSegVol  1156426.000 (1153227.000) diff=3199.000 pctdiff=0.277
BrainSegVolNotVent  1135637.000 (1136886.103) diff=-1249.103 pctdiff=-0.110
BrainSegVolNotVent  1135637.000
CerebellumVol 115990.000
VentChorVol   16612.000
3rd4th5thCSF   4177.000
CSFVol   997.000, OptChiasmVol   255.000
MaskVol 1567075.000
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    3834    3834.180
  2   3002      wm-lh-caudalanteriorcingulate    3150    3150.293
  3   3003          wm-lh-caudalmiddlefrontal    6313    6313.133
  4   3004               wm-lh-corpuscallosum       0       0.000
  5   3005                       wm-lh-cuneus    1769    1769.453
  6   3006                   wm-lh-entorhinal     908     908.430
  7   3007                     wm-lh-fusiform    6895    6894.660
  8   3008             wm-lh-inferiorparietal    9785    9785.111
  9   3009             wm-lh-inferiortemporal    7366    7365.650
 10   3010             wm-lh-isthmuscingulate    3607    3606.861
 11   3011             wm-lh-lateraloccipital    7569    7569.262
 12   3012         wm-lh-lateralorbitofrontal    5739    5739.259
 13   3013                      wm-lh-lingual    4006    4006.169
 14   3014          wm-lh-medialorbitofrontal    3596    3596.006
 15   3015               wm-lh-middletemporal    5975    5974.587
 16   3016              wm-lh-parahippocampal    1628    1627.826
 17   3017                  wm-lh-paracentral    3248    3248.455
 18   3018              wm-lh-parsopercularis    3153    3153.196
 19   3019                wm-lh-parsorbitalis     808     808.422
 20   3020             wm-lh-parstriangularis    2984    2983.516
 21   3021                wm-lh-pericalcarine    2502    2502.453
 22   3022                  wm-lh-postcentral    8140    8140.377
 23   3023           wm-lh-posteriorcingulate    4864    4863.969
 24   3024                   wm-lh-precentral   12193   12192.650
 25   3025                    wm-lh-precuneus    8386    8386.383
 26   3026     wm-lh-rostralanteriorcingulate    2341    2340.538
 27   3027         wm-lh-rostralmiddlefrontal   13413   13413.009
 28   3028              wm-lh-superiorfrontal   19154   19153.689
 29   3029             wm-lh-superiorparietal   10914   10914.403
 30   3030             wm-lh-superiortemporal    7361    7360.979
 31   3031                wm-lh-supramarginal    8190    8190.038
 32   3032                  wm-lh-frontalpole     250     249.765
 33   3033                 wm-lh-temporalpole     648     647.571
 34   3034           wm-lh-transversetemporal     703     703.380
 35   3035                       wm-lh-insula    8161    8161.229
 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    2756    2755.612
120   4002      wm-rh-caudalanteriorcingulate    3185    3185.482
121   4003          wm-rh-caudalmiddlefrontal    5015    5015.476
122   4004               wm-rh-corpuscallosum       0       0.000
123   4005                       wm-rh-cuneus    2053    2053.431
124   4006                   wm-rh-entorhinal     721     720.908
125   4007                     wm-rh-fusiform    6605    6604.547
126   4008             wm-rh-inferiorparietal   12158   12158.270
127   4009             wm-rh-inferiortemporal    6430    6429.956
128   4010             wm-rh-isthmuscingulate    3147    3147.056
129   4011             wm-rh-lateraloccipital    7412    7411.778
130   4012         wm-rh-lateralorbitofrontal    6967    6966.981
131   4013                      wm-rh-lingual    4173    4173.202
132   4014          wm-rh-medialorbitofrontal    3871    3870.739
133   4015               wm-rh-middletemporal    5838    5837.609
134   4016              wm-rh-parahippocampal    1605    1604.617
135   4017                  wm-rh-paracentral    4572    4572.180
136   4018              wm-rh-parsopercularis    2959    2958.815
137   4019                wm-rh-parsorbitalis    1131    1130.534
138   4020             wm-rh-parstriangularis    3535    3534.822
139   4021                wm-rh-pericalcarine    2413    2412.734
140   4022                  wm-rh-postcentral    7238    7237.606
141   4023           wm-rh-posteriorcingulate    4396    4395.841
142   4024                   wm-rh-precentral   13016   13015.992
143   4025                    wm-rh-precuneus    8389    8389.447
144   4026     wm-rh-rostralanteriorcingulate    2165    2165.278
145   4027         wm-rh-rostralmiddlefrontal   12097   12097.344
146   4028              wm-rh-superiorfrontal   20235   20235.414
147   4029             wm-rh-superiorparietal   10732   10731.582
148   4030             wm-rh-superiortemporal    7022    7021.965
149   4031                wm-rh-supramarginal    9521    9520.531
150   4032                  wm-rh-frontalpole     335     335.450
151   4033                 wm-rh-temporalpole     663     662.949
152   4034           wm-rh-transversetemporal     619     619.070
153   4035                       wm-rh-insula    8261    8261.174
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   27380   27380.078
237   5002       Right-UnsegmentedWhiteMatter   28233   28233.395
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/sub018/label
#--------------------------------------------
#@# BA Labels lh Fri Aug  9 00:47:03 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 365
Checking for and removing duplicates
Writing label file ./lh.BA1.label 4494
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 839
Checking for and removing duplicates
Writing label file ./lh.BA2.label 8748
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 160
Checking for and removing duplicates
Writing label file ./lh.BA3a.label 4237
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 372
Checking for and removing duplicates
Writing label file ./lh.BA3b.label 6355
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 304
Checking for and removing duplicates
Writing label file ./lh.BA4a.label 6088
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 244
Checking for and removing duplicates
Writing label file ./lh.BA4p.label 4314
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 1162
Checking for and removing duplicates
Writing label file ./lh.BA6.label 14751
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 405
Checking for and removing duplicates
Writing label file ./lh.BA44.label 4586
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 800
Checking for and removing duplicates
Writing label file ./lh.BA45.label 4222
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 930
Checking for and removing duplicates
Writing label file ./lh.V1.label 5571
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 1979
Checking for and removing duplicates
Writing label file ./lh.V2.label 10093
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 576
Checking for and removing duplicates
Writing label file ./lh.MT.label 2594
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 176
Checking for and removing duplicates
Writing label file ./lh.perirhinal.label 1375
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 100
Checking for and removing duplicates
Writing label file ./lh.BA1.thresh.label 1114
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 419
Checking for and removing duplicates
Writing label file ./lh.BA2.thresh.label 2511
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./lh.BA3a.thresh.label 1534
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 158
Checking for and removing duplicates
Writing label file ./lh.BA3b.thresh.label 2154
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 127
Checking for and removing duplicates
Writing label file ./lh.BA4a.thresh.label 2446
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 135
Checking for and removing duplicates
Writing label file ./lh.BA4p.thresh.label 1684
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 470
Checking for and removing duplicates
Writing label file ./lh.BA6.thresh.label 7505
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 185
Checking for and removing duplicates
Writing label file ./lh.BA44.thresh.label 2097
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 293
Checking for and removing duplicates
Writing label file ./lh.BA45.thresh.label 1444
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 676
Checking for and removing duplicates
Writing label file ./lh.V1.thresh.label 4081
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 882
Checking for and removing duplicates
Writing label file ./lh.V2.thresh.label 4216
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140393
Number of reverse mapping hits = 149
Checking for and removing duplicates
Writing label file ./lh.MT.thresh.label 662
mri_label2label: Done


 mris_label2annot --s sub018 --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/sub018/label
cmdline mris_label2annot --s sub018 --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 snake5
machine  x86_64
user     fkaule

subject sub018
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/sub018/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 99758 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.BA.annot

 mris_label2annot --s sub018 --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/sub018/label
cmdline mris_label2annot --s sub018 --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 snake5
machine  x86_64
user     fkaule

subject sub018
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/sub018/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 117311 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/lh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub018 lh white 

computing statistics for each annotation in ./lh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

 1117    652   2411  2.596 0.340     0.150     0.050       24     2.3  BA1
 4705   3179   8224  2.393 0.462     0.141     0.048       73     8.5  BA2
 1035    680   1095  2.050 0.468     0.126     0.034        8     1.5  BA3a
 2486   1706   4034  2.048 0.516     0.121     0.033       28     3.4  BA3b
 1588   1048   3784  2.874 0.483     0.110     0.027       12     1.9  BA4a
 1400    928   2434  2.678 0.484     0.112     0.045       18     3.0  BA4p
 9095   6141  21857  2.897 0.476     0.130     0.043      130    15.8  BA6
 2321   1632   5130  2.669 0.425     0.146     0.051       41     4.7  BA44
 3198   2184   6564  2.589 0.400     0.140     0.044       55     5.9  BA45
 3034   2100   4226  1.901 0.436     0.174     0.118      244     9.9  V1
 7288   4817  11472  2.180 0.432     0.181     0.078      174    22.2  V2
 2263   1492   4134  2.407 0.416     0.145     0.230      159    36.4  MT
 1105    796   3622  3.511 0.745     0.166     0.071       24     3.1  perirhinal

 mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub018 lh white 

computing statistics for each annotation in ./lh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

  796    422   1641  2.633 0.350     0.162     0.057       20     2.0  BA1
 2086   1444   3762  2.308 0.463     0.135     0.040       30     3.5  BA2
  849    557    863  2.020 0.445     0.131     0.036        7     1.3  BA3a
 1624   1124   2248  1.816 0.346     0.102     0.024       11     1.5  BA3b
 1522   1009   3694  2.941 0.458     0.102     0.025        9     1.7  BA4a
 1162    767   1943  2.631 0.491     0.108     0.046       16     2.5  BA4p
 4822   3276  11752  2.936 0.446     0.135     0.045       77     9.5  BA6
 1515   1090   3362  2.624 0.388     0.156     0.057       33     3.4  BA44
 1264    845   3095  2.744 0.368     0.158     0.055       31     2.9  BA45
 3279   2247   4606  1.912 0.443     0.179     0.122      256    11.6  V1
 3559   2380   5249  2.084 0.432     0.185     0.083       85    11.0  V2
  604    402   1032  2.290 0.412     0.141     0.047        9     1.2  MT
#--------------------------------------------
#@# BA Labels rh Fri Aug  9 00:51:40 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 314
Checking for and removing duplicates
Writing label file ./rh.BA1.label 4276
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 501
Checking for and removing duplicates
Writing label file ./rh.BA2.label 7188
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 262
Checking for and removing duplicates
Writing label file ./rh.BA3a.label 4242
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 370
Checking for and removing duplicates
Writing label file ./rh.BA3b.label 4892
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 545
Checking for and removing duplicates
Writing label file ./rh.BA4a.label 6292
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 302
Checking for and removing duplicates
Writing label file ./rh.BA4p.label 4775
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 1365
Checking for and removing duplicates
Writing label file ./rh.BA6.label 13621
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 741
Checking for and removing duplicates
Writing label file ./rh.BA44.label 7653
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 1304
Checking for and removing duplicates
Writing label file ./rh.BA45.label 6659
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 1009
Checking for and removing duplicates
Writing label file ./rh.V1.label 5736
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 2277
Checking for and removing duplicates
Writing label file ./rh.V2.label 10293
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 700
Checking for and removing duplicates
Writing label file ./rh.MT.label 2632
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 102
Checking for and removing duplicates
Writing label file ./rh.perirhinal.label 854
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 52
Checking for and removing duplicates
Writing label file ./rh.BA1.thresh.label 928
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 126
Checking for and removing duplicates
Writing label file ./rh.BA2.thresh.label 2814
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 48
Checking for and removing duplicates
Writing label file ./rh.BA3a.thresh.label 1746
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 257
Checking for and removing duplicates
Writing label file ./rh.BA3b.thresh.label 2440
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 140
Checking for and removing duplicates
Writing label file ./rh.BA4a.thresh.label 1528
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 150
Checking for and removing duplicates
Writing label file ./rh.BA4p.thresh.label 1639
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 770
Checking for and removing duplicates
Writing label file ./rh.BA6.thresh.label 7729
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 111
Checking for and removing duplicates
Writing label file ./rh.BA44.thresh.label 1123
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 300
Checking for and removing duplicates
Writing label file ./rh.BA45.thresh.label 1478
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 600
Checking for and removing duplicates
Writing label file ./rh.V1.thresh.label 3832
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 1069
Checking for and removing duplicates
Writing label file ./rh.V2.thresh.label 4506
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub018 --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 = sub018
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/sub018/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 140674
Number of reverse mapping hits = 92
Checking for and removing duplicates
Writing label file ./rh.MT.thresh.label 360
mri_label2label: Done


 mris_label2annot --s sub018 --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/sub018/label
cmdline mris_label2annot --s sub018 --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 snake5
machine  x86_64
user     fkaule

subject sub018
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/sub018/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 99034 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.BA.annot

 mris_label2annot --s sub018 --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/sub018/label
cmdline mris_label2annot --s sub018 --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 snake5
machine  x86_64
user     fkaule

subject sub018
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/sub018/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 118121 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label/rh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub018 rh white 

computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

  928    531   1920  2.488 0.307     0.157     0.058       21     2.5  BA1
 3550   2407   5755  2.239 0.438     0.115     0.039       33     5.8  BA2
 1097    722   1100  1.949 0.441     0.130     0.038       11     1.9  BA3a
 2235   1467   3499  2.024 0.486     0.122     0.035       27     3.2  BA3b
 1493    968   3438  2.828 0.528     0.117     0.043       36     3.4  BA4a
 1371    862   2318  2.673 0.427     0.105     0.065       32     4.4  BA4p
 9038   6079  20115  2.770 0.508     0.131     0.042      144    15.2  BA6
 3104   2109   6505  2.709 0.451     0.134     0.048       46     5.7  BA44
 4822   3257  10301  2.661 0.495     0.159     0.066      108    12.8  BA45
 3267   2258   4841  1.937 0.425     0.174     0.117       88    12.3  V1
 7626   5079  11946  2.119 0.445     0.176     0.093      389    29.3  V2
 2446   1668   4354  2.416 0.404     0.151     0.069       48     7.2  MT
  663    489   1850  2.969 0.754     0.173     0.069       14     2.0  perirhinal

 mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub018 rh white 

computing statistics for each annotation in ./rh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

  591    327   1198  2.461 0.285     0.175     0.069       16     1.9  BA1
 1814   1237   3024  2.241 0.427     0.109     0.029       14     2.1  BA2
  921    609    860  1.942 0.410     0.135     0.040        8     1.6  BA3a
 1885   1281   2678  1.882 0.424     0.110     0.029       16     2.3  BA3b
 1054    641   2371  2.830 0.576     0.118     0.055       35     2.9  BA4a
 1143    732   1919  2.683 0.411     0.109     0.071       29     4.2  BA4p
 5698   3807  12616  2.737 0.485     0.133     0.044      108    10.0  BA6
  788    545   1847  2.768 0.465     0.149     0.071       18     1.7  BA44
 1275    866   3257  2.811 0.408     0.169     0.072       32     3.5  BA45
 3083   2141   4478  1.922 0.439     0.170     0.116       79    11.2  V1
 3962   2660   5991  2.044 0.453     0.195     0.099      130    14.5  V2
  339    241    700  2.666 0.335     0.196     0.076        9     1.0  MT
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label lh Fri Aug  9 00:56:17 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub018 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

painting output onto subject sub018.
processing subject lh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 1051 points to lh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub018 lh white 

limiting computations to label ./lh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

  393    258   1336  3.300 0.587     0.155     0.080       12     1.5  ./lh.entorhinal_exvivo.label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label rh Fri Aug  9 00:56:32 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub018 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 

painting output onto subject sub018.
processing subject rh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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 814 points to rh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub018 rh white 

limiting computations to label ./rh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub018/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

  283    199   1034  3.216 0.614     0.154     0.059        4     0.8  ./rh.entorhinal_exvivo.label

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

Started at Thu Aug 8 10:53:55 CEST 2013 
Ended   at Fri Aug 9 00:56:47 CEST 2013
#@#%# recon-all-run-time-hours 14.048
recon-all -s sub018 finished without error at Fri Aug  9 00:56:47 CEST 2013