Mon May 6 20:01:32 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert /tmp/recon-all -s bert -i /space/freesurfer/test/tsd/i686/ref_subj/mri/orig/001.mgz -i /space/freesurfer/test/tsd/i686/ref_subj/mri/orig/002.mgz -i /space/freesurfer/test/tsd/i686/ref_subj/mri/orig/003.mgz -all -debug -clean -norandomness -allowcoredump -time subjid bert setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0/stable5 build-stamp.txt: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Linux node0360 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse 4194304 kbytes descriptors 32768 memorylocked 64 kbytes maxproc 30508 total used free shared buffers cached Mem: 3924864 998580 2926284 0 190184 564036 -/+ buffers/cache: 244360 3680504 Swap: 16777208 29996 16747212 ######################################## program versions used $Id: recon-all,v 1.379.2.69 2013/04/24 17:57:20 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: 2013/05/07-00:01:34-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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: 2013/05/07-00:01:37-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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: 2013/05/07-00:01:41-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:43-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:45-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:46-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:48-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:50-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:51-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:53-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:55-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:01:58-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:00-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:01-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:03-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:05-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:06-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:07-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:09-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:11-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:12-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:14-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:16-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:18-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:19-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:21-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_make_surfaces.c,v 1.127.2.5 2013/04/19 20:15:38 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:22-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:24-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:25-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:27-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:28-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:30-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $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: 2013/05/07-00:02:32-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $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: 2013/05/07-00:02:34-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:35-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:37-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:38-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/07-00:02:40-GMT BuildTimeStamp: May 3 2013 03:52:38 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: nicks Machine: node0360 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /space/freesurfer/centos4.0/stable/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /space/freesurfer/centos4.0/stable/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts/seed-*.crs.man.dat /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: No match. mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/tmp/cw256 /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/tmp/cw256': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/talairach.xfm /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/talairach.xfm': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/*.lta /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: No match. mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/optimal_preflood_height /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/optimal_preflood_height': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/optimal_skullstrip_invol /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/optimal_skullstrip_invol': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/brainmask.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/brainmask.mgz': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.mgz': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.manedit.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.manedit.mgz': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.seg.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.seg.mgz': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/tmp/control.dat /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/tmp/control.dat': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/brain.finalsurfs.manedit.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/brain.finalsurfs.manedit.mgz': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts/expert-options /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/scripts/expert-options': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/T2.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/T2.mgz': No such file or directory mv -f /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/FLAIR.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/trash mv: cannot stat `/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/FLAIR.mgz': No such file or directory /autofs/cluster/freesurfer/test/tsd/i686/bert mri_convert /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/001.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz mri_convert /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/001.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz... time:: 00:00:16 elapsed:: 00016 cmd:: mri_convert /autofs/cluster/freesurfer/test/tsd/i686/bert mri_convert /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/002.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz mri_convert /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/002.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/002.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz... time:: 00:00:16 elapsed:: 00016 cmd:: mri_convert /autofs/cluster/freesurfer/test/tsd/i686/bert mri_convert /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/003.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz mri_convert /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/003.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/freesurfer/test/subjects/x86_64/bert/mri/orig/003.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz... time:: 00:00:16 elapsed:: 00016 cmd:: mri_convert #-------------------------------------------- #@# MotionCor Mon May 6 20:05:05 EDT 2013 Found 3 runs /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /autofs/cluster/freesurfer/test/tsd/i686/bert mri_robust_template --mov /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz --average 1 --template /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001-iscale.txt /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002-iscale.txt /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003-iscale.txt --subsample 200 --lta /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.lta /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.lta /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.lta $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz'... converting source '/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz'... converting source '/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz'... converting source '/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/002.mgz ) to TP 1 ( /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/003.mgz ) to TP 1 ( /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: mapping movs and creating initial template... allow intensity scaling using median Writing final template: /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 8 minutes and 42 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf time:: 00:08:42 elapsed:: 00522 cmd:: mri_robust_template /autofs/cluster/freesurfer/test/tsd/i686/bert mri_convert /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz --conform mri_convert /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) 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 writing to /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz... time:: 00:00:12 elapsed:: 00012 cmd:: mri_convert mri_add_xform_to_header -c /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/talairach.xfm /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz INFO: extension is mgz time:: 00:00:07 elapsed:: 00007 cmd:: mri_add_xform_to_header #-------------------------------------------- #@# Talairach Mon May 6 20:14:41 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 time:: 00:02:29 elapsed:: 00149 cmd:: talairach_avi cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon May 6 20:19:29 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7614, pval=0.6675 >= threshold=0.0050) time:: 00:00:02 elapsed:: 00002 cmd:: talairach_afd awk -f /space/freesurfer/centos4.0/stable/bin/extract_talairach_avi_QA.awk /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/talairach_avi.log TalAviQA: 0.97409 z-score: 0 TalAviQA2: 23.5374 #-------------------------------------------- #@# Nu Intensity Correction Mon May 6 20:19:33 EDT 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri /space/freesurfer/centos4.0/stable/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 node0360 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 6 20:19:33 EDT 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.20719 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20719/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20719/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, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.20719/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon May 6 20:19:46 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.20719/nu0.mnc ./tmp.mri_nu_correct.mni.20719/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20719/0/ [nicks@node0360:/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/] [2013-05-06 20:19:47] running: /space/freesurfer/centos4.0/stable/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.20719/0/ ./tmp.mri_nu_correct.mni.20719/nu0.mnc ./tmp.mri_nu_correct.mni.20719/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 20 CV of field change: 0.000984265 [nicks@node0360:/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/] [2013-05-06 20:20:26] running: /space/freesurfer/centos4.0/stable/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20719/nu0.mnc ./tmp.mri_nu_correct.mni.20719/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon May 6 20:20:51 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.20719/nu1.mnc ./tmp.mri_nu_correct.mni.20719/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.20719/1/ [nicks@node0360:/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/] [2013-05-06 20:20:51] running: /space/freesurfer/centos4.0/stable/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.20719/1/ ./tmp.mri_nu_correct.mni.20719/nu1.mnc ./tmp.mri_nu_correct.mni.20719/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.000997088 [nicks@node0360:/autofs/cluster/freesurfer/test/tsd/i686/bert/mri/] [2013-05-06 20:21:12] running: /space/freesurfer/centos4.0/stable/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20719/nu1.mnc ./tmp.mri_nu_correct.mni.20719/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.20719/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20719/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/freesurfer/test/tsd/i686/bert/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.20719/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20719/ones.mgz sysname Linux hostname node0360 machine x86_64 user nicks input ./tmp.mri_nu_correct.mni.20719/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.20719/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.20719/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20719/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20719/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.20719/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20719/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20719/input.mean.dat sysname Linux hostname node0360 machine x86_64 user nicks UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20719/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.20719/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20719/ones.mgz --i ./tmp.mri_nu_correct.mni.20719/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20719/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20719/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.20719/ones.mgz --i ./tmp.mri_nu_correct.mni.20719/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20719/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20719/output.mean.dat sysname Linux hostname node0360 machine x86_64 user nicks UseRobust 0 Loading ./tmp.mri_nu_correct.mni.20719/ones.mgz Loading ./tmp.mri_nu_correct.mni.20719/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.20719/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.20719/nu2.mnc ./tmp.mri_nu_correct.mni.20719/nu2.mnc mul .96400286096517859027 Saving result to './tmp.mri_nu_correct.mni.20719/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.20719/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.20719/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.20719/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 25 seconds. mapping ( 8, 164) to ( 3, 110) Mon May 6 20:23:55 EDT 2013 mri_nu_correct.mni done time:: 00:04:22 elapsed:: 00262 cmd:: mri_nu_correct.mni mri_add_xform_to_header -c /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz time:: 00:00:05 elapsed:: 00005 cmd:: mri_add_xform_to_header #-------------------------------------------- #@# Intensity Normalization Mon May 6 20:24:01 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.106 -0.018 0.037 -5.930; 0.018 0.975 0.139 -22.800; -0.042 -0.168 1.107 -2.188; 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 = 15 Starting OpenSpline(): npoints = 15 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 81 (81), valley at 31 (31) csf peak at 40, setting threshold to 67 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 81 (81), valley at 23 (23) csf peak at 40, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 8 minutes and 24 seconds. time:: 00:08:27 elapsed:: 00507 cmd:: mri_normalize #-------------------------------------------- #@# Skull Stripping Mon May 6 20:32:30 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_em_register -skull nu.mgz /space/freesurfer/centos4.0/stable/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/space/freesurfer/centos4.0/stable/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=6.0 skull bounding box = (49, 46, 10) --> (204, 255, 206) using (101, 116, 108) as brain centroid... mean wm in atlas = 126, using box (82,90,84) --> (120, 141,132) to find MRI wm before smoothing, mri peak at 111 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.337057 @ (0.000, 0.000, 0.000) max log p = -4.330788 @ (-4.545, -4.545, -4.545) max log p = -4.299608 @ (2.273, -2.273, 2.273) max log p = -4.285196 @ (-1.136, 5.682, -5.682) max log p = -4.273677 @ (3.977, -0.568, 2.841) max log p = -4.273677 @ (0.000, 0.000, 0.000) Found translation: (0.6, -1.7, -5.1): log p = -4.274 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.3 (thresh=-4.3) 1.064 0.000 0.000 -7.413; 0.000 1.050 0.156 -25.218; 0.000 -0.112 0.997 8.982; 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) 1.064 0.000 0.000 -7.413; 0.000 1.050 0.156 -25.218; 0.000 -0.112 0.997 8.982; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.101 0.012 -0.067 -9.939; 0.000 1.079 0.229 -36.966; 0.070 -0.180 0.982 13.987; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.101 0.012 -0.067 -9.939; 0.000 1.079 0.229 -36.966; 0.070 -0.180 0.982 13.987; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.103 0.012 -0.067 -10.570; -0.000 1.081 0.229 -37.127; 0.069 -0.179 0.979 13.794; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.100 0.012 -0.067 -10.250; -0.000 1.078 0.229 -36.756; 0.069 -0.178 0.975 14.118; 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) 1.100 0.012 -0.067 -10.250; -0.000 1.078 0.229 -36.756; 0.069 -0.178 0.975 14.118; 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 1.09999 0.01219 -0.06666 -10.25042; -0.00002 1.07821 0.22894 -36.75591; 0.06912 -0.17811 0.97522 14.11849; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.09999 0.01219 -0.06666 -10.25042; -0.00002 1.07821 0.22894 -36.75591; 0.06912 -0.17811 0.97522 14.11849; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.100 0.012 -0.067 -10.250; -0.000 1.078 0.229 -36.756; 0.069 -0.178 0.975 14.118; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.3) transform before final EM align: 1.100 0.012 -0.067 -10.250; -0.000 1.078 0.229 -36.756; 0.069 -0.178 0.975 14.118; 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 1.09999 0.01219 -0.06666 -10.25042; -0.00002 1.07821 0.22894 -36.75591; 0.06912 -0.17811 0.97522 14.11849; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.09999 0.01219 -0.06666 -10.25042; -0.00002 1.07821 0.22894 -36.75591; 0.06912 -0.17811 0.97522 14.11849; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.100 0.012 -0.067 -10.250; -0.000 1.078 0.229 -36.756; 0.069 -0.178 0.975 14.118; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 78 minutes and 46 seconds. time:: 01:18:47 elapsed:: 04727 cmd:: mri_em_register mri_watershed -T1 -brain_atlas /space/freesurfer/centos4.0/stable/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=115 z=112 r=87 first estimation of the main basin volume: 2792504 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=157, y=113, z=70, Imax=255 CSF=15, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=-629994119 voxels, voxel volume =1.000 = 3664973177 mmm3 = 3664973.056 cm3 done. PostAnalyze...Basin Prior 79 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=127,y=122, z=106, r=10361 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=3, CSF_MAX=17 , nb = 808585920 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=143 , nb = 2305 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=52 , nb = 2034 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=16 , nb = 19981 LEFT_BRAIN CSF_MIN=0, CSF_intensity=3, CSF_MAX=16 , nb = 808560550 OTHER CSF_MIN=1, CSF_intensity=14, CSF_MAX=33 , nb = 325 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 17, 32, 57, 80 after analyzing : 17, 48, 57, 56 RIGHT_CER before analyzing : 143, 74, 62, 88 after analyzing : 39, 74, 74, 77 LEFT_CER before analyzing : 52, 65, 71, 90 after analyzing : 52, 69, 71, 74 RIGHT_BRAIN before analyzing : 16, 32, 58, 79 after analyzing : 16, 49, 58, 56 LEFT_BRAIN before analyzing : 16, 32, 59, 80 after analyzing : 16, 50, 59, 57 OTHER before analyzing : 33, 26, 21, 39 after analyzing : 22, 26, 26, 29 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 71.622, std = 8.923 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.97, sigma = 4.50 after rotation: sse = 2.97, sigma = 4.50 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.98, its var is 3.44 before Erosion-Dilatation 0.11% 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...51 iterations mri_strip_skull: done peeling brain Brain Size = 1837761 voxels, voxel volume = 1.000 mm3 = 1837761 mmm3 = 1837.761 cm3 ****************************** Saving brainmask.auto.mgz done time:: 00:01:20 elapsed:: 00080 cmd:: mri_watershed cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon May 6 21:52:43 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /space/freesurfer/centos4.0/stable/average/RB_all_2008-03-26.gca transforms/talairach.lta 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 '/space/freesurfer/centos4.0/stable/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=19.0 skull bounding box = (65, 59, 25) --> (191, 188, 206) using (107, 102, 116) as brain centroid... mean wm in atlas = 107, using box (92,86,94) --> (122, 117,138) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 initial log_p = -3.9 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.913651 @ (0.000, 0.000, 0.000) max log p = -3.808181 @ (-4.545, -4.545, -4.545) max log p = -3.780585 @ (2.273, 2.273, -2.273) max log p = -3.738707 @ (-1.136, 1.136, 1.136) max log p = -3.718452 @ (-0.568, 0.568, 0.568) max log p = -3.718452 @ (0.000, 0.000, 0.000) Found translation: (-4.0, -0.6, -5.1): log p = -3.718 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.7 (thresh=-3.7) 1.064 0.000 0.000 -12.315; 0.000 1.140 0.111 -29.561; 0.000 -0.161 0.906 24.547; 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=-3.5) 1.064 0.000 0.000 -12.315; 0.000 1.140 0.111 -29.561; 0.000 -0.161 0.906 24.547; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.5, old_max_log_p =-3.6 (thresh=-3.5) 1.083 0.038 0.004 -17.852; -0.034 1.118 0.109 -22.354; 0.000 -0.158 0.889 27.937; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5) 1.103 -0.035 -0.005 -10.676; 0.037 1.133 0.140 -34.954; 0.001 -0.195 0.885 32.599; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.103 -0.035 -0.005 -10.676; 0.037 1.133 0.140 -34.954; 0.001 -0.195 0.885 32.599; 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=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.009 -0.222 0.879 33.997; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.009 -0.222 0.879 33.997; 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 1.10517 -0.00597 -0.00875 -13.56926; 0.01038 1.12877 0.16217 -34.21801; 0.00940 -0.22223 0.87908 33.99701; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.10517 -0.00597 -0.00875 -13.56926; 0.01038 1.12877 0.16217 -34.21801; 0.00940 -0.22223 0.87908 33.99701; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.009 -0.222 0.879 33.997; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.4 (old=-3.9) transform before final EM align: 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.009 -0.222 0.879 33.997; 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 1.10517 -0.00597 -0.00875 -13.56926; 0.01038 1.12877 0.16217 -34.21801; 0.00940 -0.22223 0.87908 33.99701; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.10517 -0.00597 -0.00875 -13.56926; 0.01038 1.12877 0.16217 -34.21801; 0.00940 -0.22223 0.87908 33.99701; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.009 -0.222 0.879 33.997; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 59 minutes and 5 seconds. time:: 00:59:05 elapsed:: 03545 cmd:: mri_em_register #-------------------------------------- #@# CA Normalize Mon May 6 22:51:51 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /space/freesurfer/centos4.0/stable/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 '/space/freesurfer/centos4.0/stable/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=16.0 skull bounding box = (64, 58, 25) --> (191, 188, 206) using (106, 101, 116) as brain centroid... mean wm in atlas = 107, using box (90,85,94) --> (121, 116,138) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 0.982 scaling channel 0 by 0.981651 using 244171 sample points... INFO: compute sample coordinates transform 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.009 -0.222 0.879 33.997; 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 (125, 60, 24) --> (188, 159, 209) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 175.0 0 of 4947 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 62, 24) --> (128, 160, 210) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 175.0 1 of 4695 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 137, 55) --> (173, 176, 115) Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 175.0 0 of 62 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 137, 53) --> (128, 175, 117) Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 175.0 0 of 31 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 129, 95) --> (143, 189, 128) Brain_Stem: limiting intensities to 88.0 --> 175.0 0 of 255 (0.0%) samples deleted using 9990 total control points for intensity normalization... bias field = 1.005 +- 0.045 25 of 9989 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 60, 24) --> (188, 159, 209) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 166.0 0 of 4972 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 62, 24) --> (128, 160, 210) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 166.0 0 of 4883 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 137, 55) --> (173, 176, 115) Left_Cerebellum_White_Matter: limiting intensities to 87.0 --> 166.0 0 of 85 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 137, 53) --> (128, 175, 117) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 166.0 0 of 53 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 129, 95) --> (143, 189, 128) Brain_Stem: limiting intensities to 83.0 --> 166.0 0 of 261 (0.0%) samples deleted using 10254 total control points for intensity normalization... bias field = 1.028 +- 0.032 37 of 10254 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 60, 24) --> (188, 159, 209) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 165.0 0 of 4902 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (70, 62, 24) --> (128, 160, 210) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 165.0 0 of 4774 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 137, 55) --> (173, 176, 115) Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 165.0 0 of 109 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 137, 53) --> (128, 175, 117) Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 165.0 2 of 79 (2.5%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (113, 129, 95) --> (143, 189, 128) Brain_Stem: limiting intensities to 82.0 --> 165.0 0 of 288 (0.0%) samples deleted using 10152 total control points for intensity normalization... bias field = 1.024 +- 0.028 38 of 10150 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 5 minutes and 13 seconds. time:: 00:05:14 elapsed:: 00314 cmd:: mri_ca_normalize #-------------------------------------- #@# CA Reg Mon May 6 22:57:10 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /space/freesurfer/centos4.0/stable/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 reading input volume 'norm.mgz'... reading GCA '/space/freesurfer/centos4.0/stable/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.14 (predicted orig area = 7.0) 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=0.813, neg=0, invalid=96777 0001: dt=295.936000, rms=0.733 (9.886%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.714 (2.578%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.706 (1.083%), neg=0, invalid=96777 0004: dt=295.936000, rms=0.700 (0.907%), neg=0, invalid=96777 0005: dt=110.976000, rms=0.696 (0.564%), neg=0, invalid=96777 0006: dt=369.920000, rms=0.692 (0.578%), neg=0, invalid=96777 0007: dt=92.480000, rms=0.689 (0.375%), neg=0, invalid=96777 0008: dt=517.888000, rms=0.685 (0.625%), neg=0, invalid=96777 0009: dt=92.480000, rms=0.684 (0.176%), neg=0, invalid=96777 0010: dt=92.480000, rms=0.683 (0.133%), neg=0, invalid=96777 0011: dt=92.480000, rms=0.682 (0.178%), neg=0, invalid=96777 0012: dt=92.480000, rms=0.680 (0.219%), neg=0, invalid=96777 0013: dt=92.480000, rms=0.678 (0.242%), neg=0, invalid=96777 0014: dt=92.480000, rms=0.677 (0.215%), neg=0, invalid=96777 0015: dt=92.480000, rms=0.676 (0.226%), neg=0, invalid=96777 0016: dt=92.480000, rms=0.674 (0.223%), neg=0, invalid=96777 0017: dt=92.480000, rms=0.673 (0.181%), neg=0, invalid=96777 0018: dt=92.480000, rms=0.672 (0.183%), neg=0, invalid=96777 0019: dt=92.480000, rms=0.670 (0.202%), neg=0, invalid=96777 0020: dt=92.480000, rms=0.669 (0.185%), neg=0, invalid=96777 0021: dt=92.480000, rms=0.668 (0.146%), neg=0, invalid=96777 0022: dt=92.480000, rms=0.667 (0.159%), neg=0, invalid=96777 0023: dt=92.480000, rms=0.666 (0.175%), neg=0, invalid=96777 0024: dt=92.480000, rms=0.665 (0.176%), neg=0, invalid=96777 0025: dt=92.480000, rms=0.664 (0.152%), neg=0, invalid=96777 0026: dt=92.480000, rms=0.663 (0.138%), neg=0, invalid=96777 0027: dt=92.480000, rms=0.662 (0.147%), neg=0, invalid=96777 0028: dt=92.480000, rms=0.661 (0.146%), neg=0, invalid=96777 0029: dt=92.480000, rms=0.660 (0.140%), neg=0, invalid=96777 0030: dt=92.480000, rms=0.659 (0.124%), neg=0, invalid=96777 0031: dt=92.480000, rms=0.658 (0.105%), neg=0, invalid=96777 0032: dt=129.472000, rms=0.658 (0.025%), neg=0, invalid=96777 0033: dt=129.472000, rms=0.658 (0.021%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.657 (0.080%), neg=0, invalid=96777 0035: dt=129.472000, rms=0.657 (0.071%), neg=0, invalid=96777 0036: dt=129.472000, rms=0.657 (0.034%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.657, neg=0, invalid=96777 0037: dt=221.952000, rms=0.653 (0.515%), neg=0, invalid=96777 0038: dt=73.984000, rms=0.653 (0.038%), neg=0, invalid=96777 0039: dt=73.984000, rms=0.653 (0.010%), neg=0, invalid=96777 0040: dt=73.984000, rms=0.653 (0.018%), neg=0, invalid=96777 0041: dt=73.984000, rms=0.652 (0.091%), neg=0, invalid=96777 0042: dt=73.984000, rms=0.652 (0.121%), neg=0, invalid=96777 0043: dt=73.984000, rms=0.651 (0.115%), neg=0, invalid=96777 0044: dt=73.984000, rms=0.650 (0.095%), neg=0, invalid=96777 0045: dt=32.368000, rms=0.650 (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=0.658, neg=0, invalid=96777 0046: dt=62.208000, rms=0.655 (0.517%), neg=0, invalid=96777 0047: dt=248.832000, rms=0.640 (2.291%), neg=0, invalid=96777 0048: dt=31.104000, rms=0.636 (0.640%), neg=0, invalid=96777 0049: dt=82.944000, rms=0.634 (0.277%), neg=0, invalid=96777 0050: dt=103.680000, rms=0.629 (0.868%), neg=0, invalid=96777 0051: dt=20.736000, rms=0.628 (0.168%), neg=0, invalid=96777 0052: dt=20.736000, rms=0.627 (0.070%), neg=0, invalid=96777 0053: dt=20.736000, rms=0.627 (0.068%), neg=0, invalid=96777 0054: dt=20.736000, rms=0.626 (0.143%), neg=0, invalid=96777 0055: dt=20.736000, rms=0.624 (0.327%), neg=0, invalid=96777 0056: dt=20.736000, rms=0.621 (0.452%), neg=0, invalid=96777 0057: dt=20.736000, rms=0.618 (0.434%), neg=0, invalid=96777 0058: dt=20.736000, rms=0.616 (0.368%), neg=0, invalid=96777 0059: dt=20.736000, rms=0.614 (0.321%), neg=0, invalid=96777 0060: dt=20.736000, rms=0.612 (0.278%), neg=0, invalid=96777 0061: dt=20.736000, rms=0.611 (0.267%), neg=0, invalid=96777 0062: dt=20.736000, rms=0.609 (0.296%), neg=0, invalid=96777 0063: dt=20.736000, rms=0.607 (0.319%), neg=0, invalid=96777 0064: dt=20.736000, rms=0.605 (0.287%), neg=0, invalid=96777 0065: dt=20.736000, rms=0.604 (0.235%), neg=0, invalid=96777 0066: dt=20.736000, rms=0.603 (0.191%), neg=0, invalid=96777 0067: dt=20.736000, rms=0.602 (0.135%), neg=0, invalid=96777 0068: dt=20.736000, rms=0.601 (0.133%), neg=0, invalid=96777 0069: dt=20.736000, rms=0.600 (0.163%), neg=0, invalid=96777 0070: dt=20.736000, rms=0.599 (0.165%), neg=0, invalid=96777 0071: dt=20.736000, rms=0.598 (0.149%), neg=0, invalid=96777 0072: dt=20.736000, rms=0.597 (0.154%), neg=0, invalid=96777 0073: dt=20.736000, rms=0.596 (0.129%), neg=0, invalid=96777 0074: dt=20.736000, rms=0.596 (0.088%), neg=0, invalid=96777 0075: dt=20.736000, rms=0.595 (0.091%), neg=0, invalid=96777 0076: dt=20.736000, rms=0.595 (0.098%), neg=0, invalid=96777 0077: dt=20.736000, rms=0.594 (0.119%), neg=0, invalid=96777 0078: dt=20.736000, rms=0.593 (0.116%), neg=0, invalid=96777 0079: dt=82.944000, rms=0.593 (0.039%), neg=0, invalid=96777 0080: dt=82.944000, rms=0.593 (-0.088%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.593, neg=0, invalid=96777 0081: dt=36.288000, rms=0.592 (0.276%), neg=0, invalid=96777 0082: dt=103.680000, rms=0.591 (0.145%), neg=0, invalid=96777 0083: dt=103.680000, rms=0.591 (-0.311%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.623, neg=0, invalid=96777 0084: dt=11.200000, rms=0.622 (0.301%), neg=0, invalid=96777 0085: dt=11.200000, rms=0.621 (0.111%), neg=0, invalid=96777 0086: dt=11.200000, rms=0.620 (0.092%), neg=0, invalid=96777 0087: dt=11.200000, rms=0.620 (0.006%), neg=0, invalid=96777 0088: dt=11.200000, rms=0.620 (-0.144%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.620, neg=0, invalid=96777 0089: dt=11.200000, rms=0.619 (0.125%), neg=0, invalid=96777 0090: dt=11.200000, rms=0.619 (0.036%), neg=0, invalid=96777 0091: dt=11.200000, rms=0.619 (0.001%), neg=0, invalid=96777 0092: dt=11.200000, rms=0.619 (-0.040%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.666, neg=0, invalid=96777 0093: dt=1.750000, rms=0.665 (0.094%), neg=0, invalid=96777 0094: dt=0.720000, rms=0.665 (0.010%), neg=0, invalid=96777 0095: dt=0.720000, rms=0.665 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=96777 0096: dt=0.252000, rms=0.665 (0.003%), neg=0, invalid=96777 0097: dt=0.216000, rms=0.665 (0.001%), neg=0, invalid=96777 0098: dt=0.216000, rms=0.665 (0.001%), neg=0, invalid=96777 0099: dt=0.216000, rms=0.665 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.739, neg=0, invalid=96777 0100: dt=1.395492, rms=0.732 (1.005%), neg=0, invalid=96777 0101: dt=1.792000, rms=0.728 (0.508%), neg=0, invalid=96777 0102: dt=1.400000, rms=0.725 (0.410%), neg=0, invalid=96777 0103: dt=0.456522, rms=0.725 (0.068%), neg=0, invalid=96777 0104: dt=0.456522, rms=0.724 (0.047%), neg=0, invalid=96777 0105: dt=0.456522, rms=0.724 (0.069%), neg=0, invalid=96777 0106: dt=0.456522, rms=0.723 (0.081%), neg=0, invalid=96777 0107: dt=0.456522, rms=0.723 (0.085%), neg=0, invalid=96777 0108: dt=0.456522, rms=0.722 (0.050%), neg=0, invalid=96777 0109: dt=0.456522, rms=0.722 (-0.028%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.722, neg=0, invalid=96777 0110: dt=1.792000, rms=0.721 (0.223%), neg=0, invalid=96777 0111: dt=0.192000, rms=0.721 (0.007%), neg=0, invalid=96777 0112: dt=0.192000, rms=0.721 (0.001%), neg=0, invalid=96777 0113: dt=0.192000, rms=0.721 (-0.011%), 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=0.676, neg=0, invalid=96777 0114: dt=0.139423, rms=0.671 (0.816%), neg=0, invalid=96777 0115: dt=0.247093, rms=0.670 (0.088%), neg=0, invalid=96777 0116: dt=0.123547, rms=0.668 (0.370%), neg=0, invalid=96777 0117: dt=0.123547, rms=0.666 (0.260%), neg=0, invalid=96777 0118: dt=0.123547, rms=0.666 (0.079%), neg=0, invalid=96777 0119: dt=0.123547, rms=0.666 (-0.003%), neg=0, invalid=96777 0120: dt=0.028000, rms=0.666 (0.002%), neg=0, invalid=96777 0121: dt=0.080000, rms=0.666 (0.003%), neg=0, invalid=96777 0122: dt=0.112000, rms=0.665 (0.030%), neg=0, invalid=96777 0123: dt=0.448000, rms=0.665 (0.102%), neg=0, invalid=96777 0124: dt=0.112000, rms=0.664 (0.040%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.664, neg=0, invalid=96777 0125: dt=0.320000, rms=0.661 (0.497%), neg=0, invalid=96777 0126: dt=0.000000, rms=0.661 (0.003%), neg=0, invalid=96777 0127: dt=0.050000, rms=0.661 (-0.107%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.17359 (27) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (1700 voxels, overlap=0.637) Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (1700 voxels, peak = 26), gca=25.6 gca peak = 0.14022 (22) mri peak = 0.19850 (30) Right_Lateral_Ventricle (43): linear fit = 1.25 x + 0.0 (1207 voxels, overlap=0.360) Right_Lateral_Ventricle (43): linear fit = 1.25 x + 0.0 (1207 voxels, peak = 28), gca=27.6 gca peak = 0.24234 (100) mri peak = 0.09938 (96) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (560 voxels, overlap=0.923) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (560 voxels, peak = 94), gca=94.5 gca peak = 0.19192 (97) mri peak = 0.07678 (97) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (516 voxels, overlap=0.903) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (516 voxels, peak = 96), gca=95.5 gca peak = 0.24007 (63) mri peak = 0.07044 (76) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (954 voxels, overlap=0.029) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (954 voxels, peak = 75), gca=75.3 gca peak = 0.29892 (64) mri peak = 0.07287 (78) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (997 voxels, overlap=0.022) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (997 voxels, peak = 76), gca=76.5 gca peak = 0.12541 (104) mri peak = 0.10860 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (91389 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (91389 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.10510 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (96359 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (96359 voxels, peak = 106), gca=105.6 gca peak = 0.11691 (63) mri peak = 0.04323 (83) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (41687 voxels, overlap=0.008) Left_Cerebral_Cortex (3): linear fit = 1.27 x + 0.0 (41687 voxels, peak = 80), gca=80.3 gca peak = 0.13270 (63) mri peak = 0.04590 (80) Right_Cerebral_Cortex (42): linear fit = 1.27 x + 0.0 (43477 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.27 x + 0.0 (43477 voxels, peak = 80), gca=80.3 gca peak = 0.15182 (70) mri peak = 0.17533 (83) Right_Caudate (50): linear fit = 1.15 x + 0.0 (370 voxels, overlap=0.044) Right_Caudate (50): linear fit = 1.15 x + 0.0 (370 voxels, peak = 81), gca=80.8 gca peak = 0.14251 (76) mri peak = 0.11521 (81) Left_Caudate (11): linear fit = 1.03 x + 0.0 (947 voxels, overlap=0.816) Left_Caudate (11): linear fit = 1.03 x + 0.0 (947 voxels, peak = 79), gca=78.7 gca peak = 0.12116 (60) mri peak = 0.05334 (82) Left_Cerebellum_Cortex (8): linear fit = 1.36 x + 0.0 (27252 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.36 x + 0.0 (27252 voxels, peak = 81), gca=81.3 gca peak = 0.12723 (61) mri peak = 0.03961 (84) Right_Cerebellum_Cortex (47): linear fit = 1.36 x + 0.0 (28478 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.36 x + 0.0 (28478 voxels, peak = 83), gca=82.7 gca peak = 0.22684 (88) mri peak = 0.09185 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (10119 voxels, overlap=0.477) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (10119 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.05664 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (8148 voxels, overlap=0.921) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (8148 voxels, peak = 93), gca=92.7 gca peak = 0.25455 (62) mri peak = 0.09886 (79) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (444 voxels, overlap=0.073) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (444 voxels, peak = 78), gca=77.8 gca peak = 0.39668 (62) mri peak = 0.10000 (78) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (302 voxels, overlap=0.442) Right_Amygdala (54): linear fit = 1.24 x + 0.0 (302 voxels, peak = 77), gca=76.6 gca peak = 0.10129 (93) mri peak = 0.08241 (96) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (6077 voxels, overlap=0.802) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (6077 voxels, peak = 96), gca=96.3 gca peak = 0.12071 (89) mri peak = 0.09563 (96) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (5043 voxels, overlap=0.664) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (5043 voxels, peak = 94), gca=93.9 gca peak = 0.13716 (82) mri peak = 0.07100 (91) Left_Putamen (12): linear fit = 1.10 x + 0.0 (3031 voxels, overlap=0.516) Left_Putamen (12): linear fit = 1.10 x + 0.0 (3031 voxels, peak = 90), gca=89.8 gca peak = 0.15214 (84) mri peak = 0.06826 (84) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2946 voxels, overlap=0.916) Right_Putamen (51): linear fit = 1.05 x + 0.0 (2946 voxels, peak = 89), gca=88.6 gca peak = 0.08983 (85) mri peak = 0.11888 (91) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11494 voxels, overlap=0.385) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11494 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.09939 (100) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1061 voxels, overlap=0.565) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1061 voxels, peak = 97), gca=97.1 gca peak = 0.12914 (94) mri peak = 0.09091 (101) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1485 voxels, overlap=0.651) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1485 voxels, peak = 98), gca=98.2 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.50000 (28) Fourth_Ventricle (15): linear fit = 0.92 x + 0.0 (863 voxels, overlap=0.267) Fourth_Ventricle (15): linear fit = 0.92 x + 0.0 (863 voxels, peak = 25), gca=24.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) 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 1.24 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.08 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=0.661, neg=0, invalid=96777 0128: dt=110.976000, rms=0.638 (3.448%), neg=0, invalid=96777 0129: dt=369.920000, rms=0.625 (1.991%), neg=0, invalid=96777 0130: dt=129.472000, rms=0.621 (0.600%), neg=0, invalid=96777 0131: dt=295.936000, rms=0.617 (0.691%), neg=0, invalid=96777 0132: dt=73.984000, rms=0.614 (0.530%), neg=0, invalid=96777 0133: dt=517.888000, rms=0.611 (0.533%), neg=0, invalid=96777 0134: dt=129.472000, rms=0.608 (0.367%), neg=0, invalid=96777 0135: dt=110.976000, rms=0.607 (0.126%), neg=0, invalid=96777 0136: dt=295.936000, rms=0.606 (0.213%), neg=0, invalid=96777 0137: dt=92.480000, rms=0.605 (0.153%), neg=0, invalid=96777 0138: dt=1479.680000, rms=0.602 (0.601%), neg=0, invalid=96777 0139: dt=73.984000, rms=0.600 (0.351%), neg=0, invalid=96777 0140: dt=221.952000, rms=0.599 (0.078%), neg=0, invalid=96777 0141: dt=517.888000, rms=0.598 (0.225%), neg=0, invalid=96777 0142: dt=73.984000, rms=0.597 (0.076%), neg=0, invalid=96777 0143: dt=110.976000, rms=0.597 (0.016%), neg=0, invalid=96777 0144: dt=110.976000, rms=0.597 (0.053%), neg=0, invalid=96777 0145: dt=110.976000, rms=0.596 (0.075%), neg=0, invalid=96777 0146: dt=110.976000, rms=0.596 (0.096%), neg=0, invalid=96777 0147: dt=110.976000, rms=0.595 (0.119%), neg=0, invalid=96777 0148: dt=110.976000, rms=0.594 (0.140%), neg=0, invalid=96777 0149: dt=110.976000, rms=0.593 (0.151%), neg=0, invalid=96777 0150: dt=110.976000, rms=0.592 (0.156%), neg=0, invalid=96777 0151: dt=110.976000, rms=0.592 (0.155%), neg=0, invalid=96777 0152: dt=110.976000, rms=0.591 (0.161%), neg=0, invalid=96777 0153: dt=110.976000, rms=0.590 (0.164%), neg=0, invalid=96777 0154: dt=110.976000, rms=0.589 (0.155%), neg=0, invalid=96777 0155: dt=110.976000, rms=0.588 (0.145%), neg=0, invalid=96777 0156: dt=110.976000, rms=0.587 (0.138%), neg=0, invalid=96777 0157: dt=110.976000, rms=0.586 (0.121%), neg=0, invalid=96777 0158: dt=110.976000, rms=0.586 (0.121%), neg=0, invalid=96777 0159: dt=110.976000, rms=0.585 (0.118%), neg=0, invalid=96777 0160: dt=110.976000, rms=0.584 (0.097%), neg=0, invalid=96777 0161: dt=110.976000, rms=0.584 (0.079%), neg=0, invalid=96777 0162: dt=110.976000, rms=0.584 (0.066%), neg=0, invalid=96777 0163: dt=110.976000, rms=0.583 (0.121%), neg=0, invalid=96777 0164: dt=110.976000, rms=0.582 (0.110%), neg=0, invalid=96777 0165: dt=110.976000, rms=0.582 (0.085%), neg=0, invalid=96777 0166: dt=110.976000, rms=0.581 (0.055%), neg=0, invalid=96777 0167: dt=110.976000, rms=0.581 (0.119%), neg=0, invalid=96777 0168: dt=110.976000, rms=0.580 (0.134%), neg=0, invalid=96777 0169: dt=110.976000, rms=0.579 (0.095%), neg=0, invalid=96777 0170: dt=110.976000, rms=0.579 (0.050%), neg=0, invalid=96777 0171: dt=110.976000, rms=0.579 (0.052%), neg=0, invalid=96777 0172: dt=110.976000, rms=0.578 (0.133%), neg=0, invalid=96777 0173: dt=110.976000, rms=0.577 (0.090%), neg=0, invalid=96777 0174: dt=110.976000, rms=0.577 (0.065%), neg=0, invalid=96777 0175: dt=110.976000, rms=0.577 (0.068%), neg=0, invalid=96777 0176: dt=110.976000, rms=0.576 (0.089%), neg=0, invalid=96777 0177: dt=110.976000, rms=0.576 (0.097%), neg=0, invalid=96777 0178: dt=110.976000, rms=0.575 (0.067%), neg=0, invalid=96777 0179: dt=110.976000, rms=0.575 (0.068%), neg=0, invalid=96777 0180: dt=110.976000, rms=0.574 (0.074%), neg=0, invalid=96777 0181: dt=110.976000, rms=0.574 (0.075%), neg=0, invalid=96777 0182: dt=110.976000, rms=0.574 (0.052%), neg=0, invalid=96777 0183: dt=110.976000, rms=0.573 (0.055%), neg=0, invalid=96777 0184: dt=110.976000, rms=0.573 (0.041%), neg=0, invalid=96777 0185: dt=110.976000, rms=0.573 (0.098%), neg=0, invalid=96777 0186: dt=110.976000, rms=0.572 (0.073%), neg=0, invalid=96777 0187: dt=110.976000, rms=0.572 (0.040%), neg=0, invalid=96777 0188: dt=110.976000, rms=0.572 (0.025%), neg=0, invalid=96777 0189: dt=110.976000, rms=0.572 (0.048%), neg=0, invalid=96777 0190: dt=110.976000, rms=0.571 (0.076%), neg=0, invalid=96777 0191: dt=110.976000, rms=0.571 (0.052%), neg=0, invalid=96777 0192: dt=110.976000, rms=0.571 (0.043%), neg=0, invalid=96777 0193: dt=110.976000, rms=0.570 (0.017%), neg=0, invalid=96777 0194: dt=110.976000, rms=0.570 (0.036%), neg=0, invalid=96777 0195: dt=110.976000, rms=0.570 (0.084%), neg=0, invalid=96777 0196: dt=110.976000, rms=0.570 (0.039%), neg=0, invalid=96777 0197: dt=110.976000, rms=0.569 (0.029%), neg=0, invalid=96777 0198: dt=110.976000, rms=0.569 (0.017%), neg=0, invalid=96777 0199: dt=110.976000, rms=0.569 (0.047%), neg=0, invalid=96777 0200: dt=110.976000, rms=0.569 (0.054%), neg=0, invalid=96777 0201: dt=110.976000, rms=0.568 (0.038%), neg=0, invalid=96777 0202: dt=110.976000, rms=0.568 (0.042%), neg=0, invalid=96777 0203: dt=110.976000, rms=0.568 (0.035%), neg=0, invalid=96777 0204: dt=110.976000, rms=0.568 (0.046%), neg=0, invalid=96777 0205: dt=110.976000, rms=0.568 (0.039%), neg=0, invalid=96777 0206: dt=110.976000, rms=0.567 (0.029%), neg=0, invalid=96777 0207: dt=110.976000, rms=0.567 (0.031%), neg=0, invalid=96777 0208: dt=110.976000, rms=0.567 (0.034%), neg=0, invalid=96777 0209: dt=110.976000, rms=0.567 (0.036%), neg=0, invalid=96777 0210: dt=110.976000, rms=0.567 (0.036%), neg=0, invalid=96777 0211: dt=110.976000, rms=0.566 (0.033%), neg=0, invalid=96777 0212: dt=110.976000, rms=0.566 (0.031%), neg=0, invalid=96777 0213: dt=110.976000, rms=0.566 (0.031%), neg=0, invalid=96777 0214: dt=110.976000, rms=0.566 (0.032%), neg=0, invalid=96777 0215: dt=110.976000, rms=0.566 (0.017%), neg=0, invalid=96777 0216: dt=110.976000, rms=0.566 (-0.002%), neg=0, invalid=96777 0217: dt=0.000000, rms=0.566 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.566, neg=0, invalid=96777 0218: dt=369.920000, rms=0.565 (0.096%), neg=0, invalid=96777 0219: dt=110.976000, rms=0.565 (0.061%), neg=0, invalid=96777 0220: dt=27.744000, rms=0.565 (-0.000%), neg=0, invalid=96777 0221: dt=27.744000, rms=0.565 (0.002%), neg=0, invalid=96777 0222: dt=27.744000, rms=0.565 (0.001%), neg=0, invalid=96777 0223: dt=27.744000, rms=0.565 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.567, neg=0, invalid=96777 0224: dt=145.152000, rms=0.563 (0.739%), neg=0, invalid=96777 0225: dt=124.416000, rms=0.559 (0.760%), neg=0, invalid=96777 0226: dt=31.104000, rms=0.557 (0.282%), neg=0, invalid=96777 0227: dt=145.152000, rms=0.555 (0.387%), neg=0, invalid=96777 0228: dt=31.104000, rms=0.553 (0.262%), neg=0, invalid=96777 0229: dt=124.416000, rms=0.551 (0.415%), neg=0, invalid=96777 0230: dt=20.736000, rms=0.550 (0.190%), neg=0, invalid=96777 0231: dt=124.416000, rms=0.549 (0.214%), neg=0, invalid=96777 0232: dt=36.288000, rms=0.548 (0.249%), neg=0, invalid=96777 0233: dt=145.152000, rms=0.546 (0.288%), neg=0, invalid=96777 0234: dt=36.288000, rms=0.545 (0.185%), neg=0, invalid=96777 0235: dt=145.152000, rms=0.544 (0.213%), neg=0, invalid=96777 0236: dt=36.288000, rms=0.543 (0.175%), neg=0, invalid=96777 0237: dt=82.944000, rms=0.542 (0.081%), neg=0, invalid=96777 0238: dt=36.288000, rms=0.542 (0.161%), neg=0, invalid=96777 0239: dt=36.288000, rms=0.541 (0.037%), neg=0, invalid=96777 0240: dt=36.288000, rms=0.541 (0.089%), neg=0, invalid=96777 0241: dt=36.288000, rms=0.540 (0.118%), neg=0, invalid=96777 0242: dt=36.288000, rms=0.540 (0.127%), neg=0, invalid=96777 0243: dt=36.288000, rms=0.538 (0.203%), neg=0, invalid=96777 0244: dt=36.288000, rms=0.537 (0.248%), neg=0, invalid=96777 0245: dt=36.288000, rms=0.536 (0.244%), neg=0, invalid=96777 0246: dt=36.288000, rms=0.535 (0.233%), neg=0, invalid=96777 0247: dt=36.288000, rms=0.533 (0.219%), neg=0, invalid=96777 0248: dt=36.288000, rms=0.532 (0.255%), neg=0, invalid=96777 0249: dt=36.288000, rms=0.531 (0.247%), neg=0, invalid=96777 0250: dt=36.288000, rms=0.530 (0.215%), neg=0, invalid=96777 0251: dt=36.288000, rms=0.529 (0.180%), neg=0, invalid=96777 0252: dt=36.288000, rms=0.528 (0.170%), neg=0, invalid=96777 0253: dt=36.288000, rms=0.527 (0.209%), neg=0, invalid=96777 0254: dt=36.288000, rms=0.526 (0.203%), neg=0, invalid=96777 0255: dt=36.288000, rms=0.525 (0.173%), neg=0, invalid=96777 0256: dt=36.288000, rms=0.524 (0.166%), neg=0, invalid=96777 0257: dt=36.288000, rms=0.523 (0.161%), neg=0, invalid=96777 0258: dt=36.288000, rms=0.522 (0.140%), neg=0, invalid=96777 0259: dt=36.288000, rms=0.521 (0.128%), neg=0, invalid=96777 0260: dt=36.288000, rms=0.521 (0.158%), neg=0, invalid=96777 0261: dt=36.288000, rms=0.520 (0.167%), neg=0, invalid=96777 0262: dt=36.288000, rms=0.519 (0.140%), neg=0, invalid=96777 0263: dt=36.288000, rms=0.518 (0.129%), neg=0, invalid=96777 0264: dt=36.288000, rms=0.518 (0.131%), neg=0, invalid=96777 0265: dt=36.288000, rms=0.517 (0.112%), neg=0, invalid=96777 0266: dt=36.288000, rms=0.517 (0.121%), neg=0, invalid=96777 0267: dt=36.288000, rms=0.516 (0.140%), neg=0, invalid=96777 0268: dt=36.288000, rms=0.515 (0.115%), neg=0, invalid=96777 0269: dt=36.288000, rms=0.515 (0.082%), neg=0, invalid=96777 0270: dt=36.288000, rms=0.514 (0.094%), neg=0, invalid=96777 0271: dt=36.288000, rms=0.514 (0.109%), neg=0, invalid=96777 0272: dt=36.288000, rms=0.513 (0.091%), neg=0, invalid=96777 0273: dt=36.288000, rms=0.513 (0.080%), neg=0, invalid=96777 0274: dt=36.288000, rms=0.512 (0.087%), neg=0, invalid=96777 0275: dt=36.288000, rms=0.512 (0.088%), neg=0, invalid=96777 0276: dt=36.288000, rms=0.512 (0.081%), neg=0, invalid=96777 0277: dt=36.288000, rms=0.511 (0.064%), neg=0, invalid=96777 0278: dt=36.288000, rms=0.511 (0.066%), neg=0, invalid=96777 0279: dt=36.288000, rms=0.510 (0.075%), neg=0, invalid=96777 0280: dt=36.288000, rms=0.510 (0.062%), neg=0, invalid=96777 0281: dt=36.288000, rms=0.510 (0.053%), neg=0, invalid=96777 0282: dt=36.288000, rms=0.510 (0.073%), neg=0, invalid=96777 0283: dt=36.288000, rms=0.509 (0.076%), neg=0, invalid=96777 0284: dt=36.288000, rms=0.509 (0.052%), neg=0, invalid=96777 0285: dt=36.288000, rms=0.509 (0.042%), neg=0, invalid=96777 0286: dt=36.288000, rms=0.508 (0.053%), neg=0, invalid=96777 0287: dt=36.288000, rms=0.508 (0.045%), neg=0, invalid=96777 0288: dt=36.288000, rms=0.508 (0.037%), neg=0, invalid=96777 0289: dt=36.288000, rms=0.508 (0.043%), neg=0, invalid=96777 0290: dt=36.288000, rms=0.507 (0.057%), neg=0, invalid=96777 0291: dt=36.288000, rms=0.507 (0.052%), neg=0, invalid=96777 0292: dt=36.288000, rms=0.507 (0.035%), neg=0, invalid=96777 0293: dt=36.288000, rms=0.507 (0.048%), neg=0, invalid=96777 0294: dt=36.288000, rms=0.507 (0.021%), neg=0, invalid=96777 0295: dt=36.288000, rms=0.507 (0.021%), neg=0, invalid=96777 0296: dt=36.288000, rms=0.506 (0.072%), neg=0, invalid=96777 0297: dt=36.288000, rms=0.506 (0.052%), neg=0, invalid=96777 0298: dt=36.288000, rms=0.506 (0.028%), neg=0, invalid=96777 0299: dt=36.288000, rms=0.506 (0.029%), neg=0, invalid=96777 0300: dt=36.288000, rms=0.505 (0.039%), neg=0, invalid=96777 0301: dt=36.288000, rms=0.505 (0.025%), neg=0, invalid=96777 0302: dt=36.288000, rms=0.505 (0.040%), neg=0, invalid=96777 0303: dt=36.288000, rms=0.505 (0.032%), neg=0, invalid=96777 0304: dt=36.288000, rms=0.505 (0.031%), neg=0, invalid=96777 0305: dt=36.288000, rms=0.505 (0.050%), neg=0, invalid=96777 0306: dt=36.288000, rms=0.504 (0.037%), neg=0, invalid=96777 0307: dt=36.288000, rms=0.504 (0.029%), neg=0, invalid=96777 0308: dt=36.288000, rms=0.504 (0.016%), neg=0, invalid=96777 0309: dt=36.288000, rms=0.504 (0.019%), neg=0, invalid=96777 0310: dt=36.288000, rms=0.504 (0.041%), neg=0, invalid=96777 0311: dt=36.288000, rms=0.504 (0.036%), neg=0, invalid=96777 0312: dt=36.288000, rms=0.504 (0.005%), neg=0, invalid=96777 0313: dt=36.288000, rms=0.504 (0.010%), neg=0, invalid=96777 0314: dt=36.288000, rms=0.503 (0.038%), neg=0, invalid=96777 0315: dt=36.288000, rms=0.503 (0.056%), neg=0, invalid=96777 0316: dt=36.288000, rms=0.503 (0.037%), neg=0, invalid=96777 0317: dt=36.288000, rms=0.503 (0.006%), neg=0, invalid=96777 0318: dt=36.288000, rms=0.503 (-0.011%), neg=0, invalid=96777 0319: dt=0.101250, rms=0.503 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.503, neg=0, invalid=96777 0320: dt=145.152000, rms=0.501 (0.364%), neg=0, invalid=96777 0321: dt=36.288000, rms=0.501 (0.039%), neg=0, invalid=96777 0322: dt=36.288000, rms=0.501 (0.037%), neg=0, invalid=96777 0323: dt=36.288000, rms=0.500 (0.037%), neg=0, invalid=96777 0324: dt=36.288000, rms=0.500 (0.042%), neg=0, invalid=96777 0325: dt=36.288000, rms=0.500 (0.037%), neg=0, invalid=96777 0326: dt=36.288000, rms=0.500 (0.063%), neg=0, invalid=96777 0327: dt=2.268000, rms=0.500 (0.006%), neg=0, invalid=96777 0328: dt=1.134000, rms=0.500 (0.001%), neg=0, invalid=96777 0329: dt=0.567000, rms=0.500 (0.001%), neg=0, invalid=96777 0330: dt=0.141750, rms=0.500 (0.000%), neg=0, invalid=96777 0331: dt=0.070875, rms=0.500 (-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=0.512, neg=0, invalid=96777 0332: dt=0.043750, rms=0.512 (0.001%), neg=0, invalid=96777 0333: dt=0.010937, rms=0.512 (0.000%), neg=0, invalid=96777 0334: dt=0.005469, rms=0.512 (0.000%), neg=0, invalid=96777 0335: dt=0.001367, rms=0.512 (0.000%), neg=0, invalid=96777 0336: dt=0.000171, rms=0.512 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=96777 0337: dt=0.000000, rms=0.512 (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=0.552, neg=0, invalid=96777 0338: dt=17.755611, rms=0.529 (4.092%), neg=0, invalid=96777 0339: dt=11.520000, rms=0.521 (1.541%), neg=0, invalid=96777 0340: dt=7.375000, rms=0.519 (0.354%), neg=0, invalid=96777 0341: dt=5.500000, rms=0.518 (0.181%), neg=0, invalid=96777 0342: dt=7.500000, rms=0.517 (0.290%), neg=0, invalid=96777 0343: dt=3.555556, rms=0.516 (0.085%), neg=0, invalid=96777 0344: dt=13.824000, rms=0.514 (0.324%), neg=0, invalid=96777 0345: dt=2.628571, rms=0.514 (0.037%), neg=0, invalid=96777 0346: dt=2.628571, rms=0.514 (0.083%), neg=0, invalid=96777 0347: dt=2.628571, rms=0.514 (0.066%), neg=0, invalid=96777 0348: dt=2.628571, rms=0.513 (0.090%), neg=0, invalid=96777 0349: dt=2.628571, rms=0.512 (0.109%), neg=0, invalid=96777 0350: dt=2.628571, rms=0.512 (0.110%), neg=0, invalid=96777 0351: dt=2.628571, rms=0.511 (0.094%), neg=0, invalid=96777 0352: dt=2.628571, rms=0.511 (0.074%), neg=0, invalid=96777 0353: dt=2.628571, rms=0.511 (0.064%), neg=0, invalid=96777 0354: dt=2.628571, rms=0.510 (0.050%), neg=0, invalid=96777 0355: dt=2.628571, rms=0.510 (0.037%), neg=0, invalid=96777 0356: dt=2.628571, rms=0.510 (0.035%), neg=0, invalid=96777 0357: dt=2.628571, rms=0.510 (0.020%), neg=0, invalid=96777 0358: dt=2.628571, rms=0.510 (0.023%), neg=0, invalid=96777 0359: dt=2.628571, rms=0.510 (0.039%), neg=0, invalid=96777 0360: dt=2.628571, rms=0.509 (0.046%), neg=0, invalid=96777 0361: dt=2.628571, rms=0.509 (0.047%), neg=0, invalid=96777 0362: dt=2.628571, rms=0.509 (0.056%), neg=0, invalid=96777 0363: dt=2.628571, rms=0.509 (0.046%), neg=0, invalid=96777 0364: dt=2.628571, rms=0.509 (0.030%), neg=0, invalid=96777 0365: dt=2.628571, rms=0.508 (0.036%), neg=0, invalid=96777 0366: dt=2.628571, rms=0.508 (0.037%), neg=0, invalid=96777 0367: dt=2.628571, rms=0.508 (0.042%), neg=0, invalid=96777 0368: dt=2.628571, rms=0.508 (0.047%), neg=0, invalid=96777 0369: dt=2.628571, rms=0.508 (0.032%), neg=0, invalid=96777 0370: dt=2.628571, rms=0.507 (0.037%), neg=0, invalid=96777 0371: dt=2.628571, rms=0.507 (0.039%), neg=0, invalid=96777 0372: dt=2.628571, rms=0.507 (0.040%), neg=0, invalid=96777 0373: dt=2.628571, rms=0.507 (0.033%), neg=0, invalid=96777 0374: dt=2.628571, rms=0.507 (0.030%), neg=0, invalid=96777 0375: dt=2.628571, rms=0.507 (0.029%), neg=0, invalid=96777 0376: dt=2.628571, rms=0.506 (0.014%), neg=0, invalid=96777 0377: dt=2.628571, rms=0.506 (0.019%), neg=0, invalid=96777 0378: dt=2.628571, rms=0.506 (0.022%), neg=0, invalid=96777 0379: dt=2.628571, rms=0.506 (0.022%), neg=0, invalid=96777 0380: dt=4.032000, rms=0.506 (0.009%), neg=0, invalid=96777 0381: dt=4.032000, rms=0.506 (0.004%), neg=0, invalid=96777 0382: dt=4.032000, rms=0.506 (0.003%), neg=0, invalid=96777 0383: dt=4.032000, rms=0.506 (0.011%), neg=0, invalid=96777 0384: dt=4.032000, rms=0.506 (0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=96777 0385: dt=9.782383, rms=0.505 (0.157%), neg=0, invalid=96777 0386: dt=4.032000, rms=0.505 (0.028%), neg=0, invalid=96777 0387: dt=4.032000, rms=0.505 (0.007%), neg=0, invalid=96777 0388: dt=4.032000, rms=0.505 (-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=0.523, neg=0, invalid=96777 0389: dt=0.000000, rms=0.523 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.523, neg=0, invalid=96777 0390: dt=0.000000, rms=0.523 (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=0.492, neg=0, invalid=96777 0391: dt=0.148472, rms=0.488 (0.912%), neg=0, invalid=96777 0392: dt=0.080000, rms=0.486 (0.351%), neg=0, invalid=96777 0393: dt=0.121094, rms=0.484 (0.452%), neg=0, invalid=96777 0394: dt=0.080000, rms=0.483 (0.235%), neg=0, invalid=96777 0395: dt=0.005000, rms=0.483 (0.013%), neg=0, invalid=96777 0396: dt=0.005000, rms=0.483 (0.014%), neg=0, invalid=96777 0397: dt=0.005000, rms=0.482 (0.024%), neg=0, invalid=96777 0398: dt=0.005000, rms=0.482 (0.033%), neg=0, invalid=96777 0399: dt=0.005000, rms=0.482 (0.043%), neg=0, invalid=96777 0400: dt=0.005000, rms=0.482 (0.047%), neg=0, invalid=96777 0401: dt=0.005000, rms=0.482 (0.055%), neg=0, invalid=96777 0402: dt=0.005000, rms=0.481 (0.062%), neg=0, invalid=96777 0403: dt=0.005000, rms=0.481 (0.067%), neg=0, invalid=96777 0404: dt=0.005000, rms=0.481 (0.067%), neg=0, invalid=96777 0405: dt=0.005000, rms=0.480 (0.071%), neg=0, invalid=96777 0406: dt=0.005000, rms=0.480 (0.073%), neg=0, invalid=96777 0407: dt=0.005000, rms=0.480 (0.075%), neg=0, invalid=96777 0408: dt=0.005000, rms=0.479 (0.075%), neg=0, invalid=96777 0409: dt=0.005000, rms=0.479 (0.072%), neg=0, invalid=96777 0410: dt=0.005000, rms=0.479 (0.072%), neg=0, invalid=96777 0411: dt=0.005000, rms=0.478 (0.070%), neg=0, invalid=96777 0412: dt=0.005000, rms=0.478 (0.068%), neg=0, invalid=96777 0413: dt=0.005000, rms=0.478 (0.069%), neg=0, invalid=96777 0414: dt=0.005000, rms=0.477 (0.064%), neg=0, invalid=96777 0415: dt=0.005000, rms=0.477 (0.063%), neg=0, invalid=96777 0416: dt=0.005000, rms=0.477 (0.062%), neg=0, invalid=96777 0417: dt=0.005000, rms=0.476 (0.056%), neg=0, invalid=96777 0418: dt=0.005000, rms=0.476 (0.055%), neg=0, invalid=96777 0419: dt=0.005000, rms=0.476 (0.051%), neg=0, invalid=96777 0420: dt=0.005000, rms=0.476 (0.045%), neg=0, invalid=96777 0421: dt=0.005000, rms=0.475 (0.047%), neg=0, invalid=96777 0422: dt=0.005000, rms=0.475 (0.041%), neg=0, invalid=96777 0423: dt=0.005000, rms=0.475 (0.042%), neg=0, invalid=96777 0424: dt=0.005000, rms=0.475 (0.037%), neg=0, invalid=96777 0425: dt=0.005000, rms=0.475 (0.035%), neg=0, invalid=96777 0426: dt=0.005000, rms=0.475 (0.032%), neg=0, invalid=96777 0427: dt=0.005000, rms=0.474 (0.029%), neg=0, invalid=96777 0428: dt=0.005000, rms=0.474 (0.028%), neg=0, invalid=96777 0429: dt=0.005000, rms=0.474 (0.024%), neg=0, invalid=96777 0430: dt=0.005000, rms=0.474 (0.025%), neg=0, invalid=96777 0431: dt=0.005000, rms=0.474 (0.020%), neg=0, invalid=96777 0432: dt=0.112000, rms=0.474 (0.014%), neg=0, invalid=96777 0433: dt=0.028000, rms=0.474 (0.005%), neg=0, invalid=96777 0434: dt=0.028000, rms=0.474 (0.008%), neg=0, invalid=96777 0435: dt=0.028000, rms=0.474 (0.009%), neg=0, invalid=96777 0436: dt=0.028000, rms=0.474 (0.016%), neg=0, invalid=96777 0437: dt=0.028000, rms=0.474 (0.023%), neg=0, invalid=96777 0438: dt=0.028000, rms=0.474 (0.021%), neg=0, invalid=96777 0439: dt=0.028000, rms=0.473 (0.025%), neg=0, invalid=96777 0440: dt=0.028000, rms=0.473 (0.033%), neg=0, invalid=96777 0441: dt=0.014000, rms=0.473 (0.002%), neg=0, invalid=96777 0442: dt=0.014000, rms=0.473 (0.003%), neg=0, invalid=96777 0443: dt=0.014000, rms=0.473 (0.006%), neg=0, invalid=96777 0444: dt=0.014000, rms=0.473 (0.011%), neg=0, invalid=96777 0445: dt=0.014000, rms=0.473 (0.009%), neg=0, invalid=96777 0446: dt=0.112000, rms=0.473 (0.027%), neg=0, invalid=96777 0447: dt=0.112000, rms=0.473 (0.026%), neg=0, invalid=96777 0448: dt=0.112000, rms=0.473 (0.024%), neg=0, invalid=96777 0449: dt=0.028000, rms=0.473 (0.005%), neg=0, invalid=96777 0450: dt=0.028000, rms=0.473 (0.012%), neg=0, invalid=96777 0451: dt=0.028000, rms=0.473 (0.014%), neg=0, invalid=96777 0452: dt=0.028000, rms=0.473 (0.018%), neg=0, invalid=96777 0453: dt=0.028000, rms=0.472 (0.017%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=96777 0454: dt=0.112000, rms=0.471 (0.262%), neg=0, invalid=96777 0455: dt=0.112000, rms=0.470 (0.194%), neg=0, invalid=96777 0456: dt=0.112000, rms=0.470 (0.150%), neg=0, invalid=96777 0457: dt=0.112000, rms=0.469 (0.108%), neg=0, invalid=96777 0458: dt=0.007000, rms=0.469 (0.010%), neg=0, invalid=96777 0459: dt=0.007000, rms=0.469 (0.005%), neg=0, invalid=96777 0460: dt=0.007000, rms=0.469 (0.011%), neg=0, invalid=96777 0461: dt=0.007000, rms=0.469 (0.014%), neg=0, invalid=96777 0462: dt=0.007000, rms=0.469 (0.017%), neg=0, invalid=96777 0463: dt=0.007000, rms=0.469 (0.021%), neg=0, invalid=96777 0464: dt=0.007000, rms=0.469 (0.021%), neg=0, invalid=96777 0465: dt=0.007000, rms=0.468 (0.027%), neg=0, invalid=96777 0466: dt=0.007000, rms=0.468 (0.026%), neg=0, invalid=96777 0467: dt=0.007000, rms=0.468 (0.028%), neg=0, invalid=96777 0468: dt=0.007000, rms=0.468 (0.028%), neg=0, invalid=96777 0469: dt=0.007000, rms=0.468 (0.029%), neg=0, invalid=96777 0470: dt=0.007000, rms=0.468 (0.027%), neg=0, invalid=96777 0471: dt=0.007000, rms=0.468 (0.024%), neg=0, invalid=96777 0472: dt=0.007000, rms=0.468 (0.024%), neg=0, invalid=96777 0473: dt=0.007000, rms=0.468 (0.024%), neg=0, invalid=96777 0474: dt=0.112000, rms=0.467 (0.019%), neg=0, invalid=96777 0475: dt=0.007000, rms=0.467 (0.001%), neg=0, invalid=96777 0476: dt=0.007000, rms=0.467 (0.002%), neg=0, invalid=96777 0477: dt=0.007000, rms=0.467 (0.002%), neg=0, invalid=96777 0478: dt=0.007000, rms=0.467 (0.001%), neg=0, invalid=96777 0479: dt=0.007000, rms=0.467 (0.004%), neg=0, invalid=96777 0480: dt=0.007000, rms=0.467 (0.007%), neg=0, invalid=96777 0481: dt=0.007000, rms=0.467 (0.005%), 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=0.465, neg=0, invalid=96777 0482: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=96777 0483: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0484: dt=129.472000, rms=0.465 (0.080%), neg=0, invalid=96777 0485: dt=517.888000, rms=0.464 (0.180%), neg=0, invalid=96777 0486: dt=32.368000, rms=0.464 (0.016%), neg=0, invalid=96777 0487: dt=32.368000, rms=0.464 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=96777 0488: dt=31.104000, rms=0.464 (0.100%), neg=0, invalid=96777 0489: dt=36.288000, rms=0.463 (0.086%), neg=0, invalid=96777 0490: dt=36.288000, rms=0.463 (0.085%), neg=0, invalid=96777 0491: dt=36.288000, rms=0.463 (0.077%), neg=0, invalid=96777 0492: dt=36.288000, rms=0.462 (0.029%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.462, neg=0, invalid=96777 0493: dt=103.680000, rms=0.459 (0.795%), neg=0, invalid=96777 0494: dt=31.104000, rms=0.458 (0.097%), neg=0, invalid=96777 0495: dt=31.104000, rms=0.458 (0.064%), neg=0, invalid=96777 0496: dt=31.104000, rms=0.458 (0.068%), neg=0, invalid=96777 0497: dt=31.104000, rms=0.457 (0.105%), neg=0, invalid=96777 0498: dt=31.104000, rms=0.457 (0.145%), neg=0, invalid=96777 0499: dt=31.104000, rms=0.456 (0.151%), neg=0, invalid=96777 0500: dt=31.104000, rms=0.455 (0.154%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0501: dt=31.104000, rms=0.455 (0.123%), neg=0, invalid=96777 0502: dt=31.104000, rms=0.454 (0.098%), neg=0, invalid=96777 0503: dt=82.944000, rms=0.454 (0.037%), neg=0, invalid=96777 0504: dt=82.944000, rms=0.454 (0.027%), neg=0, invalid=96777 0505: dt=82.944000, rms=0.454 (0.079%), neg=0, invalid=96777 0506: dt=82.944000, rms=0.453 (0.075%), neg=0, invalid=96777 0507: dt=82.944000, rms=0.453 (0.085%), neg=0, invalid=96777 0508: dt=82.944000, rms=0.453 (0.073%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.453, neg=0, invalid=96777 0509: dt=11.200000, rms=0.452 (0.220%), neg=0, invalid=96777 0510: dt=25.600000, rms=0.451 (0.202%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0511: dt=25.600000, rms=0.451 (0.129%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0512: dt=25.600000, rms=0.450 (0.247%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 8 iterations, nbhd size=1, neg = 0 0513: dt=25.600000, rms=0.448 (0.266%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0514: dt=25.600000, rms=0.447 (0.347%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0515: dt=25.600000, rms=0.445 (0.308%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0516: dt=25.600000, rms=0.444 (0.273%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0517: dt=25.600000, rms=0.443 (0.310%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0518: dt=25.600000, rms=0.442 (0.280%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0519: dt=25.600000, rms=0.441 (0.128%), neg=0, invalid=96777 0520: dt=25.600000, rms=0.440 (0.250%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0521: dt=25.600000, rms=0.439 (0.157%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0522: dt=25.600000, rms=0.439 (0.134%), neg=0, invalid=96777 0523: dt=25.600000, rms=0.438 (0.102%), neg=0, invalid=96777 0524: dt=25.600000, rms=0.438 (0.032%), neg=0, invalid=96777 0525: dt=11.200000, rms=0.438 (0.119%), neg=0, invalid=96777 0526: dt=11.200000, rms=0.437 (0.060%), neg=0, invalid=96777 0527: dt=11.200000, rms=0.437 (0.052%), neg=0, invalid=96777 0528: dt=11.200000, rms=0.437 (0.063%), neg=0, invalid=96777 0529: dt=11.200000, rms=0.437 (0.055%), neg=0, invalid=96777 0530: dt=11.200000, rms=0.436 (0.051%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.436, neg=0, invalid=96777 0531: dt=44.800000, rms=0.434 (0.621%), neg=0, invalid=96777 0532: dt=8.000000, rms=0.433 (0.111%), neg=0, invalid=96777 0533: dt=8.000000, rms=0.433 (0.080%), neg=0, invalid=96777 0534: dt=8.000000, rms=0.432 (0.078%), neg=0, invalid=96777 0535: dt=8.000000, rms=0.432 (0.084%), neg=0, invalid=96777 0536: dt=8.000000, rms=0.432 (0.091%), neg=0, invalid=96777 0537: dt=8.000000, rms=0.431 (0.098%), neg=0, invalid=96777 0538: dt=8.000000, rms=0.431 (0.091%), neg=0, invalid=96777 0539: dt=32.000000, rms=0.431 (0.060%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.440, neg=0, invalid=96777 0540: dt=3.456000, rms=0.440 (0.089%), neg=0, invalid=96777 0541: dt=2.086957, rms=0.440 (0.028%), neg=0, invalid=96777 0542: dt=2.086957, rms=0.440 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 18 iterations, nbhd size=2, neg = 0 0543: dt=8.426036, rms=0.438 (0.274%), neg=0, invalid=96777 0544: dt=0.216000, rms=0.439 (-0.005%), neg=0, invalid=96777 0545: dt=0.216000, rms=0.439 (0.001%), neg=0, invalid=96777 0546: dt=0.216000, rms=0.438 (0.009%), neg=0, invalid=96777 0547: dt=0.216000, rms=0.438 (0.004%), neg=0, invalid=96777 0548: dt=0.216000, rms=0.438 (0.012%), neg=0, invalid=96777 0549: dt=0.216000, rms=0.438 (0.012%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.449, neg=0, invalid=96777 0550: dt=0.448000, rms=0.449 (0.021%), neg=0, invalid=96777 0551: dt=0.192000, rms=0.449 (0.003%), neg=0, invalid=96777 0552: dt=0.192000, rms=0.449 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=96777 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=1, neg = 0 0553: dt=1.792000, rms=0.448 (0.249%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0554: dt=0.448000, rms=0.447 (0.021%), neg=0, invalid=96777 0555: dt=0.448000, rms=0.447 (0.029%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0556: dt=0.448000, rms=0.447 (0.033%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0557: dt=0.448000, rms=0.447 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0558: dt=0.448000, rms=0.447 (-0.050%), 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=0.439, neg=0, invalid=96777 iter 0, gcam->neg = 453 after 25 iterations, nbhd size=2, neg = 0 0559: dt=1.645161, rms=0.413 (5.821%), neg=0, invalid=96777 0560: dt=0.000109, rms=0.413 (0.002%), neg=0, invalid=96777 0561: dt=0.000109, rms=0.413 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 0562: dt=0.000438, rms=0.413 (0.001%), neg=0, invalid=96777 0563: dt=0.000438, rms=0.413 (0.000%), neg=0, invalid=96777 0564: dt=0.000438, rms=0.413 (0.000%), neg=0, invalid=96777 0565: dt=0.000438, rms=0.413 (-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=0.403, neg=0, invalid=96777 0566: dt=0.000000, rms=0.403 (-0.119%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 0567: dt=129.472000, rms=0.403 (0.033%), neg=0, invalid=96777 0568: dt=129.472000, rms=0.403 (0.021%), neg=0, invalid=96777 0569: dt=129.472000, rms=0.403 (0.005%), neg=0, invalid=96777 0570: dt=129.472000, rms=0.403 (0.010%), neg=0, invalid=96777 0571: dt=129.472000, rms=0.403 (0.013%), neg=0, invalid=96777 0572: dt=129.472000, rms=0.403 (0.006%), neg=0, invalid=96777 0573: dt=129.472000, rms=0.403 (0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 0574: dt=0.000253, rms=0.403 (0.000%), neg=0, invalid=96777 0575: dt=0.000253, rms=0.403 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 17 iterations, nbhd size=2, neg = 0 0576: dt=145.152000, rms=0.402 (0.190%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 21 iterations, nbhd size=3, neg = 0 0577: dt=82.944000, rms=0.402 (0.026%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 32 iterations, nbhd size=4, neg = 0 0578: dt=82.944000, rms=0.402 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 2, delta 2, rms=0.002 (16.228%) 0579: dt=82.944000, rms=0.402 (0.045%), neg=0, invalid=96777 0580: dt=82.944000, rms=0.401 (0.046%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0581: dt=82.944000, rms=0.401 (0.065%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 2, delta 2, rms=0.002 (32.645%) 0582: dt=82.944000, rms=0.401 (0.064%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.401, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... iter 1, dt=0.000100: new neg 0, old_neg 4, delta 4, rms=0.002 (40.472%) 0583: dt=11.200000, rms=0.401 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 20 iterations, nbhd size=3, neg = 0 0584: dt=11.200000, rms=0.401 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 19 iterations, nbhd size=3, neg = 0 0585: dt=11.200000, rms=0.401 (0.021%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 200 iterations, nbhd size=1, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... iter 1, dt=0.000096: new neg 0, old_neg 4, delta 4, rms=0.003 (37.067%) 0586: dt=11.200000, rms=0.401 (-0.167%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.401, neg=0, invalid=96777 iter 0, gcam->neg = 17 after 31 iterations, nbhd size=4, neg = 0 0587: dt=38.400000, rms=0.399 (0.541%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=2, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 4, delta 4, rms=0.002 (47.433%) 0588: dt=25.600000, rms=0.398 (0.170%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.004, neg=5, removing folds in lattice.... iter 1, dt=0.000100: new neg 0, old_neg 5, delta 5, rms=0.002 (42.178%) 0589: dt=25.600000, rms=0.397 (0.177%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000047: new neg 0, old_neg 5, delta 5, rms=0.002 (53.091%) 0590: dt=25.600000, rms=0.397 (0.066%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000047: new neg 0, old_neg 5, delta 5, rms=0.002 (48.780%) 0591: dt=25.600000, rms=0.396 (0.168%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000099: new neg 0, old_neg 5, delta 5, rms=0.002 (53.384%) 0592: dt=25.600000, rms=0.396 (0.016%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=4, neg = 6 starting rms=0.006, neg=6, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 6, delta 6, rms=0.002 (57.574%) 0593: dt=25.600000, rms=0.396 (0.159%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 6 starting rms=0.006, neg=6, removing folds in lattice.... iter 1, dt=0.000125: new neg 1, old_neg 6, delta 5, rms=0.002 (59.964%) iter 2, dt=0.000492: new neg 0, old_neg 1, delta 1, rms=0.002 (9.146%) 0594: dt=25.600000, rms=0.396 (-0.040%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 5 starting rms=0.006, neg=5, removing folds in lattice.... iter 1, dt=0.000055: new neg 1, old_neg 5, delta 4, rms=0.002 (57.454%) iter 2, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.002 (9.395%) 0595: dt=11.200000, rms=0.395 (0.107%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=4, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000100: new neg 1, old_neg 5, delta 4, rms=0.002 (55.398%) iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.002 (9.302%) 0596: dt=44.800000, rms=0.395 (0.133%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.006, neg=5, removing folds in lattice.... iter 1, dt=0.000094: new neg 2, old_neg 5, delta 3, rms=0.002 (57.260%) iter 2, dt=0.000123: new neg 0, old_neg 2, delta 2, rms=0.002 (9.471%) 0597: dt=32.000000, rms=0.395 (0.068%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.397, neg=0, invalid=96777 iter 0, gcam->neg = 19 after 29 iterations, nbhd size=3, neg = 0 0598: dt=3.456000, rms=0.397 (0.072%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0599: dt=1.008000, rms=0.397 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 16 iterations, nbhd size=2, neg = 0 0600: dt=1.008000, rms=0.397 (0.009%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000047: new neg 0, old_neg 5, delta 5, rms=0.002 (58.244%) 0601: dt=1.008000, rms=0.397 (-0.019%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.397, neg=0, invalid=96777 iter 0, gcam->neg = 79 after 38 iterations, nbhd size=3, neg = 0 0602: dt=16.128000, rms=0.395 (0.446%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 34 iterations, nbhd size=4, neg = 0 0603: dt=1.750000, rms=0.395 (0.010%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 25 iterations, nbhd size=3, neg = 0 0604: dt=1.750000, rms=0.395 (0.029%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 27 iterations, nbhd size=4, neg = 0 0605: dt=1.750000, rms=0.395 (0.053%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 38 iterations, nbhd size=1, neg = 0 0606: dt=1.750000, rms=0.394 (0.061%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 3, delta 3, rms=0.002 (43.008%) 0607: dt=1.750000, rms=0.394 (0.039%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0608: dt=1.750000, rms=0.394 (0.028%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 8 iterations, nbhd size=1, neg = 0 0609: dt=4.032000, rms=0.394 (0.042%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 10 iterations, nbhd size=1, neg = 0 0610: dt=4.032000, rms=0.394 (0.040%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.399, neg=0, invalid=96777 0611: dt=0.000000, rms=0.399 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.399, neg=0, invalid=96777 0612: dt=0.000000, rms=0.399 (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=0.390, neg=0, invalid=96777 iter 0, gcam->neg = 311 after 38 iterations, nbhd size=4, neg = 0 0613: dt=0.792836, rms=0.381 (2.395%), neg=0, invalid=96777 0614: dt=0.000312, rms=0.381 (0.000%), neg=0, invalid=96777 0615: dt=0.000312, rms=0.381 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.381, neg=0, invalid=96777 0616: dt=0.007000, rms=0.381 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0617: dt=0.004000, rms=0.381 (0.002%), neg=0, invalid=96777 0618: dt=0.004000, rms=0.381 (0.002%), neg=0, invalid=96777 0619: dt=0.004000, rms=0.381 (0.005%), neg=0, invalid=96777 0620: dt=0.004000, rms=0.381 (0.006%), neg=0, invalid=96777 0621: dt=0.004000, rms=0.381 (0.008%), neg=0, invalid=96777 0622: dt=0.004000, rms=0.381 (0.009%), neg=0, invalid=96777 0623: dt=0.004000, rms=0.381 (0.009%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0624: dt=0.004000, rms=0.381 (0.008%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0625: dt=0.004000, rms=0.381 (0.009%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0626: dt=0.004000, rms=0.381 (0.008%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 14 hours, 25 minutes and 24 seconds. time:: 14:25:25 elapsed:: 51925 cmd:: mri_ca_register #-------------------------------------- #@# CA Reg Inv Tue May 7 13:22:37 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse time:: 00:03:47 elapsed:: 00227 cmd:: mri_ca_register #-------------------------------------- #@# Remove Neck Tue May 7 13:26:25 EDT 2013 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /space/freesurfer/centos4.0/stable/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/space/freesurfer/centos4.0/stable/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... 11044375 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 4 minutes and 15 seconds. time:: 00:04:16 elapsed:: 00256 cmd:: mri_remove_neck #-------------------------------------- #@# SkullLTA Tue May 7 13:30:42 EDT 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /space/freesurfer/centos4.0/stable/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta 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 '/space/freesurfer/centos4.0/stable/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=6.0 skull bounding box = (46, 45, 0) --> (209, 217, 205) using (100, 102, 103) as brain centroid... mean wm in atlas = 126, using box (80,81,78) --> (120, 123,128) to find MRI wm before smoothing, mri peak at 109 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-3.9 (thresh=-3.9) 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.010 -0.239 0.945 28.594; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.031 -0.002 -13.435; -0.025 1.141 0.197 -36.946; 0.010 -0.271 0.922 36.949; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.031 -0.002 -13.435; -0.025 1.141 0.197 -36.946; 0.010 -0.271 0.922 36.949; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.065 0.010 0.002 -12.004; -0.007 1.141 0.197 -38.704; 0.001 -0.270 0.922 37.120; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.064 -0.009 -0.001 -9.212; 0.010 1.144 0.197 -41.316; 0.001 -0.270 0.921 37.201; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.064 -0.009 -0.001 -9.212; 0.010 1.144 0.197 -41.316; 0.001 -0.270 0.921 37.201; 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 1.06378 -0.00866 -0.00102 -9.21189; 0.01025 1.14401 0.19708 -41.31630; 0.00085 -0.27015 0.92054 37.20064; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.06378 -0.00866 -0.00102 -9.21189; 0.01025 1.14401 0.19708 -41.31630; 0.00085 -0.27015 0.92054 37.20064; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.064 -0.009 -0.001 -9.212; 0.010 1.144 0.197 -41.316; 0.001 -0.270 0.921 37.201; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-3.9) transform before final EM align: 1.064 -0.009 -0.001 -9.212; 0.010 1.144 0.197 -41.316; 0.001 -0.270 0.921 37.201; 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 1.06378 -0.00866 -0.00102 -9.21189; 0.01025 1.14401 0.19708 -41.31630; 0.00085 -0.27015 0.92054 37.20064; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.06378 -0.00866 -0.00102 -9.21189; 0.01025 1.14401 0.19708 -41.31630; 0.00085 -0.27015 0.92054 37.20064; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = 4.4 tol 0.000000 final transform: 1.064 -0.009 -0.001 -9.212; 0.010 1.144 0.197 -41.316; 0.001 -0.270 0.921 37.201; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 63 minutes and 33 seconds. time:: 01:03:33 elapsed:: 03813 cmd:: mri_em_register #-------------------------------------- #@# SubCort Seg Tue May 7 14:34:18 EDT 2013 rm -f aseg.mgz aseg.manedit.mgz mri_ca_label -align norm.mgz transforms/talairach.m3z /space/freesurfer/centos4.0/stable/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname node0360 machine x86_64 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 cd /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /space/freesurfer/centos4.0/stable/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 /space/freesurfer/centos4.0/stable/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 /space/freesurfer/centos4.0/stable/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 = 0.18375 (27) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (1138 voxels, overlap=0.786) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (1138 voxels, peak = 28), gca=28.5 gca peak = 0.14982 (20) mri peak = 0.19852 (30) Right_Lateral_Ventricle (43): linear fit = 1.33 x + 0.0 (748 voxels, overlap=0.295) Right_Lateral_Ventricle (43): linear fit = 1.33 x + 0.0 (748 voxels, peak = 26), gca=26.5 gca peak = 0.28003 (97) mri peak = 0.15286 (98) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (303 voxels, overlap=0.894) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (303 voxels, peak = 95), gca=94.6 gca peak = 0.18160 (96) mri peak = 0.12947 (100) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (346 voxels, overlap=0.999) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (346 voxels, peak = 97), gca=97.4 gca peak = 0.27536 (62) mri peak = 0.08521 (75) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (819 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (819 voxels, peak = 73), gca=73.5 gca peak = 0.32745 (63) mri peak = 0.10358 (79) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (827 voxels, overlap=0.020) Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (827 voxels, peak = 77), gca=76.5 gca peak = 0.08597 (105) mri peak = 0.12021 (106) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45773 voxels, overlap=0.644) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45773 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.11917 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (50670 voxels, overlap=0.607) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (50670 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.04729 (77) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (34379 voxels, overlap=0.194) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (34379 voxels, peak = 78), gca=78.4 gca peak = 0.08598 (64) mri peak = 0.04907 (80) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (33152 voxels, overlap=0.113) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (33152 voxels, peak = 80), gca=80.3 gca peak = 0.24164 (71) mri peak = 0.15240 (83) Right_Caudate (50): linear fit = 1.15 x + 0.0 (479 voxels, overlap=0.017) Right_Caudate (50): linear fit = 1.15 x + 0.0 (479 voxels, peak = 82), gca=82.0 gca peak = 0.18227 (75) mri peak = 0.16408 (80) Left_Caudate (11): linear fit = 1.05 x + 0.0 (576 voxels, overlap=0.688) Left_Caudate (11): linear fit = 1.05 x + 0.0 (576 voxels, peak = 79), gca=79.1 gca peak = 0.10629 (62) mri peak = 0.06251 (82) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (27524 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.33 x + 0.0 (27524 voxels, peak = 82), gca=82.2 gca peak = 0.11668 (59) mri peak = 0.05654 (82) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (26919 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (26919 voxels, peak = 78), gca=78.2 gca peak = 0.17849 (88) mri peak = 0.14680 (96) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6124 voxels, overlap=0.122) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6124 voxels, peak = 95), gca=95.5 gca peak = 0.16819 (86) mri peak = 0.12640 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5702 voxels, overlap=0.171) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5702 voxels, peak = 94), gca=94.2 gca peak = 0.41688 (64) mri peak = 0.15177 (79) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (299 voxels, overlap=0.059) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (299 voxels, peak = 78), gca=78.4 gca peak = 0.42394 (62) mri peak = 0.14667 (81) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (223 voxels, overlap=0.050) Right_Amygdala (54): linear fit = 1.29 x + 0.0 (223 voxels, peak = 80), gca=80.3 gca peak = 0.10041 (96) mri peak = 0.10917 (96) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4342 voxels, overlap=0.860) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (4342 voxels, peak = 97), gca=97.4 gca peak = 0.13978 (88) mri peak = 0.11093 (96) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4381 voxels, overlap=0.733) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (4381 voxels, peak = 94), gca=93.7 gca peak = 0.08514 (81) mri peak = 0.07994 (91) Left_Putamen (12): linear fit = 1.08 x + 0.0 (2064 voxels, overlap=0.777) Left_Putamen (12): linear fit = 1.08 x + 0.0 (2064 voxels, peak = 87), gca=87.1 gca peak = 0.09624 (82) mri peak = 0.08167 (86) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1702 voxels, overlap=0.815) Right_Putamen (51): linear fit = 1.03 x + 0.0 (1702 voxels, peak = 85), gca=84.9 gca peak = 0.07543 (88) mri peak = 0.09777 (91) Brain_Stem (16): linear fit = 1.03 x + 0.0 (14292 voxels, overlap=0.658) Brain_Stem (16): linear fit = 1.03 x + 0.0 (14292 voxels, peak = 91), gca=91.1 gca peak = 0.12757 (95) mri peak = 0.10827 (101) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1202 voxels, overlap=0.644) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (1202 voxels, peak = 99), gca=99.3 gca peak = 0.17004 (92) mri peak = 0.10164 (101) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1288 voxels, overlap=0.771) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1288 voxels, peak = 96), gca=96.1 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.17764 (29) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (129 voxels, overlap=0.806) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (129 voxels, peak = 25), gca=25.2 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak 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 1.24 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.16 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16440 (29) mri peak = 0.18375 (27) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1138 voxels, overlap=0.781) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (1138 voxels, peak = 27), gca=27.4 gca peak = 0.14754 (27) mri peak = 0.19852 (30) Right_Lateral_Ventricle (43): linear fit = 0.99 x + 0.0 (748 voxels, overlap=0.648) Right_Lateral_Ventricle (43): linear fit = 0.99 x + 0.0 (748 voxels, peak = 27), gca=26.6 gca peak = 0.33220 (95) mri peak = 0.15286 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (303 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (303 voxels, peak = 95), gca=95.0 gca peak = 0.16602 (97) mri peak = 0.12947 (100) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (346 voxels, overlap=0.909) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (346 voxels, peak = 97), gca=96.5 gca peak = 0.20590 (73) mri peak = 0.08521 (75) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (819 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (819 voxels, peak = 73), gca=73.0 gca peak = 0.24378 (77) mri peak = 0.10358 (79) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (827 voxels, overlap=0.992) Left_Hippocampus (17): linear fit = 0.96 x + 0.0 (827 voxels, peak = 74), gca=74.3 gca peak = 0.08542 (107) mri peak = 0.12021 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45773 voxels, overlap=0.675) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45773 voxels, peak = 107), gca=107.0 gca peak = 0.08752 (107) mri peak = 0.11917 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50670 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (50670 voxels, peak = 107), gca=107.0 gca peak = 0.06419 (78) mri peak = 0.04729 (77) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (34379 voxels, overlap=0.860) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (34379 voxels, peak = 78), gca=78.0 gca peak = 0.06960 (78) mri peak = 0.04907 (80) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (33152 voxels, overlap=0.851) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (33152 voxels, peak = 77), gca=76.8 gca peak = 0.27181 (85) mri peak = 0.15240 (83) Right_Caudate (50): linear fit = 1.00 x + 0.0 (479 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (479 voxels, peak = 85), gca=85.0 gca peak = 0.18082 (79) mri peak = 0.16408 (80) Left_Caudate (11): linear fit = 1.00 x + 0.0 (576 voxels, overlap=0.627) Left_Caudate (11): linear fit = 1.00 x + 0.0 (576 voxels, peak = 79), gca=79.0 gca peak = 0.08289 (82) mri peak = 0.06251 (82) Left_Cerebellum_Cortex (8): linear fit = 1.01 x + 0.0 (27524 voxels, overlap=0.889) Left_Cerebellum_Cortex (8): linear fit = 1.01 x + 0.0 (27524 voxels, peak = 83), gca=83.2 gca peak = 0.09531 (79) mri peak = 0.05654 (82) Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (26919 voxels, overlap=0.969) Right_Cerebellum_Cortex (47): linear fit = 1.01 x + 0.0 (26919 voxels, peak = 80), gca=80.2 gca peak = 0.16649 (96) mri peak = 0.14680 (96) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6124 voxels, overlap=0.920) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6124 voxels, peak = 96), gca=95.5 gca peak = 0.13939 (94) mri peak = 0.12640 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5702 voxels, overlap=0.965) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5702 voxels, peak = 94), gca=94.0 gca peak = 0.32603 (78) mri peak = 0.15177 (79) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (299 voxels, overlap=1.018) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (299 voxels, peak = 78), gca=78.0 gca peak = 0.36270 (81) mri peak = 0.14667 (81) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (223 voxels, overlap=1.004) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (223 voxels, peak = 80), gca=79.8 gca peak = 0.10497 (96) mri peak = 0.10917 (96) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4342 voxels, overlap=0.907) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4342 voxels, peak = 96), gca=96.5 gca peak = 0.09585 (91) mri peak = 0.11093 (96) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4381 voxels, overlap=0.863) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4381 voxels, peak = 90), gca=89.6 gca peak = 0.08394 (87) mri peak = 0.07994 (91) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2064 voxels, overlap=0.973) Left_Putamen (12): linear fit = 0.99 x + 0.0 (2064 voxels, peak = 86), gca=85.7 gca peak = 0.09612 (85) mri peak = 0.08167 (86) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1702 voxels, overlap=0.989) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1702 voxels, peak = 85), gca=85.0 gca peak = 0.07106 (91) mri peak = 0.09777 (91) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14292 voxels, overlap=0.761) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14292 voxels, peak = 91), gca=90.5 gca peak = 0.13550 (99) mri peak = 0.10827 (101) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1202 voxels, overlap=0.792) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1202 voxels, peak = 99), gca=98.5 gca peak = 0.14708 (96) mri peak = 0.10164 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1288 voxels, overlap=0.883) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1288 voxels, peak = 96), gca=96.0 gca peak = 0.19677 (42) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19704 (25) mri peak = 0.17764 (29) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (129 voxels, overlap=0.776) Fourth_Ventricle (15): linear fit = 0.99 x + 0.0 (129 voxels, peak = 25), gca=24.6 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.22716 (43) gca peak Third_Ventricle = 0.19677 (42) gca peak CSF = 0.21723 (45) gca peak Left_Accumbens_area = 0.49604 (74) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63670 (62) gca peak Left_choroid_plexus = 0.08601 (47) gca peak Right_Inf_Lat_Vent = 0.22069 (38) gca peak Right_Accumbens_area = 0.31092 (83) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10190 (48) gca peak Fifth_Ventricle = 0.73407 (48) gca peak WM_hypointensities = 0.16910 (83) gca peak non_WM_hypointensities = 0.10249 (54) gca peak Optic_Chiasm = 0.34123 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.97 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 38824 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 442 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 81357 changed. image ll: -2.351, PF=1.000 pass 2: 13375 changed. image ll: -2.348, PF=1.000 pass 3: 4334 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 66 minutes and 20 seconds. time:: 01:06:21 elapsed:: 03981 cmd:: mri_ca_label mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/cc_up.lta bert will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/norm.mgz 44214 voxels in left wm, 39271 in right wm, xrange [125, 134] searching rotation angles z=[-10 4], y=[-6 8] searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 global minimum found at slice 128.8, rotations (0.61, -3.12) final transformation (x=128.8, yr=0.615, zr=-3.116): 0.998 0.054 0.011 -7.291; -0.054 0.999 -0.001 34.215; -0.011 -0.000 1.000 15.388; 0.000 0.000 0.000 1.000; updating x range to be [127, 131] in xformed coordinates best xformed slice 129 cc center is found at 129 149 103 eigenvectors: -0.000 -0.006 1.000; -0.015 -1.000 -0.006; 1.000 -0.015 0.000; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.auto.mgz... corpus callosum matter segmentation took 2.2 minutes time:: 00:02:15 elapsed:: 00135 cmd:: mri_cc #-------------------------------------- #@# Merge ASeg Tue May 7 15:42:56 EDT 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue May 7 15:42:56 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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... 409 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 59 (59) csf peak at 42, setting threshold to 70 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 84 (84), valley at 59 (59) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 12 minutes and 30 seconds. time:: 00:12:38 elapsed:: 00758 cmd:: mri_normalize #-------------------------------------------- #@# Mask BFS Tue May 7 15:55:36 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1754519 voxels in mask (pct= 10.46) Writing masked volume to brain.finalsurfs.mgz...done. time:: 00:00:09 elapsed:: 00009 cmd:: mri_mask #-------------------------------------------- #@# WM Segmentation Tue May 7 15:55:45 EDT 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 (104.0): 104.4 +- 5.8 [80.0 --> 125.0] GM (81.0) : 77.7 +- 13.2 [30.0 --> 96.0] setting bottom of white matter range to 90.9 setting top of gray matter range to 104.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 7231 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3624 filled 9151 bright non-wm voxels segmented. 3819 diagonally connected voxels added... white matter segmentation took 7.3 minutes writing output to wm.seg.mgz... time:: 00:07:19 elapsed:: 00439 cmd:: mri_segment mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz auto filling took 2.21 minutes reading wm segmentation from wm.seg.mgz... 28 voxels added to wm to prevent paths from MTL structures to cortex 3071 additional wm voxels added 0 additional wm voxels added SEG EDIT: 49107 voxels turned on, 54420 voxels turned off. writing edited volume to wm.asegedit.mgz.... time:: 00:02:14 elapsed:: 00134 cmd:: mri_edit_wm_with_aseg mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 23 found - 23 modified | TOTAL: 23 pass 2 (xy+): 0 found - 23 modified | TOTAL: 23 pass 1 (xy-): 26 found - 26 modified | TOTAL: 49 pass 2 (xy-): 0 found - 26 modified | TOTAL: 49 pass 1 (yz+): 30 found - 30 modified | TOTAL: 79 pass 2 (yz+): 0 found - 30 modified | TOTAL: 79 pass 1 (yz-): 35 found - 35 modified | TOTAL: 114 pass 2 (yz-): 0 found - 35 modified | TOTAL: 114 pass 1 (xz+): 29 found - 29 modified | TOTAL: 143 pass 2 (xz+): 0 found - 29 modified | TOTAL: 143 pass 1 (xz-): 29 found - 29 modified | TOTAL: 172 pass 2 (xz-): 0 found - 29 modified | TOTAL: 172 Iteration Number : 1 pass 1 (+++): 19 found - 19 modified | TOTAL: 19 pass 2 (+++): 0 found - 19 modified | TOTAL: 19 pass 1 (+++): 14 found - 14 modified | TOTAL: 33 pass 2 (+++): 0 found - 14 modified | TOTAL: 33 pass 1 (+++): 20 found - 20 modified | TOTAL: 53 pass 2 (+++): 0 found - 20 modified | TOTAL: 53 pass 1 (+++): 15 found - 15 modified | TOTAL: 68 pass 2 (+++): 0 found - 15 modified | TOTAL: 68 Iteration Number : 1 pass 1 (++): 61 found - 61 modified | TOTAL: 61 pass 2 (++): 0 found - 61 modified | TOTAL: 61 pass 1 (+-): 69 found - 69 modified | TOTAL: 130 pass 2 (+-): 0 found - 69 modified | TOTAL: 130 pass 1 (--): 82 found - 82 modified | TOTAL: 212 pass 2 (--): 1 found - 83 modified | TOTAL: 213 pass 3 (--): 0 found - 83 modified | TOTAL: 213 pass 1 (-+): 64 found - 64 modified | TOTAL: 277 pass 2 (-+): 0 found - 64 modified | TOTAL: 277 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 8 found - 8 modified | TOTAL: 12 pass 2 (yz+): 0 found - 8 modified | TOTAL: 12 pass 1 (yz-): 5 found - 5 modified | TOTAL: 17 pass 2 (yz-): 0 found - 5 modified | TOTAL: 17 pass 1 (xz+): 1 found - 1 modified | TOTAL: 18 pass 2 (xz+): 0 found - 1 modified | TOTAL: 18 pass 1 (xz-): 6 found - 6 modified | TOTAL: 24 pass 2 (xz-): 0 found - 6 modified | TOTAL: 24 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 3 found - 3 modified | TOTAL: 7 pass 2 (+-): 0 found - 3 modified | TOTAL: 7 pass 1 (--): 0 found - 0 modified | TOTAL: 7 pass 1 (-+): 1 found - 1 modified | TOTAL: 8 pass 2 (-+): 0 found - 1 modified | TOTAL: 8 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 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-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 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 Iteration Number : 5 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 : 5 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 : 5 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 = 562 (out of 574566: 0.097813) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done time:: 00:00:22 elapsed:: 00022 cmd:: mri_pretess #-------------------------------------------- #@# Fill Tue May 7 16:05:46 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.009 -0.222 0.879 33.997; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.105 -0.006 -0.009 -13.569; 0.010 1.129 0.162 -34.218; 0.009 -0.222 0.879 33.997; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1074 (min = 350, max = 1400), aspect = 0.51 (min = 0.10, max = 0.75) no need to search using seed (126, 120, 149), TAL = (2.0, 21.0, 8.0) talairach voxel to voxel transform 0.905 0.006 0.008 12.226; -0.007 0.855 -0.158 34.523; -0.011 0.216 1.098 -30.077; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 120, 149) --> (2.0, 21.0, 8.0) done. writing output to filled.mgz... filling took 2.8 minutes talairach cc position changed to (2.00, 21.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 21.00, 8.00) SRC: (111.86, 112.87, 158.16) search lh wm seed point around talairach space (-16.00, 21.00, 8.00), SRC: (144.43, 112.63, 157.75) 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 ... time:: 00:02:52 elapsed:: 00172 cmd:: mri_fill #-------------------------------------------- #@# Tessellate lh Tue May 7 16:08:39 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 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 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 11 (out of 274283: 0.004010) Ambiguous edge configurations... mri_pretess done time:: 00:00:10 elapsed:: 00010 cmd:: mri_pretess 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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ slice 30: 517 vertices, 579 faces slice 40: 4523 vertices, 4712 faces slice 50: 11282 vertices, 11530 faces slice 60: 19528 vertices, 19845 faces slice 70: 29160 vertices, 29503 faces slice 80: 39047 vertices, 39365 faces slice 90: 48582 vertices, 48937 faces slice 100: 59655 vertices, 60030 faces slice 110: 70060 vertices, 70482 faces slice 120: 80473 vertices, 80888 faces slice 130: 90574 vertices, 90980 faces slice 140: 100191 vertices, 100545 faces slice 150: 107988 vertices, 108280 faces slice 160: 114212 vertices, 114518 faces slice 170: 120745 vertices, 121023 faces slice 180: 126682 vertices, 126934 faces slice 190: 131522 vertices, 131724 faces slice 200: 134785 vertices, 134910 faces slice 210: 135016 vertices, 135082 faces slice 220: 135016 vertices, 135082 faces slice 230: 135016 vertices, 135082 faces slice 240: 135016 vertices, 135082 faces slice 250: 135016 vertices, 135082 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; time:: 00:00:08 elapsed:: 00008 cmd:: mri_tessellate rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 135016 voxel in cpt #1: X=-66 [v=135016,e=405246,f=270164] located at (-26.688416, -19.478306, 15.093211) For the whole surface: X=-66 [v=135016,e=405246,f=270164] One single component has been found nothing to do done time:: 00:00:05 elapsed:: 00005 cmd:: mris_extract_main_component #-------------------------------------------- #@# Smooth1 lh Tue May 7 16:09:03 EDT 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... time:: 00:00:09 elapsed:: 00009 cmd:: mris_smooth #-------------------------------------------- #@# Inflation1 lh Tue May 7 16:09:14 EDT 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts avg radius = 48.6 mm, total surface area = 72441 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.1 minutes Not saving sulc step 000: RMS=0.099 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.037 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. Not saving sulc time:: 00:01:04 elapsed:: 00064 cmd:: mris_inflate #-------------------------------------------- #@# QSphere lh Tue May 7 16:10:19 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.60 (0.00-->9.88) (max @ vno 92197 --> 92198) face area 0.02 +- 0.03 (-0.16-->0.58) scaling brain by 0.292... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.810, avgs=0 005/300: dt: 0.9000, rms radial error=177.550, avgs=0 010/300: dt: 0.9000, rms radial error=176.992, avgs=0 015/300: dt: 0.9000, rms radial error=176.259, avgs=0 020/300: dt: 0.9000, rms radial error=175.423, avgs=0 025/300: dt: 0.9000, rms radial error=174.529, avgs=0 030/300: dt: 0.9000, rms radial error=173.603, avgs=0 035/300: dt: 0.9000, rms radial error=172.659, avgs=0 040/300: dt: 0.9000, rms radial error=171.708, avgs=0 045/300: dt: 0.9000, rms radial error=170.753, avgs=0 050/300: dt: 0.9000, rms radial error=169.800, avgs=0 055/300: dt: 0.9000, rms radial error=168.849, avgs=0 060/300: dt: 0.9000, rms radial error=167.902, avgs=0 065/300: dt: 0.9000, rms radial error=166.959, avgs=0 070/300: dt: 0.9000, rms radial error=166.021, avgs=0 075/300: dt: 0.9000, rms radial error=165.088, avgs=0 080/300: dt: 0.9000, rms radial error=164.161, avgs=0 085/300: dt: 0.9000, rms radial error=163.238, avgs=0 090/300: dt: 0.9000, rms radial error=162.321, avgs=0 095/300: dt: 0.9000, rms radial error=161.408, avgs=0 100/300: dt: 0.9000, rms radial error=160.501, avgs=0 105/300: dt: 0.9000, rms radial error=159.598, avgs=0 110/300: dt: 0.9000, rms radial error=158.700, avgs=0 115/300: dt: 0.9000, rms radial error=157.808, avgs=0 120/300: dt: 0.9000, rms radial error=156.920, avgs=0 125/300: dt: 0.9000, rms radial error=156.037, avgs=0 130/300: dt: 0.9000, rms radial error=155.159, avgs=0 135/300: dt: 0.9000, rms radial error=154.288, avgs=0 140/300: dt: 0.9000, rms radial error=153.423, avgs=0 145/300: dt: 0.9000, rms radial error=152.563, avgs=0 150/300: dt: 0.9000, rms radial error=151.709, avgs=0 155/300: dt: 0.9000, rms radial error=150.858, avgs=0 160/300: dt: 0.9000, rms radial error=150.013, avgs=0 165/300: dt: 0.9000, rms radial error=149.172, avgs=0 170/300: dt: 0.9000, rms radial error=148.335, avgs=0 175/300: dt: 0.9000, rms radial error=147.504, avgs=0 180/300: dt: 0.9000, rms radial error=146.676, avgs=0 185/300: dt: 0.9000, rms radial error=145.853, avgs=0 190/300: dt: 0.9000, rms radial error=145.035, avgs=0 195/300: dt: 0.9000, rms radial error=144.221, avgs=0 200/300: dt: 0.9000, rms radial error=143.411, avgs=0 205/300: dt: 0.9000, rms radial error=142.606, avgs=0 210/300: dt: 0.9000, rms radial error=141.805, avgs=0 215/300: dt: 0.9000, rms radial error=141.009, avgs=0 220/300: dt: 0.9000, rms radial error=140.217, avgs=0 225/300: dt: 0.9000, rms radial error=139.429, avgs=0 230/300: dt: 0.9000, rms radial error=138.645, avgs=0 235/300: dt: 0.9000, rms radial error=137.866, avgs=0 240/300: dt: 0.9000, rms radial error=137.091, avgs=0 245/300: dt: 0.9000, rms radial error=136.321, avgs=0 250/300: dt: 0.9000, rms radial error=135.555, avgs=0 255/300: dt: 0.9000, rms radial error=134.793, avgs=0 260/300: dt: 0.9000, rms radial error=134.035, avgs=0 265/300: dt: 0.9000, rms radial error=133.281, avgs=0 270/300: dt: 0.9000, rms radial error=132.532, avgs=0 275/300: dt: 0.9000, rms radial error=131.786, avgs=0 280/300: dt: 0.9000, rms radial error=131.045, avgs=0 285/300: dt: 0.9000, rms radial error=130.308, avgs=0 290/300: dt: 0.9000, rms radial error=129.575, avgs=0 295/300: dt: 0.9000, rms radial error=128.847, avgs=0 300/300: dt: 0.9000, rms radial error=128.122, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16082.11 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2808.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 317.90 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00349 epoch 4 (K=640.0), pass 1, starting sse = 22.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00473 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.13 hours distance error %100000.00 time:: 00:08:02 elapsed:: 00482 cmd:: mris_sphere #-------------------------------------------- #@# Fix Topology lh Tue May 7 16:18:22 EDT 2013 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 bert 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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ before topology correction, eno=-66 (nv=135016, nf=270164, ne=405246, g=34) 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... 3771 ambiguous faces found in tessellation segmenting defects... 44 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 44 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.6228 (-4.3114) -vertex loglikelihood: -5.5160 (-2.7580) -normal dot loglikelihood: -3.5696 (-3.5696) -quad curv loglikelihood: -6.2679 (-3.1340) Total Loglikelihood : -23.9763 CORRECTING DEFECT 0 (vertices=26, convex hull=76) After retessellation of defect 0, euler #=-41 (132592,396530,263897) : difference with theory (-41) = 0 CORRECTING DEFECT 1 (vertices=29, convex hull=77) After retessellation of defect 1, euler #=-40 (132601,396590,263949) : difference with theory (-40) = 0 CORRECTING DEFECT 2 (vertices=22, convex hull=45) After retessellation of defect 2, euler #=-39 (132606,396621,263976) : difference with theory (-39) = 0 CORRECTING DEFECT 3 (vertices=20, convex hull=49) After retessellation of defect 3, euler #=-38 (132615,396666,264013) : difference with theory (-38) = 0 CORRECTING DEFECT 4 (vertices=46, convex hull=81) After retessellation of defect 4, euler #=-37 (132640,396775,264098) : difference with theory (-37) = 0 CORRECTING DEFECT 5 (vertices=50, convex hull=81) After retessellation of defect 5, euler #=-36 (132675,396916,264205) : difference with theory (-36) = 0 CORRECTING DEFECT 6 (vertices=27, convex hull=46) After retessellation of defect 6, euler #=-35 (132682,396953,264236) : difference with theory (-35) = 0 CORRECTING DEFECT 7 (vertices=7, convex hull=17) After retessellation of defect 7, euler #=-34 (132683,396959,264242) : difference with theory (-34) = 0 CORRECTING DEFECT 8 (vertices=32, convex hull=63) After retessellation of defect 8, euler #=-33 (132702,397042,264307) : difference with theory (-33) = 0 CORRECTING DEFECT 9 (vertices=37, convex hull=90) After retessellation of defect 9, euler #=-32 (132718,397127,264377) : difference with theory (-32) = 0 CORRECTING DEFECT 10 (vertices=29, convex hull=52) After retessellation of defect 10, euler #=-31 (132732,397191,264428) : difference with theory (-31) = 0 CORRECTING DEFECT 11 (vertices=14, convex hull=29) After retessellation of defect 11, euler #=-30 (132734,397209,264445) : difference with theory (-30) = 0 CORRECTING DEFECT 12 (vertices=207, convex hull=153) After retessellation of defect 12, euler #=-29 (132808,397504,264667) : difference with theory (-29) = 0 CORRECTING DEFECT 13 (vertices=57, convex hull=65) After retessellation of defect 13, euler #=-28 (132828,397590,264734) : difference with theory (-28) = 0 CORRECTING DEFECT 14 (vertices=33, convex hull=59) After retessellation of defect 14, euler #=-27 (132846,397666,264793) : difference with theory (-27) = 0 CORRECTING DEFECT 15 (vertices=42, convex hull=28) After retessellation of defect 15, euler #=-26 (132851,397692,264815) : difference with theory (-26) = 0 CORRECTING DEFECT 16 (vertices=42, convex hull=94) After retessellation of defect 16, euler #=-25 (132878,397810,264907) : difference with theory (-25) = 0 CORRECTING DEFECT 17 (vertices=14, convex hull=38) After retessellation of defect 17, euler #=-24 (132880,397826,264922) : difference with theory (-24) = 0 CORRECTING DEFECT 18 (vertices=13, convex hull=27) After retessellation of defect 18, euler #=-23 (132881,397837,264933) : difference with theory (-23) = 0 CORRECTING DEFECT 19 (vertices=44, convex hull=72) After retessellation of defect 19, euler #=-22 (132900,397926,265004) : difference with theory (-22) = 0 CORRECTING DEFECT 20 (vertices=32, convex hull=58) After retessellation of defect 20, euler #=-21 (132917,397999,265061) : difference with theory (-21) = 0 CORRECTING DEFECT 21 (vertices=170, convex hull=153) After retessellation of defect 21, euler #=-20 (132940,398140,265180) : difference with theory (-20) = 0 CORRECTING DEFECT 22 (vertices=87, convex hull=68) After retessellation of defect 22, euler #=-19 (132962,398235,265254) : difference with theory (-19) = 0 CORRECTING DEFECT 23 (vertices=17, convex hull=28) After retessellation of defect 23, euler #=-18 (132966,398255,265271) : difference with theory (-18) = 0 CORRECTING DEFECT 24 (vertices=51, convex hull=63) After retessellation of defect 24, euler #=-17 (132989,398352,265346) : difference with theory (-17) = 0 CORRECTING DEFECT 25 (vertices=285, convex hull=335) After retessellation of defect 25, euler #=-16 (133154,399011,265841) : difference with theory (-16) = 0 CORRECTING DEFECT 26 (vertices=8, convex hull=30) After retessellation of defect 26, euler #=-15 (133156,399027,265856) : difference with theory (-15) = 0 CORRECTING DEFECT 27 (vertices=70, convex hull=28) After retessellation of defect 27, euler #=-14 (133162,399053,265877) : difference with theory (-14) = 0 CORRECTING DEFECT 28 (vertices=29, convex hull=68) After retessellation of defect 28, euler #=-13 (133171,399103,265919) : difference with theory (-13) = 0 CORRECTING DEFECT 29 (vertices=34, convex hull=23) After retessellation of defect 29, euler #=-12 (133184,399151,265955) : difference with theory (-12) = 0 CORRECTING DEFECT 30 (vertices=194, convex hull=69) After retessellation of defect 30, euler #=-11 (133201,399232,266020) : difference with theory (-11) = 0 CORRECTING DEFECT 31 (vertices=23, convex hull=31) After retessellation of defect 31, euler #=-10 (133210,399269,266049) : difference with theory (-10) = 0 CORRECTING DEFECT 32 (vertices=24, convex hull=62) After retessellation of defect 32, euler #=-9 (133226,399344,266109) : difference with theory (-9) = 0 CORRECTING DEFECT 33 (vertices=61, convex hull=97) After retessellation of defect 33, euler #=-8 (133249,399452,266195) : difference with theory (-8) = 0 CORRECTING DEFECT 34 (vertices=32, convex hull=64) After retessellation of defect 34, euler #=-7 (133265,399529,266257) : difference with theory (-7) = 0 CORRECTING DEFECT 35 (vertices=30, convex hull=50) After retessellation of defect 35, euler #=-6 (133274,399575,266295) : difference with theory (-6) = 0 CORRECTING DEFECT 36 (vertices=55, convex hull=85) After retessellation of defect 36, euler #=-5 (133306,399708,266397) : difference with theory (-5) = 0 CORRECTING DEFECT 37 (vertices=36, convex hull=85) After retessellation of defect 37, euler #=-4 (133323,399797,266470) : difference with theory (-4) = 0 CORRECTING DEFECT 38 (vertices=85, convex hull=70) After retessellation of defect 38, euler #=-3 (133343,399886,266540) : difference with theory (-3) = 0 CORRECTING DEFECT 39 (vertices=23, convex hull=60) After retessellation of defect 39, euler #=-2 (133350,399926,266574) : difference with theory (-2) = 0 CORRECTING DEFECT 40 (vertices=57, convex hull=83) After retessellation of defect 40, euler #=-1 (133365,400008,266642) : difference with theory (-1) = 0 CORRECTING DEFECT 41 (vertices=30, convex hull=79) After retessellation of defect 41, euler #=0 (133382,400091,266709) : difference with theory (0) = 0 CORRECTING DEFECT 42 (vertices=138, convex hull=61) After retessellation of defect 42, euler #=1 (133397,400165,266769) : difference with theory (1) = 0 CORRECTING DEFECT 43 (vertices=68, convex hull=46) After retessellation of defect 43, euler #=2 (133401,400197,266798) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.03-->8.93) (max @ vno 91096 --> 99143) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.03-->8.93) (max @ vno 91096 --> 99143) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 165 mutations (35.3%), 303 crossovers (64.7%), 97 vertices were eliminated building final representation... 1615 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133401, nf=266798, ne=400197, g=0) writing corrected surface to /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 53.4 minutes 0 defective edges removing intersecting faces 000: 290 intersecting 001: 13 intersecting time:: 00:53:24 elapsed:: 03204 cmd:: mris_fix_topology mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 133401 - 400197 + 266798 = 2 --> 0 holes F =2V-4: 266798 = 266802-4 (0) 2E=3F: 800394 = 800394 (0) total defect index = 0 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 40 intersecting writing corrected surface to ../surf/lh.orig time:: 00:00:08 elapsed:: 00008 cmd:: mris_remove_intersection rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue May 7 17:12:02 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs bert 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 1.127.2.5 2013/04/19 20:15:38 nicks Exp $ $Id: mrisurf.c,v 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/filled.mgz... reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... 12898 bright wm thresholded. 11119 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.orig... computing class statistics... border white: 261006 voxels (1.56%) border gray 282435 voxels (1.68%) WM (101.0): 101.4 +- 5.6 [70.0 --> 110.0] GM (93.0) : 90.6 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.0 (was 70) setting MAX_BORDER_WHITE to 112.6 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 63.0 (was 40) setting MAX_GRAY to 101.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 53.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.00-->3.70) (max @ vno 133004 --> 133025) face area 0.28 +- 0.12 (0.00-->2.65) mean absolute distance = 0.89 +- 1.08 3657 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=107, GM=83 mean inside = 100.8, mean outside = 88.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=89.9, 104 (104) missing vertices, mean dist 0.5 [0.8 (%26.2)->0.9 (%73.8))] %58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.10-->4.63) (max @ vno 132779 --> 132757) face area 0.28 +- 0.14 (0.00-->2.24) mean absolute distance = 0.46 +- 0.70 4015 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3924752.2, rms=8.06 001: dt: 0.5000, sse=4289120.5, rms=6.018 (0.000%) 002: dt: 0.5000, sse=4358725.0, rms=4.584 (0.000%) 003: dt: 0.5000, sse=4415438.5, rms=3.566 (0.000%) 004: dt: 0.5000, sse=4512600.5, rms=2.892 (0.000%) 005: dt: 0.5000, sse=4526675.5, rms=2.483 (0.000%) 006: dt: 0.5000, sse=4585837.0, rms=2.248 (0.000%) 007: dt: 0.5000, sse=4586361.0, rms=2.111 (0.000%) 008: dt: 0.5000, sse=4635324.5, rms=2.029 (0.000%) rms = 1.98, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=4625102.0, rms=1.980 (0.000%) 010: dt: 0.2500, sse=3199360.0, rms=1.598 (0.000%) 011: dt: 0.2500, sse=3082546.2, rms=1.544 (0.000%) rms = 1.53, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3050876.5, rms=1.528 (0.000%) rms = 1.51, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3020993.2, rms=1.515 (0.000%) positioning took 3.0 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=92.5, 60 (13) missing vertices, mean dist -0.3 [0.5 (%73.7)->0.3 (%26.3))] %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.06-->4.98) (max @ vno 132779 --> 132757) face area 0.36 +- 0.17 (0.00-->3.23) mean absolute distance = 0.32 +- 0.43 3793 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3442878.0, rms=3.86 014: dt: 0.5000, sse=3603708.2, rms=2.408 (0.000%) 015: dt: 0.5000, sse=3813425.5, rms=1.864 (0.000%) 016: dt: 0.5000, sse=3841948.2, rms=1.627 (0.000%) 017: dt: 0.5000, sse=4033096.5, rms=1.568 (0.000%) rms = 1.57, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=4095146.8, rms=1.568 (0.000%) 019: dt: 0.2500, sse=3340684.5, rms=1.257 (0.000%) rms = 1.22, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3228030.0, rms=1.221 (0.000%) rms = 1.21, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3193764.5, rms=1.211 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=94.6, 45 (3) missing vertices, mean dist -0.2 [0.4 (%73.9)->0.2 (%26.1))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->5.16) (max @ vno 132779 --> 132757) face area 0.34 +- 0.16 (0.00-->3.33) mean absolute distance = 0.23 +- 0.32 3185 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3332544.5, rms=2.91 022: dt: 0.5000, sse=3533585.8, rms=1.592 (0.000%) 023: dt: 0.5000, sse=3672220.0, rms=1.366 (0.000%) 024: dt: 0.5000, sse=3710413.0, rms=1.307 (0.000%) rms = 1.36, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3432162.5, rms=1.146 (0.000%) 026: dt: 0.2500, sse=3333873.5, rms=1.089 (0.000%) rms = 1.09, time step reduction 2 of 3 to 0.125... rms = 1.09, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3321848.5, rms=1.086 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=95.3, 42 (1) missing vertices, mean dist -0.1 [0.2 (%58.0)->0.2 (%42.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3327290.0, rms=1.38 028: dt: 0.5000, sse=3950584.2, rms=0.980 (0.000%) rms = 1.17, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3714557.2, rms=0.897 (0.000%) rms = 0.90, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3598904.0, rms=0.896 (0.000%) rms = 0.89, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3607170.2, rms=0.892 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 9 non-cortical segments detected only using segment with 2432 vertices erasing segment 1 (vno[0] = 54527) erasing segment 2 (vno[0] = 57807) erasing segment 3 (vno[0] = 59861) erasing segment 4 (vno[0] = 95651) erasing segment 5 (vno[0] = 98310) erasing segment 6 (vno[0] = 101579) erasing segment 7 (vno[0] = 103925) erasing segment 8 (vno[0] = 104654) writing cortex label to /autofs/cluster/freesurfer/test/tsd/i686/bert/label/lh.cortex.label... LabelWrite: saving to /autofs/cluster/freesurfer/test/tsd/i686/bert/label/lh.cortex.label writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.area vertex spacing 0.89 +- 0.25 (0.05-->5.24) (max @ vno 132779 --> 132757) face area 0.33 +- 0.16 (0.00-->3.45) refinement took 13.2 minutes time:: 00:13:14 elapsed:: 00794 cmd:: mris_make_surfaces #-------------------------------------------- #@# Smooth2 lh Tue May 7 17:25:18 EDT 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/cluster/freesurfer/test/tsd/i686/bert/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... time:: 00:00:10 elapsed:: 00010 cmd:: mris_smooth #-------------------------------------------- #@# Inflation2 lh Tue May 7 17:25:28 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 48.7 mm, total surface area = 81187 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.109 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 1.1 minutes time:: 00:01:05 elapsed:: 00065 cmd:: mris_inflate 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 ~ [-0.33 0.53], k2 ~ [-0.11 0.23] total integrated curvature = 0.575*4pi (7.231) --> 0 handles ICI = 1.5, FI = 8.6, variation=152.488 140 vertices thresholded to be in [-0.05 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 104 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.021 done. time:: 00:03:37 elapsed:: 00217 cmd:: mris_curvature #----------------------------------------- #@# Curvature Stats lh Tue May 7 17:30:11 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm bert 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 [ bert/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 [ 205 ] Gb_filter = 0 WARN: S lookup min: -0.375309 WARN: S explicit min: 0.000000 vertex = 1157 time:: 00:00:11 elapsed:: 00011 cmd:: mris_curvature_stats #-------------------------------------------- #@# Sphere lh Tue May 7 17:30:22 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.275... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=node0, 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 %20.32 pass 1: epoch 2 of 3 starting distance error %20.31 unfolding complete - removing small folds... starting distance error %20.24 removing remaining folds... final distance error %20.26 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 2.14 hours time:: 02:08:23 elapsed:: 07703 cmd:: mris_sphere #-------------------------------------------- #@# Surf Reg lh Tue May 7 19:38:48 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_register -curv ../surf/lh.sphere /space/freesurfer/centos4.0/stable/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /space/freesurfer/centos4.0/stable/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=node0, 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=node0, 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 = 0.590 curvature mean = 0.020, std = 0.932 curvature mean = 0.019, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, 0.00) sse = 254571.6, tmin=3.8687 d=16.00 min @ (4.00, 0.00, 4.00) sse = 241431.4, tmin=5.8223 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 237988.2, tmin=7.9581 d=4.00 min @ (1.00, 0.00, 1.00) sse = 237108.9, tmin=10.1827 d=2.00 min @ (0.00, 0.50, -0.50) sse = 236821.4, tmin=12.4252 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 236664.4, tmin=14.6325 tol=1.0e+00, sigma=0.5, host=node0, 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 16.82 min curvature mean = 0.005, std = 0.964 curvature mean = 0.008, std = 0.942 curvature mean = 0.005, std = 0.977 curvature mean = 0.004, std = 0.975 curvature mean = 0.004, std = 0.979 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.026, std = 0.269 curvature mean = 0.004, std = 0.067 curvature mean = 0.060, std = 0.378 curvature mean = 0.004, std = 0.080 curvature mean = 0.027, std = 0.577 curvature mean = 0.004, std = 0.087 curvature mean = 0.013, std = 0.720 curvature mean = 0.004, std = 0.089 curvature mean = 0.004, std = 0.824 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 time:: 00:55:26 elapsed:: 03326 cmd:: mris_register #-------------------------------------------- #@# Jacobian white lh Tue May 7 20:34:19 EDT 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 time:: 00:00:07 elapsed:: 00007 cmd:: mris_jacobian #-------------------------------------------- #@# AvgCurv lh Tue May 7 20:34:27 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mrisp_paint -a 5 /space/freesurfer/centos4.0/stable/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 /space/freesurfer/centos4.0/stable/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... time:: 00:00:05 elapsed:: 00005 cmd:: mrisp_paint #----------------------------------------- #@# Cortical Parc lh Tue May 7 20:34:32 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /space/freesurfer/centos4.0/stable/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading atlas from /space/freesurfer/centos4.0/stable/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... 1130 labels changed using aseg relabeling using gibbs priors... 000: 3064 changed, 133401 examined... 001: 720 changed, 13053 examined... 002: 193 changed, 3899 examined... 003: 62 changed, 1091 examined... 004: 39 changed, 380 examined... 005: 23 changed, 231 examined... 006: 7 changed, 134 examined... 007: 1 changed, 46 examined... 008: 1 changed, 9 examined... 009: 1 changed, 5 examined... 010: 1 changed, 7 examined... 011: 0 changed, 7 examined... 271 labels changed using aseg 000: 109 total segments, 60 labels (186 vertices) changed 001: 48 total segments, 5 labels (11 vertices) changed 002: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1394 vertices marked for relabeling... 1394 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 2 minutes and 31 seconds. time:: 00:02:31 elapsed:: 00151 cmd:: mris_ca_label #-------------------------------------------- #@# Make Pial Surf lh Tue May 7 20:37:05 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs bert 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 1.127.2.5 2013/04/19 20:15:38 nicks Exp $ $Id: mrisurf.c,v 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/filled.mgz... reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... 12898 bright wm thresholded. 11119 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.orig... computing class statistics... border white: 261006 voxels (1.56%) border gray 282435 voxels (1.68%) WM (101.0): 101.4 +- 5.6 [70.0 --> 110.0] GM (93.0) : 90.6 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.0 (was 70) setting MAX_BORDER_WHITE to 112.6 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 63.0 (was 40) setting MAX_GRAY to 101.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 53.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107, GM=83 mean inside = 100.8, mean outside = 88.7 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 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.00-->3.70) (max @ vno 133004 --> 133025) face area 0.28 +- 0.12 (0.00-->2.65) mean absolute distance = 0.90 +- 1.08 3750 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 22 points - only 18.18% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 540 points - only 0.00% unknown mean border=89.9, 106 (105) missing vertices, mean dist 0.5 [0.8 (%26.2)->0.9 (%73.8))] %58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.10-->4.63) (max @ vno 132779 --> 132757) face area 0.28 +- 0.14 (0.00-->2.25) mean absolute distance = 0.46 +- 0.70 4054 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3937949.2, rms=8.05 001: dt: 0.5000, sse=4304417.0, rms=6.016 (0.000%) 002: dt: 0.5000, sse=4375954.0, rms=4.586 (0.000%) 003: dt: 0.5000, sse=4433176.5, rms=3.572 (0.000%) 004: dt: 0.5000, sse=4529462.0, rms=2.901 (0.000%) 005: dt: 0.5000, sse=4543870.5, rms=2.491 (0.000%) 006: dt: 0.5000, sse=4601490.5, rms=2.256 (0.000%) 007: dt: 0.5000, sse=4598664.5, rms=2.120 (0.000%) 008: dt: 0.5000, sse=4648576.5, rms=2.041 (0.000%) rms = 2.00, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=4639300.5, rms=1.996 (0.000%) 010: dt: 0.2500, sse=3210190.2, rms=1.619 (0.000%) 011: dt: 0.2500, sse=3092575.0, rms=1.568 (0.000%) rms = 1.55, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3060475.5, rms=1.551 (0.000%) rms = 1.54, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3031896.0, rms=1.539 (0.000%) positioning took 3.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 31 points - only 12.90% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 7 with 232 points - only 0.00% unknown deleting segment 9 with 111 points - only 0.00% unknown deleting segment 12 with 9 points - only 44.44% unknown deleting segment 13 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group mean border=92.5, 70 (14) missing vertices, mean dist -0.3 [0.5 (%73.7)->0.3 (%26.3))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.06-->4.96) (max @ vno 132779 --> 132757) face area 0.36 +- 0.17 (0.00-->3.23) mean absolute distance = 0.32 +- 0.44 3947 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3457890.8, rms=3.86 014: dt: 0.5000, sse=3621409.8, rms=2.416 (0.000%) 015: dt: 0.5000, sse=3831636.0, rms=1.874 (0.000%) 016: dt: 0.5000, sse=3860300.8, rms=1.638 (0.000%) 017: dt: 0.5000, sse=4051300.0, rms=1.576 (0.000%) rms = 1.58, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=3518622.8, rms=1.385 (0.000%) 019: dt: 0.2500, sse=3283044.8, rms=1.283 (0.000%) rms = 1.26, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3224597.0, rms=1.255 (0.000%) rms = 1.24, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3198041.5, rms=1.241 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 30 points - only 13.33% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 252 points - only 0.00% unknown deleting segment 5 with 160 points - only 0.00% unknown deleting segment 6 with 9 points - only 44.44% unknown deleting segment 8 with 14 points - only 0.00% unknown mean border=94.6, 66 (4) missing vertices, mean dist -0.2 [0.4 (%74.0)->0.2 (%26.0))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.03-->5.13) (max @ vno 132779 --> 132757) face area 0.34 +- 0.16 (0.00-->3.27) mean absolute distance = 0.23 +- 0.32 3222 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3338351.2, rms=2.92 022: dt: 0.5000, sse=3559668.0, rms=1.612 (0.000%) 023: dt: 0.5000, sse=3700445.0, rms=1.382 (0.000%) 024: dt: 0.5000, sse=3737717.8, rms=1.321 (0.000%) rms = 1.38, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3457266.0, rms=1.163 (0.000%) 026: dt: 0.2500, sse=3356750.5, rms=1.105 (0.000%) rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.10, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3344658.5, rms=1.102 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 0.00% unknown deleting segment 1 with 27 points - only 14.81% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 454 points - only 0.00% unknown deleting segment 4 with 9 points - only 44.44% unknown deleting segment 5 with 14 points - only 0.00% unknown mean border=95.3, 73 (1) missing vertices, mean dist -0.1 [0.2 (%58.0)->0.2 (%42.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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=3349263.0, rms=1.38 028: dt: 0.5000, sse=3983834.2, rms=0.986 (0.000%) rms = 1.18, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3743105.0, rms=0.904 (0.000%) rms = 0.90, time step reduction 2 of 3 to 0.125... rms = 0.90, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3721444.5, rms=0.898 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 14 points - only 28.57% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=73.2, 66 (66) missing vertices, mean dist 1.9 [0.0 (%0.0)->2.6 (%100.0))] %23 local maxima, %49 large gradients and %23 min vals, 2034 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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=15733763.0, rms=22.95 001: dt: 0.5000, sse=12862926.0, rms=20.342 (0.000%) 002: dt: 0.5000, sse=10623933.0, rms=18.078 (0.000%) 003: dt: 0.5000, sse=8963060.0, rms=16.156 (0.000%) 004: dt: 0.5000, sse=7841633.0, rms=14.532 (0.000%) 005: dt: 0.5000, sse=7093168.5, rms=13.185 (0.000%) 006: dt: 0.5000, sse=6556771.0, rms=12.073 (0.000%) 007: dt: 0.5000, sse=6203838.0, rms=11.075 (0.000%) 008: dt: 0.5000, sse=5921693.5, rms=10.078 (0.000%) 009: dt: 0.5000, sse=5637730.5, rms=9.009 (0.000%) 010: dt: 0.5000, sse=5362062.5, rms=7.841 (0.000%) 011: dt: 0.5000, sse=5160365.0, rms=6.622 (0.000%) 012: dt: 0.5000, sse=4994537.5, rms=5.488 (0.000%) 013: dt: 0.5000, sse=5043217.0, rms=4.595 (0.000%) 014: dt: 0.5000, sse=5088072.5, rms=4.001 (0.000%) 015: dt: 0.5000, sse=5200148.5, rms=3.679 (0.000%) 016: dt: 0.5000, sse=5219942.0, rms=3.492 (0.000%) 017: dt: 0.5000, sse=5290821.0, rms=3.396 (0.000%) 018: dt: 0.5000, sse=5283301.5, rms=3.312 (0.000%) rms = 3.29, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5317342.0, rms=3.287 (0.000%) 020: dt: 0.2500, sse=3590407.0, rms=2.533 (0.000%) 021: dt: 0.2500, sse=3412130.8, rms=2.336 (0.000%) rms = 2.30, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3321947.0, rms=2.295 (0.000%) 023: dt: 0.1250, sse=3200689.5, rms=2.201 (0.000%) rms = 2.19, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3186007.0, rms=2.188 (0.000%) positioning took 5.7 minutes mean border=71.0, 826 (16) missing vertices, mean dist 0.2 [0.2 (%40.8)->0.5 (%59.2))] %49 local maxima, %30 large gradients and %16 min vals, 658 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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=3736624.2, rms=4.26 025: dt: 0.5000, sse=3882475.8, rms=3.310 (0.000%) 026: dt: 0.5000, sse=4836011.5, rms=3.250 (0.000%) rms = 3.29, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4047863.8, rms=2.603 (0.000%) 028: dt: 0.2500, sse=3740454.2, rms=2.305 (0.000%) 029: dt: 0.2500, sse=3699488.5, rms=2.243 (0.000%) rms = 2.20, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3679980.5, rms=2.205 (0.000%) 031: dt: 0.1250, sse=3579122.2, rms=2.109 (0.000%) rms = 2.09, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3570043.5, rms=2.091 (0.000%) positioning took 2.1 minutes mean border=69.6, 1031 (8) missing vertices, mean dist 0.1 [0.2 (%37.7)->0.3 (%62.3))] %64 local maxima, %15 large gradients and %16 min vals, 640 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, 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=3669553.5, rms=2.78 rms = 2.80, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3555678.0, rms=2.381 (0.000%) 034: dt: 0.2500, sse=3571998.5, rms=2.131 (0.000%) 035: dt: 0.2500, sse=3658258.8, rms=2.056 (0.000%) rms = 2.03, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=3683338.8, rms=2.030 (0.000%) 037: dt: 0.1250, sse=3607315.8, rms=1.961 (0.000%) rms = 1.95, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3612131.0, rms=1.946 (0.000%) positioning took 1.6 minutes mean border=69.0, 1976 (7) missing vertices, mean dist 0.0 [0.2 (%45.3)->0.2 (%54.7))] %67 local maxima, %11 large gradients and %16 min vals, 550 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3623393.8, rms=2.10 rms = 2.36, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=3574567.2, rms=1.959 (0.000%) 040: dt: 0.2500, sse=3660644.2, rms=1.904 (0.000%) rms = 1.89, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=3698834.0, rms=1.889 (0.000%) 042: dt: 0.1250, sse=3649070.5, rms=1.829 (0.000%) rms = 1.82, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=3653599.2, rms=1.820 (0.000%) positioning took 1.4 minutes writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.area.pial vertex spacing 1.00 +- 0.43 (0.05-->8.79) (max @ vno 99977 --> 99972) face area 0.40 +- 0.30 (0.00-->6.08) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133401 vertices processed 25000 of 133401 vertices processed 50000 of 133401 vertices processed 75000 of 133401 vertices processed 100000 of 133401 vertices processed 125000 of 133401 vertices processed 0 of 133401 vertices processed 25000 of 133401 vertices processed 50000 of 133401 vertices processed 75000 of 133401 vertices processed 100000 of 133401 vertices processed 125000 of 133401 vertices processed thickness calculation complete, 513:677 truncations. 32392 vertices at 0 distance 91837 vertices at 1 distance 78736 vertices at 2 distance 34283 vertices at 3 distance 11156 vertices at 4 distance 3475 vertices at 5 distance 1166 vertices at 6 distance 448 vertices at 7 distance 149 vertices at 8 distance 62 vertices at 9 distance 33 vertices at 10 distance 34 vertices at 11 distance 36 vertices at 12 distance 26 vertices at 13 distance 9 vertices at 14 distance 14 vertices at 15 distance 5 vertices at 16 distance 8 vertices at 17 distance 1 vertices at 18 distance 2 vertices at 19 distance 10 vertices at 20 distance writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.thickness positioning took 26.3 minutes time:: 00:26:21 elapsed:: 01581 cmd:: mris_make_surfaces #-------------------------------------------- #@# Surf Volume lh Tue May 7 21:03:29 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] time:: 00:00:00 elapsed:: 00000 cmd:: mris_calc mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] time:: 00:00:00 elapsed:: 00000 cmd:: mris_calc mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] time:: 00:00:00 elapsed:: 00000 cmd:: mris_calc #----------------------------------------- #@# WM/GM Contrast lh Tue May 7 21:03:31 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts pctsurfcon --s bert --lh-only Log file is /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts/pctsurfcon.log Tue May 7 21:03:31 EDT 2013 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 cd /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts /space/freesurfer/centos4.0/stable/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node0360 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /space/freesurfer/centos4.0/stable mri_vol2surf --mov /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.10478/lh.wm.mgh --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz as target reference. Loading label /autofs/cluster/freesurfer/test/tsd/i686/bert/label/lh.cortex.label Reading surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 = 73761 Masking with /autofs/cluster/freesurfer/test/tsd/i686/bert/label/lh.cortex.label Writing to /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.10478/lh.wm.mgh Dim: 133401 1 1 mri_vol2surf --mov /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.10478/lh.gm.mgh --projfrac 0.3 --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz as target reference. Loading label /autofs/cluster/freesurfer/test/tsd/i686/bert/label/lh.cortex.label Reading surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/freesurfer/test/tsd/i686/bert/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 = 88038 Masking with /autofs/cluster/freesurfer/test/tsd/i686/bert/label/lh.cortex.label Writing to /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.10478/lh.gm.mgh Dim: 133401 1 1 mri_concat /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.10478/lh.wm.mgh /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.10478/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.w-g.pct.mgh --annot bert lh aparc --sum /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.w-g.pct.mgh --annot bert lh aparc --sum /autofs/cluster/freesurfer/test/tsd/i686/bert/stats/lh.w-g.pct.stats --snr sysname Linux hostname node0360 machine x86_64 user nicks 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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.w-g.pct.mgh Vertex Area is 0.658801 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1277 889.460 2 1002 caudalanteriorcingulate 815 551.323 3 1003 caudalmiddlefrontal 2945 1962.811 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2586 1594.331 6 1006 entorhinal 559 400.930 7 1007 fusiform 4462 3006.371 8 1008 inferiorparietal 5880 3983.240 9 1009 inferiortemporal 4702 3206.425 10 1010 isthmuscingulate 1351 839.951 11 1011 lateraloccipital 7553 4770.412 12 1012 lateralorbitofrontal 3583 2431.429 13 1013 lingual 4433 2928.989 14 1014 medialorbitofrontal 3131 2104.456 15 1015 middletemporal 4466 2986.692 16 1016 parahippocampal 1062 693.124 17 1017 paracentral 2010 1303.744 18 1018 parsopercularis 2403 1648.302 19 1019 parsorbitalis 775 513.475 20 1020 parstriangularis 2272 1486.065 21 1021 pericalcarine 1922 1229.319 22 1022 postcentral 5994 3738.875 23 1023 posteriorcingulate 1696 1147.837 24 1024 precentral 7245 4463.199 25 1025 precuneus 5709 3759.036 26 1026 rostralanteriorcingulate 1081 702.617 27 1027 rostralmiddlefrontal 8598 5663.775 28 1028 superiorfrontal 10202 6945.263 29 1029 superiorparietal 7988 5169.099 30 1030 superiortemporal 5502 3696.509 31 1031 supramarginal 6944 4645.574 32 1032 frontalpole 282 181.952 33 1033 temporalpole 693 490.516 34 1034 transversetemporal 778 473.163 35 1035 insula 3372 2262.565 Reporting on 34 segmentations mri_segstats done Cleaning up time:: 00:00:26 elapsed:: 00026 cmd:: pctsurfcon #----------------------------------------- #@# Parcellation Stats lh Tue May 7 21:03:57 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 bert lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1277 889 2361 2.693 0.659 0.111 0.026 9 1.4 bankssts 815 551 1348 2.311 0.455 0.135 0.031 13 0.9 caudalanteriorcingulate 2945 1963 5885 2.645 0.557 0.125 0.033 30 4.1 caudalmiddlefrontal 2586 1594 3004 1.792 0.490 0.162 0.062 49 6.9 cuneus 559 401 1687 3.099 0.656 0.145 0.057 7 1.3 entorhinal 4462 3006 8658 2.569 0.722 0.142 0.057 69 11.6 fusiform 5880 3983 11251 2.538 0.595 0.136 0.045 76 10.5 inferiorparietal 4702 3206 11113 2.897 0.695 0.149 0.057 74 10.9 inferiortemporal 1351 840 2042 2.192 0.643 0.139 0.073 159 3.2 isthmuscingulate 7553 4770 11988 2.243 0.638 0.153 0.062 122 19.6 lateraloccipital 3583 2431 7842 2.833 0.699 0.149 0.052 56 7.8 lateralorbitofrontal 4433 2929 5433 1.744 0.508 0.144 0.050 69 9.3 lingual 3131 2104 6430 2.597 0.891 0.148 0.259 152 10.9 medialorbitofrontal 4466 2987 11317 3.109 0.677 0.142 0.044 71 8.2 middletemporal 1062 693 1866 2.399 0.650 0.091 0.020 6 0.8 parahippocampal 2010 1304 3625 2.531 0.612 0.116 0.035 17 3.1 paracentral 2403 1648 5360 2.948 0.504 0.122 0.034 25 3.1 parsopercularis 775 513 2008 3.183 0.545 0.132 0.040 11 1.2 parsorbitalis 2272 1486 4350 2.651 0.553 0.125 0.036 28 3.5 parstriangularis 1922 1229 1735 1.542 0.399 0.134 0.049 23 3.8 pericalcarine 5994 3739 9344 2.192 0.768 0.117 0.054 98 15.3 postcentral 1696 1148 3174 2.496 0.561 0.143 0.046 29 3.2 posteriorcingulate 7245 4463 14296 2.915 0.671 0.117 0.048 127 16.4 precentral 5709 3759 9237 2.349 0.596 0.130 0.042 70 9.2 precuneus 1081 703 2419 3.072 0.572 0.141 0.047 19 1.9 rostralanteriorcingulate 8598 5664 16001 2.473 0.580 0.142 0.065 1115 27.7 rostralmiddlefrontal 10202 6945 23223 2.929 0.620 0.128 0.040 117 15.7 superiorfrontal 7988 5169 13590 2.309 0.583 0.129 0.049 106 18.3 superiorparietal 5502 3697 12168 2.911 0.665 0.124 0.035 61 8.0 superiortemporal 6944 4646 14344 2.742 0.612 0.133 0.041 90 11.2 supramarginal 282 182 793 2.981 0.578 0.185 0.093 8 1.2 frontalpole 693 491 2879 3.891 0.541 0.188 0.106 17 2.8 temporalpole 778 473 1273 2.484 0.548 0.140 0.044 10 1.4 transversetemporal 3372 2263 7050 3.090 0.733 0.111 0.048 37 5.0 insula time:: 00:01:12 elapsed:: 00072 cmd:: mris_anatomical_stats #----------------------------------------- #@# Cortical Parc 2 lh Tue May 7 21:05:10 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /space/freesurfer/centos4.0/stable/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading atlas from /space/freesurfer/centos4.0/stable/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... 126 labels changed using aseg relabeling using gibbs priors... 000: 9099 changed, 133401 examined... 001: 2259 changed, 35351 examined... 002: 723 changed, 11680 examined... 003: 312 changed, 4023 examined... 004: 147 changed, 1780 examined... 005: 87 changed, 862 examined... 006: 55 changed, 506 examined... 007: 36 changed, 298 examined... 008: 21 changed, 204 examined... 009: 11 changed, 91 examined... 010: 4 changed, 57 examined... 011: 3 changed, 30 examined... 012: 2 changed, 16 examined... 013: 3 changed, 12 examined... 014: 3 changed, 17 examined... 015: 2 changed, 16 examined... 016: 2 changed, 14 examined... 017: 2 changed, 10 examined... 018: 1 changed, 10 examined... 019: 3 changed, 7 examined... 020: 1 changed, 13 examined... 021: 0 changed, 7 examined... 64 labels changed using aseg 000: 296 total segments, 212 labels (2167 vertices) changed 001: 92 total segments, 9 labels (44 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 139 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 804 vertices marked for relabeling... 804 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 2 minutes and 48 seconds. time:: 00:02:48 elapsed:: 00168 cmd:: mris_ca_label #----------------------------------------- #@# Parcellation Stats 2 lh Tue May 7 21:08:00 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 bert lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1174 789 2059 2.321 0.615 0.147 0.044 18 2.1 G_and_S_frontomargin 1723 1133 2833 2.257 0.643 0.161 0.056 30 4.3 G_and_S_occipital_inf 1705 968 3098 2.591 0.559 0.130 0.055 50 4.4 G_and_S_paracentral 1315 862 3227 3.249 0.596 0.152 0.047 21 2.6 G_and_S_subcentral 768 491 1687 2.587 0.553 0.159 0.053 14 1.7 G_and_S_transv_frontopol 2297 1537 4745 2.821 0.566 0.124 0.036 25 3.2 G_and_S_cingul-Ant 1440 1009 2675 2.656 0.631 0.117 0.026 12 1.6 G_and_S_cingul-Mid-Ant 1283 906 2328 2.492 0.507 0.118 0.030 12 1.5 G_and_S_cingul-Mid-Post 524 346 1256 2.884 0.415 0.174 0.073 12 1.6 G_cingul-Post-dorsal 319 183 456 2.129 0.628 0.138 0.049 6 0.7 G_cingul-Post-ventral 2226 1354 2571 1.695 0.438 0.164 0.067 45 6.5 G_cuneus 1264 864 3221 3.019 0.514 0.137 0.041 17 2.0 G_front_inf-Opercular 254 160 615 2.860 0.393 0.146 0.053 6 0.5 G_front_inf-Orbital 1442 936 3446 2.900 0.483 0.145 0.046 26 2.8 G_front_inf-Triangul 4171 2758 9960 2.770 0.579 0.150 0.054 71 9.0 G_front_middle 6791 4567 17251 3.090 0.590 0.141 0.049 94 12.6 G_front_sup 522 330 1345 3.517 0.575 0.135 0.086 10 1.3 G_Ins_lg_and_S_cent_ins 687 438 2126 3.666 0.685 0.114 0.037 11 1.0 G_insular_short 2239 1452 4915 2.754 0.547 0.166 0.064 45 5.5 G_occipital_middle 1471 967 2667 2.295 0.582 0.143 0.091 27 7.7 G_occipital_sup 1745 1154 4011 2.761 0.593 0.160 0.077 38 6.7 G_oc-temp_lat-fusifor 2995 1926 3770 1.714 0.537 0.158 0.059 58 7.4 G_oc-temp_med-Lingual 1074 723 2640 2.829 0.748 0.125 0.044 13 1.8 G_oc-temp_med-Parahip 2347 1591 6423 3.111 0.702 0.162 0.115 1028 16.4 G_orbital 2564 1738 6206 2.831 0.514 0.155 0.058 45 5.6 G_pariet_inf-Angular 3318 2257 7771 2.879 0.632 0.141 0.045 50 5.7 G_pariet_inf-Supramar 3446 2196 7116 2.516 0.594 0.141 0.051 56 6.6 G_parietal_sup 2216 1321 3735 2.189 0.581 0.126 0.092 65 10.6 G_postcentral 2912 1635 7036 3.183 0.646 0.123 0.066 68 9.8 G_precentral 2598 1706 4908 2.363 0.571 0.143 0.046 41 5.1 G_precuneus 1154 784 2977 2.669 0.668 0.164 0.427 93 4.7 G_rectus 545 357 1053 3.118 1.148 0.179 0.482 38 3.9 G_subcallosal 567 347 1107 2.628 0.603 0.154 0.047 9 1.0 G_temp_sup-G_T_transv 2164 1465 6446 3.249 0.633 0.156 0.054 38 5.0 G_temp_sup-Lateral 376 248 987 3.785 0.594 0.132 0.055 5 0.9 G_temp_sup-Plan_polar 1149 764 2434 2.798 0.582 0.122 0.032 13 1.5 G_temp_sup-Plan_tempo 3072 2081 8305 3.023 0.624 0.165 0.072 64 9.0 G_temporal_inf 2750 1823 7903 3.270 0.559 0.155 0.052 54 6.0 G_temporal_middle 382 248 469 2.085 0.396 0.097 0.019 2 0.3 Lat_Fis-ant-Horizont 406 270 643 2.882 0.430 0.110 0.025 2 0.5 Lat_Fis-ant-Vertical 1502 980 2126 2.813 0.553 0.116 0.029 11 1.8 Lat_Fis-post 2314 1349 2766 1.873 0.530 0.160 0.080 42 8.2 Pole_occipital 1714 1203 5806 3.364 0.794 0.165 0.081 32 5.4 Pole_temporal 2607 1702 2693 1.745 0.583 0.130 0.050 32 4.5 S_calcarine 3074 2031 3675 2.051 0.749 0.097 0.025 14 3.1 S_central 1076 728 1560 2.274 0.513 0.100 0.022 6 1.0 S_cingul-Marginalis 520 336 868 2.768 0.522 0.117 0.033 4 0.7 S_circular_insula_ant 1644 1126 2730 2.790 0.603 0.102 0.045 13 2.0 S_circular_insula_inf 1961 1343 3126 2.793 0.474 0.091 0.018 7 1.5 S_circular_insula_sup 649 452 1477 3.088 0.833 0.130 0.046 8 1.1 S_collat_transv_ant 416 293 494 1.742 0.434 0.140 0.042 3 0.8 S_collat_transv_post 2563 1697 4581 2.491 0.568 0.115 0.034 24 3.7 S_front_inf 1499 1002 2024 2.129 0.439 0.121 0.034 13 2.0 S_front_middle 2429 1666 4225 2.516 0.495 0.107 0.030 23 2.8 S_front_sup 645 440 1018 2.343 0.488 0.100 0.021 4 0.6 S_interm_prim-Jensen 3337 2211 4875 2.203 0.562 0.116 0.030 28 4.1 S_intrapariet_and_P_trans 1280 852 1642 2.145 0.562 0.124 0.035 9 1.8 S_oc_middle_and_Lunatus 831 548 1016 1.976 0.423 0.096 0.021 4 0.7 S_oc_sup_and_transversal 374 249 550 2.392 0.425 0.120 0.038 4 0.5 S_occipital_ant 1090 745 1672 2.367 0.519 0.111 0.027 7 1.2 S_oc-temp_lat 2134 1477 2844 2.110 0.466 0.105 0.021 13 2.0 S_oc-temp_med_and_Lingual 387 261 611 2.586 0.503 0.131 0.037 4 0.6 S_orbital_lateral 681 492 1162 2.263 0.765 0.120 0.040 10 1.5 S_orbital_med-olfact 1272 869 2289 2.593 0.667 0.147 0.056 21 3.4 S_orbital-H_Shaped 2643 1706 3667 2.310 0.621 0.119 0.032 22 3.5 S_parieto_occipital 939 535 879 1.999 0.619 0.155 0.095 164 2.5 S_pericallosal 2871 1866 3651 2.060 0.497 0.117 0.040 28 5.3 S_postcentral 1471 1000 2228 2.597 0.491 0.113 0.034 10 1.7 S_precentral-inf-part 1151 778 1749 2.665 0.488 0.104 0.024 6 1.1 S_precentral-sup-part 776 519 1216 2.390 0.888 0.140 0.033 11 1.0 S_suborbital 743 495 1164 2.291 0.582 0.136 0.043 9 1.2 S_subparietal 1096 743 1620 2.739 0.771 0.126 0.031 7 1.6 S_temporal_inf 4778 3239 8171 2.548 0.564 0.112 0.028 38 5.3 S_temporal_sup 409 257 497 2.334 0.580 0.130 0.034 5 0.6 S_temporal_transverse time:: 00:01:14 elapsed:: 00074 cmd:: mris_anatomical_stats #----------------------------------------- #@# Cortical Parc 3 lh Tue May 7 21:09:16 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /space/freesurfer/centos4.0/stable/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading atlas from /space/freesurfer/centos4.0/stable/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... 1309 labels changed using aseg relabeling using gibbs priors... 000: 2658 changed, 133401 examined... 001: 628 changed, 11375 examined... 002: 174 changed, 3451 examined... 003: 84 changed, 1072 examined... 004: 38 changed, 503 examined... 005: 21 changed, 232 examined... 006: 9 changed, 115 examined... 007: 6 changed, 51 examined... 008: 2 changed, 30 examined... 009: 0 changed, 15 examined... 186 labels changed using aseg 000: 74 total segments, 41 labels (237 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 42 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 511 vertices marked for relabeling... 511 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 2 minutes and 28 seconds. time:: 00:02:28 elapsed:: 00148 cmd:: mris_ca_label #----------------------------------------- #@# Parcellation Stats 3 lh Tue May 7 21:11:47 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 bert lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1532 1043 2849 2.508 0.555 0.125 0.032 20 1.8 caudalanteriorcingulate 3092 2052 6177 2.662 0.553 0.125 0.034 32 4.4 caudalmiddlefrontal 3505 2186 4359 1.896 0.550 0.149 0.054 57 8.1 cuneus 479 358 1572 3.233 0.590 0.142 0.048 5 0.9 entorhinal 4166 2792 7540 2.485 0.707 0.139 0.054 61 10.5 fusiform 5862 3949 11083 2.515 0.604 0.135 0.044 75 10.4 inferiorparietal 4718 3235 11664 2.936 0.679 0.155 0.062 81 11.9 inferiortemporal 1355 846 2061 2.202 0.657 0.140 0.073 159 3.2 isthmuscingulate 7736 4882 12257 2.240 0.637 0.152 0.061 124 19.6 lateraloccipital 3941 2687 8855 2.851 0.748 0.158 0.064 77 11.1 lateralorbitofrontal 4433 2927 5430 1.743 0.510 0.145 0.050 71 9.5 lingual 2355 1584 4929 2.495 0.869 0.148 0.318 134 8.0 medialorbitofrontal 5572 3748 13281 3.001 0.698 0.136 0.041 78 9.5 middletemporal 1077 703 1883 2.387 0.646 0.091 0.020 6 0.9 parahippocampal 2250 1476 4178 2.555 0.612 0.115 0.034 18 3.4 paracentral 2099 1424 4636 2.911 0.509 0.124 0.034 22 2.8 parsopercularis 1101 722 2316 2.743 0.551 0.116 0.032 11 1.5 parsorbitalis 2838 1867 5622 2.735 0.556 0.126 0.041 36 4.8 parstriangularis 1916 1226 1747 1.552 0.406 0.133 0.049 22 3.7 pericalcarine 6821 4280 10455 2.193 0.756 0.120 0.055 112 18.2 postcentral 1838 1243 3323 2.483 0.552 0.142 0.044 31 3.4 posteriorcingulate 7206 4451 14186 2.913 0.674 0.117 0.048 126 16.2 precentral 5468 3606 9117 2.366 0.577 0.132 0.042 69 8.7 precuneus 1494 972 3112 3.001 0.618 0.136 0.041 24 2.3 rostralanteriorcingulate 5700 3771 10671 2.507 0.604 0.141 0.073 1070 21.9 rostralmiddlefrontal 11551 7786 25812 2.855 0.653 0.133 0.042 145 18.9 superiorfrontal 6325 4103 11008 2.353 0.582 0.129 0.051 83 14.5 superiorparietal 7353 4962 17323 2.998 0.720 0.131 0.043 91 12.8 superiortemporal 6635 4453 13739 2.760 0.605 0.132 0.040 85 10.4 supramarginal 777 473 1268 2.468 0.535 0.140 0.044 10 1.4 transversetemporal 3076 2062 6645 3.113 0.727 0.111 0.049 35 4.6 insula time:: 00:01:11 elapsed:: 00071 cmd:: mris_anatomical_stats #-------------------------------------------- #@# Tessellate rh Tue May 7 21:12:59 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 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+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 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 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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 = 4 (out of 276717: 0.001446) Ambiguous edge configurations... mri_pretess done time:: 00:00:10 elapsed:: 00010 cmd:: mri_pretess 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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ slice 30: 626 vertices, 708 faces slice 40: 4418 vertices, 4604 faces slice 50: 11414 vertices, 11671 faces slice 60: 19953 vertices, 20256 faces slice 70: 30064 vertices, 30425 faces slice 80: 39981 vertices, 40308 faces slice 90: 49981 vertices, 50359 faces slice 100: 61266 vertices, 61668 faces slice 110: 71351 vertices, 71759 faces slice 120: 81762 vertices, 82156 faces slice 130: 91718 vertices, 92099 faces slice 140: 100555 vertices, 100887 faces slice 150: 107717 vertices, 108002 faces slice 160: 113767 vertices, 114049 faces slice 170: 120339 vertices, 120618 faces slice 180: 126228 vertices, 126492 faces slice 190: 131123 vertices, 131335 faces slice 200: 134453 vertices, 134575 faces slice 210: 134838 vertices, 134902 faces slice 220: 134838 vertices, 134902 faces slice 230: 134838 vertices, 134902 faces slice 240: 134838 vertices, 134902 faces slice 250: 134838 vertices, 134902 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; time:: 00:00:08 elapsed:: 00008 cmd:: mri_tessellate rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 134838 voxel in cpt #1: X=-64 [v=134838,e=404706,f=269804] located at (26.154505, -20.123133, 17.801474) For the whole surface: X=-64 [v=134838,e=404706,f=269804] One single component has been found nothing to do done time:: 00:00:05 elapsed:: 00005 cmd:: mris_extract_main_component #-------------------------------------------- #@# Smooth1 rh Tue May 7 21:13:23 EDT 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... time:: 00:00:09 elapsed:: 00009 cmd:: mris_smooth #-------------------------------------------- #@# Inflation1 rh Tue May 7 21:13:33 EDT 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts avg radius = 48.8 mm, total surface area = 72643 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.1 minutes Not saving sulc step 000: RMS=0.098 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.028 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc time:: 00:01:07 elapsed:: 00067 cmd:: mris_inflate #-------------------------------------------- #@# QSphere rh Tue May 7 21:14:41 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.60 (0.00-->8.28) (max @ vno 96170 --> 96171) face area 0.02 +- 0.03 (-0.13-->0.65) scaling brain by 0.291... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.790, avgs=0 005/300: dt: 0.9000, rms radial error=177.529, avgs=0 010/300: dt: 0.9000, rms radial error=176.969, avgs=0 015/300: dt: 0.9000, rms radial error=176.232, avgs=0 020/300: dt: 0.9000, rms radial error=175.394, avgs=0 025/300: dt: 0.9000, rms radial error=174.497, avgs=0 030/300: dt: 0.9000, rms radial error=173.569, avgs=0 035/300: dt: 0.9000, rms radial error=172.625, avgs=0 040/300: dt: 0.9000, rms radial error=171.674, avgs=0 045/300: dt: 0.9000, rms radial error=170.720, avgs=0 050/300: dt: 0.9000, rms radial error=169.767, avgs=0 055/300: dt: 0.9000, rms radial error=168.817, avgs=0 060/300: dt: 0.9000, rms radial error=167.872, avgs=0 065/300: dt: 0.9000, rms radial error=166.930, avgs=0 070/300: dt: 0.9000, rms radial error=165.993, avgs=0 075/300: dt: 0.9000, rms radial error=165.061, avgs=0 080/300: dt: 0.9000, rms radial error=164.134, avgs=0 085/300: dt: 0.9000, rms radial error=163.211, avgs=0 090/300: dt: 0.9000, rms radial error=162.294, avgs=0 095/300: dt: 0.9000, rms radial error=161.382, avgs=0 100/300: dt: 0.9000, rms radial error=160.476, avgs=0 105/300: dt: 0.9000, rms radial error=159.574, avgs=0 110/300: dt: 0.9000, rms radial error=158.676, avgs=0 115/300: dt: 0.9000, rms radial error=157.784, avgs=0 120/300: dt: 0.9000, rms radial error=156.897, avgs=0 125/300: dt: 0.9000, rms radial error=156.015, avgs=0 130/300: dt: 0.9000, rms radial error=155.137, avgs=0 135/300: dt: 0.9000, rms radial error=154.264, avgs=0 140/300: dt: 0.9000, rms radial error=153.396, avgs=0 145/300: dt: 0.9000, rms radial error=152.533, avgs=0 150/300: dt: 0.9000, rms radial error=151.675, avgs=0 155/300: dt: 0.9000, rms radial error=150.822, avgs=0 160/300: dt: 0.9000, rms radial error=149.973, avgs=0 165/300: dt: 0.9000, rms radial error=149.129, avgs=0 170/300: dt: 0.9000, rms radial error=148.290, avgs=0 175/300: dt: 0.9000, rms radial error=147.456, avgs=0 180/300: dt: 0.9000, rms radial error=146.626, avgs=0 185/300: dt: 0.9000, rms radial error=145.801, avgs=0 190/300: dt: 0.9000, rms radial error=144.980, avgs=0 195/300: dt: 0.9000, rms radial error=144.164, avgs=0 200/300: dt: 0.9000, rms radial error=143.352, avgs=0 205/300: dt: 0.9000, rms radial error=142.545, avgs=0 210/300: dt: 0.9000, rms radial error=141.743, avgs=0 215/300: dt: 0.9000, rms radial error=140.945, avgs=0 220/300: dt: 0.9000, rms radial error=140.151, avgs=0 225/300: dt: 0.9000, rms radial error=139.362, avgs=0 230/300: dt: 0.9000, rms radial error=138.577, avgs=0 235/300: dt: 0.9000, rms radial error=137.796, avgs=0 240/300: dt: 0.9000, rms radial error=137.020, avgs=0 245/300: dt: 0.9000, rms radial error=136.248, avgs=0 250/300: dt: 0.9000, rms radial error=135.481, avgs=0 255/300: dt: 0.9000, rms radial error=134.717, avgs=0 260/300: dt: 0.9000, rms radial error=133.958, avgs=0 265/300: dt: 0.9000, rms radial error=133.205, avgs=0 270/300: dt: 0.9000, rms radial error=132.456, avgs=0 275/300: dt: 0.9000, rms radial error=131.712, avgs=0 280/300: dt: 0.9000, rms radial error=130.971, avgs=0 285/300: dt: 0.9000, rms radial error=130.235, avgs=0 290/300: dt: 0.9000, rms radial error=129.502, avgs=0 295/300: dt: 0.9000, rms radial error=128.774, avgs=0 300/300: dt: 0.9000, rms radial error=128.050, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16076.51 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 2821.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 319.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00479 epoch 4 (K=640.0), pass 1, starting sse = 21.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00750 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.16 hours distance error %100000.00 time:: 00:09:41 elapsed:: 00581 cmd:: mris_sphere #-------------------------------------------- #@# Fix Topology rh Tue May 7 21:24:23 EDT 2013 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 bert 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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ before topology correction, eno=-64 (nv=134838, nf=269804, ne=404706, g=33) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 3648 ambiguous faces found in tessellation segmenting defects... 38 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 38 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.5748 (-4.2874) -vertex loglikelihood: -5.5366 (-2.7683) -normal dot loglikelihood: -3.5962 (-3.5962) -quad curv loglikelihood: -6.4185 (-3.2092) Total Loglikelihood : -24.1261 CORRECTING DEFECT 0 (vertices=72, convex hull=97) After retessellation of defect 0, euler #=-35 (132591,396733,264107) : difference with theory (-35) = 0 CORRECTING DEFECT 1 (vertices=54, convex hull=72) After retessellation of defect 1, euler #=-34 (132612,396825,264179) : difference with theory (-34) = 0 CORRECTING DEFECT 2 (vertices=34, convex hull=84) After retessellation of defect 2, euler #=-33 (132628,396905,264244) : difference with theory (-33) = 0 CORRECTING DEFECT 3 (vertices=10, convex hull=26) After retessellation of defect 3, euler #=-32 (132631,396921,264258) : difference with theory (-32) = 0 CORRECTING DEFECT 4 (vertices=6, convex hull=24) After retessellation of defect 4, euler #=-31 (132633,396933,264269) : difference with theory (-31) = 0 CORRECTING DEFECT 5 (vertices=43, convex hull=79) After retessellation of defect 5, euler #=-30 (132663,397056,264363) : difference with theory (-30) = 0 CORRECTING DEFECT 6 (vertices=25, convex hull=53) After retessellation of defect 6, euler #=-29 (132672,397107,264406) : difference with theory (-29) = 0 CORRECTING DEFECT 7 (vertices=53, convex hull=77) After retessellation of defect 7, euler #=-28 (132698,397220,264494) : difference with theory (-28) = 0 CORRECTING DEFECT 8 (vertices=83, convex hull=113) After retessellation of defect 8, euler #=-27 (132742,397408,264639) : difference with theory (-27) = 0 CORRECTING DEFECT 9 (vertices=25, convex hull=58) After retessellation of defect 9, euler #=-26 (132751,397456,264679) : difference with theory (-26) = 0 CORRECTING DEFECT 10 (vertices=35, convex hull=30) After retessellation of defect 10, euler #=-25 (132759,397492,264708) : difference with theory (-25) = 0 CORRECTING DEFECT 11 (vertices=34, convex hull=54) After retessellation of defect 11, euler #=-24 (132775,397559,264760) : difference with theory (-24) = 0 CORRECTING DEFECT 12 (vertices=23, convex hull=40) After retessellation of defect 12, euler #=-23 (132784,397603,264796) : difference with theory (-23) = 0 CORRECTING DEFECT 13 (vertices=24, convex hull=71) After retessellation of defect 13, euler #=-22 (132798,397673,264853) : difference with theory (-22) = 0 CORRECTING DEFECT 14 (vertices=46, convex hull=84) After retessellation of defect 14, euler #=-21 (132824,397788,264943) : difference with theory (-21) = 0 CORRECTING DEFECT 15 (vertices=60, convex hull=122) After retessellation of defect 15, euler #=-20 (132860,397952,265072) : difference with theory (-20) = 0 CORRECTING DEFECT 16 (vertices=299, convex hull=104) After retessellation of defect 16, euler #=-19 (132918,398174,265237) : difference with theory (-19) = 0 CORRECTING DEFECT 17 (vertices=25, convex hull=37) After retessellation of defect 17, euler #=-18 (132922,398199,265259) : difference with theory (-18) = 0 CORRECTING DEFECT 18 (vertices=193, convex hull=90) After retessellation of defect 18, euler #=-17 (132955,398338,265366) : difference with theory (-17) = 0 CORRECTING DEFECT 19 (vertices=118, convex hull=56) After retessellation of defect 19, euler #=-16 (132973,398418,265429) : difference with theory (-16) = 0 CORRECTING DEFECT 20 (vertices=133, convex hull=53) After retessellation of defect 20, euler #=-15 (132988,398483,265480) : difference with theory (-15) = 0 CORRECTING DEFECT 21 (vertices=42, convex hull=74) After retessellation of defect 21, euler #=-14 (133011,398579,265554) : difference with theory (-14) = 0 CORRECTING DEFECT 22 (vertices=42, convex hull=79) After retessellation of defect 22, euler #=-13 (133033,398676,265630) : difference with theory (-13) = 0 CORRECTING DEFECT 23 (vertices=96, convex hull=128) After retessellation of defect 23, euler #=-12 (133089,398902,265801) : difference with theory (-12) = 0 CORRECTING DEFECT 24 (vertices=24, convex hull=28) After retessellation of defect 24, euler #=-11 (133097,398934,265826) : difference with theory (-11) = 0 CORRECTING DEFECT 25 (vertices=57, convex hull=53) After retessellation of defect 25, euler #=-10 (133100,398965,265855) : difference with theory (-10) = 0 CORRECTING DEFECT 26 (vertices=64, convex hull=113) After retessellation of defect 26, euler #=-9 (133144,399147,265994) : difference with theory (-9) = 0 CORRECTING DEFECT 27 (vertices=20, convex hull=37) After retessellation of defect 27, euler #=-8 (133152,399183,266023) : difference with theory (-8) = 0 CORRECTING DEFECT 28 (vertices=66, convex hull=93) After retessellation of defect 28, euler #=-7 (133189,399333,266137) : difference with theory (-7) = 0 CORRECTING DEFECT 29 (vertices=78, convex hull=106) After retessellation of defect 29, euler #=-6 (133215,399456,266235) : difference with theory (-6) = 0 CORRECTING DEFECT 30 (vertices=21, convex hull=38) After retessellation of defect 30, euler #=-5 (133225,399499,266269) : difference with theory (-5) = 0 CORRECTING DEFECT 31 (vertices=156, convex hull=96) After retessellation of defect 31, euler #=-4 (133241,399592,266347) : difference with theory (-4) = 0 CORRECTING DEFECT 32 (vertices=18, convex hull=30) After retessellation of defect 32, euler #=-3 (133243,399608,266362) : difference with theory (-3) = 0 CORRECTING DEFECT 33 (vertices=72, convex hull=74) After retessellation of defect 33, euler #=-2 (133257,399679,266420) : difference with theory (-2) = 0 CORRECTING DEFECT 34 (vertices=25, convex hull=60) After retessellation of defect 34, euler #=-1 (133268,399735,266466) : difference with theory (-1) = 0 CORRECTING DEFECT 35 (vertices=47, convex hull=67) After retessellation of defect 35, euler #=0 (133286,399817,266531) : difference with theory (0) = 0 CORRECTING DEFECT 36 (vertices=20, convex hull=53) After retessellation of defect 36, euler #=1 (133297,399871,266575) : difference with theory (1) = 0 CORRECTING DEFECT 37 (vertices=35, convex hull=34) After retessellation of defect 37, euler #=2 (133299,399891,266594) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.07-->8.27) (max @ vno 82382 --> 86137) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.07-->8.27) (max @ vno 82382 --> 86137) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 116 mutations (34.1%), 224 crossovers (65.9%), 112 vertices were eliminated building final representation... 1539 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133299, nf=266594, ne=399891, g=0) writing corrected surface to /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 46.2 minutes 0 defective edges removing intersecting faces 000: 292 intersecting 001: 30 intersecting time:: 00:46:14 elapsed:: 02774 cmd:: mris_fix_topology mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 133299 - 399891 + 266594 = 2 --> 0 holes F =2V-4: 266594 = 266598-4 (0) 2E=3F: 799782 = 799782 (0) total defect index = 0 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 60 intersecting 001: 6 intersecting writing corrected surface to ../surf/rh.orig time:: 00:00:09 elapsed:: 00009 cmd:: mris_remove_intersection rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue May 7 22:10:54 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs bert 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 1.127.2.5 2013/04/19 20:15:38 nicks Exp $ $Id: mrisurf.c,v 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/filled.mgz... reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... 13228 bright wm thresholded. 11116 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.orig... computing class statistics... border white: 261006 voxels (1.56%) border gray 282435 voxels (1.68%) WM (101.0): 101.3 +- 5.7 [70.0 --> 110.0] GM (93.0) : 90.6 +- 9.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.1 (was 70) setting MAX_BORDER_WHITE to 112.7 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 63.1 (was 40) setting MAX_GRAY to 101.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 53.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.03-->3.70) (max @ vno 122410 --> 133252) face area 0.28 +- 0.12 (0.00-->2.03) mean absolute distance = 0.91 +- 1.06 4101 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=107, GM=83 mean inside = 100.9, mean outside = 88.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=90.0, 65 (65) missing vertices, mean dist 0.5 [0.8 (%25.9)->1.0 (%74.1))] %59 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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 0.93 +- 0.27 (0.09-->4.64) (max @ vno 72422 --> 73394) face area 0.28 +- 0.14 (0.00-->2.03) mean absolute distance = 0.47 +- 0.70 3934 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3948430.2, rms=8.15 001: dt: 0.5000, sse=4273279.5, rms=6.093 (0.000%) 002: dt: 0.5000, sse=4294418.0, rms=4.635 (0.000%) 003: dt: 0.5000, sse=4372118.0, rms=3.594 (0.000%) 004: dt: 0.5000, sse=4395030.0, rms=2.887 (0.000%) 005: dt: 0.5000, sse=4420704.0, rms=2.442 (0.000%) 006: dt: 0.5000, sse=4431424.0, rms=2.179 (0.000%) 007: dt: 0.5000, sse=4458692.5, rms=2.030 (0.000%) 008: dt: 0.5000, sse=4442972.0, rms=1.937 (0.000%) 009: dt: 0.5000, sse=4474960.5, rms=1.882 (0.000%) rms = 1.85, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=4466542.0, rms=1.849 (0.000%) 011: dt: 0.2500, sse=3170677.2, rms=1.499 (0.000%) rms = 1.46, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3075290.5, rms=1.457 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3034001.0, rms=1.447 (0.000%) positioning took 2.9 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 mean border=92.7, 66 (7) missing vertices, mean dist -0.3 [0.5 (%73.7)->0.3 (%26.3))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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-->5.01) (max @ vno 72422 --> 73394) face area 0.36 +- 0.17 (0.00-->2.86) mean absolute distance = 0.32 +- 0.43 4079 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3497227.0, rms=3.92 014: dt: 0.5000, sse=3626936.2, rms=2.455 (0.000%) 015: dt: 0.5000, sse=3837566.5, rms=1.884 (0.000%) 016: dt: 0.5000, sse=3852196.2, rms=1.624 (0.000%) 017: dt: 0.5000, sse=4059346.5, rms=1.543 (0.000%) rms = 1.54, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=4107496.5, rms=1.535 (0.000%) 019: dt: 0.2500, sse=3395565.0, rms=1.240 (0.000%) rms = 1.21, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3280460.0, rms=1.212 (0.000%) rms = 1.20, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3256183.0, rms=1.204 (0.000%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=94.8, 36 (1) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.2 (%26.2))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->5.15) (max @ vno 72422 --> 73394) face area 0.34 +- 0.16 (0.00-->2.82) mean absolute distance = 0.24 +- 0.33 3585 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3404273.5, rms=2.95 022: dt: 0.5000, sse=3615482.8, rms=1.633 (0.000%) 023: dt: 0.5000, sse=3748809.2, rms=1.359 (0.000%) 024: dt: 0.5000, sse=3772793.8, rms=1.302 (0.000%) rms = 1.34, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3505369.5, rms=1.154 (0.000%) 026: dt: 0.2500, sse=3403599.5, rms=1.102 (0.000%) rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.10, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3391600.2, rms=1.100 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=95.5, 30 (0) missing vertices, mean dist -0.1 [0.3 (%57.8)->0.2 (%42.2))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3395739.8, rms=1.38 028: dt: 0.5000, sse=4046763.5, rms=0.985 (0.000%) rms = 1.17, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3809517.0, rms=0.912 (0.000%) rms = 0.91, time step reduction 2 of 3 to 0.125... rms = 0.91, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3787890.0, rms=0.907 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 12 non-cortical segments detected only using segment with 2249 vertices erasing segment 1 (vno[0] = 58195) erasing segment 2 (vno[0] = 59497) erasing segment 3 (vno[0] = 86277) erasing segment 4 (vno[0] = 94581) erasing segment 5 (vno[0] = 99420) erasing segment 6 (vno[0] = 102443) erasing segment 7 (vno[0] = 103832) erasing segment 8 (vno[0] = 105154) erasing segment 9 (vno[0] = 106391) erasing segment 10 (vno[0] = 132764) erasing segment 11 (vno[0] = 132975) writing cortex label to /autofs/cluster/freesurfer/test/tsd/i686/bert/label/rh.cortex.label... LabelWrite: saving to /autofs/cluster/freesurfer/test/tsd/i686/bert/label/rh.cortex.label writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.area vertex spacing 0.89 +- 0.25 (0.04-->5.15) (max @ vno 72422 --> 73394) face area 0.33 +- 0.16 (0.00-->2.77) refinement took 12.9 minutes time:: 00:12:57 elapsed:: 00777 cmd:: mris_make_surfaces #-------------------------------------------- #@# Smooth2 rh Tue May 7 22:23:55 EDT 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/cluster/freesurfer/test/tsd/i686/bert/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... time:: 00:00:10 elapsed:: 00010 cmd:: mris_smooth #-------------------------------------------- #@# Inflation2 rh Tue May 7 22:24:05 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 49.0 mm, total surface area = 81494 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.109 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.036 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 1.1 minutes time:: 00:01:04 elapsed:: 00064 cmd:: mris_inflate 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 161 vertices thresholded to be in k1 ~ [-0.69 0.47], k2 ~ [-0.18 0.25] total integrated curvature = 0.455*4pi (5.712) --> 1 handles ICI = 1.4, FI = 8.6, variation=149.368 139 vertices thresholded to be in [-0.07 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 99 vertices thresholded to be in [-0.18 0.15] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.021 done. time:: 00:03:34 elapsed:: 00214 cmd:: mris_curvature #----------------------------------------- #@# Curvature Stats rh Tue May 7 22:28:45 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm bert 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 [ bert/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 [ 228 ] Gb_filter = 0 WARN: S lookup min: -0.360398 WARN: S explicit min: 0.000000 vertex = 16 time:: 00:00:11 elapsed:: 00011 cmd:: mris_curvature_stats #-------------------------------------------- #@# Sphere rh Tue May 7 22:28:57 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.274... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=node0, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.38 pass 1: epoch 2 of 3 starting distance error %20.33 unfolding complete - removing small folds... starting distance error %20.20 removing remaining folds... final distance error %20.22 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 2.05 hours time:: 02:02:59 elapsed:: 07379 cmd:: mris_sphere #-------------------------------------------- #@# Surf Reg rh Wed May 8 00:31:56 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_register -curv ../surf/rh.sphere /space/freesurfer/centos4.0/stable/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /space/freesurfer/centos4.0/stable/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=node0, 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=node0, 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 = 0.597 curvature mean = 0.033, std = 0.937 curvature mean = 0.019, std = 0.862 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 368213.0, tmin=2.1026 d=32.00 min @ (0.00, 0.00, -8.00) sse = 301179.9, tmin=4.2168 d=16.00 min @ (4.00, 4.00, 0.00) sse = 282185.8, tmin=6.3389 d=8.00 min @ (-2.00, -2.00, 0.00) sse = 282176.2, tmin=8.5117 d=4.00 min @ (1.00, 1.00, 1.00) sse = 279443.8, tmin=10.7177 d=1.00 min @ (0.00, 0.00, -0.25) sse = 279354.5, tmin=15.1206 tol=1.0e+00, sigma=0.5, host=node0, 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 17.30 min curvature mean = 0.009, std = 0.955 curvature mean = 0.008, std = 0.943 curvature mean = 0.008, std = 0.966 curvature mean = 0.004, std = 0.976 curvature mean = 0.006, std = 0.966 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.024, std = 0.260 curvature mean = 0.006, std = 0.070 curvature mean = 0.060, std = 0.387 curvature mean = 0.006, std = 0.084 curvature mean = 0.025, std = 0.589 curvature mean = 0.006, std = 0.090 curvature mean = 0.014, std = 0.729 curvature mean = 0.007, std = 0.093 curvature mean = 0.004, std = 0.831 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 1107: 80 negative triangles time:: 01:24:17 elapsed:: 05057 cmd:: mris_register #-------------------------------------------- #@# Jacobian white rh Wed May 8 01:56:14 EDT 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 time:: 00:00:05 elapsed:: 00005 cmd:: mris_jacobian #-------------------------------------------- #@# AvgCurv rh Wed May 8 01:56:19 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mrisp_paint -a 5 /space/freesurfer/centos4.0/stable/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 /space/freesurfer/centos4.0/stable/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... time:: 00:00:03 elapsed:: 00003 cmd:: mrisp_paint #----------------------------------------- #@# Cortical Parc rh Wed May 8 01:56:23 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /space/freesurfer/centos4.0/stable/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading atlas from /space/freesurfer/centos4.0/stable/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... 1391 labels changed using aseg relabeling using gibbs priors... 000: 2803 changed, 133299 examined... 001: 664 changed, 12131 examined... 002: 173 changed, 3733 examined... 003: 66 changed, 1030 examined... 004: 28 changed, 406 examined... 005: 15 changed, 153 examined... 006: 9 changed, 91 examined... 007: 7 changed, 56 examined... 008: 0 changed, 34 examined... 192 labels changed using aseg 000: 95 total segments, 58 labels (351 vertices) changed 001: 39 total segments, 2 labels (4 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 52 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1490 vertices marked for relabeling... 1490 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 2 minutes and 30 seconds. time:: 00:02:29 elapsed:: 00149 cmd:: mris_ca_label #-------------------------------------------- #@# Make Pial Surf rh Wed May 8 01:58:53 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs bert 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 1.127.2.5 2013/04/19 20:15:38 nicks Exp $ $Id: mrisurf.c,v 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/filled.mgz... reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... 13228 bright wm thresholded. 11116 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.orig... computing class statistics... border white: 261006 voxels (1.56%) border gray 282435 voxels (1.68%) WM (101.0): 101.3 +- 5.7 [70.0 --> 110.0] GM (93.0) : 90.6 +- 9.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 73.1 (was 70) setting MAX_BORDER_WHITE to 112.7 (was 105) setting MIN_BORDER_WHITE to 83.0 (was 85) setting MAX_CSF to 63.1 (was 40) setting MAX_GRAY to 101.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 53.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=107, GM=83 mean inside = 100.9, mean outside = 88.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.03-->3.70) (max @ vno 122410 --> 133252) face area 0.28 +- 0.12 (0.00-->2.03) mean absolute distance = 0.91 +- 1.06 4111 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 20 points - only 0.00% unknown deleting segment 5 with 31 points - only 0.00% unknown deleting segment 6 with 32 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown mean border=90.0, 65 (65) missing vertices, mean dist 0.5 [0.8 (%25.9)->1.0 (%74.1))] %59 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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 0.93 +- 0.27 (0.07-->4.64) (max @ vno 72422 --> 73394) face area 0.28 +- 0.14 (0.00-->2.03) mean absolute distance = 0.47 +- 0.70 3940 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3949591.0, rms=8.14 001: dt: 0.5000, sse=4274792.0, rms=6.091 (0.000%) 002: dt: 0.5000, sse=4295222.5, rms=4.634 (0.000%) 003: dt: 0.5000, sse=4373208.0, rms=3.592 (0.000%) 004: dt: 0.5000, sse=4396251.0, rms=2.886 (0.000%) 005: dt: 0.5000, sse=4422541.0, rms=2.441 (0.000%) 006: dt: 0.5000, sse=4431775.0, rms=2.178 (0.000%) 007: dt: 0.5000, sse=4457003.0, rms=2.029 (0.000%) 008: dt: 0.5000, sse=4441665.0, rms=1.937 (0.000%) 009: dt: 0.5000, sse=4474755.0, rms=1.881 (0.000%) rms = 1.85, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=4463881.0, rms=1.848 (0.000%) 011: dt: 0.2500, sse=3169045.2, rms=1.498 (0.000%) rms = 1.46, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3072192.2, rms=1.456 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3034450.0, rms=1.446 (0.000%) positioning took 3.0 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 removing 2 vertex label from ripped group deleting segment 6 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 19 points - only 0.00% unknown deleting segment 11 with 24 points - only 0.00% unknown deleting segment 12 with 24 points - only 50.00% unknown deleting segment 14 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 points - only 0.00% unknown mean border=92.7, 67 (7) missing vertices, mean dist -0.3 [0.5 (%73.7)->0.3 (%26.3))] %74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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-->5.01) (max @ vno 72422 --> 73394) face area 0.36 +- 0.17 (0.00-->2.86) mean absolute distance = 0.32 +- 0.43 4081 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3500315.0, rms=3.92 014: dt: 0.5000, sse=3631355.8, rms=2.455 (0.000%) 015: dt: 0.5000, sse=3838484.0, rms=1.883 (0.000%) 016: dt: 0.5000, sse=3856625.8, rms=1.624 (0.000%) 017: dt: 0.5000, sse=4057592.0, rms=1.543 (0.000%) rms = 1.53, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=4109926.0, rms=1.534 (0.000%) 019: dt: 0.2500, sse=3396415.0, rms=1.240 (0.000%) rms = 1.21, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3280779.0, rms=1.211 (0.000%) rms = 1.20, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3255793.2, rms=1.203 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 22 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 4 with 30 points - only 0.00% unknown deleting segment 5 with 27 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown mean border=94.8, 41 (2) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.2 (%26.2))] %86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->5.15) (max @ vno 72422 --> 73394) face area 0.34 +- 0.16 (0.00-->2.82) mean absolute distance = 0.24 +- 0.33 3584 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3403429.0, rms=2.95 022: dt: 0.5000, sse=3615441.2, rms=1.632 (0.000%) 023: dt: 0.5000, sse=3748219.0, rms=1.358 (0.000%) 024: dt: 0.5000, sse=3775592.8, rms=1.301 (0.000%) rms = 1.34, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3507275.8, rms=1.153 (0.000%) 026: dt: 0.2500, sse=3406310.5, rms=1.101 (0.000%) rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.10, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=3394040.8, rms=1.099 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 19 points - only 0.00% unknown deleting segment 2 with 31 points - only 0.00% unknown deleting segment 3 with 29 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=95.5, 27 (0) missing vertices, mean dist -0.1 [0.3 (%57.8)->0.2 (%42.2))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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=3398268.8, rms=1.38 028: dt: 0.5000, sse=4050016.8, rms=0.985 (0.000%) rms = 1.17, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3813013.8, rms=0.912 (0.000%) rms = 0.91, time step reduction 2 of 3 to 0.125... rms = 0.91, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3790934.2, rms=0.907 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=73.5, 37 (37) missing vertices, mean dist 1.9 [0.1 (%0.0)->2.6 (%100.0))] %24 local maxima, %47 large gradients and %24 min vals, 1871 gradients ignored tol=1.0e-04, sigma=2.0, host=node0, 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=15614372.0, rms=22.80 001: dt: 0.5000, sse=12793596.0, rms=20.241 (0.000%) 002: dt: 0.5000, sse=10574154.0, rms=18.003 (0.000%) 003: dt: 0.5000, sse=8905682.0, rms=16.106 (0.000%) 004: dt: 0.5000, sse=7759680.0, rms=14.508 (0.000%) 005: dt: 0.5000, sse=7007887.0, rms=13.171 (0.000%) 006: dt: 0.5000, sse=6519351.0, rms=12.047 (0.000%) 007: dt: 0.5000, sse=6177069.5, rms=11.037 (0.000%) 008: dt: 0.5000, sse=5924464.0, rms=10.035 (0.000%) 009: dt: 0.5000, sse=5645433.5, rms=8.972 (0.000%) 010: dt: 0.5000, sse=5392095.5, rms=7.823 (0.000%) 011: dt: 0.5000, sse=5157161.5, rms=6.611 (0.000%) 012: dt: 0.5000, sse=4998219.0, rms=5.425 (0.000%) 013: dt: 0.5000, sse=4972568.5, rms=4.486 (0.000%) 014: dt: 0.5000, sse=5067462.0, rms=3.881 (0.000%) 015: dt: 0.5000, sse=5133948.5, rms=3.562 (0.000%) 016: dt: 0.5000, sse=5184149.0, rms=3.389 (0.000%) 017: dt: 0.5000, sse=5224871.5, rms=3.286 (0.000%) 018: dt: 0.5000, sse=5249397.5, rms=3.221 (0.000%) rms = 3.18, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5268855.0, rms=3.182 (0.000%) 020: dt: 0.2500, sse=3503636.8, rms=2.402 (0.000%) 021: dt: 0.2500, sse=3325955.0, rms=2.194 (0.000%) rms = 2.16, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3239823.5, rms=2.157 (0.000%) 023: dt: 0.1250, sse=3112279.5, rms=2.057 (0.000%) rms = 2.04, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3087096.2, rms=2.043 (0.000%) positioning took 5.7 minutes mean border=71.2, 911 (8) missing vertices, mean dist 0.2 [0.2 (%39.4)->0.5 (%60.6))] %50 local maxima, %28 large gradients and %17 min vals, 510 gradients ignored tol=1.0e-04, sigma=1.0, host=node0, 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=3640658.8, rms=4.22 025: dt: 0.5000, sse=3778194.5, rms=3.202 (0.000%) 026: dt: 0.5000, sse=4672865.0, rms=3.128 (0.000%) rms = 3.20, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3908469.0, rms=2.465 (0.000%) 028: dt: 0.2500, sse=3619261.8, rms=2.165 (0.000%) 029: dt: 0.2500, sse=3577792.8, rms=2.104 (0.000%) rms = 2.07, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3542165.0, rms=2.073 (0.000%) 031: dt: 0.1250, sse=3443457.8, rms=1.974 (0.000%) rms = 1.96, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3438925.8, rms=1.958 (0.000%) positioning took 2.1 minutes mean border=69.8, 1069 (6) missing vertices, mean dist 0.1 [0.2 (%36.7)->0.3 (%63.3))] %64 local maxima, %13 large gradients and %17 min vals, 533 gradients ignored tol=1.0e-04, sigma=0.5, host=node0, 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=3537982.5, rms=2.69 rms = 2.71, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3420961.8, rms=2.271 (0.000%) 034: dt: 0.2500, sse=3429625.8, rms=2.004 (0.000%) 035: dt: 0.2500, sse=3521043.5, rms=1.932 (0.000%) rms = 1.91, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=3541521.5, rms=1.908 (0.000%) 037: dt: 0.1250, sse=3469620.8, rms=1.842 (0.000%) rms = 1.83, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3468030.8, rms=1.828 (0.000%) positioning took 1.6 minutes mean border=69.3, 2114 (4) missing vertices, mean dist 0.0 [0.2 (%45.8)->0.2 (%54.2))] %67 local maxima, %10 large gradients and %17 min vals, 392 gradients ignored tol=1.0e-04, sigma=0.2, host=node0, 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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3478108.5, rms=1.98 rms = 2.26, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=3433476.0, rms=1.837 (0.000%) rms = 1.79, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=3528513.2, rms=1.787 (0.000%) rms = 1.75, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=3480250.2, rms=1.745 (0.000%) positioning took 0.9 minutes writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.area.pial vertex spacing 0.99 +- 0.42 (0.08-->7.06) (max @ vno 90998 --> 91011) face area 0.39 +- 0.30 (0.00-->6.39) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133299 vertices processed 25000 of 133299 vertices processed 50000 of 133299 vertices processed 75000 of 133299 vertices processed 100000 of 133299 vertices processed 125000 of 133299 vertices processed 0 of 133299 vertices processed 25000 of 133299 vertices processed 50000 of 133299 vertices processed 75000 of 133299 vertices processed 100000 of 133299 vertices processed 125000 of 133299 vertices processed thickness calculation complete, 584:640 truncations. 32611 vertices at 0 distance 91149 vertices at 1 distance 79898 vertices at 2 distance 34278 vertices at 3 distance 11295 vertices at 4 distance 3527 vertices at 5 distance 1144 vertices at 6 distance 367 vertices at 7 distance 134 vertices at 8 distance 53 vertices at 9 distance 35 vertices at 10 distance 23 vertices at 11 distance 22 vertices at 12 distance 22 vertices at 13 distance 6 vertices at 14 distance 5 vertices at 15 distance 7 vertices at 16 distance 12 vertices at 17 distance 12 vertices at 18 distance 9 vertices at 19 distance 7 vertices at 20 distance writing curvature file /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.thickness positioning took 25.9 minutes time:: 00:25:53 elapsed:: 01553 cmd:: mris_make_surfaces #-------------------------------------------- #@# Surf Volume rh Wed May 8 02:24:47 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] time:: 00:00:00 elapsed:: 00000 cmd:: mris_calc mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] time:: 00:00:00 elapsed:: 00000 cmd:: mris_calc mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] time:: 00:00:00 elapsed:: 00000 cmd:: mris_calc #----------------------------------------- #@# WM/GM Contrast rh Wed May 8 02:24:48 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts pctsurfcon --s bert --rh-only Log file is /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts/pctsurfcon.log Wed May 8 02:24:48 EDT 2013 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 cd /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts /space/freesurfer/centos4.0/stable/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node0360 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /space/freesurfer/centos4.0/stable mri_vol2surf --mov /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.15461/rh.wm.mgh --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz as target reference. Loading label /autofs/cluster/freesurfer/test/tsd/i686/bert/label/rh.cortex.label Reading surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 = 74337 Masking with /autofs/cluster/freesurfer/test/tsd/i686/bert/label/rh.cortex.label Writing to /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.15461/rh.wm.mgh Dim: 133299 1 1 mri_vol2surf --mov /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.15461/rh.gm.mgh --projfrac 0.3 --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/orig.mgz as target reference. Loading label /autofs/cluster/freesurfer/test/tsd/i686/bert/label/rh.cortex.label Reading surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/freesurfer/test/tsd/i686/bert/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 = 88261 Masking with /autofs/cluster/freesurfer/test/tsd/i686/bert/label/rh.cortex.label Writing to /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.15461/rh.gm.mgh Dim: 133299 1 1 mri_concat /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.15461/rh.wm.mgh /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/tmp.pctsurfcon.15461/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.w-g.pct.mgh --annot bert rh aparc --sum /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.w-g.pct.mgh --annot bert rh aparc --sum /autofs/cluster/freesurfer/test/tsd/i686/bert/stats/rh.w-g.pct.stats --snr sysname Linux hostname node0360 machine x86_64 user nicks 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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.w-g.pct.mgh Vertex Area is 0.662138 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1087 746.730 2 2002 caudalanteriorcingulate 1301 895.890 3 2003 caudalmiddlefrontal 2824 1854.027 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2313 1489.953 6 2006 entorhinal 417 290.190 7 2007 fusiform 4275 2991.606 8 2008 inferiorparietal 7205 4922.135 9 2009 inferiortemporal 4428 3062.847 10 2010 isthmuscingulate 1187 774.685 11 2011 lateraloccipital 7809 5103.807 12 2012 lateralorbitofrontal 3915 2694.955 13 2013 lingual 4433 2898.375 14 2014 medialorbitofrontal 3027 2096.418 15 2015 middletemporal 4679 3230.428 16 2016 parahippocampal 1057 698.752 17 2017 paracentral 2190 1457.244 18 2018 parsopercularis 1941 1293.662 19 2019 parsorbitalis 1361 882.745 20 2020 parstriangularis 2607 1747.475 21 2021 pericalcarine 2220 1420.442 22 2022 postcentral 6115 3854.081 23 2023 posteriorcingulate 1839 1300.936 24 2024 precentral 7611 4629.466 25 2025 precuneus 5937 3950.674 26 2026 rostralanteriorcingulate 1073 707.809 27 2027 rostralmiddlefrontal 8326 5511.135 28 2028 superiorfrontal 9144 6127.457 29 2029 superiorparietal 8317 5373.504 30 2030 superiortemporal 5173 3454.948 31 2031 supramarginal 5561 3802.418 32 2032 frontalpole 538 351.050 33 2033 temporalpole 488 358.806 34 2034 transversetemporal 596 334.858 35 2035 insula 3670 2352.847 Reporting on 34 segmentations mri_segstats done Cleaning up time:: 00:00:20 elapsed:: 00020 cmd:: pctsurfcon #----------------------------------------- #@# Parcellation Stats rh Wed May 8 02:25:09 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 bert rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1087 747 1817 2.425 0.647 0.101 0.026 7 1.1 bankssts 1301 896 2510 2.561 0.605 0.141 0.034 19 1.9 caudalanteriorcingulate 2824 1854 5655 2.800 0.530 0.118 0.032 25 3.8 caudalmiddlefrontal 2313 1490 2750 1.780 0.570 0.164 0.070 49 6.7 cuneus 417 290 1579 3.565 0.616 0.138 0.054 4 1.0 entorhinal 4275 2992 8025 2.524 0.633 0.143 0.047 70 8.5 fusiform 7205 4922 14688 2.649 0.532 0.139 0.047 145 13.1 inferiorparietal 4428 3063 10972 2.987 0.689 0.159 0.070 141 14.4 inferiortemporal 1187 775 1899 2.272 0.673 0.139 0.053 20 2.5 isthmuscingulate 7809 5104 11855 2.134 0.595 0.147 0.056 123 17.6 lateraloccipital 3915 2695 8210 2.796 0.711 0.148 0.062 76 9.8 lateralorbitofrontal 4433 2898 5958 1.929 0.559 0.152 0.062 86 12.3 lingual 3027 2096 6030 2.625 0.790 0.146 0.059 58 7.5 medialorbitofrontal 4679 3230 11256 2.901 0.704 0.145 0.063 83 11.6 middletemporal 1057 699 1927 2.492 0.586 0.100 0.026 8 1.1 parahippocampal 2190 1457 3709 2.402 0.524 0.131 0.053 30 5.3 paracentral 1941 1294 4117 2.980 0.518 0.125 0.037 20 2.8 parsopercularis 1361 883 3302 2.906 0.680 0.148 0.054 24 3.0 parsorbitalis 2607 1747 5364 2.701 0.541 0.129 0.041 33 4.0 parstriangularis 2220 1420 2131 1.613 0.531 0.131 0.052 30 5.2 pericalcarine 6115 3854 9180 2.111 0.723 0.121 0.047 114 12.3 postcentral 1839 1301 3435 2.426 0.639 0.143 0.043 29 3.2 posteriorcingulate 7611 4629 14525 2.806 0.685 0.117 0.047 109 17.2 precentral 5937 3951 10107 2.416 0.574 0.127 0.038 69 9.3 precuneus 1073 708 2334 2.914 0.680 0.150 0.043 19 2.0 rostralanteriorcingulate 8326 5511 16423 2.583 0.547 0.141 0.054 124 15.7 rostralmiddlefrontal 9144 6127 21085 3.027 0.602 0.129 0.037 99 14.0 superiorfrontal 8317 5374 14246 2.332 0.541 0.130 0.045 116 15.1 superiorparietal 5173 3455 11549 2.942 0.602 0.124 0.041 63 8.8 superiortemporal 5561 3802 11089 2.701 0.603 0.133 0.042 71 9.1 supramarginal 538 351 1327 2.697 0.523 0.159 0.053 10 1.2 frontalpole 488 359 2062 4.087 0.383 0.177 0.093 10 1.9 temporalpole 596 335 882 2.436 0.489 0.119 0.034 6 0.8 transversetemporal 3670 2353 7404 3.182 0.765 0.127 0.115 86 20.8 insula time:: 00:01:11 elapsed:: 00071 cmd:: mris_anatomical_stats #----------------------------------------- #@# Cortical Parc 2 rh Wed May 8 02:26:21 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /space/freesurfer/centos4.0/stable/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading atlas from /space/freesurfer/centos4.0/stable/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... 36 labels changed using aseg relabeling using gibbs priors... 000: 9151 changed, 133299 examined... 001: 2209 changed, 35257 examined... 002: 672 changed, 11507 examined... 003: 283 changed, 3808 examined... 004: 153 changed, 1594 examined... 005: 92 changed, 843 examined... 006: 46 changed, 516 examined... 007: 30 changed, 262 examined... 008: 19 changed, 162 examined... 009: 10 changed, 118 examined... 010: 6 changed, 55 examined... 011: 3 changed, 28 examined... 012: 4 changed, 19 examined... 013: 3 changed, 23 examined... 014: 2 changed, 21 examined... 015: 2 changed, 12 examined... 016: 3 changed, 10 examined... 017: 3 changed, 15 examined... 018: 0 changed, 10 examined... 9 labels changed using aseg 000: 288 total segments, 204 labels (2421 vertices) changed 001: 105 total segments, 21 labels (90 vertices) changed 002: 86 total segments, 2 labels (3 vertices) changed 003: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 155 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1216 vertices marked for relabeling... 1216 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 2 minutes and 48 seconds. time:: 00:02:48 elapsed:: 00168 cmd:: mris_ca_label #----------------------------------------- #@# Parcellation Stats 2 rh Wed May 8 02:29:09 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 bert rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1144 753 2330 2.644 0.563 0.153 0.082 21 2.8 G_and_S_frontomargin 1162 781 2068 2.372 0.624 0.140 0.050 15 2.2 G_and_S_occipital_inf 1479 892 2286 2.246 0.556 0.140 0.063 24 4.0 G_and_S_paracentral 1295 884 3114 3.004 0.622 0.154 0.054 22 3.0 G_and_S_subcentral 1344 916 3267 2.750 0.512 0.152 0.055 24 2.9 G_and_S_transv_frontopol 3034 2040 5949 2.836 0.561 0.132 0.040 40 4.8 G_and_S_cingul-Ant 1482 1041 3001 2.766 0.489 0.124 0.030 14 1.9 G_and_S_cingul-Mid-Ant 1551 1105 2927 2.536 0.555 0.122 0.035 15 2.0 G_and_S_cingul-Mid-Post 380 283 988 2.820 0.477 0.190 0.076 9 1.2 G_cingul-Post-dorsal 233 141 526 2.864 0.682 0.171 0.074 6 0.6 G_cingul-Post-ventral 2224 1427 2555 1.654 0.498 0.162 0.070 46 6.5 G_cuneus 1129 735 3036 3.182 0.349 0.141 0.046 17 2.1 G_front_inf-Opercular 483 314 1334 3.086 0.405 0.173 0.096 12 1.4 G_front_inf-Orbital 1426 931 3573 2.953 0.500 0.145 0.061 25 2.8 G_front_inf-Triangul 3877 2507 9299 2.831 0.502 0.149 0.053 67 8.3 G_front_middle 5633 3736 14972 3.166 0.610 0.139 0.046 77 11.0 G_front_sup 633 413 1554 3.543 0.606 0.130 0.121 10 1.2 G_Ins_lg_and_S_cent_ins 662 406 1989 3.623 0.805 0.142 0.054 12 1.5 G_insular_short 1932 1287 4459 2.670 0.573 0.165 0.068 42 4.8 G_occipital_middle 1853 1195 3075 2.135 0.538 0.145 0.048 26 3.8 G_occipital_sup 2065 1397 4389 2.559 0.537 0.155 0.059 47 5.0 G_oc-temp_lat-fusifor 2825 1786 4150 1.983 0.594 0.165 0.077 72 9.8 G_oc-temp_med-Lingual 1298 835 3158 3.029 0.887 0.142 0.064 20 3.7 G_oc-temp_med-Parahip 2551 1776 7266 3.095 0.726 0.170 0.071 65 7.9 G_orbital 2878 1946 7223 2.860 0.476 0.164 0.066 101 6.9 G_pariet_inf-Angular 2907 1999 7200 2.965 0.480 0.155 0.056 55 6.4 G_pariet_inf-Supramar 2829 1769 5913 2.587 0.532 0.139 0.061 60 6.7 G_parietal_sup 2249 1296 3601 2.198 0.675 0.117 0.045 30 4.5 G_postcentral 3128 1720 7160 3.176 0.612 0.118 0.061 69 10.2 G_precentral 3058 2033 5869 2.382 0.525 0.139 0.046 47 5.6 G_precuneus 790 596 2034 2.483 0.807 0.188 0.107 25 3.6 G_rectus 345 215 754 3.419 0.717 0.101 0.053 4 0.5 G_subcallosal 438 240 796 2.584 0.509 0.128 0.046 6 0.8 G_temp_sup-G_T_transv 1673 1104 4888 3.204 0.526 0.156 0.059 32 4.2 G_temp_sup-Lateral 586 410 1543 3.324 0.749 0.106 0.033 3 0.7 G_temp_sup-Plan_polar 733 489 1551 3.010 0.699 0.117 0.046 9 1.2 G_temp_sup-Plan_tempo 2755 1894 7327 2.951 0.649 0.170 0.086 121 11.1 G_temporal_inf 2593 1812 7500 3.106 0.643 0.159 0.079 59 8.6 G_temporal_middle 469 327 657 2.241 0.364 0.096 0.018 2 0.4 Lat_Fis-ant-Horizont 227 158 373 2.878 0.547 0.131 0.033 2 0.3 Lat_Fis-ant-Vertical 1518 1011 2088 2.529 0.692 0.105 0.024 9 1.5 Lat_Fis-post 3745 2341 4631 1.861 0.565 0.161 0.068 72 10.3 Pole_occipital 1628 1189 5657 3.640 0.668 0.171 0.082 33 5.1 Pole_temporal 2451 1653 2651 1.811 0.684 0.128 0.052 30 5.7 S_calcarine 3040 1963 3564 2.008 0.760 0.110 0.034 22 4.5 S_central 1401 939 2149 2.438 0.524 0.108 0.029 10 1.7 S_cingul-Marginalis 650 430 1150 3.195 0.492 0.110 0.029 4 0.8 S_circular_insula_ant 1319 835 1894 2.814 0.552 0.112 0.192 48 15.5 S_circular_insula_inf 1555 1050 2484 2.753 0.490 0.093 0.018 6 1.2 S_circular_insula_sup 694 486 1317 2.637 0.819 0.136 0.035 8 1.1 S_collat_transv_ant 492 324 605 2.011 0.443 0.160 0.056 6 1.3 S_collat_transv_post 2148 1436 3314 2.425 0.449 0.120 0.034 19 3.0 S_front_inf 1874 1254 2721 2.287 0.458 0.117 0.030 15 2.1 S_front_middle 2061 1419 3861 2.669 0.624 0.122 0.031 19 2.6 S_front_sup 665 470 837 2.092 0.439 0.106 0.018 3 0.6 S_interm_prim-Jensen 2995 1987 4390 2.360 0.513 0.121 0.032 26 4.0 S_intrapariet_and_P_trans 1361 939 1889 2.211 0.505 0.125 0.033 12 1.9 S_oc_middle_and_Lunatus 1217 827 1333 1.797 0.405 0.112 0.026 8 1.4 S_oc_sup_and_transversal 768 502 1090 2.444 0.496 0.124 0.036 7 1.2 S_occipital_ant 645 458 1128 2.813 0.647 0.126 0.034 5 0.9 S_oc-temp_lat 2137 1525 3158 2.294 0.496 0.107 0.024 13 2.3 S_oc-temp_med_and_Lingual 535 356 675 2.281 0.558 0.121 0.027 4 0.6 S_orbital_lateral 951 671 1534 2.271 0.735 0.119 0.038 14 1.7 S_orbital_med-olfact 1441 978 2409 2.467 0.544 0.140 0.054 20 3.2 S_orbital-H_Shaped 2124 1416 3169 2.487 0.502 0.113 0.032 16 2.8 S_parieto_occipital 1865 1167 1999 2.127 0.709 0.132 0.034 29 2.7 S_pericallosal 2632 1770 3674 2.205 0.507 0.112 0.044 63 4.3 S_postcentral 1873 1223 3016 2.672 0.434 0.101 0.024 11 1.9 S_precentral-inf-part 1151 779 1598 2.397 0.406 0.123 0.035 10 1.7 S_precentral-sup-part 474 309 956 2.899 0.565 0.140 0.042 8 0.8 S_suborbital 803 538 1303 2.313 0.658 0.121 0.033 8 1.1 S_subparietal 1425 965 2365 2.611 0.491 0.135 0.040 18 2.4 S_temporal_inf 5270 3598 8495 2.428 0.496 0.107 0.027 41 5.7 S_temporal_sup 403 265 644 2.847 0.459 0.103 0.019 2 0.4 S_temporal_transverse time:: 00:01:20 elapsed:: 00080 cmd:: mris_anatomical_stats #----------------------------------------- #@# Cortical Parc 3 rh Wed May 8 02:30:31 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /space/freesurfer/centos4.0/stable/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 1.693.2.6 2013/04/26 19:03:01 nicks Exp $ reading atlas from /space/freesurfer/centos4.0/stable/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... 1170 labels changed using aseg relabeling using gibbs priors... 000: 2601 changed, 133299 examined... 001: 622 changed, 11308 examined... 002: 154 changed, 3426 examined... 003: 64 changed, 890 examined... 004: 40 changed, 364 examined... 005: 26 changed, 208 examined... 006: 16 changed, 139 examined... 007: 7 changed, 76 examined... 008: 8 changed, 40 examined... 009: 4 changed, 27 examined... 010: 3 changed, 16 examined... 011: 3 changed, 16 examined... 012: 4 changed, 13 examined... 013: 2 changed, 16 examined... 014: 2 changed, 10 examined... 015: 1 changed, 10 examined... 016: 1 changed, 7 examined... 017: 1 changed, 9 examined... 018: 0 changed, 5 examined... 155 labels changed using aseg 000: 53 total segments, 20 labels (108 vertices) changed 001: 34 total segments, 1 labels (2 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 871 vertices marked for relabeling... 871 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 2 minutes and 28 seconds. time:: 00:02:29 elapsed:: 00149 cmd:: mris_ca_label #----------------------------------------- #@# Parcellation Stats 3 rh Wed May 8 02:33:00 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 bert rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 1285 887 2460 2.545 0.607 0.142 0.034 19 1.8 caudalanteriorcingulate 2823 1859 5537 2.762 0.541 0.118 0.032 25 3.8 caudalmiddlefrontal 2877 1856 3540 1.862 0.568 0.153 0.062 53 7.4 cuneus 506 350 1739 3.451 0.612 0.136 0.049 5 1.1 entorhinal 3786 2640 6958 2.518 0.631 0.142 0.047 61 7.5 fusiform 6678 4550 13605 2.664 0.525 0.140 0.048 133 12.3 inferiorparietal 4827 3360 11985 2.950 0.697 0.159 0.068 149 15.0 inferiortemporal 1211 788 1909 2.272 0.673 0.136 0.049 19 2.3 isthmuscingulate 8092 5295 12258 2.133 0.592 0.148 0.057 128 18.3 lateraloccipital 4249 2928 9529 2.802 0.726 0.159 0.074 92 12.1 lateralorbitofrontal 4471 2914 5998 1.924 0.557 0.152 0.062 86 12.4 lingual 2429 1703 5081 2.652 0.843 0.152 0.065 53 6.7 medialorbitofrontal 5492 3774 12673 2.840 0.710 0.141 0.059 97 12.8 middletemporal 1034 679 1816 2.472 0.576 0.100 0.026 8 1.1 parahippocampal 2247 1506 3849 2.405 0.519 0.133 0.055 31 5.5 paracentral 1967 1307 4136 2.982 0.509 0.126 0.038 21 2.9 parsopercularis 1497 987 3398 2.900 0.571 0.138 0.055 23 3.0 parsorbitalis 2749 1832 5600 2.711 0.554 0.134 0.048 38 4.6 parstriangularis 2167 1391 2062 1.598 0.516 0.132 0.052 29 5.1 pericalcarine 6624 4172 9946 2.133 0.712 0.121 0.050 128 14.6 postcentral 1886 1340 3525 2.436 0.634 0.143 0.043 29 3.3 posteriorcingulate 7396 4497 14386 2.829 0.681 0.117 0.046 106 16.8 precentral 5943 3964 10257 2.421 0.572 0.129 0.040 70 9.7 precuneus 1209 802 2516 2.882 0.675 0.147 0.041 20 2.2 rostralanteriorcingulate 5483 3594 10673 2.541 0.567 0.137 0.046 76 9.8 rostralmiddlefrontal 12491 8323 27381 2.907 0.610 0.130 0.039 146 19.7 superiorfrontal 7192 4642 12557 2.352 0.550 0.129 0.043 95 11.7 superiorparietal 6720 4550 15531 2.984 0.706 0.127 0.052 85 12.6 superiortemporal 5313 3642 10574 2.686 0.623 0.132 0.041 67 8.4 supramarginal 559 310 843 2.465 0.472 0.118 0.035 6 0.8 transversetemporal 3461 2221 7080 3.190 0.712 0.123 0.101 78 19.3 insula time:: 00:01:11 elapsed:: 00071 cmd:: mris_anatomical_stats #-------------------------------------------- #@# Cortical ribbon mask Wed May 8 02:34:12 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon bert SUBJECTS_DIR is /autofs/cluster/freesurfer/test/tsd/i686 loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 11 writing volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/ribbon.mgz writing ribbon files time:: 00:27:51 elapsed:: 01671 cmd:: mris_volmask #-------------------------------------------- #@# ASeg Stats Wed May 8 03:02:04 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert 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 /space/freesurfer/centos4.0/stable/ASegStatsLUT.txt --subject bert $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 /space/freesurfer/centos4.0/stable/ASegStatsLUT.txt --subject bert sysname Linux hostname node0360 machine x86_64 user nicks UseRobust 0 atlas_icv (eTIV) = 1594882 mm^3 (det: 1.221473 ) Computing euler number orig.nofix lheno = -66, rheno = -64 orig.nofix lhholes = 34, rhholes = 33 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 237947.199 237662.000 diff= 285.2 pctdiff= 0.120 rhCtxGM: 238312.857 238026.000 diff= 286.9 pctdiff= 0.120 lhCtxWM: 240888.938 240615.500 diff= 273.4 pctdiff= 0.114 rhCtxWM: 244738.223 245519.500 diff= -781.3 pctdiff=-0.319 SubCortGMVol 60460.000 SupraTentVol 1038907.218 (1037805.000) diff=1102.218 pctdiff=0.106 SupraTentVolNotVent 1023476.218 (1022374.000) diff=1102.218 pctdiff=0.108 BrainSegVol 1193318.000 (1190790.000) diff=2528.000 pctdiff=0.212 BrainSegVolNotVent 1174082.000 (1173867.218) diff=214.782 pctdiff=0.018 BrainSegVolNotVent 1174082.000 CerebellumVol 151429.000 VentChorVol 15431.000 3rd4th5thCSF 3805.000 CSFVol 1282.000, OptChiasmVol 274.000 MaskVol 1830156.000 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 6563 6562.566 4 5 Left-Inf-Lat-Vent 228 228.278 5 7 Left-Cerebellum-White-Matter 15708 15708.169 6 8 Left-Cerebellum-Cortex 58536 58535.703 7 10 Left-Thalamus-Proper 8150 8150.375 8 11 Left-Caudate 3214 3213.715 9 12 Left-Putamen 5671 5671.442 10 13 Left-Pallidum 1654 1654.214 11 14 3rd-Ventricle 997 997.478 12 15 4th-Ventricle 1714 1714.229 13 16 Brain-Stem 25995 25995.365 14 17 Left-Hippocampus 4540 4540.183 15 18 Left-Amygdala 1539 1539.050 16 24 CSF 1259 1259.169 17 26 Left-Accumbens-area 518 517.656 18 28 Left-VentralDC 4588 4587.726 19 30 Left-vessel 64 64.420 20 31 Left-choroid-plexus 1421 1420.912 23 43 Right-Lateral-Ventricle 6040 6039.915 24 44 Right-Inf-Lat-Vent 160 160.270 25 46 Right-Cerebellum-White-Matter 15695 15694.527 26 47 Right-Cerebellum-Cortex 61434 61433.523 27 49 Right-Thalamus-Proper 8133 8132.870 28 50 Right-Caudate 3105 3105.158 29 51 Right-Putamen 5097 5097.402 30 52 Right-Pallidum 1551 1550.578 31 53 Right-Hippocampus 4502 4501.988 32 54 Right-Amygdala 1346 1346.472 33 58 Right-Accumbens-area 544 543.683 34 60 Right-VentralDC 4400 4400.178 35 62 Right-vessel 47 47.467 36 63 Right-choroid-plexus 1467 1466.694 37 72 5th-Ventricle 14 14.129 38 77 WM-hypointensities 1003 1002.589 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 3 2.809 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 268 268.207 45 251 CC_Posterior 934 933.868 46 252 CC_Mid_Posterior 479 479.463 47 253 CC_Central 645 644.703 48 254 CC_Mid_Anterior 552 551.760 49 255 CC_Anterior 1068 1068.465 Reporting on 45 segmentations mri_segstats done time:: 00:11:25 elapsed:: 00685 cmd:: mri_segstats #----------------------------------------- #@# AParc-to-ASeg Wed May 8 03:13:32 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert mri_aparc2aseg --s bert --volmask SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 subject bert outvol /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading lh pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial Loading lh annotations from /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading rh pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial Loading rh annotations from /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 = 474092 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aparc+aseg.mgz time:: 00:04:00 elapsed:: 00240 cmd:: mri_aparc2aseg /autofs/cluster/freesurfer/test/tsd/i686/bert mri_aparc2aseg --s bert --volmask --a2009s SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 subject bert outvol /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading lh pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial Loading lh annotations from /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading rh pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial Loading rh annotations from /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/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 = 474092 Used brute-force search on 0 voxels Writing output aseg to /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aparc.a2009s+aseg.mgz time:: 00:04:14 elapsed:: 00254 cmd:: mri_aparc2aseg #----------------------------------------- #@# WMParc Wed May 8 03:21:49 EDT 2013 /autofs/cluster/freesurfer/test/tsd/i686/bert mri_aparc2aseg --s bert --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 subject bert outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading lh pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial Loading lh annotations from /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading rh pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial Loading rh annotations from /autofs/cluster/freesurfer/test/tsd/i686/bert/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/ribbon.mgz Loading filled from /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9130 vertices from left hemi Ripped 8635 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 /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/freesurfer/test/tsd/i686/bert/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 = 958000 Used brute-force search on 36 voxels Fixing Parahip LH WM Found 19 clusters 0 k 3.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 2.000000 7 k 1.000000 8 k 1.000000 9 k 4.000000 10 k 1.000000 11 k 1.000000 12 k 2.000000 13 k 3.000000 14 k 1.000000 15 k 2.000000 16 k 1796.000000 17 k 1.000000 18 k 1.000000 Fixing Parahip RH WM Found 11 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 1813.000000 4 k 1.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 2.000000 Writing output aseg to mri/wmparc.mgz time:: 00:09:03 elapsed:: 00543 cmd:: mri_aparc2aseg /autofs/cluster/freesurfer/test/tsd/i686/bert 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 bert --surf-wm-vol --ctab /space/freesurfer/centos4.0/stable/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 bert --surf-wm-vol --ctab /space/freesurfer/centos4.0/stable/WMParcStatsLUT.txt --etiv sysname Linux hostname node0360 machine x86_64 user nicks UseRobust 0 atlas_icv (eTIV) = 1594882 mm^3 (det: 1.221473 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 237947.199 237662.000 diff= 285.2 pctdiff= 0.120 rhCtxGM: 238312.857 238026.000 diff= 286.9 pctdiff= 0.120 lhCtxWM: 240888.938 240615.500 diff= 273.4 pctdiff= 0.114 rhCtxWM: 244738.223 245519.500 diff= -781.3 pctdiff=-0.319 SubCortGMVol 60460.000 SupraTentVol 1038907.218 (1037805.000) diff=1102.218 pctdiff=0.106 SupraTentVolNotVent 1023476.218 (1022374.000) diff=1102.218 pctdiff=0.108 BrainSegVol 1193318.000 (1190790.000) diff=2528.000 pctdiff=0.212 BrainSegVolNotVent 1174082.000 (1173867.218) diff=214.782 pctdiff=0.018 BrainSegVolNotVent 1174082.000 CerebellumVol 151429.000 VentChorVol 15431.000 3rd4th5thCSF 3805.000 CSFVol 1282.000, OptChiasmVol 274.000 MaskVol 1830156.000 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 2898 2897.939 2 3002 wm-lh-caudalanteriorcingulate 2932 2932.122 3 3003 wm-lh-caudalmiddlefrontal 5572 5571.792 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2837 2836.977 6 3006 wm-lh-entorhinal 1009 1009.087 7 3007 wm-lh-fusiform 6821 6821.363 8 3008 wm-lh-inferiorparietal 10000 10000.129 9 3009 wm-lh-inferiortemporal 6792 6792.187 10 3010 wm-lh-isthmuscingulate 3243 3243.086 11 3011 wm-lh-lateraloccipital 9656 9656.379 12 3012 wm-lh-lateralorbitofrontal 7196 7195.533 13 3013 wm-lh-lingual 5435 5435.420 14 3014 wm-lh-medialorbitofrontal 4230 4230.417 15 3015 wm-lh-middletemporal 5681 5680.940 16 3016 wm-lh-parahippocampal 1833 1832.799 17 3017 wm-lh-paracentral 4260 4259.718 18 3018 wm-lh-parsopercularis 4118 4117.734 19 3019 wm-lh-parsorbitalis 834 834.227 20 3020 wm-lh-parstriangularis 3758 3757.698 21 3021 wm-lh-pericalcarine 3160 3160.492 22 3022 wm-lh-postcentral 6955 6954.763 23 3023 wm-lh-posteriorcingulate 4230 4230.259 24 3024 wm-lh-precentral 13342 13342.065 25 3025 wm-lh-precuneus 10584 10584.230 26 3026 wm-lh-rostralanteriorcingulate 3145 3145.316 27 3027 wm-lh-rostralmiddlefrontal 14213 14213.491 28 3028 wm-lh-superiorfrontal 19116 19116.023 29 3029 wm-lh-superiorparietal 12424 12423.932 30 3030 wm-lh-superiortemporal 8270 8269.999 31 3031 wm-lh-supramarginal 11016 11015.670 32 3032 wm-lh-frontalpole 202 202.454 33 3033 wm-lh-temporalpole 748 748.340 34 3034 wm-lh-transversetemporal 813 813.216 35 3035 wm-lh-insula 10005 10005.378 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 2498 2497.529 120 4002 wm-rh-caudalanteriorcingulate 3595 3595.209 121 4003 wm-rh-caudalmiddlefrontal 6548 6547.880 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2465 2464.678 124 4006 wm-rh-entorhinal 610 609.606 125 4007 wm-rh-fusiform 7019 7018.993 126 4008 wm-rh-inferiorparietal 10713 10712.556 127 4009 wm-rh-inferiortemporal 5518 5518.344 128 4010 wm-rh-isthmuscingulate 3058 3058.317 129 4011 wm-rh-lateraloccipital 11099 11099.086 130 4012 wm-rh-lateralorbitofrontal 7740 7740.332 131 4013 wm-rh-lingual 5634 5634.430 132 4014 wm-rh-medialorbitofrontal 4759 4758.773 133 4015 wm-rh-middletemporal 6468 6467.785 134 4016 wm-rh-parahippocampal 1890 1890.351 135 4017 wm-rh-paracentral 4815 4814.986 136 4018 wm-rh-parsopercularis 3472 3472.415 137 4019 wm-rh-parsorbitalis 1634 1634.487 138 4020 wm-rh-parstriangularis 4429 4428.714 139 4021 wm-rh-pericalcarine 3318 3318.409 140 4022 wm-rh-postcentral 7892 7891.608 141 4023 wm-rh-posteriorcingulate 5029 5029.047 142 4024 wm-rh-precentral 13867 13866.507 143 4025 wm-rh-precuneus 10571 10571.420 144 4026 wm-rh-rostralanteriorcingulate 2379 2379.337 145 4027 wm-rh-rostralmiddlefrontal 12774 12773.556 146 4028 wm-rh-superiorfrontal 18232 18232.387 147 4029 wm-rh-superiorparietal 12393 12393.058 148 4030 wm-rh-superiortemporal 7169 7169.222 149 4031 wm-rh-supramarginal 10592 10591.624 150 4032 wm-rh-frontalpole 510 509.752 151 4033 wm-rh-temporalpole 585 584.558 152 4034 wm-rh-transversetemporal 706 706.367 153 4035 wm-rh-insula 10696 10696.416 154 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 34165 34165.434 237 5002 Right-UnsegmentedWhiteMatter 35453 35453.477 238 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 time:: 00:20:30 elapsed:: 01230 cmd:: mri_segstats /autofs/cluster/freesurfer/test/tsd/i686/bert/label #-------------------------------------------- #@# BA Labels lh Wed May 8 03:51:23 EDT 2013 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /autofs/cluster/freesurfer/test/tsd/i686; ln -s /space/freesurfer/centos4.0/stable/subjects/fsaverage; cd - time:: 00:00:00 elapsed:: 00000 cmd:: ln mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA1.label --trgsubject bert --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 286 Checking for and removing duplicates Writing label file ./lh.BA1.label 4415 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA2.label --trgsubject bert --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 432 Checking for and removing duplicates Writing label file ./lh.BA2.label 8341 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done time:: 00:00:20 elapsed:: 00020 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA3a.label --trgsubject bert --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4217 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA3b.label --trgsubject bert --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 374 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6357 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA4a.label --trgsubject bert --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 534 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6318 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA4p.label --trgsubject bert --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 354 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4424 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA6.label --trgsubject bert --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 979 Checking for and removing duplicates Writing label file ./lh.BA6.label 14568 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done time:: 00:00:26 elapsed:: 00026 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA44.label --trgsubject bert --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 323 Checking for and removing duplicates Writing label file ./lh.BA44.label 4504 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done time:: 00:00:17 elapsed:: 00017 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA45.label --trgsubject bert --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 1085 Checking for and removing duplicates Writing label file ./lh.BA45.label 4507 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.V1.label --trgsubject bert --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 1459 Checking for and removing duplicates Writing label file ./lh.V1.label 6100 LabelWrite: saving to ./lh.V1.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.V2.label --trgsubject bert --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 3369 Checking for and removing duplicates Writing label file ./lh.V2.label 11483 LabelWrite: saving to ./lh.V2.label mri_label2label: Done time:: 00:00:22 elapsed:: 00022 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.MT.label --trgsubject bert --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 436 Checking for and removing duplicates Writing label file ./lh.MT.label 2454 LabelWrite: saving to ./lh.MT.label mri_label2label: Done time:: 00:00:17 elapsed:: 00017 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.perirhinal.label --trgsubject bert --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1261 LabelWrite: saving to ./lh.perirhinal.label mri_label2label: Done time:: 00:00:15 elapsed:: 00015 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA1.thresh.label --trgsubject bert --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 79 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1093 LabelWrite: saving to ./lh.BA1.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA2.thresh.label --trgsubject bert --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 66 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2158 LabelWrite: saving to ./lh.BA2.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA3a.thresh.label --trgsubject bert --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1539 LabelWrite: saving to ./lh.BA3a.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA3b.thresh.label --trgsubject bert --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 133 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2129 LabelWrite: saving to ./lh.BA3b.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA4a.thresh.label --trgsubject bert --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 330 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2649 LabelWrite: saving to ./lh.BA4a.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA4p.thresh.label --trgsubject bert --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1648 LabelWrite: saving to ./lh.BA4p.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA6.thresh.label --trgsubject bert --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 310 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7345 LabelWrite: saving to ./lh.BA6.thresh.label mri_label2label: Done time:: 00:00:20 elapsed:: 00020 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA44.thresh.label --trgsubject bert --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2042 LabelWrite: saving to ./lh.BA44.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA45.thresh.label --trgsubject bert --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 501 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1652 LabelWrite: saving to ./lh.BA45.thresh.label mri_label2label: Done time:: 00:00:15 elapsed:: 00015 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.V1.thresh.label --trgsubject bert --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 875 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4280 LabelWrite: saving to ./lh.V1.thresh.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.V2.thresh.label --trgsubject bert --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 1633 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4967 LabelWrite: saving to ./lh.V2.thresh.label mri_label2label: Done time:: 00:00:17 elapsed:: 00017 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.MT.thresh.label --trgsubject bert --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133401 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 601 LabelWrite: saving to ./lh.MT.thresh.label mri_label2label: Done time:: 00:00:14 elapsed:: 00014 cmd:: mri_label2label mris_label2annot --s bert --hemi lh --ctab /space/freesurfer/centos4.0/stable/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 /space/freesurfer/centos4.0/stable/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/label cmdline mris_label2annot --s bert --hemi lh --ctab /space/freesurfer/centos4.0/stable/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 node0360 machine x86_64 user nicks subject bert hemi lh SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 ColorTable /space/freesurfer/centos4.0/stable/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/tsd/i686/bert/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 92825 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/tsd/i686/bert/label/lh.BA.annot time:: 00:00:04 elapsed:: 00004 cmd:: mris_label2annot mris_label2annot --s bert --hemi lh --ctab /space/freesurfer/centos4.0/stable/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 /space/freesurfer/centos4.0/stable/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/label cmdline mris_label2annot --s bert --hemi lh --ctab /space/freesurfer/centos4.0/stable/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 node0360 machine x86_64 user nicks subject bert hemi lh SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 ColorTable /space/freesurfer/centos4.0/stable/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/tsd/i686/bert/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 110049 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/tsd/i686/bert/label/lh.BA.thresh.annot time:: 00:00:03 elapsed:: 00003 cmd:: mris_label2annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab bert lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /space/freesurfer/centos4.0/stable/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 1073 573 2003 2.443 0.507 0.143 0.091 31 4.7 BA1 3547 2339 5203 2.171 0.580 0.120 0.043 37 7.2 BA2 1005 646 875 1.799 0.482 0.124 0.035 7 1.5 BA3a 2348 1499 3222 1.898 0.678 0.108 0.057 45 6.7 BA3b 1928 1049 3613 2.944 0.584 0.120 0.084 79 9.1 BA4a 1342 848 2240 2.774 0.648 0.103 0.037 10 2.1 BA4p 8338 5495 19764 3.033 0.627 0.123 0.037 88 12.1 BA6 2040 1408 4629 2.914 0.544 0.135 0.038 24 3.2 BA44 3690 2446 7514 2.737 0.552 0.134 0.044 50 6.7 BA45 3491 2201 3508 1.565 0.449 0.141 0.056 51 8.3 V1 9002 5675 11456 1.893 0.555 0.157 0.065 162 24.5 V2 1918 1240 3201 2.464 0.474 0.137 0.045 26 3.3 MT 854 585 1958 2.732 0.718 0.111 0.033 6 1.1 perirhinal time:: 00:00:13 elapsed:: 00013 cmd:: mris_anatomical_stats mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab bert lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /space/freesurfer/centos4.0/stable/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 662 334 1188 2.424 0.531 0.162 0.214 49 7.8 BA1 1297 866 2046 2.119 0.537 0.106 0.028 9 1.6 BA2 825 533 688 1.770 0.443 0.128 0.038 6 1.3 BA3a 1432 934 1544 1.555 0.442 0.083 0.020 7 1.0 BA3b 1904 1038 3523 2.976 0.586 0.110 0.066 33 6.5 BA4a 1057 682 1633 2.593 0.643 0.112 0.043 30 2.0 BA4p 4418 2852 10587 3.063 0.590 0.118 0.045 69 8.5 BA6 1387 971 3092 2.861 0.523 0.138 0.040 18 2.3 BA44 1571 1031 3524 2.898 0.557 0.143 0.044 25 2.9 BA45 3713 2325 3753 1.561 0.440 0.139 0.055 55 8.8 V1 4604 2847 5296 1.790 0.529 0.164 0.078 95 14.6 V2 482 300 988 2.896 0.502 0.143 0.047 7 0.8 MT time:: 00:00:12 elapsed:: 00012 cmd:: mris_anatomical_stats #-------------------------------------------- #@# BA Labels rh Wed May 8 03:59:19 EDT 2013 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA1.label --trgsubject bert --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 278 Checking for and removing duplicates Writing label file ./rh.BA1.label 4240 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA2.label --trgsubject bert --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 483 Checking for and removing duplicates Writing label file ./rh.BA2.label 7170 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA3a.label --trgsubject bert --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4165 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA3b.label --trgsubject bert --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 316 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4838 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA4a.label --trgsubject bert --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 546 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6293 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA4p.label --trgsubject bert --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 314 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4787 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA6.label --trgsubject bert --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 922 Checking for and removing duplicates Writing label file ./rh.BA6.label 13178 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done time:: 00:00:24 elapsed:: 00024 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA44.label --trgsubject bert --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 1004 Checking for and removing duplicates Writing label file ./rh.BA44.label 7916 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA45.label --trgsubject bert --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 1373 Checking for and removing duplicates Writing label file ./rh.BA45.label 6728 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.V1.label --trgsubject bert --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 1582 Checking for and removing duplicates Writing label file ./rh.V1.label 6309 LabelWrite: saving to ./rh.V1.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.V2.label --trgsubject bert --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 3321 Checking for and removing duplicates Writing label file ./rh.V2.label 11337 LabelWrite: saving to ./rh.V2.label mri_label2label: Done time:: 00:00:21 elapsed:: 00021 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.MT.label --trgsubject bert --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 349 Checking for and removing duplicates Writing label file ./rh.MT.label 2281 LabelWrite: saving to ./rh.MT.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.perirhinal.label --trgsubject bert --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 804 LabelWrite: saving to ./rh.perirhinal.label mri_label2label: Done time:: 00:00:15 elapsed:: 00015 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA1.thresh.label --trgsubject bert --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 962 LabelWrite: saving to ./rh.BA1.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA2.thresh.label --trgsubject bert --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2798 LabelWrite: saving to ./rh.BA2.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA3a.thresh.label --trgsubject bert --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 52 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1750 LabelWrite: saving to ./rh.BA3a.thresh.label mri_label2label: Done time:: 00:00:15 elapsed:: 00015 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA3b.thresh.label --trgsubject bert --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 173 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2356 LabelWrite: saving to ./rh.BA3b.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA4a.thresh.label --trgsubject bert --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1554 LabelWrite: saving to ./rh.BA4a.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA4p.thresh.label --trgsubject bert --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1562 LabelWrite: saving to ./rh.BA4p.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA6.thresh.label --trgsubject bert --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 425 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7384 LabelWrite: saving to ./rh.BA6.thresh.label mri_label2label: Done time:: 00:00:19 elapsed:: 00019 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA44.thresh.label --trgsubject bert --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1130 LabelWrite: saving to ./rh.BA44.thresh.label mri_label2label: Done time:: 00:00:16 elapsed:: 00016 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA45.thresh.label --trgsubject bert --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 372 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1550 LabelWrite: saving to ./rh.BA45.thresh.label mri_label2label: Done time:: 00:00:15 elapsed:: 00015 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.V1.thresh.label --trgsubject bert --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 989 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4221 LabelWrite: saving to ./rh.V1.thresh.label mri_label2label: Done time:: 00:00:18 elapsed:: 00018 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.V2.thresh.label --trgsubject bert --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 1532 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4969 LabelWrite: saving to ./rh.V2.thresh.label mri_label2label: Done time:: 00:00:17 elapsed:: 00017 cmd:: mri_label2label mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.MT.thresh.label --trgsubject bert --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = bert 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 /autofs/cluster/freesurfer/test/tsd/i686 FREESURFER_HOME /space/freesurfer/centos4.0/stable Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/tsd/i686/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/tsd/i686/bert/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 133299 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 288 LabelWrite: saving to ./rh.MT.thresh.label mri_label2label: Done time:: 00:00:15 elapsed:: 00015 cmd:: mri_label2label mris_label2annot --s bert --hemi rh --ctab /space/freesurfer/centos4.0/stable/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 /space/freesurfer/centos4.0/stable/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/label cmdline mris_label2annot --s bert --hemi rh --ctab /space/freesurfer/centos4.0/stable/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 node0360 machine x86_64 user nicks subject bert hemi rh SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 ColorTable /space/freesurfer/centos4.0/stable/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/tsd/i686/bert/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 92050 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/tsd/i686/bert/label/rh.BA.annot time:: 00:00:04 elapsed:: 00004 cmd:: mris_label2annot mris_label2annot --s bert --hemi rh --ctab /space/freesurfer/centos4.0/stable/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 /space/freesurfer/centos4.0/stable/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 /autofs/cluster/freesurfer/test/tsd/i686/bert/label cmdline mris_label2annot --s bert --hemi rh --ctab /space/freesurfer/centos4.0/stable/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 node0360 machine x86_64 user nicks subject bert hemi rh SUBJECTS_DIR /autofs/cluster/freesurfer/test/tsd/i686 ColorTable /space/freesurfer/centos4.0/stable/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/tsd/i686/bert/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 110894 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/tsd/i686/bert/label/rh.BA.thresh.annot time:: 00:00:03 elapsed:: 00003 cmd:: mris_label2annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab bert rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /space/freesurfer/centos4.0/stable/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 923 468 1649 2.456 0.557 0.142 0.062 18 2.8 BA1 3442 2266 5214 2.243 0.525 0.114 0.043 73 5.7 BA2 1073 685 905 1.684 0.408 0.126 0.044 9 2.0 BA3a 2048 1297 2442 1.655 0.614 0.116 0.041 23 3.6 BA3b 1700 968 3113 2.778 0.605 0.123 0.056 28 4.3 BA4a 1221 802 2038 2.647 0.596 0.121 0.047 13 2.4 BA4p 7073 4525 15730 2.977 0.671 0.122 0.046 100 16.1 BA6 3624 2409 7407 2.836 0.533 0.113 0.030 31 4.4 BA44 4960 3284 10547 2.751 0.576 0.139 0.052 72 9.4 BA45 3989 2498 4259 1.620 0.513 0.140 0.062 71 10.9 V1 8791 5720 11864 1.975 0.564 0.163 0.068 174 24.8 V2 1859 1288 3156 2.528 0.496 0.128 0.036 19 2.6 MT 546 384 1528 2.995 0.715 0.121 0.035 4 0.9 perirhinal time:: 00:00:13 elapsed:: 00013 cmd:: mris_anatomical_stats mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab bert rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /space/freesurfer/centos4.0/stable/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 655 327 1167 2.479 0.500 0.129 0.054 11 1.7 BA1 1733 1146 2761 2.267 0.577 0.108 0.052 57 3.4 BA2 943 578 718 1.693 0.404 0.126 0.046 8 2.0 BA3a 1672 1085 1759 1.504 0.495 0.100 0.028 11 1.8 BA3b 1072 595 1662 2.524 0.614 0.139 0.087 25 4.6 BA4a 1017 681 1734 2.679 0.655 0.123 0.047 12 1.9 BA4p 4523 2886 9859 2.941 0.669 0.120 0.044 67 9.8 BA6 862 572 2088 3.084 0.407 0.129 0.044 12 1.4 BA44 1397 931 3497 2.975 0.507 0.143 0.045 23 2.6 BA45 3780 2392 4016 1.618 0.518 0.139 0.062 65 10.3 V1 4549 2865 5374 1.808 0.539 0.167 0.077 105 15.2 V2 202 144 371 2.590 0.585 0.115 0.029 1 0.3 MT time:: 00:00:12 elapsed:: 00012 cmd:: mris_anatomical_stats /autofs/cluster/freesurfer/test/tsd/i686/bert/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Wed May 8 04:07:14 EDT 2013 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /autofs/cluster/freesurfer/test/tsd/i686; ln -s /space/freesurfer/centos4.0/stable/subjects/lh.EC_average; cd - time:: 00:00:00 elapsed:: 00000 cmd:: ln mris_spherical_average -erode 1 -orig white -t 0.4 -o bert label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject bert. processing subject lh.EC_average... reading output surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 888 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label time:: 00:00:19 elapsed:: 00019 cmd:: mris_spherical_average mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label bert lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 316 220 925 2.772 0.803 0.115 0.028 3 0.4 ./lh.entorhinal_exvivo.label time:: 00:00:12 elapsed:: 00012 cmd:: mris_anatomical_stats #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Wed May 8 04:07:46 EDT 2013 INFO: rh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to rh.EC_average subject... cd /autofs/cluster/freesurfer/test/tsd/i686; ln -s /space/freesurfer/centos4.0/stable/subjects/rh.EC_average; cd - time:: 00:00:00 elapsed:: 00000 cmd:: ln mris_spherical_average -erode 1 -orig white -t 0.4 -o bert label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject bert. processing subject rh.EC_average... reading output surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 702 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label time:: 00:00:19 elapsed:: 00019 cmd:: mris_spherical_average mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label bert rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/cluster/freesurfer/test/tsd/i686/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/tsd/i686/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/tsd/i686/bert/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 222 147 761 3.273 0.614 0.127 0.046 2 0.5 ./rh.entorhinal_exvivo.label time:: 00:00:12 elapsed:: 00012 cmd:: mris_anatomical_stats #------------------------------------------ Started at Mon May 6 20:01:31 EDT 2013 Ended at Wed May 8 04:08:17 EDT 2013 #@#%# recon-all-run-time-hours 32.113 recon-all -s bert finished without error at Wed May 8 04:08:18 EDT 2013 New invocation of recon-all Mon Oct 31 15:47:39 CET 2016 /usr/local/bin/freesurfer/subjects/bert /usr/local/bin/freesurfer/bin/recon-all -s bert -all subjid bert setenv SUBJECTS_DIR /usr/local/bin/freesurfer/subjects FREESURFER_HOME /usr/local/bin/freesurfer Actual FREESURFER_HOME /usr/local/bin/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 47869 maxlocks unlimited maxsignal 47869 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12294800 1732552 3849224 37828 6713024 10154452 Swap: 12571644 0 12571644 ######################################## 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: 2016/10/31-14:47:39-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:40-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:41-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-14:47:42-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/bin/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/bin/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/bin/freesurfer Previous: /space/freesurfer/centos4.0/stable #-------------------------------------------- #@# MotionCor Mon Oct 31 15:47:43 CET 2016 Found 3 runs /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /usr/local/bin/freesurfer/subjects/bert mri_robust_template --mov /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/bin/freesurfer/subjects/bert/mri/orig/001-iscale.txt /usr/local/bin/freesurfer/subjects/bert/mri/orig/002-iscale.txt /usr/local/bin/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.lta $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz ) to TP 1 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz ) to TP 1 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: mapping movs and creating initial template... allow intensity scaling using median Writing final template: /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 2 minutes and 17 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf /usr/local/bin/freesurfer/subjects/bert mri_convert /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz --conform mri_convert /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) 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 writing to /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/bin/freesurfer/subjects/bert/mri/transforms/talairach.xfm /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 31 15:50:10 CET 2016 /usr/local/bin/freesurfer/subjects/bert/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Oct 31 15:50:11 CET 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Mon Oct 31 16:27:44 CET 2016 /usr/local/bin/freesurfer/subjects/bert /usr/local/bin/freesurfer/bin/recon-all -s bert -all subjid bert setenv SUBJECTS_DIR /usr/local/bin/freesurfer/subjects FREESURFER_HOME /usr/local/bin/freesurfer Actual FREESURFER_HOME /usr/local/bin/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 47869 maxlocks unlimited maxsignal 47869 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12294800 1754272 3608804 39888 6931724 10130416 Swap: 12571644 0 12571644 ######################################## 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: 2016/10/31-15:27:44-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-15:27:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-15:27:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:47-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:47-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:47-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:27:47-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/bin/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/bin/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/bin/freesurfer Previous: /space/freesurfer/centos4.0/stable #-------------------------------------------- #@# MotionCor Mon Oct 31 16:27:48 CET 2016 Found 3 runs /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /usr/local/bin/freesurfer/subjects/bert mri_robust_template --mov /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/bin/freesurfer/subjects/bert/mri/orig/001-iscale.txt /usr/local/bin/freesurfer/subjects/bert/mri/orig/002-iscale.txt /usr/local/bin/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.lta $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz ) to TP 1 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz ) to TP 1 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: mapping movs and creating initial template... allow intensity scaling using median Writing final template: /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 2 minutes and 15 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf /usr/local/bin/freesurfer/subjects/bert mri_convert /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz --conform mri_convert /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) 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 writing to /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/bin/freesurfer/subjects/bert/mri/transforms/talairach.xfm /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 31 16:30:12 CET 2016 /usr/local/bin/freesurfer/subjects/bert/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Oct 31 16:30:14 CET 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Mon Oct 31 16:40:11 CET 2016 /usr/local/bin/freesurfer/subjects/bert /usr/local/bin/freesurfer/bin/recon-all -s bert -all subjid bert setenv SUBJECTS_DIR /usr/local/bin/freesurfer/subjects FREESURFER_HOME /usr/local/bin/freesurfer Actual FREESURFER_HOME /usr/local/bin/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 47869 maxlocks unlimited maxsignal 47869 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12294800 1801580 3460428 43028 7032792 10080140 Swap: 12571644 0 12571644 ######################################## 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: 2016/10/31-15:40:11-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:12-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:13-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic 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: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/31-15:40:14-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: albert Machine: unanderra Platform: Linux PlatformVersion: 4.4.0-45-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/bin/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/bin/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/bin/freesurfer Previous: /space/freesurfer/centos4.0/stable #-------------------------------------------- #@# MotionCor Mon Oct 31 16:40:15 CET 2016 Found 3 runs /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /usr/local/bin/freesurfer/subjects/bert mri_robust_template --mov /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/bin/freesurfer/subjects/bert/mri/orig/001-iscale.txt /usr/local/bin/freesurfer/subjects/bert/mri/orig/002-iscale.txt /usr/local/bin/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.lta /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.lta $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz'... converting source '/usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/002.mgz ) to TP 1 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/003.mgz ) to TP 1 ( /usr/local/bin/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: mapping movs and creating initial template... allow intensity scaling using median Writing final template: /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 2 minutes and 19 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf /usr/local/bin/freesurfer/subjects/bert mri_convert /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz --conform mri_convert /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/bin/freesurfer/subjects/bert/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) 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 writing to /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/bin/freesurfer/subjects/bert/mri/transforms/talairach.xfm /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz /usr/local/bin/freesurfer/subjects/bert/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 31 16:42:43 CET 2016 /usr/local/bin/freesurfer/subjects/bert/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Oct 31 16:42:45 CET 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting