Fri Sep 18 11:37:01 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon /share/apps/freesurfer-5.3.0/bin/recon-all -all -subject af1021_recon -FLAIR /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/T2_FLAIR/001.mgz -FLAIRpial -hippo-subfields -qcache subjid af1021_recon setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori FREESURFER_HOME /share/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /share/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux compute-0-14.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 41943040 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 335872 Fri Sep 18 11:46:46 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon /share/apps/freesurfer-5.3.0/bin/recon-all -all -subject af1021_recon -FLAIR /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/T2_FLAIR/001.mgz -FLAIRpial -no-isrunning subjid af1021_recon setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori FREESURFER_HOME /share/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /share/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux compute-0-4.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 41943040 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 401408 total used free shared buffers cached Mem: 49449548 48105692 1343856 0 247548 46726220 -/+ buffers/cache: 1131924 48317624 Swap: 1020116 224 1019892 ######################################## 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: 2015/09/18-15:46:46-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/09/18-15:46:46-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/09/18-15:46:46-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:46-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:46-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:46-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:48-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/09/18-15:46:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/09/18-15:46:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/09/18-15:46:49-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: twilliams Machine: compute-0-4.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /share/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /share/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Fri Sep 18 11:46:49 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon mri_convert /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/T2_FLAIR/001.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/FLAIRraw.mgz mri_convert /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/T2_FLAIR/001.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/FLAIRraw.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/T2_FLAIR/001.mgz... TR=6000.00, TE=475.00, TI=2100.00, flip angle=120.00 i_ras = (0.0313814, -0.959852, 0.278747) j_ras = (0.0851089, -0.275305, -0.957582) k_ras = (-0.995877, -0.053774, -0.0730522) writing to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/FLAIRraw.mgz... #-------------------------------------------- #@# MotionCor Fri Sep 18 11:46:55 EDT 2015 Found 1 runs /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/001.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/rawavg.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon mri_convert /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/rawavg.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz --conform mri_convert /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/rawavg.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/rawavg.mgz... TR=2530.00, TE=3.32, TI=1100.00, flip angle=7.00 i_ras = (0.03293, -0.976376, 0.213556) j_ras = (0.0460134, -0.211964, -0.976194) k_ras = (-0.998398, -0.0419726, -0.0379467) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz... mri_add_xform_to_header -c /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/talairach.xfm /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Sep 18 11:47:12 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Sep 18 11:51:21 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6523, pval=0.3663 >= threshold=0.0050) awk -f /share/apps/freesurfer-5.3.0/bin/extract_talairach_avi_QA.awk /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/talairach_avi.log tal_QC_AZS /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/talairach_avi.log TalAviQA: 0.97649 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Sep 18 11:51:21 EDT 2015 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri /share/apps/freesurfer-5.3.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux compute-0-4.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux Fri Sep 18 11:51:21 EDT 2015 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.13557 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13557/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13557/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=2530.00, TE=3.32, TI=1100.00, flip angle=7.00 i_ras = (-1, 1.11759e-08, -5.58794e-08) j_ras = (-8.9407e-08, -1.40863e-08, -1) k_ras = (-8.56817e-08, 1, -9.42964e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.13557/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Sep 18 11:51:33 EDT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.13557/nu0.mnc ./tmp.mri_nu_correct.mni.13557/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13557/0/ [twilliams@compute-0-4.local:/share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/] [2015-09-18 11:51:33] running: /share/apps/freesurfer-5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13557/0/ ./tmp.mri_nu_correct.mni.13557/nu0.mnc ./tmp.mri_nu_correct.mni.13557/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 34 CV of field change: 0.000963465 [twilliams@compute-0-4.local:/share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/] [2015-09-18 11:53:14] running: /share/apps/freesurfer-5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13557/nu0.mnc ./tmp.mri_nu_correct.mni.13557/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Sep 18 11:54:02 EDT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.13557/nu1.mnc ./tmp.mri_nu_correct.mni.13557/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.13557/1/ [twilliams@compute-0-4.local:/share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/] [2015-09-18 11:54:02] running: /share/apps/freesurfer-5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.13557/1/ ./tmp.mri_nu_correct.mni.13557/nu1.mnc ./tmp.mri_nu_correct.mni.13557/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000979503 [twilliams@compute-0-4.local:/share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/] [2015-09-18 11:54:48] running: /share/apps/freesurfer-5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.13557/nu1.mnc ./tmp.mri_nu_correct.mni.13557/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.13557/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13557/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.13557/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.13557/ones.mgz sysname Linux hostname compute-0-4.local machine x86_64 user twilliams input ./tmp.mri_nu_correct.mni.13557/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.13557/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.13557/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13557/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13557/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.13557/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.13557/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13557/input.mean.dat sysname Linux hostname compute-0-4.local machine x86_64 user twilliams UseRobust 0 Loading ./tmp.mri_nu_correct.mni.13557/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.13557/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.13557/ones.mgz --i ./tmp.mri_nu_correct.mni.13557/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13557/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13557/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.13557/ones.mgz --i ./tmp.mri_nu_correct.mni.13557/nu2.mnc --sum ./tmp.mri_nu_correct.mni.13557/sum.junk --avgwf ./tmp.mri_nu_correct.mni.13557/output.mean.dat sysname Linux hostname compute-0-4.local machine x86_64 user twilliams UseRobust 0 Loading ./tmp.mri_nu_correct.mni.13557/ones.mgz Loading ./tmp.mri_nu_correct.mni.13557/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.13557/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.13557/nu2.mnc ./tmp.mri_nu_correct.mni.13557/nu2.mnc mul .98442569500605742890 Saving result to './tmp.mri_nu_correct.mni.13557/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.13557/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.13557/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.13557/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.11759e-08, -5.58794e-08) j_ras = (-8.9407e-08, -1.40863e-08, -1) k_ras = (-8.56817e-08, 1, -9.42964e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 1 minutes and 2 seconds. mapping (10, 177) to ( 3, 110) Fri Sep 18 11:57:50 EDT 2015 mri_nu_correct.mni done mri_add_xform_to_header -c /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Sep 18 11:57:53 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.115 0.031 0.034 -4.191; -0.056 1.037 0.031 -32.102; -0.044 0.050 1.091 20.356; 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 = 21 Starting OpenSpline(): npoints = 21 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 65 (65), valley at 42 (42) csf peak at 32, setting threshold to 54 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 65 (65), valley at 30 (30) csf peak at 32, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 33 seconds. #-------------------------------------------- #@# Skull Stripping Fri Sep 18 12:00:27 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_em_register -skull nu.mgz /share/apps/freesurfer-5.3.0/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 '/share/apps/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (48, 22, 43) --> (202, 255, 232) using (99, 100, 138) as brain centroid... mean wm in atlas = 126, using box (80,71,115) --> (117, 128,161) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.414641 @ (-9.091, 9.091, -27.273) max log p = -4.338395 @ (13.636, 4.545, 4.545) max log p = -4.272542 @ (-2.273, 2.273, 2.273) max log p = -4.265767 @ (-3.409, 1.136, 1.136) max log p = -4.256771 @ (0.568, -0.568, 0.568) max log p = -4.256326 @ (0.284, 0.284, -0.284) Found translation: (-0.3, 16.8, -19.0): log p = -4.256 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.3 (thresh=-4.3) 1.140 0.000 -0.150 0.823; 0.000 1.150 0.000 1.109; 0.150 0.000 1.140 -62.984; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.150 0.000 0.000 -20.170; 0.000 1.150 0.000 1.109; 0.000 0.000 1.064 -33.885; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.150 0.000 0.000 -20.170; 0.000 1.150 0.000 1.109; 0.000 0.000 1.064 -33.885; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.086 -0.001 -0.034 -9.301; -0.000 1.192 -0.037 1.729; 0.036 0.036 1.063 -40.372; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.106 0.040 -0.001 -20.543; -0.036 1.192 -0.037 8.241; 0.001 0.036 1.043 -33.213; 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=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.105 0.020 -0.008 -17.365; -0.017 1.194 -0.038 4.829; 0.010 0.036 1.044 -34.585; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.104 0.020 -0.008 -17.198; -0.017 1.194 -0.038 4.829; 0.010 0.036 1.044 -34.585; 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 1.10372 0.01993 -0.00848 -17.19772; -0.01746 1.19363 -0.03774 4.82913; 0.00972 0.03607 1.04449 -34.58549; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.10372 0.01993 -0.00848 -17.19772; -0.01746 1.19363 -0.03774 4.82913; 0.00972 0.03607 1.04449 -34.58549; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.104 0.020 -0.008 -17.198; -0.017 1.194 -0.038 4.829; 0.010 0.036 1.044 -34.585; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.7) transform before final EM align: 1.104 0.020 -0.008 -17.198; -0.017 1.194 -0.038 4.829; 0.010 0.036 1.044 -34.585; 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 1.10372 0.01993 -0.00848 -17.19772; -0.01746 1.19363 -0.03774 4.82913; 0.00972 0.03607 1.04449 -34.58549; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.10372 0.01993 -0.00848 -17.19772; -0.01746 1.19363 -0.03774 4.82913; 0.00972 0.03607 1.04449 -34.58549; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.2 tol 0.000000 final transform: 1.104 0.020 -0.008 -17.198; -0.017 1.194 -0.038 4.829; 0.010 0.036 1.044 -34.585; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 29 minutes and 17 seconds. mri_watershed -T1 -brain_atlas /share/apps/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=98 z=135 r=88 first estimation of the main basin volume: 2861614 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=148, y=81, z=97, Imax=255 CSF=13, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=27226732861 voxels, voxel volume =1.000 = 27226732861 mmm3 = 27226732.544 cm3 done. PostAnalyze...Basin Prior 22 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=128,y=101, z=127, r=9753 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=39 , nb = 44226 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=35 , nb = 3258 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 2736 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=38 , nb = 19098 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 18648 OTHER CSF_MIN=0, CSF_intensity=19, CSF_MAX=40 , nb = 486 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 39, 43, 46, 64 after analyzing : 39, 45, 46, 49 RIGHT_CER before analyzing : 35, 35, 36, 79 after analyzing : 20, 35, 36, 46 LEFT_CER before analyzing : 21, 30, 43, 70 after analyzing : 21, 38, 43, 46 RIGHT_BRAIN before analyzing : 38, 41, 44, 64 after analyzing : 38, 43, 44, 48 LEFT_BRAIN before analyzing : 38, 41, 44, 64 after analyzing : 38, 43, 44, 48 OTHER before analyzing : 40, 28, 19, 37 after analyzing : 25, 28, 28, 30 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.684, std = 7.062 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.61, sigma = 6.20 after rotation: sse = 4.61, sigma = 6.20 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.32, its var is 6.99 before Erosion-Dilatation 2.22% 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...50 iterations mri_strip_skull: done peeling brain Brain Size = 1605317 voxels, voxel volume = 1.000 mm3 = 1605317 mmm3 = 1605.317 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Sep 18 12:30:13 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /share/apps/freesurfer-5.3.0/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 '/share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.9 skull bounding box = (64, 38, 43) --> (191, 154, 216) using (106, 77, 130) as brain centroid... mean wm in atlas = 107, using box (90,63,109) --> (121, 91,151) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.025071 @ (-9.091, 27.273, -27.273) max log p = -3.787479 @ (4.545, -4.545, 4.545) max log p = -3.766387 @ (2.273, -2.273, 2.273) max log p = -3.755645 @ (-1.136, -1.136, -1.136) max log p = -3.720972 @ (1.705, -0.568, -1.705) max log p = -3.720972 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 18.7, -23.3): log p = -3.721 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.7 (thresh=-3.7) 1.150 0.000 0.000 -20.982; 0.000 1.150 0.000 3.733; 0.000 0.000 1.000 -23.295; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.150 0.000 0.000 -20.982; 0.000 1.150 0.000 3.733; 0.000 0.000 1.000 -23.295; 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=-3.1, old_max_log_p =-3.4 (thresh=-3.4) 1.125 0.074 -0.034 -22.700; -0.074 1.167 -0.065 19.839; 0.041 0.077 1.015 -38.185; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.127 0.036 -0.033 -19.229; -0.035 1.170 -0.032 10.360; 0.043 0.038 0.998 -32.239; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.127 0.036 -0.033 -19.229; -0.035 1.170 -0.032 10.360; 0.043 0.038 0.998 -32.239; 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=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.125 0.026 -0.049 -15.419; -0.026 1.169 -0.033 8.848; 0.061 0.038 1.001 -35.560; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.125 0.026 -0.049 -15.419; -0.026 1.169 -0.033 8.848; 0.061 0.038 1.001 -35.560; 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 1.12464 0.02574 -0.04885 -15.41854; -0.02626 1.16925 -0.03276 8.84788; 0.06120 0.03830 1.00051 -35.56002; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.12464 0.02574 -0.04885 -15.41854; -0.02626 1.16925 -0.03276 8.84788; 0.06120 0.03830 1.00051 -35.56002; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.125 0.026 -0.049 -15.419; -0.026 1.169 -0.033 8.848; 0.061 0.038 1.001 -35.560; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.1 (old=-4.4) transform before final EM align: 1.125 0.026 -0.049 -15.419; -0.026 1.169 -0.033 8.848; 0.061 0.038 1.001 -35.560; 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 1.12464 0.02574 -0.04885 -15.41854; -0.02626 1.16925 -0.03276 8.84788; 0.06120 0.03830 1.00051 -35.56002; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.12464 0.02574 -0.04885 -15.41854; -0.02626 1.16925 -0.03276 8.84788; 0.06120 0.03830 1.00051 -35.56002; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 3.7 after pass:transform: ( 1.12, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 011: -log(p) = 3.7 after pass:transform: ( 1.12, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 012: -log(p) = 3.7 after pass:transform: ( 1.12, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 013: -log(p) = 3.7 after pass:transform: ( 1.12, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 014: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 015: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 016: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 017: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 018: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 019: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 021: -log(p) = 3.7 tol 0.000000 final transform: 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 23 minutes and 21 seconds. #-------------------------------------- #@# CA Normalize Fri Sep 18 12:53:34 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.9 skull bounding box = (64, 38, 43) --> (191, 154, 216) using (106, 77, 130) as brain centroid... mean wm in atlas = 107, using box (90,63,109) --> (121, 91,151) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 244171 sample points... INFO: compute sample coordinates transform 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 43, 49) --> (187, 145, 217) Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 153.0 24 of 125 (19.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 43, 51) --> (131, 144, 218) Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 153.0 0 of 51 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 113, 69) --> (171, 151, 124) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 153.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 113, 69) --> (127, 150, 125) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 153.0 0 of 8 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 110, 103) --> (142, 168, 137) Brain_Stem: limiting intensities to 104.0 --> 153.0 5 of 10 (50.0%) samples deleted using 201 total control points for intensity normalization... bias field = 0.986 +- 0.063 0 of 172 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 43, 49) --> (187, 145, 217) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 145.0 0 of 148 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 43, 51) --> (131, 144, 218) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 145.0 0 of 89 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 113, 69) --> (171, 151, 124) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 145.0 0 of 32 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 113, 69) --> (127, 150, 125) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 145.0 0 of 48 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 110, 103) --> (142, 168, 137) Brain_Stem: limiting intensities to 82.0 --> 145.0 0 of 94 (0.0%) samples deleted using 411 total control points for intensity normalization... bias field = 0.976 +- 0.069 0 of 411 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 43, 49) --> (187, 145, 217) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 146.0 0 of 263 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 43, 51) --> (131, 144, 218) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 146.0 0 of 194 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 113, 69) --> (171, 151, 124) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 146.0 0 of 85 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 113, 69) --> (127, 150, 125) Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 146.0 0 of 77 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 110, 103) --> (142, 168, 137) Brain_Stem: limiting intensities to 76.0 --> 146.0 0 of 127 (0.0%) samples deleted using 746 total control points for intensity normalization... bias field = 0.983 +- 0.047 1 of 746 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 45 seconds. #-------------------------------------- #@# CA Reg Fri Sep 18 12:55:20 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.32 (predicted orig area = 6.0) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.734, neg=0, invalid=96777 0001: dt=129.472000, rms=0.678 (7.633%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.665 (2.018%), neg=0, invalid=96777 0003: dt=369.920000, rms=0.654 (1.569%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.649 (0.783%), neg=0, invalid=96777 0005: dt=369.920000, rms=0.645 (0.656%), neg=0, invalid=96777 0006: dt=92.480000, rms=0.642 (0.464%), neg=0, invalid=96777 0007: dt=1479.680000, rms=0.633 (1.424%), neg=0, invalid=96777 0008: dt=92.480000, rms=0.629 (0.567%), neg=0, invalid=96777 0009: dt=295.936000, rms=0.627 (0.277%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.627 (0.044%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.627 (0.045%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.626 (0.067%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.626 (0.107%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.625 (0.122%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.624 (0.154%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.623 (0.165%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.622 (0.163%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.621 (0.161%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.620 (0.165%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.619 (0.164%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.618 (0.152%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.617 (0.150%), neg=0, invalid=96777 0023: dt=73.984000, rms=0.616 (0.143%), neg=0, invalid=96777 0024: dt=73.984000, rms=0.615 (0.133%), neg=0, invalid=96777 0025: dt=73.984000, rms=0.614 (0.127%), neg=0, invalid=96777 0026: dt=73.984000, rms=0.614 (0.126%), neg=0, invalid=96777 0027: dt=73.984000, rms=0.613 (0.131%), neg=0, invalid=96777 0028: dt=73.984000, rms=0.612 (0.116%), neg=0, invalid=96777 0029: dt=73.984000, rms=0.612 (0.101%), neg=0, invalid=96777 0030: dt=443.904000, rms=0.611 (0.018%), neg=0, invalid=96777 0031: dt=443.904000, rms=0.611 (-0.021%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=96777 0032: dt=129.472000, rms=0.611 (0.055%), neg=0, invalid=96777 0033: dt=517.888000, rms=0.610 (0.180%), neg=0, invalid=96777 0034: dt=27.744000, rms=0.610 (0.004%), neg=0, invalid=96777 0035: dt=27.744000, rms=0.610 (0.003%), neg=0, invalid=96777 0036: dt=27.744000, rms=0.610 (-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=0.614, neg=0, invalid=96777 0037: dt=124.416000, rms=0.608 (0.976%), neg=0, invalid=96777 0038: dt=82.944000, rms=0.602 (0.989%), neg=0, invalid=96777 0039: dt=25.920000, rms=0.600 (0.330%), neg=0, invalid=96777 0040: dt=145.152000, rms=0.595 (0.831%), neg=0, invalid=96777 0041: dt=20.736000, rms=0.593 (0.272%), neg=0, invalid=96777 0042: dt=124.416000, rms=0.590 (0.594%), neg=0, invalid=96777 0043: dt=36.288000, rms=0.588 (0.272%), neg=0, invalid=96777 0044: dt=82.944000, rms=0.586 (0.338%), neg=0, invalid=96777 0045: dt=20.736000, rms=0.585 (0.154%), neg=0, invalid=96777 0046: dt=20.736000, rms=0.584 (0.122%), neg=0, invalid=96777 0047: dt=20.736000, rms=0.583 (0.161%), neg=0, invalid=96777 0048: dt=20.736000, rms=0.582 (0.209%), neg=0, invalid=96777 0049: dt=20.736000, rms=0.581 (0.260%), neg=0, invalid=96777 0050: dt=20.736000, rms=0.579 (0.303%), neg=0, invalid=96777 0051: dt=20.736000, rms=0.577 (0.326%), neg=0, invalid=96777 0052: dt=20.736000, rms=0.575 (0.337%), neg=0, invalid=96777 0053: dt=20.736000, rms=0.573 (0.338%), neg=0, invalid=96777 0054: dt=20.736000, rms=0.571 (0.327%), neg=0, invalid=96777 0055: dt=20.736000, rms=0.569 (0.322%), neg=0, invalid=96777 0056: dt=20.736000, rms=0.568 (0.309%), neg=0, invalid=96777 0057: dt=20.736000, rms=0.566 (0.312%), neg=0, invalid=96777 0058: dt=20.736000, rms=0.564 (0.294%), neg=0, invalid=96777 0059: dt=20.736000, rms=0.563 (0.264%), neg=0, invalid=96777 0060: dt=20.736000, rms=0.561 (0.233%), neg=0, invalid=96777 0061: dt=20.736000, rms=0.560 (0.213%), neg=0, invalid=96777 0062: dt=20.736000, rms=0.559 (0.201%), neg=0, invalid=96777 0063: dt=20.736000, rms=0.558 (0.192%), neg=0, invalid=96777 0064: dt=20.736000, rms=0.557 (0.165%), neg=0, invalid=96777 0065: dt=20.736000, rms=0.556 (0.149%), neg=0, invalid=96777 0066: dt=20.736000, rms=0.556 (0.122%), neg=0, invalid=96777 0067: dt=20.736000, rms=0.555 (0.116%), neg=0, invalid=96777 0068: dt=124.416000, rms=0.555 (0.055%), neg=0, invalid=96777 0069: dt=124.416000, rms=0.555 (-0.336%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=96777 0070: dt=36.288000, rms=0.554 (0.098%), neg=0, invalid=96777 0071: dt=103.680000, rms=0.553 (0.137%), neg=0, invalid=96777 0072: dt=20.736000, rms=0.553 (0.041%), neg=0, invalid=96777 0073: dt=20.736000, rms=0.553 (0.024%), neg=0, invalid=96777 0074: dt=20.736000, rms=0.553 (0.022%), neg=0, invalid=96777 0075: dt=20.736000, rms=0.553 (0.021%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 0076: dt=5.714286, rms=0.572 (0.046%), neg=0, invalid=96777 0077: dt=2.000000, rms=0.572 (0.004%), neg=0, invalid=96777 0078: dt=2.000000, rms=0.572 (0.000%), neg=0, invalid=96777 0079: dt=2.000000, rms=0.572 (-0.017%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 0080: dt=0.175000, rms=0.572 (0.000%), neg=0, invalid=96777 0081: dt=0.150000, rms=0.572 (0.001%), neg=0, invalid=96777 0082: dt=0.000000, rms=0.572 (0.001%), neg=0, invalid=96777 0083: dt=0.000000, rms=0.572 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.623, neg=0, invalid=96777 0084: dt=5.468041, rms=0.609 (2.243%), neg=0, invalid=96777 0085: dt=1.783133, rms=0.609 (0.048%), neg=0, invalid=96777 0086: dt=1.783133, rms=0.609 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=96777 0087: dt=0.000000, rms=0.609 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.663, neg=0, invalid=96777 0088: dt=1.087533, rms=0.660 (0.518%), neg=0, invalid=96777 0089: dt=2.248276, rms=0.654 (0.868%), neg=0, invalid=96777 0090: dt=0.486842, rms=0.653 (0.081%), neg=0, invalid=96777 0091: dt=0.486842, rms=0.653 (0.055%), neg=0, invalid=96777 0092: dt=0.486842, rms=0.653 (0.073%), neg=0, invalid=96777 0093: dt=0.486842, rms=0.652 (0.060%), neg=0, invalid=96777 0094: dt=0.486842, rms=0.652 (0.011%), neg=0, invalid=96777 0095: dt=1.792000, rms=0.652 (0.076%), neg=0, invalid=96777 0096: dt=0.256000, rms=0.652 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=96777 0097: dt=1.068966, rms=0.651 (0.110%), neg=0, invalid=96777 0098: dt=0.000050, rms=0.651 (0.000%), neg=0, invalid=96777 0099: dt=0.000050, rms=0.651 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.624, neg=0, invalid=96777 0100: dt=0.448000, rms=0.611 (2.176%), neg=0, invalid=96777 0101: dt=0.000000, rms=0.611 (0.005%), neg=0, invalid=96777 0102: dt=0.050000, rms=0.611 (-0.274%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=96777 0103: dt=0.000000, rms=0.611 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.06288 (16) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1228 voxels, overlap=0.470) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1228 voxels, peak = 13), gca=13.1 gca peak = 0.14022 (22) mri peak = 0.10084 (18) Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (587 voxels, overlap=0.185) Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (587 voxels, peak = 15), gca=15.3 gca peak = 0.24234 (100) mri peak = 0.13387 (101) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (488 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (488 voxels, peak = 102), gca=101.5 gca peak = 0.19192 (97) mri peak = 0.06268 (101) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (327 voxels, overlap=0.995) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (327 voxels, peak = 99), gca=99.4 gca peak = 0.24007 (63) mri peak = 0.08797 (67) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (811 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (811 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.08419 (64) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (846 voxels, overlap=0.993) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (846 voxels, peak = 63), gca=63.0 gca peak = 0.12541 (104) mri peak = 0.08746 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65753 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65753 voxels, peak = 110), gca=109.7 gca peak = 0.13686 (104) mri peak = 0.07674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (67757 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (67757 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.03794 (62) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (29182 voxels, overlap=0.996) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (29182 voxels, peak = 62), gca=62.1 gca peak = 0.13270 (63) mri peak = 0.04143 (63) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (30965 voxels, overlap=0.997) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (30965 voxels, peak = 62), gca=62.1 gca peak = 0.15182 (70) mri peak = 0.09260 (77) Right_Caudate (50): linear fit = 1.08 x + 0.0 (595 voxels, overlap=0.788) Right_Caudate (50): linear fit = 1.08 x + 0.0 (595 voxels, peak = 75), gca=75.2 gca peak = 0.14251 (76) mri peak = 0.08276 (84) Left_Caudate (11): linear fit = 1.07 x + 0.0 (703 voxels, overlap=0.894) Left_Caudate (11): linear fit = 1.07 x + 0.0 (703 voxels, peak = 81), gca=80.9 gca peak = 0.12116 (60) mri peak = 0.04348 (63) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (22807 voxels, overlap=0.923) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (22807 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.04500 (67) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (24802 voxels, overlap=0.741) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (24802 voxels, peak = 67), gca=67.4 gca peak = 0.22684 (88) mri peak = 0.07986 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (8180 voxels, overlap=0.689) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (8180 voxels, peak = 92), gca=92.0 gca peak = 0.21067 (87) mri peak = 0.08266 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7699 voxels, overlap=0.732) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7699 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.07459 (62) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (370 voxels, overlap=0.996) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (370 voxels, peak = 62), gca=62.0 gca peak = 0.39668 (62) mri peak = 0.10496 (60) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (350 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (350 voxels, peak = 59), gca=59.2 gca peak = 0.10129 (93) mri peak = 0.05850 (100) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5078 voxels, overlap=0.613) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5078 voxels, peak = 104), gca=103.7 gca peak = 0.12071 (89) mri peak = 0.06003 (97) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4135 voxels, overlap=0.783) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4135 voxels, peak = 96), gca=95.7 gca peak = 0.13716 (82) mri peak = 0.05371 (87) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2285 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2285 voxels, peak = 87), gca=86.5 gca peak = 0.15214 (84) mri peak = 0.05107 (83) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2324 voxels, overlap=1.001) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2324 voxels, peak = 82), gca=81.9 gca peak = 0.08983 (85) mri peak = 0.06644 (93) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11527 voxels, overlap=0.742) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11527 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.07171 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (835 voxels, overlap=0.575) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (835 voxels, peak = 104), gca=103.5 gca peak = 0.12914 (94) mri peak = 0.07282 (104) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1183 voxels, overlap=0.613) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1183 voxels, peak = 104), gca=103.9 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.17887 (18) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (255 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (255 voxels, peak = 16), gca=16.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.62 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=0.645, neg=0, invalid=96777 0104: dt=129.472000, rms=0.638 (1.114%), neg=0, invalid=96777 0105: dt=221.952000, rms=0.634 (0.627%), neg=0, invalid=96777 0106: dt=129.472000, rms=0.632 (0.330%), neg=0, invalid=96777 0107: dt=92.480000, rms=0.631 (0.154%), neg=0, invalid=96777 0108: dt=221.952000, rms=0.629 (0.350%), neg=0, invalid=96777 0109: dt=32.368000, rms=0.628 (0.087%), neg=0, invalid=96777 0110: dt=92.480000, rms=0.628 (0.071%), neg=0, invalid=96777 0111: dt=295.936000, rms=0.626 (0.286%), neg=0, invalid=96777 0112: dt=32.368000, rms=0.625 (0.085%), neg=0, invalid=96777 0113: dt=55.488000, rms=0.625 (0.038%), neg=0, invalid=96777 0114: dt=55.488000, rms=0.625 (0.048%), neg=0, invalid=96777 0115: dt=55.488000, rms=0.624 (0.077%), neg=0, invalid=96777 0116: dt=55.488000, rms=0.624 (0.107%), neg=0, invalid=96777 0117: dt=55.488000, rms=0.623 (0.120%), neg=0, invalid=96777 0118: dt=55.488000, rms=0.622 (0.141%), neg=0, invalid=96777 0119: dt=55.488000, rms=0.621 (0.146%), neg=0, invalid=96777 0120: dt=55.488000, rms=0.620 (0.141%), neg=0, invalid=96777 0121: dt=55.488000, rms=0.619 (0.134%), neg=0, invalid=96777 0122: dt=55.488000, rms=0.619 (0.126%), neg=0, invalid=96777 0123: dt=55.488000, rms=0.618 (0.114%), neg=0, invalid=96777 0124: dt=55.488000, rms=0.617 (0.105%), neg=0, invalid=96777 0125: dt=55.488000, rms=0.617 (0.105%), neg=0, invalid=96777 0126: dt=55.488000, rms=0.616 (0.092%), neg=0, invalid=96777 0127: dt=55.488000, rms=0.616 (0.082%), neg=0, invalid=96777 0128: dt=55.488000, rms=0.615 (0.067%), neg=0, invalid=96777 0129: dt=55.488000, rms=0.615 (0.058%), neg=0, invalid=96777 0130: dt=55.488000, rms=0.614 (0.069%), neg=0, invalid=96777 0131: dt=55.488000, rms=0.614 (0.087%), neg=0, invalid=96777 0132: dt=55.488000, rms=0.613 (0.078%), neg=0, invalid=96777 0133: dt=55.488000, rms=0.613 (0.066%), neg=0, invalid=96777 0134: dt=55.488000, rms=0.613 (0.040%), neg=0, invalid=96777 0135: dt=55.488000, rms=0.612 (0.037%), neg=0, invalid=96777 0136: dt=55.488000, rms=0.612 (0.064%), neg=0, invalid=96777 0137: dt=55.488000, rms=0.612 (0.089%), neg=0, invalid=96777 0138: dt=55.488000, rms=0.611 (0.089%), neg=0, invalid=96777 0139: dt=55.488000, rms=0.611 (0.069%), neg=0, invalid=96777 0140: dt=55.488000, rms=0.610 (0.064%), neg=0, invalid=96777 0141: dt=55.488000, rms=0.610 (0.038%), neg=0, invalid=96777 0142: dt=55.488000, rms=0.610 (0.033%), neg=0, invalid=96777 0143: dt=55.488000, rms=0.609 (0.088%), neg=0, invalid=96777 0144: dt=55.488000, rms=0.609 (0.077%), neg=0, invalid=96777 0145: dt=55.488000, rms=0.608 (0.054%), neg=0, invalid=96777 0146: dt=55.488000, rms=0.608 (0.042%), neg=0, invalid=96777 0147: dt=55.488000, rms=0.608 (0.023%), neg=0, invalid=96777 0148: dt=55.488000, rms=0.608 (0.037%), neg=0, invalid=96777 0149: dt=55.488000, rms=0.607 (0.061%), neg=0, invalid=96777 0150: dt=55.488000, rms=0.607 (0.059%), neg=0, invalid=96777 0151: dt=55.488000, rms=0.607 (0.048%), neg=0, invalid=96777 0152: dt=55.488000, rms=0.607 (0.044%), neg=0, invalid=96777 0153: dt=55.488000, rms=0.606 (0.029%), neg=0, invalid=96777 0154: dt=55.488000, rms=0.606 (0.030%), neg=0, invalid=96777 0155: dt=55.488000, rms=0.606 (0.045%), neg=0, invalid=96777 0156: dt=55.488000, rms=0.606 (0.042%), neg=0, invalid=96777 0157: dt=55.488000, rms=0.605 (0.033%), neg=0, invalid=96777 0158: dt=55.488000, rms=0.605 (0.038%), neg=0, invalid=96777 0159: dt=55.488000, rms=0.605 (0.034%), neg=0, invalid=96777 0160: dt=55.488000, rms=0.605 (0.026%), neg=0, invalid=96777 0161: dt=55.488000, rms=0.605 (0.037%), neg=0, invalid=96777 0162: dt=55.488000, rms=0.604 (0.042%), neg=0, invalid=96777 0163: dt=55.488000, rms=0.604 (0.040%), neg=0, invalid=96777 0164: dt=55.488000, rms=0.604 (0.034%), neg=0, invalid=96777 0165: dt=55.488000, rms=0.604 (0.032%), neg=0, invalid=96777 0166: dt=55.488000, rms=0.604 (0.030%), neg=0, invalid=96777 0167: dt=55.488000, rms=0.603 (0.029%), neg=0, invalid=96777 0168: dt=55.488000, rms=0.603 (0.020%), neg=0, invalid=96777 0169: dt=55.488000, rms=0.603 (0.026%), neg=0, invalid=96777 0170: dt=55.488000, rms=0.603 (0.023%), neg=0, invalid=96777 0171: dt=55.488000, rms=0.603 (0.019%), neg=0, invalid=96777 0172: dt=295.936000, rms=0.603 (0.037%), neg=0, invalid=96777 0173: dt=18.496000, rms=0.603 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.603, neg=0, invalid=96777 0174: dt=32.368000, rms=0.602 (0.031%), neg=0, invalid=96777 0175: dt=92.480000, rms=0.602 (0.035%), neg=0, invalid=96777 0176: dt=369.920000, rms=0.602 (0.067%), neg=0, invalid=96777 0177: dt=92.480000, rms=0.602 (0.036%), neg=0, invalid=96777 0178: dt=92.480000, rms=0.601 (0.027%), neg=0, invalid=96777 0179: dt=92.480000, rms=0.601 (0.018%), neg=0, invalid=96777 0180: dt=92.480000, rms=0.601 (0.021%), neg=0, invalid=96777 0181: dt=92.480000, rms=0.601 (0.019%), neg=0, invalid=96777 0182: dt=129.472000, rms=0.601 (0.030%), neg=0, invalid=96777 0183: dt=32.368000, rms=0.601 (-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=0.602, neg=0, invalid=96777 0184: dt=82.944000, rms=0.599 (0.537%), neg=0, invalid=96777 0185: dt=82.944000, rms=0.593 (0.905%), neg=0, invalid=96777 0186: dt=36.288000, rms=0.591 (0.430%), neg=0, invalid=96777 0187: dt=331.776000, rms=0.583 (1.317%), neg=0, invalid=96777 0188: dt=21.160173, rms=0.578 (0.871%), neg=0, invalid=96777 0189: dt=36.288000, rms=0.576 (0.239%), neg=0, invalid=96777 0190: dt=145.152000, rms=0.573 (0.499%), neg=0, invalid=96777 0191: dt=20.736000, rms=0.572 (0.260%), neg=0, invalid=96777 0192: dt=497.664000, rms=0.564 (1.416%), neg=0, invalid=96777 0193: dt=20.736000, rms=0.563 (0.218%), neg=0, invalid=96777 0194: dt=124.416000, rms=0.561 (0.375%), neg=0, invalid=96777 0195: dt=31.104000, rms=0.560 (0.107%), neg=0, invalid=96777 0196: dt=103.680000, rms=0.559 (0.202%), neg=0, invalid=96777 0197: dt=20.736000, rms=0.558 (0.070%), neg=0, invalid=96777 0198: dt=145.152000, rms=0.557 (0.329%), neg=0, invalid=96777 0199: dt=25.920000, rms=0.556 (0.022%), neg=0, invalid=96777 0200: dt=25.920000, rms=0.556 (0.068%), neg=0, invalid=96777 0201: dt=25.920000, rms=0.556 (0.086%), neg=0, invalid=96777 0202: dt=25.920000, rms=0.556 (0.015%), neg=0, invalid=96777 0203: dt=12.960000, rms=0.555 (0.040%), neg=0, invalid=96777 0204: dt=3.240000, rms=0.555 (0.009%), neg=0, invalid=96777 0205: dt=1.620000, rms=0.555 (0.003%), neg=0, invalid=96777 0206: dt=0.141750, rms=0.555 (0.001%), neg=0, invalid=96777 0207: dt=0.000138, rms=0.555 (0.000%), neg=0, invalid=96777 0208: dt=0.000035, rms=0.555 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=96777 0209: dt=103.680000, rms=0.553 (0.436%), neg=0, invalid=96777 0210: dt=36.288000, rms=0.552 (0.228%), neg=0, invalid=96777 0211: dt=124.416000, rms=0.550 (0.253%), neg=0, invalid=96777 0212: dt=20.736000, rms=0.549 (0.126%), neg=0, invalid=96777 0213: dt=145.152000, rms=0.548 (0.185%), neg=0, invalid=96777 0214: dt=36.288000, rms=0.548 (0.165%), neg=0, invalid=96777 0215: dt=82.944000, rms=0.547 (0.060%), neg=0, invalid=96777 0216: dt=36.288000, rms=0.546 (0.134%), neg=0, invalid=96777 0217: dt=20.736000, rms=0.546 (0.019%), neg=0, invalid=96777 0218: dt=20.736000, rms=0.546 (0.038%), neg=0, invalid=96777 0219: dt=20.736000, rms=0.546 (0.052%), neg=0, invalid=96777 0220: dt=20.736000, rms=0.546 (0.070%), neg=0, invalid=96777 0221: dt=20.736000, rms=0.545 (0.093%), neg=0, invalid=96777 0222: dt=20.736000, rms=0.544 (0.108%), neg=0, invalid=96777 0223: dt=20.736000, rms=0.544 (0.029%), neg=0, invalid=96777 0224: dt=20.736000, rms=0.544 (0.043%), neg=0, invalid=96777 0225: dt=20.736000, rms=0.544 (0.024%), neg=0, invalid=96777 0226: dt=10.368000, rms=0.544 (0.010%), neg=0, invalid=96777 0227: dt=6.480000, rms=0.544 (0.010%), neg=0, invalid=96777 0228: dt=0.567000, rms=0.544 (-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=0.549, neg=0, invalid=96777 0229: dt=11.200000, rms=0.546 (0.641%), neg=0, invalid=96777 0230: dt=11.200000, rms=0.543 (0.567%), neg=0, invalid=96777 0231: dt=44.800000, rms=0.532 (1.884%), neg=0, invalid=96777 0232: dt=44.800000, rms=0.524 (1.527%), neg=0, invalid=96777 0233: dt=11.200000, rms=0.523 (0.261%), neg=0, invalid=96777 0234: dt=44.800000, rms=0.518 (0.900%), neg=0, invalid=96777 0235: dt=8.648649, rms=0.517 (0.223%), neg=0, invalid=96777 0236: dt=11.200000, rms=0.516 (0.281%), neg=0, invalid=96777 0237: dt=32.000000, rms=0.513 (0.424%), neg=0, invalid=96777 0238: dt=12.000000, rms=0.512 (0.255%), neg=0, invalid=96777 0239: dt=11.200000, rms=0.511 (0.132%), neg=0, invalid=96777 0240: dt=11.200000, rms=0.510 (0.207%), neg=0, invalid=96777 0241: dt=11.200000, rms=0.510 (0.102%), neg=0, invalid=96777 0242: dt=38.400000, rms=0.508 (0.305%), neg=0, invalid=96777 0243: dt=6.400000, rms=0.507 (0.194%), neg=0, invalid=96777 0244: dt=44.800000, rms=0.505 (0.492%), neg=0, invalid=96777 0245: dt=11.200000, rms=0.504 (0.112%), neg=0, invalid=96777 0246: dt=128.000000, rms=0.501 (0.531%), neg=0, invalid=96777 0247: dt=8.265060, rms=0.499 (0.403%), neg=0, invalid=96777 0248: dt=11.200000, rms=0.499 (0.168%), neg=0, invalid=96777 0249: dt=11.200000, rms=0.498 (0.083%), neg=0, invalid=96777 0250: dt=11.200000, rms=0.498 (0.049%), neg=0, invalid=96777 0251: dt=11.200000, rms=0.498 (0.076%), neg=0, invalid=96777 0252: dt=11.200000, rms=0.497 (0.102%), neg=0, invalid=96777 0253: dt=11.200000, rms=0.496 (0.134%), neg=0, invalid=96777 0254: dt=11.200000, rms=0.496 (0.178%), neg=0, invalid=96777 0255: dt=11.200000, rms=0.494 (0.215%), neg=0, invalid=96777 0256: dt=11.200000, rms=0.493 (0.216%), neg=0, invalid=96777 0257: dt=11.200000, rms=0.492 (0.226%), neg=0, invalid=96777 0258: dt=11.200000, rms=0.491 (0.241%), neg=0, invalid=96777 0259: dt=11.200000, rms=0.490 (0.239%), neg=0, invalid=96777 0260: dt=11.200000, rms=0.489 (0.224%), neg=0, invalid=96777 0261: dt=11.200000, rms=0.488 (0.225%), neg=0, invalid=96777 0262: dt=11.200000, rms=0.487 (0.212%), neg=0, invalid=96777 0263: dt=11.200000, rms=0.486 (0.197%), neg=0, invalid=96777 0264: dt=11.200000, rms=0.485 (0.168%), neg=0, invalid=96777 0265: dt=11.200000, rms=0.484 (0.159%), neg=0, invalid=96777 0266: dt=11.200000, rms=0.483 (0.142%), neg=0, invalid=96777 0267: dt=11.200000, rms=0.483 (0.138%), neg=0, invalid=96777 0268: dt=11.200000, rms=0.482 (0.110%), neg=0, invalid=96777 0269: dt=11.200000, rms=0.482 (0.109%), neg=0, invalid=96777 0270: dt=11.200000, rms=0.481 (0.108%), neg=0, invalid=96777 0271: dt=11.200000, rms=0.481 (0.098%), neg=0, invalid=96777 0272: dt=11.200000, rms=0.480 (0.091%), neg=0, invalid=96777 0273: dt=11.200000, rms=0.480 (0.077%), neg=0, invalid=96777 0274: dt=11.200000, rms=0.480 (0.065%), neg=0, invalid=96777 0275: dt=11.200000, rms=0.479 (0.070%), neg=0, invalid=96777 0276: dt=11.200000, rms=0.479 (0.081%), neg=0, invalid=96777 0277: dt=11.200000, rms=0.479 (0.059%), neg=0, invalid=96777 0278: dt=11.200000, rms=0.478 (0.051%), neg=0, invalid=96777 0279: dt=11.200000, rms=0.478 (0.046%), neg=0, invalid=96777 0280: dt=11.200000, rms=0.478 (0.053%), neg=0, invalid=96777 0281: dt=11.200000, rms=0.478 (0.058%), neg=0, invalid=96777 0282: dt=11.200000, rms=0.477 (0.038%), neg=0, invalid=96777 0283: dt=11.200000, rms=0.477 (0.057%), neg=0, invalid=96777 0284: dt=11.200000, rms=0.477 (0.052%), neg=0, invalid=96777 0285: dt=11.200000, rms=0.477 (0.038%), neg=0, invalid=96777 0286: dt=11.200000, rms=0.477 (0.024%), neg=0, invalid=96777 0287: dt=11.200000, rms=0.476 (0.038%), neg=0, invalid=96777 0288: dt=11.200000, rms=0.476 (0.057%), neg=0, invalid=96777 0289: dt=11.200000, rms=0.476 (0.046%), neg=0, invalid=96777 0290: dt=11.200000, rms=0.476 (0.030%), neg=0, invalid=96777 0291: dt=11.200000, rms=0.476 (0.022%), neg=0, invalid=96777 0292: dt=11.200000, rms=0.476 (0.036%), neg=0, invalid=96777 0293: dt=11.200000, rms=0.475 (0.035%), neg=0, invalid=96777 0294: dt=11.200000, rms=0.475 (0.027%), neg=0, invalid=96777 0295: dt=11.200000, rms=0.475 (0.032%), neg=0, invalid=96777 0296: dt=11.200000, rms=0.475 (0.028%), neg=0, invalid=96777 0297: dt=11.200000, rms=0.475 (0.037%), neg=0, invalid=96777 0298: dt=11.200000, rms=0.475 (0.018%), neg=0, invalid=96777 0299: dt=11.200000, rms=0.475 (0.022%), neg=0, invalid=96777 0300: dt=11.200000, rms=0.474 (0.027%), neg=0, invalid=96777 0301: dt=11.200000, rms=0.474 (0.025%), neg=0, invalid=96777 0302: dt=11.200000, rms=0.474 (0.016%), neg=0, invalid=96777 0303: dt=11.200000, rms=0.474 (0.005%), neg=0, invalid=96777 0304: dt=11.200000, rms=0.474 (0.010%), neg=0, invalid=96777 0305: dt=11.200000, rms=0.474 (0.004%), neg=0, invalid=96777 0306: dt=11.200000, rms=0.474 (0.008%), neg=0, invalid=96777 0307: dt=11.200000, rms=0.474 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=96777 0308: dt=32.000000, rms=0.472 (0.367%), neg=0, invalid=96777 0309: dt=11.200000, rms=0.472 (0.099%), neg=0, invalid=96777 0310: dt=32.000000, rms=0.471 (0.105%), neg=0, invalid=96777 0311: dt=6.400000, rms=0.471 (0.027%), neg=0, invalid=96777 0312: dt=6.400000, rms=0.471 (0.027%), neg=0, invalid=96777 0313: dt=6.400000, rms=0.471 (0.021%), neg=0, invalid=96777 0314: dt=6.400000, rms=0.471 (0.017%), neg=0, invalid=96777 0315: dt=44.800000, rms=0.471 (0.054%), neg=0, invalid=96777 0316: dt=6.400000, rms=0.471 (0.012%), neg=0, invalid=96777 0317: dt=6.400000, rms=0.471 (0.005%), neg=0, invalid=96777 0318: dt=6.400000, rms=0.471 (-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=0.495, neg=0, invalid=96777 0319: dt=0.000000, rms=0.495 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=96777 0320: dt=0.000000, rms=0.495 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.544, neg=0, invalid=96777 0321: dt=1.555556, rms=0.538 (1.150%), neg=0, invalid=96777 0322: dt=0.448000, rms=0.537 (0.040%), neg=0, invalid=96777 0323: dt=0.448000, rms=0.537 (-0.019%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.537, neg=0, invalid=96777 0324: dt=0.931034, rms=0.537 (0.147%), neg=0, invalid=96777 0325: dt=0.256000, rms=0.537 (0.006%), neg=0, invalid=96777 0326: dt=0.256000, rms=0.537 (-0.003%), 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=0.490, neg=0, invalid=96777 0327: dt=0.150330, rms=0.486 (0.954%), neg=0, invalid=96777 0328: dt=0.132386, rms=0.483 (0.605%), neg=0, invalid=96777 0329: dt=0.320000, rms=0.477 (1.110%), neg=0, invalid=96777 0330: dt=0.112000, rms=0.477 (0.192%), neg=0, invalid=96777 0331: dt=0.112000, rms=0.476 (0.168%), neg=0, invalid=96777 0332: dt=0.112000, rms=0.475 (0.145%), neg=0, invalid=96777 0333: dt=0.112000, rms=0.474 (0.125%), neg=0, invalid=96777 0334: dt=0.320000, rms=0.473 (0.319%), neg=0, invalid=96777 0335: dt=0.112000, rms=0.473 (0.075%), neg=0, invalid=96777 0336: dt=0.448000, rms=0.471 (0.276%), neg=0, invalid=96777 0337: dt=0.320000, rms=0.471 (0.135%), neg=0, invalid=96777 0338: dt=0.112000, rms=0.471 (0.037%), neg=0, invalid=96777 0339: dt=0.112000, rms=0.470 (0.039%), neg=0, invalid=96777 0340: dt=0.112000, rms=0.470 (0.066%), neg=0, invalid=96777 0341: dt=0.112000, rms=0.470 (0.029%), neg=0, invalid=96777 0342: dt=0.112000, rms=0.470 (0.058%), neg=0, invalid=96777 0343: dt=0.112000, rms=0.469 (0.024%), neg=0, invalid=96777 0344: dt=0.112000, rms=0.469 (0.027%), neg=0, invalid=96777 0345: dt=0.112000, rms=0.469 (0.040%), neg=0, invalid=96777 0346: dt=0.112000, rms=0.469 (0.068%), neg=0, invalid=96777 0347: dt=0.112000, rms=0.469 (0.073%), neg=0, invalid=96777 0348: dt=0.112000, rms=0.468 (0.078%), neg=0, invalid=96777 0349: dt=0.112000, rms=0.468 (0.085%), neg=0, invalid=96777 0350: dt=0.028000, rms=0.468 (0.006%), neg=0, invalid=96777 0351: dt=0.028000, rms=0.468 (0.003%), neg=0, invalid=96777 0352: dt=0.112000, rms=0.468 (0.005%), neg=0, invalid=96777 0353: dt=0.112000, rms=0.468 (0.011%), neg=0, invalid=96777 0354: dt=0.320000, rms=0.468 (0.020%), neg=0, invalid=96777 0355: dt=0.112000, rms=0.468 (0.008%), neg=0, invalid=96777 0356: dt=0.112000, rms=0.467 (0.009%), neg=0, invalid=96777 0357: dt=0.112000, rms=0.467 (0.014%), neg=0, invalid=96777 0358: dt=0.112000, rms=0.467 (0.016%), neg=0, invalid=96777 0359: dt=0.056000, rms=0.467 (0.002%), neg=0, invalid=96777 0360: dt=0.056000, rms=0.467 (0.007%), neg=0, invalid=96777 0361: dt=0.056000, rms=0.467 (0.007%), neg=0, invalid=96777 0362: dt=0.056000, rms=0.467 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=96777 0363: dt=0.112000, rms=0.466 (0.230%), neg=0, invalid=96777 0364: dt=0.112000, rms=0.465 (0.173%), neg=0, invalid=96777 0365: dt=0.112000, rms=0.465 (0.132%), neg=0, invalid=96777 0366: dt=0.448000, rms=0.463 (0.384%), neg=0, invalid=96777 0367: dt=0.028000, rms=0.463 (0.002%), neg=0, invalid=96777 0368: dt=0.028000, rms=0.463 (0.001%), neg=0, invalid=96777 0369: dt=0.028000, rms=0.463 (0.007%), neg=0, invalid=96777 0370: dt=0.028000, rms=0.463 (0.007%), neg=0, invalid=96777 0371: dt=0.028000, rms=0.463 (0.011%), neg=0, invalid=96777 0372: dt=0.028000, rms=0.463 (0.010%), neg=0, invalid=96777 0373: dt=0.112000, rms=0.463 (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=0.461, neg=0, invalid=96777 0374: dt=0.000000, rms=0.461 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=96777 0375: dt=295.936000, rms=0.460 (0.109%), neg=0, invalid=96777 0376: dt=55.488000, rms=0.460 (0.029%), neg=0, invalid=96777 0377: dt=55.488000, rms=0.460 (0.019%), neg=0, invalid=96777 0378: dt=55.488000, rms=0.460 (0.015%), neg=0, invalid=96777 0379: dt=55.488000, rms=0.460 (0.017%), neg=0, invalid=96777 0380: dt=55.488000, rms=0.460 (0.033%), neg=0, invalid=96777 0381: dt=55.488000, rms=0.460 (0.031%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.460, neg=0, invalid=96777 0382: dt=36.288000, rms=0.459 (0.061%), neg=0, invalid=96777 0383: dt=82.944000, rms=0.459 (0.098%), neg=0, invalid=96777 0384: dt=62.208000, rms=0.458 (0.105%), neg=0, invalid=96777 0385: dt=25.920000, rms=0.458 (0.068%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0386: dt=25.920000, rms=0.458 (0.039%), neg=0, invalid=96777 0387: dt=25.920000, rms=0.458 (0.055%), neg=0, invalid=96777 0388: dt=25.920000, rms=0.457 (0.067%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0389: dt=25.920000, rms=0.457 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0390: dt=25.920000, rms=0.457 (0.032%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=96777 0391: dt=82.944000, rms=0.455 (0.416%), neg=0, invalid=96777 0392: dt=25.920000, rms=0.454 (0.139%), neg=0, invalid=96777 0393: dt=25.920000, rms=0.454 (0.074%), neg=0, invalid=96777 0394: dt=25.920000, rms=0.454 (0.090%), neg=0, invalid=96777 0395: dt=25.920000, rms=0.453 (0.105%), neg=0, invalid=96777 0396: dt=25.920000, rms=0.453 (0.102%), neg=0, invalid=96777 0397: dt=25.920000, rms=0.452 (0.123%), neg=0, invalid=96777 0398: dt=25.920000, rms=0.452 (0.109%), neg=0, invalid=96777 0399: dt=25.920000, rms=0.452 (0.018%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0400: dt=25.600000, rms=0.450 (0.355%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0401: dt=44.800000, rms=0.448 (0.534%), neg=0, invalid=96777 0402: dt=8.671329, rms=0.447 (0.223%), neg=0, invalid=96777 0403: dt=8.671329, rms=0.446 (0.124%), neg=0, invalid=96777 0404: dt=8.671329, rms=0.446 (0.124%), neg=0, invalid=96777 0405: dt=8.671329, rms=0.445 (0.223%), neg=0, invalid=96777 0406: dt=8.671329, rms=0.444 (0.245%), neg=0, invalid=96777 0407: dt=8.671329, rms=0.443 (0.269%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0408: dt=8.671329, rms=0.442 (0.237%), neg=0, invalid=96777 0409: dt=8.671329, rms=0.441 (0.220%), neg=0, invalid=96777 0410: dt=8.671329, rms=0.440 (0.209%), neg=0, invalid=96777 0411: dt=8.671329, rms=0.439 (0.171%), neg=0, invalid=96777 0412: dt=8.671329, rms=0.438 (0.160%), neg=0, invalid=96777 0413: dt=8.671329, rms=0.438 (0.150%), neg=0, invalid=96777 0414: dt=8.671329, rms=0.437 (0.160%), neg=0, invalid=96777 0415: dt=8.671329, rms=0.436 (0.162%), neg=0, invalid=96777 0416: dt=8.671329, rms=0.435 (0.155%), neg=0, invalid=96777 0417: dt=8.671329, rms=0.435 (0.142%), neg=0, invalid=96777 0418: dt=8.671329, rms=0.434 (0.119%), neg=0, invalid=96777 0419: dt=8.671329, rms=0.434 (0.108%), neg=0, invalid=96777 0420: dt=11.200000, rms=0.434 (0.020%), neg=0, invalid=96777 0421: dt=11.200000, rms=0.434 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=96777 0422: dt=38.400000, rms=0.431 (0.636%), neg=0, invalid=96777 0423: dt=9.600000, rms=0.430 (0.191%), neg=0, invalid=96777 0424: dt=9.600000, rms=0.430 (0.088%), neg=0, invalid=96777 0425: dt=9.600000, rms=0.429 (0.096%), neg=0, invalid=96777 0426: dt=9.600000, rms=0.429 (0.143%), neg=0, invalid=96777 0427: dt=9.600000, rms=0.428 (0.115%), neg=0, invalid=96777 0428: dt=9.600000, rms=0.428 (0.143%), neg=0, invalid=96777 0429: dt=9.600000, rms=0.427 (0.082%), neg=0, invalid=96777 0430: dt=9.600000, rms=0.427 (0.088%), neg=0, invalid=96777 0431: dt=9.600000, rms=0.427 (0.038%), neg=0, invalid=96777 0432: dt=6.400000, rms=0.427 (0.017%), neg=0, invalid=96777 0433: dt=6.400000, rms=0.427 (0.013%), neg=0, invalid=96777 0434: dt=6.400000, rms=0.427 (0.024%), neg=0, invalid=96777 0435: dt=6.400000, rms=0.427 (0.005%), neg=0, invalid=96777 0436: dt=6.400000, rms=0.426 (0.020%), neg=0, invalid=96777 0437: dt=6.400000, rms=0.426 (0.021%), neg=0, invalid=96777 0438: dt=6.400000, rms=0.426 (0.026%), neg=0, invalid=96777 0439: dt=6.400000, rms=0.426 (0.026%), neg=0, invalid=96777 0440: dt=6.400000, rms=0.426 (0.027%), neg=0, invalid=96777 0441: dt=6.400000, rms=0.426 (0.030%), neg=0, invalid=96777 0442: dt=6.400000, rms=0.426 (0.029%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.431, neg=0, invalid=96777 0443: dt=0.000000, rms=0.431 (0.001%), neg=0, invalid=96777 0444: dt=0.000000, rms=0.431 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.431, neg=0, invalid=96777 0445: dt=2.304000, rms=0.431 (0.021%), neg=0, invalid=96777 0446: dt=1.008000, rms=0.431 (0.005%), neg=0, invalid=96777 0447: dt=1.008000, rms=0.431 (0.007%), neg=0, invalid=96777 0448: dt=1.008000, rms=0.431 (-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=0.440, neg=0, invalid=96777 0449: dt=0.500000, rms=0.440 (0.044%), neg=0, invalid=96777 0450: dt=0.256000, rms=0.440 (0.006%), neg=0, invalid=96777 0451: dt=0.256000, rms=0.440 (-0.005%), 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 = 1 after 0 iterations, nbhd size=0, neg = 0 0452: dt=1.280000, rms=0.439 (0.149%), neg=0, invalid=96777 0453: dt=0.007000, rms=0.439 (0.000%), neg=0, invalid=96777 0454: dt=0.007000, rms=0.439 (-0.001%), 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=0.429, neg=0, invalid=96777 iter 0, gcam->neg = 491 after 21 iterations, nbhd size=2, neg = 0 0455: dt=1.695409, rms=0.402 (6.248%), neg=0, invalid=96777 0456: dt=0.000188, rms=0.402 (-0.003%), neg=0, invalid=96777 0457: dt=0.000188, rms=0.402 (0.000%), neg=0, invalid=96777 0458: dt=0.000188, rms=0.402 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 0459: dt=0.000438, rms=0.402 (0.000%), neg=0, invalid=96777 0460: dt=0.000000, rms=0.402 (0.001%), neg=0, invalid=96777 0461: dt=0.000000, rms=0.402 (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=0.391, neg=0, invalid=96777 0462: dt=0.000000, rms=0.392 (-0.254%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0463: dt=27.744000, rms=0.392 (0.002%), neg=0, invalid=96777 0464: dt=6.936000, rms=0.392 (0.000%), neg=0, invalid=96777 0465: dt=6.936000, rms=0.392 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0466: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0467: dt=36.288000, rms=0.392 (0.022%), neg=0, invalid=96777 0468: dt=36.288000, rms=0.392 (0.008%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0469: dt=36.288000, rms=0.392 (0.010%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0470: dt=36.288000, rms=0.392 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=2, neg = 0 0471: dt=8.000000, rms=0.392 (0.033%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0472: dt=2.800000, rms=0.392 (0.007%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 18 iterations, nbhd size=2, neg = 0 0473: dt=2.800000, rms=0.392 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 38 iterations, nbhd size=4, neg = 0 0474: dt=2.800000, rms=0.392 (-0.020%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 iter 0, gcam->neg = 39 after 117 iterations, nbhd size=4, neg = 0 0475: dt=32.000000, rms=0.391 (0.336%), neg=0, invalid=96777 iter 0, gcam->neg = 22 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.003 (15.808%) 0476: dt=19.200000, rms=0.390 (0.146%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 33 iterations, nbhd size=4, neg = 0 0477: dt=19.200000, rms=0.390 (0.121%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 37 iterations, nbhd size=4, neg = 0 0478: dt=19.200000, rms=0.389 (0.123%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 18 iterations, nbhd size=2, neg = 0 0479: dt=19.200000, rms=0.389 (0.193%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 31 iterations, nbhd size=3, neg = 0 0480: dt=19.200000, rms=0.388 (0.191%), neg=0, invalid=96777 iter 0, gcam->neg = 31 after 49 iterations, nbhd size=4, neg = 0 0481: dt=19.200000, rms=0.387 (0.112%), neg=0, invalid=96777 iter 0, gcam->neg = 53 after 200 iterations, nbhd size=2, neg = 6 starting rms=0.004, neg=6, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 6, delta 6, rms=0.003 (21.731%) 0482: dt=19.200000, rms=0.387 (0.066%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 3, delta 3, rms=0.003 (13.466%) 0483: dt=11.200000, rms=0.387 (0.076%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 13 iterations, nbhd size=1, neg = 0 0484: dt=19.200000, rms=0.387 (0.081%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000188: new neg 0, old_neg 2, delta 2, rms=0.002 (41.275%) 0485: dt=38.400000, rms=0.386 (0.092%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... iter 1, dt=0.000039: new neg 0, old_neg 3, delta 3, rms=0.002 (25.158%) 0486: dt=38.400000, rms=0.386 (0.121%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000156: new neg 0, old_neg 2, delta 2, rms=0.002 (42.482%) 0487: dt=32.000000, rms=0.385 (0.058%), neg=0, invalid=96777 0488: dt=32.000000, rms=0.385 (0.042%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0489: dt=32.000000, rms=0.385 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 35 after 200 iterations, nbhd size=2, neg = 6 starting rms=0.005, neg=6, removing folds in lattice.... iter 1, dt=0.000039: new neg 0, old_neg 6, delta 6, rms=0.003 (49.959%) 0490: dt=32.000000, rms=0.385 (0.038%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 42 iterations, nbhd size=3, neg = 0 0491: dt=32.000000, rms=0.385 (0.019%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 2, delta 2, rms=0.002 (49.031%) 0492: dt=2.000000, rms=0.388 (0.015%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 23 iterations, nbhd size=4, neg = 0 0493: dt=1.008000, rms=0.388 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 32 iterations, nbhd size=4, neg = 0 0494: dt=1.008000, rms=0.388 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 23 iterations, nbhd size=3, neg = 0 0495: dt=1.008000, rms=0.388 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 35 iterations, nbhd size=4, neg = 0 0496: dt=1.008000, rms=0.388 (-0.022%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 iter 0, gcam->neg = 18 after 9 iterations, nbhd size=1, neg = 0 0497: dt=11.520000, rms=0.386 (0.302%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 42 iterations, nbhd size=4, neg = 0 0498: dt=2.880000, rms=0.386 (0.056%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 28 iterations, nbhd size=3, neg = 0 0499: dt=2.880000, rms=0.386 (0.061%), neg=0, invalid=96777 iter 0, gcam->neg = 26 after 36 iterations, nbhd size=3, neg = 0 0500: dt=2.880000, rms=0.386 (0.079%), neg=0, invalid=96777 iter 0, gcam->neg = 35 after 41 iterations, nbhd size=4, neg = 0 0501: dt=2.880000, rms=0.385 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 38 after 50 iterations, nbhd size=4, neg = 0 0502: dt=2.880000, rms=0.385 (0.080%), neg=0, invalid=96777 iter 0, gcam->neg = 53 after 50 iterations, nbhd size=1, neg = 0 0503: dt=2.880000, rms=0.385 (0.084%), neg=0, invalid=96777 iter 0, gcam->neg = 53 after 64 iterations, nbhd size=2, neg = 0 0504: dt=2.880000, rms=0.384 (0.114%), neg=0, invalid=96777 iter 0, gcam->neg = 57 after 53 iterations, nbhd size=4, neg = 0 0505: dt=2.880000, rms=0.384 (0.105%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 17 iterations, nbhd size=2, neg = 0 0506: dt=3.456000, rms=0.384 (0.029%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 0507: dt=0.000000, rms=0.389 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 0508: dt=0.000000, rms=0.389 (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=0.381, neg=0, invalid=96777 iter 0, gcam->neg = 336 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0509: dt=0.831800, 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 iter 0, gcam->neg = 583 after 24 iterations, nbhd size=2, neg = 0 0510: dt=1.024000, rms=0.364 (4.419%), neg=0, invalid=96777 0511: dt=0.000000, rms=0.364 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 83 after 7 iterations, nbhd size=1, neg = 0 0512: dt=0.050000, rms=0.364 (-0.224%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 3 hours, 42 minutes and 33 seconds. #-------------------------------------- #@# CA Reg Inv Fri Sep 18 16:37:53 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri Sep 18 16:39:16 EDT 2015 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11328081 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 32 seconds. #-------------------------------------- #@# SkullLTA Fri Sep 18 16:40:48 EDT 2015 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /share/apps/freesurfer-5.3.0/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 '/share/apps/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (51, 21, 36) --> (205, 199, 234) using (102, 80, 135) as brain centroid... mean wm in atlas = 126, using box (83,58,111) --> (120, 101,159) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.125 0.026 -0.048 -15.419; -0.028 1.257 -0.035 0.428; 0.066 0.041 1.076 -46.180; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.125 0.026 -0.048 -15.419; -0.028 1.257 -0.035 0.428; 0.066 0.041 1.076 -46.180; 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=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.125 0.071 -0.015 -24.287; -0.068 1.226 -0.105 19.659; 0.027 0.118 1.013 -40.832; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.125 0.071 -0.015 -24.287; -0.068 1.226 -0.105 19.659; 0.027 0.118 1.013 -40.832; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.123 0.083 0.000 -27.783; -0.077 1.227 -0.105 20.331; 0.009 0.117 1.014 -38.526; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.123 0.082 -0.008 -26.598; -0.077 1.227 -0.105 19.863; 0.018 0.118 1.011 -38.970; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12330 0.08215 -0.00781 -26.59829; -0.07717 1.22713 -0.10526 19.86253; 0.01776 0.11781 1.01146 -38.96956; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.12330 0.08215 -0.00781 -26.59829; -0.07717 1.22713 -0.10526 19.86253; 0.01776 0.11781 1.01146 -38.96956; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.123 0.082 -0.008 -26.598; -0.077 1.227 -0.105 19.863; 0.018 0.118 1.011 -38.970; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-3.9) transform before final EM align: 1.123 0.082 -0.008 -26.598; -0.077 1.227 -0.105 19.863; 0.018 0.118 1.011 -38.970; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12330 0.08215 -0.00781 -26.59829; -0.07717 1.22713 -0.10526 19.86253; 0.01776 0.11781 1.01146 -38.96956; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.12330 0.08215 -0.00781 -26.59829; -0.07717 1.22713 -0.10526 19.86253; 0.01776 0.11781 1.01146 -38.96956; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.2 tol 0.000000 final transform: 1.123 0.082 -0.008 -26.598; -0.077 1.227 -0.105 19.863; 0.018 0.118 1.011 -38.970; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 26 minutes and 32 seconds. #-------------------------------------- #@# SubCort Seg Fri Sep 18 17:07:21 EDT 2015 mri_ca_label -align norm.mgz transforms/talairach.m3z /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname compute-0-4.local machine x86_64 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori cd /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.09459 (17) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (295 voxels, overlap=0.733) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (295 voxels, peak = 18), gca=17.7 gca peak = 0.14982 (20) mri peak = 0.12979 (18) Right_Lateral_Ventricle (43): linear fit = 0.73 x + 0.0 (293 voxels, overlap=0.350) Right_Lateral_Ventricle (43): linear fit = 0.73 x + 0.0 (293 voxels, peak = 14), gca=14.5 gca peak = 0.28003 (97) mri peak = 0.13559 (101) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (295 voxels, overlap=0.972) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (295 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.13392 (104) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (341 voxels, overlap=0.730) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (341 voxels, peak = 100), gca=100.3 gca peak = 0.27536 (62) mri peak = 0.09703 (66) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (634 voxels, overlap=0.833) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (634 voxels, peak = 65), gca=64.8 gca peak = 0.32745 (63) mri peak = 0.08626 (64) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (659 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (659 voxels, peak = 63), gca=63.0 gca peak = 0.08597 (105) mri peak = 0.09879 (110) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (31933 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (31933 voxels, peak = 110), gca=109.7 gca peak = 0.09209 (106) mri peak = 0.08616 (110) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (35313 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (35313 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.04550 (62) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28117 voxels, overlap=0.894) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28117 voxels, peak = 62), gca=62.1 gca peak = 0.08598 (64) mri peak = 0.04446 (63) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (30013 voxels, overlap=0.902) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (30013 voxels, peak = 62), gca=61.8 gca peak = 0.24164 (71) mri peak = 0.11658 (81) Right_Caudate (50): linear fit = 1.11 x + 0.0 (609 voxels, overlap=0.602) Right_Caudate (50): linear fit = 1.11 x + 0.0 (609 voxels, peak = 78), gca=78.5 gca peak = 0.18227 (75) mri peak = 0.10822 (84) Left_Caudate (11): linear fit = 1.02 x + 0.0 (725 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.02 x + 0.0 (725 voxels, peak = 77), gca=76.9 gca peak = 0.10629 (62) mri peak = 0.05300 (65) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (20841 voxels, overlap=0.948) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (20841 voxels, peak = 67), gca=66.7 gca peak = 0.11668 (59) mri peak = 0.05284 (64) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (20925 voxels, overlap=0.812) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (20925 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.10493 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5613 voxels, overlap=0.815) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5613 voxels, peak = 92), gca=92.0 gca peak = 0.16819 (86) mri peak = 0.09965 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4640 voxels, overlap=0.592) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4640 voxels, peak = 92), gca=91.6 gca peak = 0.41688 (64) mri peak = 0.07809 (69) Left_Amygdala (18): linear fit = 1.05 x + 0.0 (396 voxels, overlap=1.041) Left_Amygdala (18): linear fit = 1.05 x + 0.0 (396 voxels, peak = 68), gca=67.5 gca peak = 0.42394 (62) mri peak = 0.08540 (59) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (208 voxels, overlap=1.041) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (208 voxels, peak = 58), gca=58.0 gca peak = 0.10041 (96) mri peak = 0.07405 (100) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3699 voxels, overlap=0.715) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3699 voxels, peak = 98), gca=98.4 gca peak = 0.13978 (88) mri peak = 0.07095 (95) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3883 voxels, overlap=0.873) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3883 voxels, peak = 94), gca=93.7 gca peak = 0.08514 (81) mri peak = 0.06872 (80) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1913 voxels, overlap=0.932) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1913 voxels, peak = 84), gca=83.8 gca peak = 0.09624 (82) mri peak = 0.06355 (80) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1571 voxels, overlap=0.979) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1571 voxels, peak = 82), gca=81.6 gca peak = 0.07543 (88) mri peak = 0.06917 (93) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11184 voxels, overlap=0.733) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11184 voxels, peak = 94), gca=93.7 gca peak = 0.12757 (95) mri peak = 0.08799 (99) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (993 voxels, overlap=0.649) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (993 voxels, peak = 102), gca=102.1 gca peak = 0.17004 (92) mri peak = 0.07610 (107) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1001 voxels, overlap=0.702) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1001 voxels, peak = 101), gca=100.7 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.16180 (18) Fourth_Ventricle (15): linear fit = 0.64 x + 0.0 (115 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.64 x + 0.0 (115 voxels, peak = 15), gca=14.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.69 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.21595 (18) mri peak = 0.09459 (17) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (295 voxels, overlap=0.973) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (295 voxels, peak = 18), gca=17.7 gca peak = 0.22747 (15) mri peak = 0.12979 (18) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (293 voxels, overlap=0.851) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (293 voxels, peak = 15), gca=15.4 gca peak = 0.30534 (100) mri peak = 0.13559 (101) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (295 voxels, overlap=0.821) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (295 voxels, peak = 100), gca=100.5 gca peak = 0.18300 (100) mri peak = 0.13392 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (341 voxels, overlap=0.885) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (341 voxels, peak = 100), gca=100.0 gca peak = 0.26329 (65) mri peak = 0.09703 (66) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (634 voxels, overlap=0.988) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (634 voxels, peak = 65), gca=65.0 gca peak = 0.31612 (63) mri peak = 0.08626 (64) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (659 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (659 voxels, peak = 63), gca=63.0 gca peak = 0.08168 (110) mri peak = 0.09879 (110) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31933 voxels, overlap=0.747) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31933 voxels, peak = 110), gca=110.0 gca peak = 0.08583 (111) mri peak = 0.08616 (110) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35313 voxels, overlap=0.753) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35313 voxels, peak = 111), gca=111.0 gca peak = 0.07862 (62) mri peak = 0.04550 (62) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28117 voxels, overlap=0.930) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28117 voxels, peak = 61), gca=61.1 gca peak = 0.09119 (62) mri peak = 0.04446 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (30013 voxels, overlap=0.948) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (30013 voxels, peak = 64), gca=63.5 gca peak = 0.22081 (81) mri peak = 0.11658 (81) Right_Caudate (50): linear fit = 0.99 x + 0.0 (609 voxels, overlap=1.004) Right_Caudate (50): linear fit = 0.99 x + 0.0 (609 voxels, peak = 80), gca=79.8 gca peak = 0.18185 (77) mri peak = 0.10822 (84) Left_Caudate (11): linear fit = 1.00 x + 0.0 (725 voxels, overlap=1.002) Left_Caudate (11): linear fit = 1.00 x + 0.0 (725 voxels, peak = 77), gca=77.0 gca peak = 0.09845 (66) mri peak = 0.05300 (65) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (20841 voxels, overlap=0.998) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (20841 voxels, peak = 65), gca=65.0 gca peak = 0.12109 (64) mri peak = 0.05284 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20925 voxels, overlap=0.987) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20925 voxels, peak = 66), gca=65.6 gca peak = 0.17465 (92) mri peak = 0.10493 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5613 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5613 voxels, peak = 92), gca=91.5 gca peak = 0.16064 (92) mri peak = 0.09965 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4640 voxels, overlap=0.975) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4640 voxels, peak = 92), gca=91.5 gca peak = 0.30715 (67) mri peak = 0.07809 (69) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (396 voxels, overlap=1.036) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (396 voxels, peak = 68), gca=68.0 gca peak = 0.42272 (58) mri peak = 0.08540 (59) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (208 voxels, overlap=1.027) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (208 voxels, peak = 58), gca=58.0 gca peak = 0.09900 (97) mri peak = 0.07405 (100) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3699 voxels, overlap=0.811) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3699 voxels, peak = 99), gca=99.4 gca peak = 0.09644 (91) mri peak = 0.07095 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3883 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3883 voxels, peak = 91), gca=91.5 gca peak = 0.08482 (85) mri peak = 0.06872 (80) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1913 voxels, overlap=0.998) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1913 voxels, peak = 84), gca=83.7 gca peak = 0.10657 (82) mri peak = 0.06355 (80) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1571 voxels, overlap=0.987) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1571 voxels, peak = 81), gca=80.8 gca peak = 0.06520 (88) mri peak = 0.06917 (93) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11184 voxels, overlap=0.854) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11184 voxels, peak = 87), gca=86.7 gca peak = 0.12361 (98) mri peak = 0.08799 (99) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (993 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (993 voxels, peak = 98), gca=98.5 gca peak = 0.15683 (101) mri peak = 0.07610 (107) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1001 voxels, overlap=0.913) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1001 voxels, peak = 102), gca=101.5 gca peak = 0.25227 (26) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.32391 (16) mri peak = 0.16180 (18) Fourth_Ventricle (15): linear fit = 0.96 x + 0.0 (115 voxels, overlap=0.730) Fourth_Ventricle (15): linear fit = 0.96 x + 0.0 (115 voxels, peak = 15), gca=15.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.25227 (26) gca peak CSF = 0.21139 (27) gca peak Left_Accumbens_area = 0.37770 (71) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65202 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.32842 (33) gca peak Right_Accumbens_area = 0.26557 (79) gca peak Right_vessel = 0.80912 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (30) gca peak WM_hypointensities = 0.16549 (85) gca peak non_WM_hypointensities = 0.11940 (55) gca peak Optic_Chiasm = 0.34853 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 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 16350 gm and wm labels changed (%18 to gray, %82 to white out of all changed labels) 274 hippocampal voxels changed. 3 amygdala voxels changed. pass 1: 71200 changed. image ll: -2.149, PF=1.000 pass 2: 11173 changed. image ll: -2.147, PF=1.000 pass 3: 3575 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 23 minutes and 23 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/cc_up.lta af1021_recon will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/cc_up.lta reading aseg from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/aseg.auto_noCCseg.mgz reading norm from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/norm.mgz 32006 voxels in left wm, 84205 in right wm, xrange [120, 133] searching rotation angles z=[-9 5], y=[-10 4] searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 global minimum found at slice 129.0, rotations (-2.68, -2.57) final transformation (x=129.0, yr=-2.685, zr=-2.573): 0.998 0.045 -0.047 1.587; -0.045 0.999 0.002 47.595; 0.047 -0.000 0.999 -9.897; 0.000 0.000 0.000 1.000; updating x range to be [126, 131] in xformed coordinates best xformed slice 129 cc center is found at 129 155 168 eigenvectors: 0.000 -0.007 1.000; 0.205 -0.979 -0.007; 0.979 0.205 0.001; error in mid anterior detected - correcting... error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.1 minutes #-------------------------------------- #@# Merge ASeg Fri Sep 18 17:31:48 EDT 2015 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Sep 18 17:31:48 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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... 2842 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 68 (68), valley at 31 (31) csf peak at 10, setting threshold to 48 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 68 (68), valley at 31 (31) csf peak at 10, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 58 seconds. #-------------------------------------------- #@# Mask BFS Fri Sep 18 17:35:48 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1558913 voxels in mask (pct= 9.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Sep 18 17:35:50 EDT 2015 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 (105.0): 104.6 +- 6.2 [80.0 --> 125.0] GM (73.0) : 71.5 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 81.1 setting top of gray matter range to 90.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5040 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5172 filled 759 bright non-wm voxels segmented. 2815 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.67 minutes reading wm segmentation from wm.seg.mgz... 259 voxels added to wm to prevent paths from MTL structures to cortex 1780 additional wm voxels added 0 additional wm voxels added SEG EDIT: 35946 voxels turned on, 40715 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 8 found - 8 modified | TOTAL: 26 pass 2 (xy-): 0 found - 8 modified | TOTAL: 26 pass 1 (yz+): 24 found - 24 modified | TOTAL: 50 pass 2 (yz+): 0 found - 24 modified | TOTAL: 50 pass 1 (yz-): 31 found - 31 modified | TOTAL: 81 pass 2 (yz-): 0 found - 31 modified | TOTAL: 81 pass 1 (xz+): 11 found - 11 modified | TOTAL: 92 pass 2 (xz+): 0 found - 11 modified | TOTAL: 92 pass 1 (xz-): 15 found - 15 modified | TOTAL: 107 pass 2 (xz-): 0 found - 15 modified | TOTAL: 107 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 6 found - 6 modified | TOTAL: 10 pass 2 (+++): 0 found - 6 modified | TOTAL: 10 pass 1 (+++): 9 found - 9 modified | TOTAL: 19 pass 2 (+++): 0 found - 9 modified | TOTAL: 19 pass 1 (+++): 13 found - 13 modified | TOTAL: 32 pass 2 (+++): 0 found - 13 modified | TOTAL: 32 Iteration Number : 1 pass 1 (++): 63 found - 63 modified | TOTAL: 63 pass 2 (++): 0 found - 63 modified | TOTAL: 63 pass 1 (+-): 123 found - 123 modified | TOTAL: 186 pass 2 (+-): 0 found - 123 modified | TOTAL: 186 pass 1 (--): 108 found - 108 modified | TOTAL: 294 pass 2 (--): 0 found - 108 modified | TOTAL: 294 pass 1 (-+): 135 found - 135 modified | TOTAL: 429 pass 2 (-+): 0 found - 135 modified | TOTAL: 429 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 7 found - 7 modified | TOTAL: 9 pass 2 (yz+): 0 found - 7 modified | TOTAL: 9 pass 1 (yz-): 6 found - 6 modified | TOTAL: 15 pass 2 (yz-): 0 found - 6 modified | TOTAL: 15 pass 1 (xz+): 5 found - 5 modified | TOTAL: 20 pass 2 (xz+): 0 found - 5 modified | TOTAL: 20 pass 1 (xz-): 1 found - 1 modified | TOTAL: 21 pass 2 (xz-): 0 found - 1 modified | TOTAL: 21 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 2 found - 2 modified | TOTAL: 5 pass 2 (--): 0 found - 2 modified | TOTAL: 5 pass 1 (-+): 2 found - 2 modified | TOTAL: 7 pass 2 (-+): 0 found - 2 modified | TOTAL: 7 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 597 (out of 529595: 0.112728) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Sep 18 17:38:14 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1362 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (126, 112, 88), TAL = (2.0, -40.0, 16.0) talairach voxel to voxel transform 0.886 -0.021 0.042 15.340; 0.018 0.854 0.029 -6.252; -0.055 -0.032 0.995 34.827; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 112, 88) --> (2.0, -40.0, 16.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, -40.00, 16.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -40.00, 16.00) SRC: (112.34, 93.87, 112.94) search lh wm seed point around talairach space (-16.00, -40.00, 16.00), SRC: (144.23, 94.52, 110.95) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Fri Sep 18 17:39:12 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 3 found - 3 modified | TOTAL: 11 pass 2 (xz+): 0 found - 3 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 254789: 0.005887) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 797 vertices, 889 faces slice 60: 5526 vertices, 5728 faces slice 70: 12871 vertices, 13135 faces slice 80: 21291 vertices, 21628 faces slice 90: 31254 vertices, 31595 faces slice 100: 41085 vertices, 41421 faces slice 110: 51073 vertices, 51413 faces slice 120: 62569 vertices, 62982 faces slice 130: 74831 vertices, 75282 faces slice 140: 86318 vertices, 86660 faces slice 150: 96554 vertices, 96931 faces slice 160: 106040 vertices, 106351 faces slice 170: 114009 vertices, 114302 faces slice 180: 121009 vertices, 121278 faces slice 190: 127640 vertices, 127884 faces slice 200: 132807 vertices, 133000 faces slice 210: 135887 vertices, 135989 faces slice 220: 136234 vertices, 136278 faces slice 230: 136234 vertices, 136278 faces slice 240: 136234 vertices, 136278 faces slice 250: 136234 vertices, 136278 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 136234 voxel in cpt #1: X=-44 [v=136234,e=408834,f=272556] located at (-26.273779, -3.643892, 33.029758) For the whole surface: X=-44 [v=136234,e=408834,f=272556] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Sep 18 17:39:20 EDT 2015 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri Sep 18 17:39:26 EDT 2015 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts avg radius = 46.9 mm, total surface area = 71799 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Sep 18 17:39:54 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.58 (0.00-->6.87) (max @ vno 55345 --> 56522) face area 0.02 +- 0.03 (-0.21-->0.62) scaling brain by 0.302... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.289, avgs=0 005/300: dt: 0.9000, rms radial error=177.030, avgs=0 010/300: dt: 0.9000, rms radial error=176.476, avgs=0 015/300: dt: 0.9000, rms radial error=175.748, avgs=0 020/300: dt: 0.9000, rms radial error=174.917, avgs=0 025/300: dt: 0.9000, rms radial error=174.028, avgs=0 030/300: dt: 0.9000, rms radial error=173.106, avgs=0 035/300: dt: 0.9000, rms radial error=172.167, avgs=0 040/300: dt: 0.9000, rms radial error=171.221, avgs=0 045/300: dt: 0.9000, rms radial error=170.271, avgs=0 050/300: dt: 0.9000, rms radial error=169.322, avgs=0 055/300: dt: 0.9000, rms radial error=168.376, avgs=0 060/300: dt: 0.9000, rms radial error=167.433, avgs=0 065/300: dt: 0.9000, rms radial error=166.497, avgs=0 070/300: dt: 0.9000, rms radial error=165.565, avgs=0 075/300: dt: 0.9000, rms radial error=164.639, avgs=0 080/300: dt: 0.9000, rms radial error=163.717, avgs=0 085/300: dt: 0.9000, rms radial error=162.800, avgs=0 090/300: dt: 0.9000, rms radial error=161.888, avgs=0 095/300: dt: 0.9000, rms radial error=160.980, avgs=0 100/300: dt: 0.9000, rms radial error=160.078, avgs=0 105/300: dt: 0.9000, rms radial error=159.180, avgs=0 110/300: dt: 0.9000, rms radial error=158.288, avgs=0 115/300: dt: 0.9000, rms radial error=157.400, avgs=0 120/300: dt: 0.9000, rms radial error=156.517, avgs=0 125/300: dt: 0.9000, rms radial error=155.639, avgs=0 130/300: dt: 0.9000, rms radial error=154.766, avgs=0 135/300: dt: 0.9000, rms radial error=153.897, avgs=0 140/300: dt: 0.9000, rms radial error=153.033, avgs=0 145/300: dt: 0.9000, rms radial error=152.174, avgs=0 150/300: dt: 0.9000, rms radial error=151.319, avgs=0 155/300: dt: 0.9000, rms radial error=150.469, avgs=0 160/300: dt: 0.9000, rms radial error=149.624, avgs=0 165/300: dt: 0.9000, rms radial error=148.783, avgs=0 170/300: dt: 0.9000, rms radial error=147.947, avgs=0 175/300: dt: 0.9000, rms radial error=147.115, avgs=0 180/300: dt: 0.9000, rms radial error=146.288, avgs=0 185/300: dt: 0.9000, rms radial error=145.466, avgs=0 190/300: dt: 0.9000, rms radial error=144.647, avgs=0 195/300: dt: 0.9000, rms radial error=143.834, avgs=0 200/300: dt: 0.9000, rms radial error=143.025, avgs=0 205/300: dt: 0.9000, rms radial error=142.220, avgs=0 210/300: dt: 0.9000, rms radial error=141.419, avgs=0 215/300: dt: 0.9000, rms radial error=140.623, avgs=0 220/300: dt: 0.9000, rms radial error=139.832, avgs=0 225/300: dt: 0.9000, rms radial error=139.044, avgs=0 230/300: dt: 0.9000, rms radial error=138.262, avgs=0 235/300: dt: 0.9000, rms radial error=137.483, avgs=0 240/300: dt: 0.9000, rms radial error=136.709, avgs=0 245/300: dt: 0.9000, rms radial error=135.939, avgs=0 250/300: dt: 0.9000, rms radial error=135.173, avgs=0 255/300: dt: 0.9000, rms radial error=134.412, avgs=0 260/300: dt: 0.9000, rms radial error=133.654, avgs=0 265/300: dt: 0.9000, rms radial error=132.901, avgs=0 270/300: dt: 0.9000, rms radial error=132.153, avgs=0 275/300: dt: 0.9000, rms radial error=131.408, avgs=0 280/300: dt: 0.9000, rms radial error=130.668, avgs=0 285/300: dt: 0.9000, rms radial error=129.932, avgs=0 290/300: dt: 0.9000, rms radial error=129.199, avgs=0 295/300: dt: 0.9000, rms radial error=128.471, avgs=0 300/300: dt: 0.9000, rms radial error=127.747, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16087.29 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 = 2736.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 292.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00482 epoch 4 (K=640.0), pass 1, starting sse = 20.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00731 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri Sep 18 17:43:44 EDT 2015 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 af1021_recon lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-44 (nv=136234, nf=272556, ne=408834, g=23) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 3927 ambiguous faces found in tessellation segmenting defects... 28 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 28 defects to be corrected 0 vertices coincident reading input surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2548 (-4.6274) -vertex loglikelihood: -6.1560 (-3.0780) -normal dot loglikelihood: -3.6201 (-3.6201) -quad curv loglikelihood: -6.3204 (-3.1602) Total Loglikelihood : -25.3512 CORRECTING DEFECT 0 (vertices=50, convex hull=98) After retessellation of defect 0, euler #=-22 (133881,400806,266903) : difference with theory (-25) = -3 CORRECTING DEFECT 1 (vertices=29, convex hull=86) After retessellation of defect 1, euler #=-21 (133890,400866,266955) : difference with theory (-24) = -3 CORRECTING DEFECT 2 (vertices=9, convex hull=27) After retessellation of defect 2, euler #=-20 (133891,400877,266966) : difference with theory (-23) = -3 CORRECTING DEFECT 3 (vertices=259, convex hull=205) After retessellation of defect 3, euler #=-19 (133940,401120,267161) : difference with theory (-22) = -3 CORRECTING DEFECT 4 (vertices=6, convex hull=16) After retessellation of defect 4, euler #=-18 (133941,401125,267166) : difference with theory (-21) = -3 CORRECTING DEFECT 5 (vertices=136, convex hull=145) After retessellation of defect 5, euler #=-17 (133985,401326,267324) : difference with theory (-20) = -3 CORRECTING DEFECT 6 (vertices=46, convex hull=67) After retessellation of defect 6, euler #=-16 (134012,401437,267409) : difference with theory (-19) = -3 CORRECTING DEFECT 7 (vertices=87, convex hull=95) After retessellation of defect 7, euler #=-17 (134064,401642,267561) : difference with theory (-18) = -1 CORRECTING DEFECT 8 (vertices=5, convex hull=20) After retessellation of defect 8, euler #=-16 (134064,401647,267567) : difference with theory (-17) = -1 CORRECTING DEFECT 9 (vertices=11, convex hull=10) After retessellation of defect 9, euler #=-15 (134064,401650,267571) : difference with theory (-16) = -1 CORRECTING DEFECT 10 (vertices=42, convex hull=70) After retessellation of defect 10, euler #=-14 (134090,401754,267650) : difference with theory (-15) = -1 CORRECTING DEFECT 11 (vertices=36, convex hull=27) After retessellation of defect 11, euler #=-13 (134096,401780,267671) : difference with theory (-14) = -1 CORRECTING DEFECT 12 (vertices=23, convex hull=20) After retessellation of defect 12, euler #=-12 (134099,401796,267685) : difference with theory (-13) = -1 CORRECTING DEFECT 13 (vertices=28, convex hull=44) After retessellation of defect 13, euler #=-11 (134108,401839,267720) : difference with theory (-12) = -1 CORRECTING DEFECT 14 (vertices=134, convex hull=112) After retessellation of defect 14, euler #=-10 (134163,402056,267883) : difference with theory (-11) = -1 CORRECTING DEFECT 15 (vertices=887, convex hull=214) After retessellation of defect 15, euler #=-9 (134225,402346,268112) : difference with theory (-10) = -1 CORRECTING DEFECT 16 (vertices=29, convex hull=51) After retessellation of defect 16, euler #=-9 (134239,402410,268162) : difference with theory (-9) = 0 CORRECTING DEFECT 17 (vertices=27, convex hull=74) After retessellation of defect 17, euler #=-8 (134255,402487,268224) : difference with theory (-8) = 0 CORRECTING DEFECT 18 (vertices=19, convex hull=50) After retessellation of defect 18, euler #=-7 (134264,402532,268261) : difference with theory (-7) = 0 CORRECTING DEFECT 19 (vertices=39, convex hull=45) After retessellation of defect 19, euler #=-6 (134269,402567,268292) : difference with theory (-6) = 0 CORRECTING DEFECT 20 (vertices=67, convex hull=66) After retessellation of defect 20, euler #=-5 (134287,402654,268362) : difference with theory (-5) = 0 CORRECTING DEFECT 21 (vertices=17, convex hull=30) After retessellation of defect 21, euler #=-4 (134291,402677,268382) : difference with theory (-4) = 0 CORRECTING DEFECT 22 (vertices=61, convex hull=95) After retessellation of defect 22, euler #=-3 (134321,402814,268490) : difference with theory (-3) = 0 CORRECTING DEFECT 23 (vertices=57, convex hull=58) After retessellation of defect 23, euler #=-2 (134337,402886,268547) : difference with theory (-2) = 0 CORRECTING DEFECT 24 (vertices=78, convex hull=95) After retessellation of defect 24, euler #=-1 (134358,402990,268631) : difference with theory (-1) = 0 CORRECTING DEFECT 25 (vertices=23, convex hull=49) After retessellation of defect 25, euler #=0 (134365,403028,268663) : difference with theory (0) = 0 CORRECTING DEFECT 26 (vertices=116, convex hull=100) normal vector of length zero at vertex 136109 with 4 faces After retessellation of defect 26, euler #=1 (134381,403122,268742) : difference with theory (1) = 0 CORRECTING DEFECT 27 (vertices=41, convex hull=36) After retessellation of defect 27, euler #=2 (134383,403143,268762) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.11-->7.44) (max @ vno 125519 --> 129730) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.11-->7.44) (max @ vno 125519 --> 129730) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 97 mutations (34.2%), 187 crossovers (65.8%), 249 vertices were eliminated building final representation... 1851 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134383, nf=268762, ne=403143, g=0) writing corrected surface to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 21.0 minutes 0 defective edges removing intersecting faces 000: 221 intersecting 001: 3 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 134383 - 403143 + 268762 = 2 --> 0 holes F =2V-4: 268762 = 268766-4 (0) 2E=3F: 806286 = 806286 (0) total defect index = 0 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 17 intersecting 001: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Sep 18 18:04:52 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... 12571 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.88 3457 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.54 2734 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4892828.0, rms=9.92 001: dt: 0.5000, sse=5566344.5, rms=7.099 (0.000%) 002: dt: 0.5000, sse=5952963.5, rms=5.421 (0.000%) 003: dt: 0.5000, sse=6270257.5, rms=4.412 (0.000%) 004: dt: 0.5000, sse=6511372.5, rms=3.793 (0.000%) 005: dt: 0.5000, sse=6646172.5, rms=3.482 (0.000%) 006: dt: 0.5000, sse=6745737.0, rms=3.293 (0.000%) 007: dt: 0.5000, sse=6787876.0, rms=3.217 (0.000%) 008: dt: 0.5000, sse=6808347.0, rms=3.145 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6803474.0, rms=3.126 (0.000%) 010: dt: 0.2500, sse=4088440.0, rms=2.113 (0.000%) 011: dt: 0.2500, sse=3761433.0, rms=1.869 (0.000%) 012: dt: 0.2500, sse=3615080.2, rms=1.813 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3566575.0, rms=1.783 (0.000%) rms = 1.75, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3509653.8, rms=1.752 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.8, 41 (6) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.3 (%26.2))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.03-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.40) mean absolute distance = 0.25 +- 0.37 3083 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4100091.8, rms=4.66 015: dt: 0.5000, sse=4396954.0, rms=2.790 (0.000%) rms = 2.79, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4865183.0, rms=2.785 (0.000%) 017: dt: 0.2500, sse=4087599.5, rms=1.708 (0.000%) 018: dt: 0.2500, sse=3957018.2, rms=1.512 (0.000%) rms = 1.47, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3845835.0, rms=1.475 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3799473.8, rms=1.433 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.2, 21 (3) missing vertices, mean dist -0.1 [0.3 (%71.9)->0.2 (%28.1))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.50) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3251 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4001116.2, rms=3.27 021: dt: 0.5000, sse=4304313.5, rms=2.448 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4040074.0, rms=1.739 (0.000%) 023: dt: 0.2500, sse=3963482.8, rms=1.400 (0.000%) 024: dt: 0.2500, sse=3935912.5, rms=1.316 (0.000%) rms = 1.32, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3913786.8, rms=1.301 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.0, 29 (2) missing vertices, mean dist -0.0 [0.2 (%56.4)->0.2 (%43.6))] %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3929055.0, rms=1.62 rms = 1.67, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=3991274.2, rms=1.215 (0.000%) 027: dt: 0.2500, sse=4167403.5, rms=0.985 (0.000%) rms = 0.99, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4168569.0, rms=0.984 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 23 non-cortical segments detected only using segment with 2182 vertices erasing segment 1 (vno[0] = 57470) erasing segment 2 (vno[0] = 77359) erasing segment 3 (vno[0] = 78446) erasing segment 4 (vno[0] = 82313) erasing segment 5 (vno[0] = 83246) erasing segment 6 (vno[0] = 89295) erasing segment 7 (vno[0] = 93408) erasing segment 8 (vno[0] = 95380) erasing segment 9 (vno[0] = 97413) erasing segment 10 (vno[0] = 97437) erasing segment 11 (vno[0] = 97489) erasing segment 12 (vno[0] = 98344) erasing segment 13 (vno[0] = 98353) erasing segment 14 (vno[0] = 98456) erasing segment 15 (vno[0] = 99252) erasing segment 16 (vno[0] = 99310) erasing segment 17 (vno[0] = 100095) erasing segment 18 (vno[0] = 101770) erasing segment 19 (vno[0] = 101844) erasing segment 20 (vno[0] = 105977) erasing segment 21 (vno[0] = 106623) erasing segment 22 (vno[0] = 134247) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/lh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.curv writing smoothed area to lh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.area vertex spacing 0.89 +- 0.25 (0.07-->6.52) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.26) refinement took 4.9 minutes #-------------------------------------------- #@# Smooth2 lh Fri Sep 18 18:09:47 EDT 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Fri Sep 18 18:09:51 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.0 mm, total surface area = 81870 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 135 vertices thresholded to be in k1 ~ [-0.29 0.32], k2 ~ [-0.11 0.20] total integrated curvature = 0.529*4pi (6.644) --> 0 handles ICI = 1.6, FI = 9.9, variation=171.984 96 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 127 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Fri Sep 18 18:11:43 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 257 ] Gb_filter = 0 WARN: S lookup min: -0.486032 WARN: S explicit min: 0.000000 vertex = 245 #-------------------------------------------- #@# Sphere lh Fri Sep 18 18:11:49 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.282... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %19.78 pass 1: epoch 2 of 3 starting distance error %19.78 unfolding complete - removing small folds... starting distance error %19.73 removing remaining folds... final distance error %19.74 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.70 hours #-------------------------------------------- #@# Surf Reg lh Fri Sep 18 18:54:05 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_register -curv ../surf/lh.sphere /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, 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 = 0.578 curvature mean = 0.039, std = 0.935 curvature mean = 0.022, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 337229.2, tmin=0.9398 d=32.00 min @ (0.00, -8.00, 0.00) sse = 281077.2, tmin=1.8950 d=16.00 min @ (4.00, 0.00, -4.00) sse = 254592.3, tmin=2.9242 d=8.00 min @ (0.00, 2.00, 2.00) sse = 252122.2, tmin=4.0004 d=4.00 min @ (0.00, 0.00, -1.00) sse = 251389.0, tmin=5.1086 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 250911.2, tmin=6.2262 d=1.00 min @ (0.25, 0.00, 0.00) sse = 250884.6, tmin=7.3191 d=0.50 min @ (-0.12, -0.12, 0.00) sse = 250849.5, tmin=8.4035 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.40 min curvature mean = 0.014, std = 0.962 curvature mean = 0.010, std = 0.940 curvature mean = 0.012, std = 0.974 curvature mean = 0.004, std = 0.973 curvature mean = 0.009, std = 0.975 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.028, std = 0.295 curvature mean = 0.003, std = 0.067 curvature mean = 0.066, std = 0.342 curvature mean = 0.003, std = 0.080 curvature mean = 0.032, std = 0.527 curvature mean = 0.003, std = 0.086 curvature mean = 0.017, std = 0.669 curvature mean = 0.003, std = 0.088 curvature mean = 0.007, std = 0.776 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri Sep 18 19:18:45 EDT 2015 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri Sep 18 19:18:47 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Sep 18 19:18:48 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1080 labels changed using aseg relabeling using gibbs priors... 000: 2998 changed, 134383 examined... 001: 687 changed, 12813 examined... 002: 158 changed, 3844 examined... 003: 54 changed, 949 examined... 004: 20 changed, 327 examined... 005: 10 changed, 130 examined... 006: 6 changed, 57 examined... 007: 4 changed, 36 examined... 008: 2 changed, 28 examined... 009: 1 changed, 15 examined... 010: 0 changed, 6 examined... 221 labels changed using aseg 000: 102 total segments, 59 labels (226 vertices) changed 001: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1230 vertices marked for relabeling... 1230 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 41 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Sep 18 19:19:29 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... 12571 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.89 3533 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 58 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 4 with 589 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 20 points - only 0.00% unknown mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.55 2833 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4906516.0, rms=9.91 001: dt: 0.5000, sse=5584919.0, rms=7.087 (0.000%) 002: dt: 0.5000, sse=5971842.0, rms=5.412 (0.000%) 003: dt: 0.5000, sse=6295095.5, rms=4.407 (0.000%) 004: dt: 0.5000, sse=6537852.5, rms=3.792 (0.000%) 005: dt: 0.5000, sse=6681860.0, rms=3.482 (0.000%) 006: dt: 0.5000, sse=6780486.5, rms=3.292 (0.000%) 007: dt: 0.5000, sse=6830326.5, rms=3.216 (0.000%) 008: dt: 0.5000, sse=6847692.5, rms=3.144 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6848157.5, rms=3.126 (0.000%) 010: dt: 0.2500, sse=4112707.0, rms=2.115 (0.000%) 011: dt: 0.2500, sse=3785237.8, rms=1.871 (0.000%) 012: dt: 0.2500, sse=3640015.2, rms=1.816 (0.000%) rms = 1.79, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3591487.2, rms=1.786 (0.000%) rms = 1.76, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3534378.5, rms=1.756 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 141 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 5 with 502 points - only 0.00% unknown deleting segment 9 with 13 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown mean border=83.8, 44 (9) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.3 (%26.3))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.03-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.39) mean absolute distance = 0.26 +- 0.38 3165 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4128960.2, rms=4.65 015: dt: 0.5000, sse=4428448.0, rms=2.790 (0.000%) rms = 2.79, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4907061.5, rms=2.785 (0.000%) 017: dt: 0.2500, sse=4118854.8, rms=1.714 (0.000%) 018: dt: 0.2500, sse=3989801.5, rms=1.519 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3879248.2, rms=1.482 (0.000%) rms = 1.44, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3831904.5, rms=1.441 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 535 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 47 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown mean border=86.2, 34 (5) missing vertices, mean dist -0.1 [0.3 (%71.8)->0.2 (%28.2))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.50) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3329 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4035464.2, rms=3.27 021: dt: 0.5000, sse=4342159.0, rms=2.452 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4076464.0, rms=1.749 (0.000%) 023: dt: 0.2500, sse=4000122.5, rms=1.416 (0.000%) 024: dt: 0.2500, sse=3970749.2, rms=1.332 (0.000%) rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.32, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3948572.0, rms=1.317 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 540 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 15 points - only 0.00% unknown mean border=87.0, 44 (4) missing vertices, mean dist -0.0 [0.2 (%56.3)->0.2 (%43.7))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=3964720.0, rms=1.63 rms = 1.67, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4029283.2, rms=1.228 (0.000%) 027: dt: 0.2500, sse=4209924.5, rms=1.001 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4211571.0, rms=0.999 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.1, 61 (61) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.5 (%100.0))] %19 local maxima, %48 large gradients and %29 min vals, 2550 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21194238.0, rms=26.91 001: dt: 0.5000, sse=16177710.0, rms=22.987 (0.000%) 002: dt: 0.5000, sse=12511884.0, rms=19.660 (0.000%) 003: dt: 0.5000, sse=9935601.0, rms=16.892 (0.000%) 004: dt: 0.5000, sse=8271835.0, rms=14.595 (0.000%) 005: dt: 0.5000, sse=7201807.5, rms=12.715 (0.000%) 006: dt: 0.5000, sse=6564423.0, rms=11.197 (0.000%) 007: dt: 0.5000, sse=6195552.5, rms=9.892 (0.000%) 008: dt: 0.5000, sse=5944976.5, rms=8.753 (0.000%) 009: dt: 0.5000, sse=5813457.5, rms=7.736 (0.000%) 010: dt: 0.5000, sse=5740933.0, rms=6.837 (0.000%) 011: dt: 0.5000, sse=5759568.0, rms=6.034 (0.000%) 012: dt: 0.5000, sse=5744825.0, rms=5.300 (0.000%) 013: dt: 0.5000, sse=5830524.5, rms=4.707 (0.000%) 014: dt: 0.5000, sse=5884602.5, rms=4.272 (0.000%) 015: dt: 0.5000, sse=5996652.5, rms=3.978 (0.000%) 016: dt: 0.5000, sse=6030062.0, rms=3.778 (0.000%) 017: dt: 0.5000, sse=6088289.0, rms=3.652 (0.000%) 018: dt: 0.5000, sse=6084106.0, rms=3.556 (0.000%) 019: dt: 0.5000, sse=6118176.0, rms=3.493 (0.000%) 020: dt: 0.5000, sse=6138362.0, rms=3.442 (0.000%) rms = 3.41, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=6133908.5, rms=3.410 (0.000%) 022: dt: 0.2500, sse=4409242.5, rms=2.794 (0.000%) 023: dt: 0.2500, sse=4266424.5, rms=2.634 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=4153288.2, rms=2.616 (0.000%) 025: dt: 0.1250, sse=4016203.5, rms=2.546 (0.000%) rms = 2.54, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3998913.8, rms=2.540 (0.000%) positioning took 2.6 minutes mean border=57.8, 972 (24) missing vertices, mean dist 0.2 [0.2 (%44.9)->0.6 (%55.1))] %39 local maxima, %33 large gradients and %23 min vals, 1002 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4627678.0, rms=4.69 027: dt: 0.5000, sse=4770570.5, rms=3.666 (0.000%) 028: dt: 0.5000, sse=6037900.0, rms=3.553 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=5907187.5, rms=3.553 (0.000%) 030: dt: 0.2500, sse=4851860.0, rms=2.808 (0.000%) 031: dt: 0.2500, sse=4736925.5, rms=2.609 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4666506.5, rms=2.577 (0.000%) 033: dt: 0.1250, sse=4528337.5, rms=2.472 (0.000%) rms = 2.45, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=4520418.0, rms=2.452 (0.000%) positioning took 0.8 minutes mean border=56.1, 1173 (20) missing vertices, mean dist 0.1 [0.2 (%38.1)->0.4 (%61.9))] %55 local maxima, %17 large gradients and %23 min vals, 1161 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4670800.5, rms=3.31 rms = 3.27, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=4854815.5, rms=3.274 (0.000%) 036: dt: 0.2500, sse=4860777.5, rms=2.608 (0.000%) 037: dt: 0.2500, sse=4851694.0, rms=2.465 (0.000%) rms = 2.45, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4837670.0, rms=2.453 (0.000%) 039: dt: 0.1250, sse=4716520.5, rms=2.329 (0.000%) rms = 2.31, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4717036.5, rms=2.314 (0.000%) positioning took 0.6 minutes mean border=55.3, 2461 (17) missing vertices, mean dist 0.0 [0.2 (%44.6)->0.3 (%55.4))] %58 local maxima, %14 large gradients and %22 min vals, 909 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4740523.0, rms=2.51 rms = 2.90, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4649935.5, rms=2.347 (0.000%) rms = 2.30, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4802499.5, rms=2.302 (0.000%) 043: dt: 0.1250, sse=4712826.5, rms=2.250 (0.000%) rms = 2.23, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4740258.0, rms=2.234 (0.000%) positioning took 0.5 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.06-->8.04) (max @ vno 92642 --> 92643) face area 0.41 +- 0.32 (0.00-->11.66) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 714:1242 truncations. 27368 vertices at 0 distance 86933 vertices at 1 distance 84333 vertices at 2 distance 39033 vertices at 3 distance 12967 vertices at 4 distance 3966 vertices at 5 distance 1355 vertices at 6 distance 478 vertices at 7 distance 174 vertices at 8 distance 91 vertices at 9 distance 55 vertices at 10 distance 40 vertices at 11 distance 27 vertices at 12 distance 18 vertices at 13 distance 20 vertices at 14 distance 20 vertices at 15 distance 10 vertices at 16 distance 8 vertices at 17 distance 7 vertices at 18 distance 15 vertices at 19 distance 16 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.thickness positioning took 10.6 minutes #-------------------------------------------- #@# Surf Volume lh Fri Sep 18 19:30:07 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Fri Sep 18 19:30:07 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts pctsurfcon --s af1021_recon --lh-only Log file is /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts/pctsurfcon.log Fri Sep 18 19:30:07 EDT 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori cd /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-4.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.9895/lh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 = 73830 Masking with /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.9895/lh.wm.mgh Dim: 134383 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.9895/lh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 = 87912 Masking with /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.9895/lh.gm.mgh Dim: 134383 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.9895/lh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.9895/lh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/af1021_recon/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-4.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.w-g.pct.mgh Vertex Area is 0.663955 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1569 1086.962 2 1002 caudalanteriorcingulate 814 522.250 3 1003 caudalmiddlefrontal 2764 1864.563 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 1883 1217.582 6 1006 entorhinal 629 417.842 7 1007 fusiform 4799 3219.453 8 1008 inferiorparietal 6854 4603.135 9 1009 inferiortemporal 4719 3154.068 10 1010 isthmuscingulate 1422 922.708 11 1011 lateraloccipital 8366 5390.013 12 1012 lateralorbitofrontal 3788 2557.312 13 1013 lingual 5325 3458.724 14 1014 medialorbitofrontal 2410 1593.298 15 1015 middletemporal 4533 3092.269 16 1016 parahippocampal 1136 726.788 17 1017 paracentral 1942 1265.307 18 1018 parsopercularis 2937 2028.785 19 1019 parsorbitalis 925 609.904 20 1020 parstriangularis 1947 1316.733 21 1021 pericalcarine 2184 1389.921 22 1022 postcentral 6527 4170.566 23 1023 posteriorcingulate 1726 1180.100 24 1024 precentral 7435 4766.086 25 1025 precuneus 5912 4054.477 26 1026 rostralanteriorcingulate 1079 697.362 27 1027 rostralmiddlefrontal 8007 5515.635 28 1028 superiorfrontal 9959 6792.604 29 1029 superiorparietal 7689 5110.637 30 1030 superiortemporal 6200 4140.839 31 1031 supramarginal 5569 3709.949 32 1032 frontalpole 276 193.698 33 1033 temporalpole 656 457.104 34 1034 transversetemporal 842 513.617 35 1035 insula 3107 2035.490 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Fri Sep 18 19:30:15 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 1569 1087 2846 2.470 0.540 0.111 0.029 12 1.9 bankssts 814 522 1559 2.657 0.511 0.147 0.039 13 1.3 caudalanteriorcingulate 2764 1865 5278 2.590 0.605 0.136 0.065 52 8.5 caudalmiddlefrontal 1883 1218 2578 1.945 0.462 0.164 0.063 34 4.8 cuneus 629 418 1608 3.005 0.670 0.123 0.047 6 1.1 entorhinal 4799 3219 10709 2.888 0.620 0.158 0.084 105 13.2 fusiform 6854 4603 13088 2.536 0.549 0.143 0.058 117 14.7 inferiorparietal 4719 3154 10526 2.879 0.821 0.146 0.074 96 12.7 inferiortemporal 1422 923 2608 2.632 0.682 0.152 0.066 34 3.6 isthmuscingulate 8366 5390 12445 2.104 0.543 0.147 0.051 122 17.4 lateraloccipital 3788 2557 7888 2.761 0.732 0.149 0.064 71 9.7 lateralorbitofrontal 5325 3459 8278 2.196 0.571 0.159 0.066 97 13.5 lingual 2410 1593 4399 2.420 0.716 0.157 0.126 120 10.9 medialorbitofrontal 4533 3092 11432 2.911 0.733 0.138 0.048 72 8.4 middletemporal 1136 727 2152 2.531 0.618 0.117 0.038 10 1.8 parahippocampal 1942 1265 3245 2.339 0.465 0.132 0.077 99 7.9 paracentral 2937 2029 6285 2.714 0.437 0.131 0.043 41 5.4 parsopercularis 925 610 2379 2.896 0.587 0.161 0.097 26 3.7 parsorbitalis 1947 1317 4111 2.709 0.597 0.133 0.045 26 3.3 parstriangularis 2184 1390 2455 1.864 0.460 0.131 0.064 32 5.8 pericalcarine 6527 4171 10629 2.256 0.706 0.132 0.045 87 12.6 postcentral 1726 1180 3384 2.703 0.618 0.158 0.056 33 4.0 posteriorcingulate 7435 4766 13528 2.580 0.615 0.136 0.055 100 17.0 precentral 5912 4054 10262 2.340 0.554 0.141 0.047 93 11.5 precuneus 1079 697 2505 3.053 0.797 0.162 0.058 22 2.4 rostralanteriorcingulate 8007 5516 16686 2.540 0.652 0.158 0.065 158 20.4 rostralmiddlefrontal 9959 6793 23602 2.971 0.637 0.148 0.061 162 23.7 superiorfrontal 7689 5111 12720 2.221 0.556 0.141 0.056 303 14.4 superiorparietal 6200 4141 14442 2.932 0.637 0.127 0.045 86 12.0 superiortemporal 5569 3710 11797 2.797 0.595 0.142 0.058 133 13.1 supramarginal 276 194 794 3.001 0.443 0.251 0.169 14 1.9 frontalpole 656 457 2583 3.475 0.840 0.187 0.093 19 2.7 temporalpole 842 514 1541 2.532 0.532 0.136 0.067 13 2.5 transversetemporal 3107 2035 6910 3.267 0.828 0.115 0.052 34 5.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Sep 18 19:30:29 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 179 labels changed using aseg relabeling using gibbs priors... 000: 9263 changed, 134383 examined... 001: 2241 changed, 35608 examined... 002: 713 changed, 11519 examined... 003: 297 changed, 4013 examined... 004: 158 changed, 1678 examined... 005: 79 changed, 867 examined... 006: 30 changed, 433 examined... 007: 18 changed, 185 examined... 008: 20 changed, 114 examined... 009: 6 changed, 89 examined... 010: 2 changed, 37 examined... 011: 2 changed, 12 examined... 012: 0 changed, 8 examined... 83 labels changed using aseg 000: 295 total segments, 214 labels (2830 vertices) changed 001: 94 total segments, 13 labels (124 vertices) changed 002: 83 total segments, 2 labels (2 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 114 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 539 vertices marked for relabeling... 539 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 48 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Sep 18 19:31:17 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 1044 704 2096 2.370 0.735 0.179 0.081 28 3.5 G_and_S_frontomargin 1688 1144 2994 2.335 0.514 0.158 0.099 37 3.5 G_and_S_occipital_inf 1472 894 2367 2.186 0.499 0.136 0.066 92 4.3 G_and_S_paracentral 1587 1041 3502 2.903 0.618 0.158 0.065 30 4.0 G_and_S_subcentral 663 455 1664 2.513 0.705 0.218 0.129 28 2.9 G_and_S_transv_frontopol 1976 1323 4356 3.077 0.733 0.154 0.053 33 4.1 G_and_S_cingul-Ant 1112 754 2209 2.684 0.556 0.123 0.033 10 1.5 G_and_S_cingul-Mid-Ant 1276 897 2484 2.655 0.533 0.143 0.048 17 2.6 G_and_S_cingul-Mid-Post 499 338 1286 3.134 0.581 0.169 0.061 11 1.2 G_cingul-Post-dorsal 283 163 457 2.356 0.791 0.160 0.103 8 1.2 G_cingul-Post-ventral 1654 1038 2207 1.878 0.429 0.167 0.070 33 4.8 G_cuneus 1528 1070 4089 2.897 0.386 0.150 0.058 33 4.0 G_front_inf-Opercular 410 262 1120 3.172 0.420 0.183 0.166 19 2.5 G_front_inf-Orbital 1299 876 3374 2.836 0.522 0.148 0.048 21 2.6 G_front_inf-Triangul 4000 2727 10188 2.890 0.593 0.173 0.088 111 14.8 G_front_middle 7440 5014 19252 3.058 0.608 0.160 0.078 151 24.0 G_front_sup 535 343 1404 3.611 0.772 0.114 0.076 6 0.9 G_Ins_lg_and_S_cent_ins 631 402 2180 3.971 0.728 0.133 0.074 13 2.2 G_insular_short 2945 1862 6553 2.636 0.539 0.159 0.056 59 6.5 G_occipital_middle 1516 971 2603 2.173 0.556 0.160 0.060 28 3.6 G_occipital_sup 1895 1262 4711 2.914 0.541 0.169 0.067 43 5.5 G_oc-temp_lat-fusifor 3719 2357 6067 2.167 0.612 0.168 0.081 83 10.8 G_oc-temp_med-Lingual 1284 806 2923 2.948 0.757 0.119 0.044 12 2.4 G_oc-temp_med-Parahip 2602 1768 6810 2.853 0.722 0.168 0.083 65 8.5 G_orbital 2245 1491 4933 2.650 0.594 0.159 0.087 59 6.4 G_pariet_inf-Angular 3257 2163 8092 2.971 0.565 0.149 0.065 104 9.2 G_pariet_inf-Supramar 2706 1804 5389 2.333 0.651 0.140 0.050 39 5.3 G_parietal_sup 2617 1582 4881 2.413 0.638 0.138 0.052 43 5.9 G_postcentral 3048 1777 6360 2.821 0.551 0.138 0.063 49 8.5 G_precentral 2656 1817 5675 2.464 0.545 0.159 0.062 61 7.1 G_precuneus 999 678 2286 2.524 0.667 0.177 0.087 30 3.7 G_rectus 455 265 613 2.246 0.853 0.180 0.399 81 6.0 G_subcallosal 678 404 1384 2.701 0.621 0.155 0.084 13 2.5 G_temp_sup-G_T_transv 2426 1583 7578 3.248 0.656 0.149 0.064 55 6.9 G_temp_sup-Lateral 472 300 1165 3.386 0.704 0.140 0.073 9 1.4 G_temp_sup-Plan_polar 1035 733 2165 2.605 0.519 0.105 0.025 7 1.0 G_temp_sup-Plan_tempo 2200 1477 6192 3.104 0.781 0.165 0.098 53 6.6 G_temporal_inf 2671 1810 7865 3.119 0.710 0.153 0.059 54 6.1 G_temporal_middle 336 219 471 2.630 0.609 0.106 0.027 2 0.3 Lat_Fis-ant-Horizont 335 228 489 2.542 0.390 0.101 0.024 1 0.3 Lat_Fis-ant-Vertical 1339 887 1831 2.608 0.530 0.118 0.037 12 2.0 Lat_Fis-post 2543 1542 3017 1.778 0.469 0.145 0.058 40 6.3 Pole_occipital 1821 1237 6082 3.416 0.828 0.180 0.098 49 6.6 Pole_temporal 3040 2002 3962 2.090 0.526 0.131 0.050 39 6.5 S_calcarine 3197 2176 3438 1.791 0.518 0.133 0.046 32 5.8 S_central 887 631 1369 2.269 0.495 0.127 0.039 9 1.4 S_cingul-Marginalis 443 296 771 2.963 0.515 0.108 0.030 3 0.6 S_circular_insula_ant 1433 957 2440 2.720 0.653 0.083 0.018 5 1.1 S_circular_insula_inf 1741 1170 2689 2.718 0.485 0.108 0.028 11 2.1 S_circular_insula_sup 1179 797 2515 3.040 0.701 0.145 0.067 21 2.8 S_collat_transv_ant 449 298 528 2.255 0.397 0.138 0.042 4 0.8 S_collat_transv_post 2543 1729 3928 2.308 0.476 0.121 0.034 22 3.6 S_front_inf 1454 1017 2437 2.405 0.499 0.133 0.038 14 2.5 S_front_middle 2382 1646 3991 2.454 0.481 0.119 0.044 23 3.9 S_front_sup 265 180 662 3.024 0.574 0.167 0.059 5 0.7 S_interm_prim-Jensen 3328 2241 4676 2.197 0.469 0.131 0.044 37 5.2 S_intrapariet_and_P_trans 1417 933 1584 1.908 0.376 0.139 0.041 16 2.4 S_oc_middle_and_Lunatus 1294 845 1645 2.023 0.381 0.127 0.081 212 1.7 S_oc_sup_and_transversal 1256 861 1655 2.247 0.368 0.138 0.053 22 3.2 S_occipital_ant 767 527 1093 2.424 0.380 0.109 0.026 5 0.8 S_oc-temp_lat 2026 1414 3093 2.454 0.521 0.133 0.040 20 3.4 S_oc-temp_med_and_Lingual 295 200 396 2.142 0.409 0.118 0.033 2 0.4 S_orbital_lateral 758 511 1028 2.279 0.685 0.108 0.022 5 0.6 S_orbital_med-olfact 1192 802 2190 2.744 0.742 0.140 0.054 20 2.6 S_orbital-H_Shaped 2585 1762 3493 2.160 0.573 0.129 0.035 25 3.9 S_parieto_occipital 899 577 1088 2.445 0.593 0.166 0.056 25 2.0 S_pericallosal 2287 1540 3313 2.368 0.432 0.122 0.035 21 3.4 S_postcentral 1848 1286 2967 2.418 0.475 0.117 0.030 13 2.3 S_precentral-inf-part 708 512 1073 2.437 0.409 0.117 0.027 4 0.9 S_precentral-sup-part 610 421 970 2.538 0.712 0.137 0.037 6 0.9 S_suborbital 902 607 1504 2.444 0.551 0.131 0.042 10 1.5 S_subparietal 1506 1018 2327 2.393 0.703 0.124 0.047 20 3.6 S_temporal_inf 5987 4106 10562 2.571 0.485 0.120 0.036 55 8.8 S_temporal_sup 355 249 502 2.456 0.397 0.130 0.034 3 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fri Sep 18 19:31:31 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1246 labels changed using aseg relabeling using gibbs priors... 000: 2899 changed, 134383 examined... 001: 703 changed, 12164 examined... 002: 174 changed, 3786 examined... 003: 80 changed, 984 examined... 004: 31 changed, 481 examined... 005: 20 changed, 188 examined... 006: 19 changed, 104 examined... 007: 15 changed, 97 examined... 008: 9 changed, 79 examined... 009: 8 changed, 51 examined... 010: 7 changed, 43 examined... 011: 2 changed, 40 examined... 012: 3 changed, 12 examined... 013: 1 changed, 13 examined... 014: 2 changed, 7 examined... 015: 0 changed, 11 examined... 270 labels changed using aseg 000: 75 total segments, 42 labels (284 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 559 vertices marked for relabeling... 559 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 41 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Sep 18 19:32:12 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 1574 1020 3075 2.771 0.615 0.137 0.038 21 2.6 caudalanteriorcingulate 2790 1889 5344 2.588 0.604 0.136 0.065 53 8.5 caudalmiddlefrontal 3021 1949 4183 1.987 0.491 0.153 0.055 49 6.8 cuneus 558 368 1483 3.026 0.714 0.123 0.044 5 1.0 entorhinal 4232 2860 8916 2.793 0.549 0.153 0.062 77 10.4 fusiform 6608 4440 12747 2.537 0.556 0.144 0.058 115 14.4 inferiorparietal 4968 3307 11929 2.988 0.839 0.152 0.077 100 13.7 inferiortemporal 1407 915 2553 2.616 0.684 0.152 0.065 33 3.5 isthmuscingulate 8664 5564 12876 2.096 0.544 0.148 0.063 149 19.5 lateraloccipital 3858 2621 8587 2.805 0.797 0.159 0.073 89 11.2 lateralorbitofrontal 5325 3467 8286 2.194 0.574 0.158 0.066 97 13.4 lingual 2045 1355 3818 2.418 0.700 0.146 0.067 43 5.5 medialorbitofrontal 6012 4085 13762 2.799 0.729 0.133 0.044 83 10.6 middletemporal 1153 736 2192 2.540 0.626 0.119 0.038 10 1.9 parahippocampal 2324 1519 3959 2.403 0.502 0.131 0.070 84 8.5 paracentral 2484 1726 5249 2.697 0.412 0.129 0.042 36 4.4 parsopercularis 1044 703 2499 2.938 0.535 0.137 0.082 23 3.1 parsorbitalis 2501 1674 5268 2.659 0.610 0.136 0.045 32 4.6 parstriangularis 2132 1360 2408 1.874 0.459 0.132 0.065 31 5.7 pericalcarine 7110 4600 11730 2.272 0.693 0.133 0.045 94 13.4 postcentral 1828 1248 3517 2.706 0.602 0.156 0.055 34 4.2 posteriorcingulate 7573 4836 13641 2.585 0.614 0.137 0.055 121 17.5 precentral 5628 3866 9871 2.325 0.574 0.142 0.048 91 11.3 precuneus 1486 977 3186 2.911 0.844 0.176 0.155 99 7.8 rostralanteriorcingulate 5507 3770 11640 2.593 0.637 0.156 0.058 96 12.8 rostralmiddlefrontal 11109 7601 25989 2.871 0.663 0.155 0.070 211 29.9 superiorfrontal 6092 4053 10336 2.283 0.545 0.142 0.059 283 11.3 superiorparietal 8066 5437 19340 2.938 0.675 0.131 0.049 117 16.6 superiortemporal 5253 3495 10948 2.793 0.592 0.141 0.058 127 12.4 supramarginal 829 505 1516 2.526 0.527 0.137 0.068 13 2.5 transversetemporal 2749 1829 6403 3.266 0.819 0.110 0.047 27 4.7 insula #-------------------------------------------- #@# Tessellate rh Fri Sep 18 19:32:28 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 254379: 0.001572) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 60: 1433 vertices, 1540 faces slice 70: 6181 vertices, 6407 faces slice 80: 13052 vertices, 13308 faces slice 90: 21514 vertices, 21856 faces slice 100: 31864 vertices, 32228 faces slice 110: 42481 vertices, 42864 faces slice 120: 54336 vertices, 54740 faces slice 130: 67248 vertices, 67687 faces slice 140: 79843 vertices, 80285 faces slice 150: 91429 vertices, 91817 faces slice 160: 101695 vertices, 102034 faces slice 170: 109545 vertices, 109817 faces slice 180: 117416 vertices, 117726 faces slice 190: 124512 vertices, 124785 faces slice 200: 130623 vertices, 130864 faces slice 210: 135029 vertices, 135167 faces slice 220: 135960 vertices, 135992 faces slice 230: 135960 vertices, 135992 faces slice 240: 135960 vertices, 135992 faces slice 250: 135960 vertices, 135992 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 135960 voxel in cpt #1: X=-32 [v=135960,e=407976,f=271984] located at (25.719248, 2.998522, 35.666489) For the whole surface: X=-32 [v=135960,e=407976,f=271984] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Fri Sep 18 19:32:35 EDT 2015 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Fri Sep 18 19:32:38 EDT 2015 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts avg radius = 45.7 mm, total surface area = 70897 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Fri Sep 18 19:33:05 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.56 (0.00-->6.85) (max @ vno 45690 --> 46760) face area 0.03 +- 0.03 (-0.09-->0.76) scaling brain by 0.311... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.055, avgs=0 005/300: dt: 0.9000, rms radial error=176.795, avgs=0 010/300: dt: 0.9000, rms radial error=176.236, avgs=0 015/300: dt: 0.9000, rms radial error=175.501, avgs=0 020/300: dt: 0.9000, rms radial error=174.671, avgs=0 025/300: dt: 0.9000, rms radial error=173.782, avgs=0 030/300: dt: 0.9000, rms radial error=172.860, avgs=0 035/300: dt: 0.9000, rms radial error=171.922, avgs=0 040/300: dt: 0.9000, rms radial error=170.976, avgs=0 045/300: dt: 0.9000, rms radial error=170.028, avgs=0 050/300: dt: 0.9000, rms radial error=169.081, avgs=0 055/300: dt: 0.9000, rms radial error=168.137, avgs=0 060/300: dt: 0.9000, rms radial error=167.196, avgs=0 065/300: dt: 0.9000, rms radial error=166.260, avgs=0 070/300: dt: 0.9000, rms radial error=165.328, avgs=0 075/300: dt: 0.9000, rms radial error=164.400, avgs=0 080/300: dt: 0.9000, rms radial error=163.478, avgs=0 085/300: dt: 0.9000, rms radial error=162.561, avgs=0 090/300: dt: 0.9000, rms radial error=161.649, avgs=0 095/300: dt: 0.9000, rms radial error=160.741, avgs=0 100/300: dt: 0.9000, rms radial error=159.838, avgs=0 105/300: dt: 0.9000, rms radial error=158.940, avgs=0 110/300: dt: 0.9000, rms radial error=158.047, avgs=0 115/300: dt: 0.9000, rms radial error=157.159, avgs=0 120/300: dt: 0.9000, rms radial error=156.276, avgs=0 125/300: dt: 0.9000, rms radial error=155.398, avgs=0 130/300: dt: 0.9000, rms radial error=154.524, avgs=0 135/300: dt: 0.9000, rms radial error=153.656, avgs=0 140/300: dt: 0.9000, rms radial error=152.792, avgs=0 145/300: dt: 0.9000, rms radial error=151.932, avgs=0 150/300: dt: 0.9000, rms radial error=151.078, avgs=0 155/300: dt: 0.9000, rms radial error=150.228, avgs=0 160/300: dt: 0.9000, rms radial error=149.383, avgs=0 165/300: dt: 0.9000, rms radial error=148.543, avgs=0 170/300: dt: 0.9000, rms radial error=147.707, avgs=0 175/300: dt: 0.9000, rms radial error=146.875, avgs=0 180/300: dt: 0.9000, rms radial error=146.049, avgs=0 185/300: dt: 0.9000, rms radial error=145.227, avgs=0 190/300: dt: 0.9000, rms radial error=144.410, avgs=0 195/300: dt: 0.9000, rms radial error=143.598, avgs=0 200/300: dt: 0.9000, rms radial error=142.790, avgs=0 205/300: dt: 0.9000, rms radial error=141.986, avgs=0 210/300: dt: 0.9000, rms radial error=141.187, avgs=0 215/300: dt: 0.9000, rms radial error=140.392, avgs=0 220/300: dt: 0.9000, rms radial error=139.602, avgs=0 225/300: dt: 0.9000, rms radial error=138.816, avgs=0 230/300: dt: 0.9000, rms radial error=138.035, avgs=0 235/300: dt: 0.9000, rms radial error=137.257, avgs=0 240/300: dt: 0.9000, rms radial error=136.484, avgs=0 245/300: dt: 0.9000, rms radial error=135.716, avgs=0 250/300: dt: 0.9000, rms radial error=134.951, avgs=0 255/300: dt: 0.9000, rms radial error=134.191, avgs=0 260/300: dt: 0.9000, rms radial error=133.436, avgs=0 265/300: dt: 0.9000, rms radial error=132.684, avgs=0 270/300: dt: 0.9000, rms radial error=131.937, avgs=0 275/300: dt: 0.9000, rms radial error=131.193, avgs=0 280/300: dt: 0.9000, rms radial error=130.454, avgs=0 285/300: dt: 0.9000, rms radial error=129.719, avgs=0 290/300: dt: 0.9000, rms radial error=128.988, avgs=0 295/300: dt: 0.9000, rms radial error=128.262, avgs=0 300/300: dt: 0.9000, rms radial error=127.539, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15904.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 2638.92 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 = 268.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00631 epoch 4 (K=640.0), pass 1, starting sse = 15.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/13 = 0.00492 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Fri Sep 18 19:36:53 EDT 2015 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 af1021_recon rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-32 (nv=135960, nf=271984, ne=407976, g=17) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 2506 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 11 24 defects to be corrected 0 vertices coincident reading input surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2556 (-4.6278) -vertex loglikelihood: -6.1765 (-3.0883) -normal dot loglikelihood: -3.6583 (-3.6583) -quad curv loglikelihood: -6.5684 (-3.2842) Total Loglikelihood : -25.6589 CORRECTING DEFECT 0 (vertices=31, convex hull=61) After retessellation of defect 0, euler #=-22 (134430,402642,268190) : difference with theory (-21) = 1 CORRECTING DEFECT 1 (vertices=29, convex hull=82) After retessellation of defect 1, euler #=-21 (134444,402716,268251) : difference with theory (-20) = 1 CORRECTING DEFECT 2 (vertices=23, convex hull=70) After retessellation of defect 2, euler #=-20 (134461,402794,268313) : difference with theory (-19) = 1 CORRECTING DEFECT 3 (vertices=6, convex hull=14) After retessellation of defect 3, euler #=-19 (134462,402801,268320) : difference with theory (-18) = 1 CORRECTING DEFECT 4 (vertices=42, convex hull=70) After retessellation of defect 4, euler #=-18 (134489,402912,268405) : difference with theory (-17) = 1 CORRECTING DEFECT 5 (vertices=30, convex hull=83) After retessellation of defect 5, euler #=-17 (134506,402998,268475) : difference with theory (-16) = 1 CORRECTING DEFECT 6 (vertices=54, convex hull=37) After retessellation of defect 6, euler #=-16 (134512,403026,268498) : difference with theory (-15) = 1 CORRECTING DEFECT 7 (vertices=121, convex hull=132) After retessellation of defect 7, euler #=-15 (134549,403197,268633) : difference with theory (-14) = 1 CORRECTING DEFECT 8 (vertices=159, convex hull=78) After retessellation of defect 8, euler #=-14 (134579,403327,268734) : difference with theory (-13) = 1 CORRECTING DEFECT 9 (vertices=47, convex hull=87) After retessellation of defect 9, euler #=-13 (134601,403433,268819) : difference with theory (-12) = 1 CORRECTING DEFECT 10 (vertices=6, convex hull=22) After retessellation of defect 10, euler #=-12 (134602,403442,268828) : difference with theory (-11) = 1 CORRECTING DEFECT 11 (vertices=113, convex hull=118) After retessellation of defect 11, euler #=-10 (134645,403628,268973) : difference with theory (-10) = 0 CORRECTING DEFECT 12 (vertices=28, convex hull=62) After retessellation of defect 12, euler #=-9 (134656,403684,269019) : difference with theory (-9) = 0 CORRECTING DEFECT 13 (vertices=219, convex hull=70) After retessellation of defect 13, euler #=-8 (134669,403754,269077) : difference with theory (-8) = 0 CORRECTING DEFECT 14 (vertices=198, convex hull=101) After retessellation of defect 14, euler #=-7 (134705,403905,269193) : difference with theory (-7) = 0 CORRECTING DEFECT 15 (vertices=25, convex hull=31) After retessellation of defect 15, euler #=-6 (134708,403923,269209) : difference with theory (-6) = 0 CORRECTING DEFECT 16 (vertices=87, convex hull=122) After retessellation of defect 16, euler #=-5 (134741,404073,269327) : difference with theory (-5) = 0 CORRECTING DEFECT 17 (vertices=23, convex hull=54) After retessellation of defect 17, euler #=-4 (134751,404126,269371) : difference with theory (-4) = 0 CORRECTING DEFECT 18 (vertices=15, convex hull=23) After retessellation of defect 18, euler #=-3 (134754,404142,269385) : difference with theory (-3) = 0 CORRECTING DEFECT 19 (vertices=16, convex hull=15) After retessellation of defect 19, euler #=-2 (134754,404146,269390) : difference with theory (-2) = 0 CORRECTING DEFECT 20 (vertices=19, convex hull=51) After retessellation of defect 20, euler #=-1 (134766,404200,269433) : difference with theory (-1) = 0 CORRECTING DEFECT 21 (vertices=118, convex hull=65) After retessellation of defect 21, euler #=0 (134777,404262,269485) : difference with theory (0) = 0 CORRECTING DEFECT 22 (vertices=105, convex hull=95) After retessellation of defect 22, euler #=1 (134796,404361,269566) : difference with theory (1) = 0 CORRECTING DEFECT 23 (vertices=33, convex hull=60) After retessellation of defect 23, euler #=2 (134806,404412,269608) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.10-->8.46) (max @ vno 51160 --> 56118) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.10-->8.46) (max @ vno 51160 --> 56118) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (37.2%), 137 crossovers (62.8%), 85 vertices were eliminated building final representation... 1154 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134806, nf=269608, ne=404412, g=0) writing corrected surface to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 13.8 minutes 0 defective edges removing intersecting faces 000: 171 intersecting 001: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 134806 - 404412 + 269608 = 2 --> 0 holes F =2V-4: 269608 = 269612-4 (0) 2E=3F: 808824 = 808824 (0) total defect index = 0 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 43 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri Sep 18 19:50:45 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 7.9 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.72 +- 0.91 3825 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=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.8, 20 (20) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.33) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2614 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5028703.0, rms=9.93 001: dt: 0.5000, sse=5798095.0, rms=7.145 (0.000%) 002: dt: 0.5000, sse=6203343.0, rms=5.512 (0.000%) 003: dt: 0.5000, sse=6482051.5, rms=4.508 (0.000%) 004: dt: 0.5000, sse=6737260.0, rms=3.876 (0.000%) 005: dt: 0.5000, sse=6852365.5, rms=3.535 (0.000%) 006: dt: 0.5000, sse=6976557.5, rms=3.322 (0.000%) 007: dt: 0.5000, sse=7006738.0, rms=3.233 (0.000%) 008: dt: 0.5000, sse=7047161.5, rms=3.151 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7017312.0, rms=3.132 (0.000%) 010: dt: 0.2500, sse=4336957.5, rms=2.129 (0.000%) 011: dt: 0.2500, sse=4010876.8, rms=1.885 (0.000%) 012: dt: 0.2500, sse=3853105.2, rms=1.832 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3813539.0, rms=1.801 (0.000%) rms = 1.76, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3750707.5, rms=1.764 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.7, 51 (5) missing vertices, mean dist -0.2 [0.4 (%72.0)->0.3 (%28.0))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.59) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.38 3687 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4287212.5, rms=4.33 015: dt: 0.5000, sse=4680078.5, rms=2.730 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4372707.5, rms=2.168 (0.000%) 017: dt: 0.2500, sse=4217287.5, rms=1.751 (0.000%) 018: dt: 0.2500, sse=4125774.8, rms=1.579 (0.000%) 019: dt: 0.2500, sse=4071074.8, rms=1.525 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4054175.8, rms=1.503 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4010530.0, rms=1.472 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.0, 39 (3) missing vertices, mean dist -0.1 [0.3 (%71.2)->0.2 (%28.8))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->4.66) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.90) mean absolute distance = 0.22 +- 0.31 3608 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4208390.0, rms=3.25 022: dt: 0.5000, sse=4531338.0, rms=2.426 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4266951.5, rms=1.765 (0.000%) 024: dt: 0.2500, sse=4186573.8, rms=1.436 (0.000%) 025: dt: 0.2500, sse=4155218.8, rms=1.354 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4130778.0, rms=1.353 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4097113.2, rms=1.324 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.8, 53 (1) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4112361.8, rms=1.66 rms = 1.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=5244013.0, rms=1.628 (0.000%) 029: dt: 0.2500, sse=4485060.5, rms=1.269 (0.000%) 030: dt: 0.2500, sse=4692758.0, rms=1.096 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.06, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4654068.0, rms=1.065 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 15 non-cortical segments detected only using segment with 2313 vertices erasing segment 1 (vno[0] = 45502) erasing segment 2 (vno[0] = 50090) erasing segment 3 (vno[0] = 83943) erasing segment 4 (vno[0] = 94873) erasing segment 5 (vno[0] = 94892) erasing segment 6 (vno[0] = 94904) erasing segment 7 (vno[0] = 95880) erasing segment 8 (vno[0] = 96851) erasing segment 9 (vno[0] = 99617) erasing segment 10 (vno[0] = 101371) erasing segment 11 (vno[0] = 102196) erasing segment 12 (vno[0] = 102270) erasing segment 13 (vno[0] = 103084) erasing segment 14 (vno[0] = 103867) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/rh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.curv writing smoothed area to rh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.area vertex spacing 0.89 +- 0.25 (0.02-->4.59) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.87) refinement took 5.2 minutes #-------------------------------------------- #@# Smooth2 rh Fri Sep 18 19:55:55 EDT 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Fri Sep 18 19:55:58 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 45.8 mm, total surface area = 81367 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.117 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 148 vertices thresholded to be in k1 ~ [-0.39 0.34], k2 ~ [-0.11 0.11] total integrated curvature = 0.562*4pi (7.068) --> 0 handles ICI = 1.4, FI = 8.6, variation=149.358 111 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 126 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats rh Fri Sep 18 19:57:58 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 247 ] Gb_filter = 0 WARN: S lookup min: -0.713181 WARN: S explicit min: 0.000000 vertex = 427 #-------------------------------------------- #@# Sphere rh Fri Sep 18 19:58:04 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.290... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %20.08 pass 1: epoch 2 of 3 starting distance error %20.00 unfolding complete - removing small folds... starting distance error %19.91 removing remaining folds... final distance error %19.93 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.72 hours #-------------------------------------------- #@# Surf Reg rh Fri Sep 18 20:41:31 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_register -curv ../surf/rh.sphere /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, 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 = 0.590 curvature mean = 0.038, std = 0.931 curvature mean = 0.022, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 16.00) sse = 377629.5, tmin=0.9568 d=32.00 min @ (0.00, 8.00, 0.00) sse = 333386.8, tmin=1.9129 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 314571.8, tmin=2.8801 d=8.00 min @ (0.00, 2.00, -2.00) sse = 313948.2, tmin=3.8850 d=4.00 min @ (0.00, -1.00, 1.00) sse = 312803.1, tmin=4.9172 d=2.00 min @ (0.00, 0.00, -0.50) sse = 312781.5, tmin=5.9776 d=1.00 min @ (0.00, 0.00, 0.25) sse = 312736.7, tmin=7.0393 d=0.50 min @ (0.00, -0.12, 0.00) sse = 312731.5, tmin=8.0708 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.07 min curvature mean = 0.024, std = 0.960 curvature mean = 0.007, std = 0.938 curvature mean = 0.021, std = 0.970 curvature mean = 0.004, std = 0.972 curvature mean = 0.020, std = 0.970 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.028, std = 0.391 curvature mean = 0.006, std = 0.070 curvature mean = 0.049, std = 0.262 curvature mean = 0.006, std = 0.083 curvature mean = 0.023, std = 0.409 curvature mean = 0.006, std = 0.089 curvature mean = 0.013, std = 0.517 curvature mean = 0.007, std = 0.092 curvature mean = 0.004, std = 0.605 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Fri Sep 18 21:04:59 EDT 2015 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Fri Sep 18 21:05:02 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri Sep 18 21:05:07 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1183 labels changed using aseg relabeling using gibbs priors... 000: 3078 changed, 134806 examined... 001: 690 changed, 13166 examined... 002: 181 changed, 3798 examined... 003: 67 changed, 1081 examined... 004: 28 changed, 395 examined... 005: 9 changed, 155 examined... 006: 8 changed, 65 examined... 007: 5 changed, 43 examined... 008: 1 changed, 21 examined... 009: 0 changed, 7 examined... 153 labels changed using aseg 000: 96 total segments, 57 labels (478 vertices) changed 001: 40 total segments, 2 labels (2 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1134 vertices marked for relabeling... 1134 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 43 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri Sep 18 21:05:50 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 7.9 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.73 +- 0.92 3426 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 384 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=80.8, 25 (24) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.33) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2648 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5038844.0, rms=9.92 001: dt: 0.5000, sse=5814627.5, rms=7.139 (0.000%) 002: dt: 0.5000, sse=6222935.5, rms=5.509 (0.000%) 003: dt: 0.5000, sse=6502243.5, rms=4.506 (0.000%) 004: dt: 0.5000, sse=6758716.5, rms=3.876 (0.000%) 005: dt: 0.5000, sse=6871853.0, rms=3.535 (0.000%) 006: dt: 0.5000, sse=6998138.5, rms=3.322 (0.000%) 007: dt: 0.5000, sse=7027588.5, rms=3.234 (0.000%) 008: dt: 0.5000, sse=7068909.0, rms=3.152 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7037584.5, rms=3.133 (0.000%) 010: dt: 0.2500, sse=4353948.5, rms=2.132 (0.000%) 011: dt: 0.2500, sse=4026537.0, rms=1.889 (0.000%) 012: dt: 0.2500, sse=3868687.5, rms=1.836 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3828527.0, rms=1.805 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3765107.0, rms=1.768 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 297 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 22 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown mean border=83.7, 55 (6) missing vertices, mean dist -0.2 [0.4 (%71.9)->0.3 (%28.1))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.59) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.39 3727 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4305371.5, rms=4.33 015: dt: 0.5000, sse=4697748.0, rms=2.730 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4391852.0, rms=2.169 (0.000%) 017: dt: 0.2500, sse=4239539.5, rms=1.753 (0.000%) 018: dt: 0.2500, sse=4146410.0, rms=1.581 (0.000%) 019: dt: 0.2500, sse=4091415.0, rms=1.528 (0.000%) rms = 1.51, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4074417.2, rms=1.506 (0.000%) rms = 1.48, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4030618.8, rms=1.475 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 300 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=86.0, 40 (3) missing vertices, mean dist -0.1 [0.3 (%71.1)->0.2 (%28.9))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->4.66) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.90) mean absolute distance = 0.22 +- 0.31 2768 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4228552.0, rms=3.25 022: dt: 0.5000, sse=4553882.5, rms=2.425 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4287966.5, rms=1.766 (0.000%) 024: dt: 0.2500, sse=4205730.0, rms=1.439 (0.000%) 025: dt: 0.2500, sse=4176810.0, rms=1.357 (0.000%) rms = 1.36, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4150228.8, rms=1.357 (0.000%) rms = 1.33, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4117656.2, rms=1.327 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 304 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=86.8, 54 (1) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4133005.5, rms=1.67 rms = 1.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=5277291.5, rms=1.628 (0.000%) 029: dt: 0.2500, sse=4514169.5, rms=1.271 (0.000%) 030: dt: 0.2500, sse=4722153.5, rms=1.099 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4683113.5, rms=1.068 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=60.2, 49 (49) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.6 (%100.0))] %19 local maxima, %45 large gradients and %32 min vals, 2376 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21254276.0, rms=26.82 001: dt: 0.5000, sse=16363014.0, rms=23.004 (0.000%) 002: dt: 0.5000, sse=12765346.0, rms=19.767 (0.000%) 003: dt: 0.5000, sse=10241108.0, rms=17.081 (0.000%) 004: dt: 0.5000, sse=8602027.0, rms=14.855 (0.000%) 005: dt: 0.5000, sse=7530341.0, rms=13.020 (0.000%) 006: dt: 0.5000, sse=6845582.0, rms=11.543 (0.000%) 007: dt: 0.5000, sse=6417503.0, rms=10.267 (0.000%) 008: dt: 0.5000, sse=6131376.5, rms=9.129 (0.000%) 009: dt: 0.5000, sse=5967624.0, rms=8.078 (0.000%) 010: dt: 0.5000, sse=5861806.0, rms=7.133 (0.000%) 011: dt: 0.5000, sse=5848593.0, rms=6.277 (0.000%) 012: dt: 0.5000, sse=5832226.5, rms=5.527 (0.000%) 013: dt: 0.5000, sse=5939219.5, rms=4.900 (0.000%) 014: dt: 0.5000, sse=5983240.5, rms=4.446 (0.000%) 015: dt: 0.5000, sse=6110336.0, rms=4.119 (0.000%) 016: dt: 0.5000, sse=6144840.5, rms=3.911 (0.000%) 017: dt: 0.5000, sse=6209216.0, rms=3.767 (0.000%) 018: dt: 0.5000, sse=6223545.5, rms=3.676 (0.000%) 019: dt: 0.5000, sse=6279600.0, rms=3.602 (0.000%) rms = 3.56, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6271217.5, rms=3.560 (0.000%) 021: dt: 0.2500, sse=4564613.0, rms=2.979 (0.000%) 022: dt: 0.2500, sse=4422597.5, rms=2.819 (0.000%) rms = 2.80, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4324017.0, rms=2.795 (0.000%) 024: dt: 0.1250, sse=4158617.8, rms=2.716 (0.000%) rms = 2.71, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4138553.0, rms=2.705 (0.000%) positioning took 2.6 minutes mean border=58.0, 1051 (3) missing vertices, mean dist 0.2 [0.2 (%44.6)->0.6 (%55.4))] %38 local maxima, %31 large gradients and %26 min vals, 876 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4744649.0, rms=4.66 026: dt: 0.5000, sse=4932263.5, rms=3.755 (0.000%) 027: dt: 0.5000, sse=6193329.5, rms=3.613 (0.000%) rms = 3.60, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=6060425.5, rms=3.598 (0.000%) 029: dt: 0.2500, sse=5033093.5, rms=2.879 (0.000%) 030: dt: 0.2500, sse=4903777.0, rms=2.686 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4841873.5, rms=2.672 (0.000%) 032: dt: 0.1250, sse=4692738.0, rms=2.562 (0.000%) rms = 2.54, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4682554.5, rms=2.544 (0.000%) positioning took 0.8 minutes mean border=56.5, 1317 (2) missing vertices, mean dist 0.1 [0.2 (%39.1)->0.4 (%60.9))] %52 local maxima, %18 large gradients and %25 min vals, 951 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4820253.0, rms=3.30 rms = 3.35, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4659440.5, rms=2.937 (0.000%) 035: dt: 0.2500, sse=4677714.0, rms=2.701 (0.000%) 036: dt: 0.2500, sse=4850115.0, rms=2.628 (0.000%) rms = 2.60, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4909077.0, rms=2.601 (0.000%) 038: dt: 0.1250, sse=4805551.5, rms=2.527 (0.000%) rms = 2.51, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4821908.5, rms=2.510 (0.000%) positioning took 0.7 minutes mean border=55.8, 2795 (2) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.3 (%55.4))] %55 local maxima, %14 large gradients and %25 min vals, 833 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4845860.5, rms=2.70 rms = 3.04, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4771183.0, rms=2.552 (0.000%) 041: dt: 0.2500, sse=4952673.0, rms=2.493 (0.000%) rms = 2.47, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5020869.0, rms=2.470 (0.000%) 043: dt: 0.1250, sse=4939721.0, rms=2.406 (0.000%) rms = 2.39, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4966083.0, rms=2.389 (0.000%) positioning took 0.6 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.area.pial vertex spacing 1.01 +- 0.44 (0.05-->7.36) (max @ vno 101451 --> 134658) face area 0.40 +- 0.31 (0.00-->5.11) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 817:1388 truncations. 25712 vertices at 0 distance 83583 vertices at 1 distance 85081 vertices at 2 distance 42066 vertices at 3 distance 14483 vertices at 4 distance 4522 vertices at 5 distance 1434 vertices at 6 distance 510 vertices at 7 distance 240 vertices at 8 distance 129 vertices at 9 distance 62 vertices at 10 distance 49 vertices at 11 distance 41 vertices at 12 distance 55 vertices at 13 distance 25 vertices at 14 distance 15 vertices at 15 distance 11 vertices at 16 distance 16 vertices at 17 distance 6 vertices at 18 distance 6 vertices at 19 distance 6 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.thickness positioning took 11.2 minutes #-------------------------------------------- #@# Surf Volume rh Fri Sep 18 21:17:00 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Fri Sep 18 21:17:00 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts pctsurfcon --s af1021_recon --rh-only Log file is /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts/pctsurfcon.log Fri Sep 18 21:17:00 EDT 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori cd /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-4.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.15805/rh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 = 73363 Masking with /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.15805/rh.wm.mgh Dim: 134806 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.15805/rh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 = 87880 Masking with /share/VA_Imaging/Projects/shayes/tori/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.15805/rh.gm.mgh Dim: 134806 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.15805/rh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/tmp.pctsurfcon.15805/rh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/af1021_recon/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-4.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.w-g.pct.mgh Vertex Area is 0.661523 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1561 1094.279 2 2002 caudalanteriorcingulate 1237 808.057 3 2003 caudalmiddlefrontal 2992 2066.130 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2205 1402.712 6 2006 entorhinal 634 426.316 7 2007 fusiform 5330 3566.980 8 2008 inferiorparietal 8292 5603.694 9 2009 inferiortemporal 4337 2926.609 10 2010 isthmuscingulate 1237 797.656 11 2011 lateraloccipital 7249 4645.855 12 2012 lateralorbitofrontal 3685 2487.292 13 2013 lingual 5101 3366.425 14 2014 medialorbitofrontal 2789 1878.021 15 2015 middletemporal 4389 3011.584 16 2016 parahippocampal 1269 805.625 17 2017 paracentral 2191 1352.664 18 2018 parsopercularis 2339 1549.661 19 2019 parsorbitalis 1100 797.024 20 2020 parstriangularis 2143 1427.397 21 2021 pericalcarine 2366 1577.206 22 2022 postcentral 5734 3554.974 23 2023 posteriorcingulate 1898 1275.721 24 2024 precentral 7196 4670.821 25 2025 precuneus 6268 4230.708 26 2026 rostralanteriorcingulate 744 478.121 27 2027 rostralmiddlefrontal 8736 5933.263 28 2028 superiorfrontal 9154 6337.103 29 2029 superiorparietal 7347 4721.856 30 2030 superiortemporal 5905 3912.371 31 2031 supramarginal 6011 3964.572 32 2032 frontalpole 442 293.571 33 2033 temporalpole 533 364.143 34 2034 transversetemporal 700 410.010 35 2035 insula 3150 2052.494 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Fri Sep 18 21:17:08 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 1561 1094 3002 2.678 0.485 0.130 0.035 19 2.4 bankssts 1237 808 2367 2.551 0.785 0.166 0.061 25 3.0 caudalanteriorcingulate 2992 2066 6062 2.585 0.499 0.137 0.046 38 5.9 caudalmiddlefrontal 2205 1403 3387 2.051 0.517 0.169 0.086 49 9.2 cuneus 634 426 1927 3.126 0.819 0.170 0.086 12 2.2 entorhinal 5330 3567 12008 2.899 0.695 0.153 0.068 105 14.5 fusiform 8292 5604 15300 2.399 0.581 0.155 0.121 246 21.1 inferiorparietal 4337 2927 9814 2.877 0.759 0.156 0.079 129 15.6 inferiortemporal 1237 798 2164 2.590 0.689 0.154 0.064 23 3.0 isthmuscingulate 7249 4646 11880 2.292 0.556 0.155 0.061 126 19.1 lateraloccipital 3685 2487 7638 2.612 0.796 0.170 0.081 96 12.3 lateralorbitofrontal 5101 3366 7867 2.227 0.600 0.168 0.074 179 16.0 lingual 2789 1878 5572 2.502 0.836 0.164 0.082 77 9.4 medialorbitofrontal 4389 3012 11288 3.047 0.663 0.154 0.094 116 11.5 middletemporal 1269 806 2365 2.560 0.570 0.114 0.042 11 2.4 parahippocampal 2191 1353 3558 2.496 0.525 0.129 0.089 66 4.0 paracentral 2339 1550 4616 2.769 0.453 0.132 0.053 31 4.9 parsopercularis 1100 797 3032 2.804 0.762 0.183 0.085 24 3.8 parsorbitalis 2143 1427 4207 2.505 0.567 0.141 0.053 31 4.3 parstriangularis 2366 1577 2810 1.917 0.542 0.157 0.071 41 7.1 pericalcarine 5734 3555 8484 2.120 0.694 0.129 0.051 73 13.2 postcentral 1898 1276 3714 2.598 0.800 0.172 0.066 40 5.1 posteriorcingulate 7196 4671 12734 2.528 0.630 0.140 1.530 436 15.2 precentral 6268 4231 11187 2.497 0.576 0.151 0.055 105 14.0 precuneus 744 478 1623 2.703 0.966 0.152 0.061 13 1.9 rostralanteriorcingulate 8736 5933 16125 2.265 0.678 0.166 0.089 328 30.7 rostralmiddlefrontal 9154 6337 21312 2.865 0.688 0.149 0.059 145 21.0 superiorfrontal 7347 4722 11901 2.222 0.549 0.141 0.051 102 15.6 superiorparietal 5905 3912 14316 3.092 0.761 0.143 0.064 112 13.4 superiortemporal 6011 3965 11381 2.675 0.591 0.138 0.053 91 12.0 supramarginal 442 294 1025 2.457 0.870 0.211 0.099 19 1.8 frontalpole 533 364 1986 3.610 1.126 0.198 0.122 20 2.2 temporalpole 700 410 1223 2.508 0.372 0.132 0.073 11 1.4 transversetemporal 3150 2052 6867 3.245 0.861 0.133 0.109 89 18.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri Sep 18 21:17:22 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 14 labels changed using aseg relabeling using gibbs priors... 000: 9872 changed, 134806 examined... 001: 2371 changed, 37485 examined... 002: 750 changed, 11992 examined... 003: 325 changed, 4245 examined... 004: 164 changed, 1795 examined... 005: 78 changed, 888 examined... 006: 32 changed, 429 examined... 007: 15 changed, 184 examined... 008: 6 changed, 91 examined... 009: 5 changed, 32 examined... 010: 2 changed, 24 examined... 011: 0 changed, 12 examined... 13 labels changed using aseg 000: 304 total segments, 216 labels (2977 vertices) changed 001: 102 total segments, 14 labels (41 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 183 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 603 vertices marked for relabeling... 603 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 50 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri Sep 18 21:18:13 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 1163 800 2042 2.012 0.761 0.177 0.071 27 3.4 G_and_S_frontomargin 1251 835 2755 2.819 0.508 0.158 0.054 20 2.8 G_and_S_occipital_inf 1356 737 2063 2.331 0.480 0.133 0.130 62 3.3 G_and_S_paracentral 1501 1007 3314 2.933 0.554 0.165 0.060 28 3.6 G_and_S_subcentral 782 527 2033 2.685 0.732 0.228 0.130 94 4.5 G_and_S_transv_frontopol 2350 1592 4837 2.825 0.773 0.151 0.068 43 6.1 G_and_S_cingul-Ant 1401 973 3008 2.850 0.553 0.152 0.052 23 3.0 G_and_S_cingul-Mid-Ant 1421 960 2709 2.673 0.511 0.146 0.054 22 2.9 G_and_S_cingul-Mid-Post 471 315 1242 3.117 0.748 0.211 0.103 14 2.1 G_cingul-Post-dorsal 304 181 571 2.691 0.527 0.167 0.094 8 1.2 G_cingul-Post-ventral 1881 1212 2632 1.893 0.495 0.171 0.094 44 8.8 G_cuneus 1462 965 3383 2.858 0.429 0.158 0.075 32 4.3 G_front_inf-Opercular 323 215 849 2.839 0.616 0.172 0.076 8 0.9 G_front_inf-Orbital 1064 709 2498 2.675 0.563 0.150 0.056 18 2.1 G_front_inf-Triangul 3653 2521 8798 2.637 0.646 0.174 0.111 132 16.5 G_front_middle 6709 4532 17152 2.986 0.693 0.164 0.069 136 18.3 G_front_sup 451 302 1293 3.915 0.967 0.133 0.366 43 11.4 G_Ins_lg_and_S_cent_ins 639 401 2034 3.861 0.730 0.142 0.076 15 1.9 G_insular_short 2060 1295 4462 2.587 0.459 0.158 0.061 41 5.0 G_occipital_middle 1892 1174 3280 2.283 0.581 0.146 0.050 27 4.2 G_occipital_sup 2040 1306 4855 2.979 0.621 0.165 0.080 54 5.9 G_oc-temp_lat-fusifor 3192 2075 5344 2.293 0.624 0.179 0.089 68 11.8 G_oc-temp_med-Lingual 1663 1044 4542 3.124 0.790 0.153 0.078 36 5.2 G_oc-temp_med-Parahip 2806 1911 7753 2.907 0.785 0.202 0.115 139 13.3 G_orbital 2777 1871 6397 2.678 0.695 0.176 0.084 111 9.5 G_pariet_inf-Angular 2733 1750 5996 2.902 0.568 0.148 0.059 52 6.1 G_pariet_inf-Supramar 2272 1486 4318 2.343 0.532 0.149 0.058 35 5.7 G_parietal_sup 2264 1255 3443 2.176 0.631 0.123 0.060 32 6.9 G_postcentral 2603 1566 5283 2.671 0.605 0.135 4.131 373 5.5 G_precentral 2905 1977 6145 2.478 0.524 0.160 0.061 59 7.2 G_precuneus 798 514 2067 2.836 0.559 0.180 0.078 27 2.6 G_rectus 329 224 413 1.692 0.808 0.125 0.109 9 1.2 G_subcallosal 500 292 973 2.511 0.415 0.144 0.088 9 1.3 G_temp_sup-G_T_transv 2215 1464 7183 3.533 0.693 0.174 0.075 49 6.6 G_temp_sup-Lateral 635 418 1822 3.608 0.731 0.158 0.091 13 2.0 G_temp_sup-Plan_polar 915 615 1816 2.606 0.499 0.122 0.058 14 1.8 G_temp_sup-Plan_tempo 2136 1437 5775 3.092 0.864 0.171 0.089 62 8.3 G_temporal_inf 2544 1739 7644 3.187 0.593 0.169 0.090 72 7.9 G_temporal_middle 344 232 556 2.292 0.471 0.128 0.041 4 0.6 Lat_Fis-ant-Horizont 139 94 258 2.540 0.293 0.085 0.020 1 0.1 Lat_Fis-ant-Vertical 1959 1307 2908 2.591 0.463 0.125 0.038 19 3.0 Lat_Fis-post 3298 2062 5023 2.086 0.582 0.174 0.089 86 12.8 Pole_occipital 1763 1222 6098 3.305 0.956 0.194 0.126 92 9.1 Pole_temporal 2839 1892 3519 2.043 0.553 0.153 0.058 125 6.9 S_calcarine 2760 1918 2905 1.726 0.478 0.136 0.054 30 5.3 S_central 1377 940 2170 2.469 0.513 0.136 0.044 17 2.4 S_cingul-Marginalis 627 439 1000 2.741 0.410 0.116 0.034 4 1.0 S_circular_insula_ant 1396 887 2181 2.664 0.584 0.095 0.033 8 1.7 S_circular_insula_inf 1454 970 2330 2.768 0.622 0.121 0.046 14 3.0 S_circular_insula_sup 925 612 2177 3.197 0.784 0.152 0.078 16 3.4 S_collat_transv_ant 796 532 924 2.075 0.472 0.155 0.057 10 1.8 S_collat_transv_post 2741 1827 4526 2.421 0.532 0.130 0.041 27 4.8 S_front_inf 2270 1513 3386 2.015 0.562 0.155 0.070 43 5.4 S_front_middle 2366 1656 3856 2.318 0.489 0.117 0.037 21 3.7 S_front_sup 509 342 685 2.248 0.500 0.130 0.056 7 0.9 S_interm_prim-Jensen 3052 2026 4138 2.091 0.510 0.140 0.047 38 5.9 S_intrapariet_and_P_trans 1209 811 1624 2.072 0.435 0.136 0.046 13 2.3 S_oc_middle_and_Lunatus 1088 714 1286 1.990 0.360 0.131 0.043 11 1.8 S_oc_sup_and_transversal 924 620 1295 2.443 0.308 0.125 0.036 8 1.4 S_occipital_ant 1239 877 2009 2.535 0.383 0.134 0.043 15 2.2 S_oc-temp_lat 2261 1550 3372 2.452 0.446 0.117 0.033 16 3.1 S_oc-temp_med_and_Lingual 476 334 638 2.083 0.480 0.127 0.042 4 0.8 S_orbital_lateral 767 556 1110 1.862 0.586 0.116 0.032 6 1.1 S_orbital_med-olfact 1325 896 2304 2.359 0.709 0.161 0.067 25 3.5 S_orbital-H_Shaped 2691 1777 3908 2.428 0.629 0.140 0.043 31 4.9 S_parieto_occipital 1593 997 1596 1.969 0.732 0.156 0.056 28 3.6 S_pericallosal 2179 1449 2732 2.012 0.426 0.114 0.033 17 3.1 S_postcentral 1973 1375 3582 2.580 0.519 0.125 0.039 19 3.0 S_precentral-inf-part 796 540 1133 2.456 0.511 0.125 0.037 6 1.3 S_precentral-sup-part 174 128 329 2.768 0.867 0.153 0.040 2 0.3 S_suborbital 958 650 1788 2.641 0.487 0.141 0.049 11 1.9 S_subparietal 1097 736 1770 2.640 0.547 0.139 0.140 32 2.5 S_temporal_inf 7134 4904 12511 2.548 0.537 0.134 0.119 166 13.0 S_temporal_sup 304 208 390 2.361 0.215 0.129 0.031 3 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Fri Sep 18 21:18:29 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1166 labels changed using aseg relabeling using gibbs priors... 000: 2638 changed, 134806 examined... 001: 614 changed, 11352 examined... 002: 165 changed, 3301 examined... 003: 83 changed, 1023 examined... 004: 30 changed, 457 examined... 005: 15 changed, 180 examined... 006: 4 changed, 84 examined... 007: 1 changed, 25 examined... 008: 1 changed, 7 examined... 009: 1 changed, 7 examined... 010: 1 changed, 7 examined... 011: 1 changed, 7 examined... 012: 1 changed, 7 examined... 013: 1 changed, 7 examined... 014: 1 changed, 7 examined... 015: 0 changed, 8 examined... 119 labels changed using aseg 000: 59 total segments, 26 labels (123 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 57 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 724 vertices marked for relabeling... 724 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Fri Sep 18 21:19:09 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/af1021_recon/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 1205 788 2343 2.587 0.767 0.166 0.060 25 2.9 caudalanteriorcingulate 3010 2070 6052 2.594 0.501 0.137 0.046 39 5.9 caudalmiddlefrontal 2707 1748 4104 2.075 0.512 0.163 0.068 53 8.4 cuneus 634 429 1922 3.128 0.829 0.168 0.086 12 2.2 entorhinal 4675 3113 10129 2.891 0.694 0.149 0.066 87 12.1 fusiform 7762 5232 14182 2.395 0.591 0.156 0.127 238 20.1 inferiorparietal 4988 3372 11604 2.876 0.751 0.157 0.078 143 17.3 inferiortemporal 1255 806 2180 2.589 0.685 0.153 0.064 23 3.0 isthmuscingulate 7508 4803 12412 2.294 0.560 0.156 0.062 134 19.9 lateraloccipital 4239 2871 9044 2.518 0.841 0.181 0.088 158 15.4 lateralorbitofrontal 5145 3397 7890 2.225 0.597 0.168 0.072 173 16.0 lingual 2179 1461 4686 2.582 0.806 0.167 0.081 62 7.6 medialorbitofrontal 5350 3681 13176 2.986 0.646 0.151 0.087 128 13.5 middletemporal 1201 766 2255 2.562 0.566 0.114 0.043 11 2.3 parahippocampal 2234 1388 3653 2.502 0.530 0.129 0.088 67 4.0 paracentral 2416 1596 4714 2.757 0.449 0.132 0.052 33 4.9 parsopercularis 1216 832 2845 2.734 0.734 0.156 0.072 20 3.2 parsorbitalis 2299 1539 4517 2.477 0.582 0.139 0.049 33 4.4 parstriangularis 2441 1605 2858 1.898 0.538 0.159 0.087 51 9.4 pericalcarine 6148 3839 9026 2.113 0.683 0.130 0.050 77 14.0 postcentral 1989 1331 3872 2.595 0.802 0.172 0.067 42 5.5 posteriorcingulate 7051 4583 12463 2.525 0.631 0.141 1.561 435 15.2 precentral 6302 4234 11461 2.507 0.569 0.152 0.056 109 14.4 precuneus 890 572 1873 2.709 0.928 0.148 0.058 14 2.1 rostralanteriorcingulate 5955 4085 11609 2.349 0.665 0.165 0.094 170 21.8 rostralmiddlefrontal 12021 8260 26064 2.694 0.761 0.154 0.064 276 30.6 superiorfrontal 6248 4036 10278 2.238 0.555 0.139 0.050 84 12.9 superiorparietal 7757 5185 18912 3.077 0.795 0.148 0.066 159 18.6 superiortemporal 5807 3836 10950 2.669 0.580 0.137 0.052 87 11.4 supramarginal 705 415 1233 2.509 0.373 0.131 0.072 11 1.4 transversetemporal 2927 1917 6435 3.253 0.846 0.126 0.104 76 16.9 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Fri Sep 18 21:19:24 EDT 2015 bbregister --s af1021_recon --mov /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/FLAIRraw.mgz --lta /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/FLAIRraw.lta --init-fsl --T2 Log file is /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/FLAIRraw.dat.log Fri Sep 18 21:19:24 EDT 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori cd /share/VA_Imaging/Projects/shayes/tori/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/bbregister --s af1021_recon --mov /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/FLAIRraw.mgz --lta /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/FLAIRraw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux compute-0-4.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_convert /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/FLAIRraw.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/tmp.bbregister.16058/template.nii mri_convert /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/FLAIRraw.mgz /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/tmp.bbregister.16058/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/orig/FLAIRraw.mgz... TR=6000.00, TE=475.00, TI=2100.00, flip angle=120.00 i_ras = (0.0313814, -0.959852, 0.278747) j_ras = (0.0851089, -0.275305, -0.957582) k_ras = (-0.995877, -0.053774, -0.0730522) writing to /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/tmp.bbregister.16058/template.nii... fslregister --s af1021_recon --mov /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/tmp.bbregister.16058/template.nii --reg /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/tmp.bbregister.16058/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /share/VA_Imaging/Projects/shayes/tori/af1021_recon/mri/transforms/tmp.bbregister.16058/fslregister --dof 6 --fsvol brainmask.mgz ERROR: cannot find /share/apps/fsl/etc/flirtsch/xyztrans.sch Linux compute-0-4.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all -s af1021_recon exited with ERRORS at Fri Sep 18 21:19:25 EDT 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Oct 20 10:20:25 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon /share/apps/freesurfer-5.3.0/bin/recon-all -all -subject af1021_recon -FLAIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/T2_FLAIR/001.mgz -FLAIRpial -no-isrunning subjid af1021_recon setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /share/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux compute-0-1.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 41943040 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 401408 total used free shared buffers cached Mem: 49449548 45677700 3771848 0 252408 44175464 -/+ buffers/cache: 1249828 48199720 Swap: 1020116 244 1019872 ######################################## 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: 2015/10/20-14:20:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/10/20-14:20:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/10/20-14:20:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:27-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:28-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:29-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:29-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:29-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:29-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:30-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:30-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:30-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:31-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:31-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:31-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:32-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:32-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:32-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:33-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:33-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:33-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:33-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:34-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:34-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/10/20-14:20:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/10/20-14:20:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/10/20-14:20:38-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: twilliams Machine: compute-0-1.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /share/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /share/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Tue Oct 20 10:20:38 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/T2_FLAIR/001.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/T2_FLAIR/001.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/T2_FLAIR/001.mgz... TR=6000.00, TE=475.00, TI=2100.00, flip angle=120.00 i_ras = (0.0313814, -0.959852, 0.278747) j_ras = (0.0851089, -0.275305, -0.957582) k_ras = (-0.995877, -0.053774, -0.0730522) writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz... #-------------------------------------------- #@# MotionCor Tue Oct 20 10:20:43 EDT 2015 Found 1 runs /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/001.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz --conform mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz... TR=2530.00, TE=3.32, TI=1100.00, flip angle=7.00 i_ras = (0.03293, -0.976376, 0.213556) j_ras = (0.0460134, -0.211964, -0.976194) k_ras = (-0.998398, -0.0419726, -0.0379467) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz... mri_add_xform_to_header -c /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/talairach.xfm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Oct 20 10:21:02 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Oct 20 10:26:35 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6523, pval=0.3663 >= threshold=0.0050) awk -f /share/apps/freesurfer-5.3.0/bin/extract_talairach_avi_QA.awk /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/talairach_avi.log tal_QC_AZS /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/talairach_avi.log TalAviQA: 0.97649 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Oct 20 10:26:37 EDT 2015 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri /share/apps/freesurfer-5.3.0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux compute-0-1.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux Tue Oct 20 10:26:37 EDT 2015 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.17083 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17083/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17083/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=2530.00, TE=3.32, TI=1100.00, flip angle=7.00 i_ras = (-1, 1.11759e-08, -5.58794e-08) j_ras = (-8.9407e-08, -1.40863e-08, -1) k_ras = (-8.56817e-08, 1, -9.42964e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17083/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Oct 20 10:26:50 EDT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.17083/nu0.mnc ./tmp.mri_nu_correct.mni.17083/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17083/0/ [twilliams@compute-0-1.local:/share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/] [2015-10-20 10:26:50] running: /share/apps/freesurfer-5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17083/0/ ./tmp.mri_nu_correct.mni.17083/nu0.mnc ./tmp.mri_nu_correct.mni.17083/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 34 CV of field change: 0.000963465 [twilliams@compute-0-1.local:/share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/] [2015-10-20 10:29:01] running: /share/apps/freesurfer-5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17083/nu0.mnc ./tmp.mri_nu_correct.mni.17083/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Tue Oct 20 10:29:49 EDT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.17083/nu1.mnc ./tmp.mri_nu_correct.mni.17083/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17083/1/ [twilliams@compute-0-1.local:/share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/] [2015-10-20 10:29:49] running: /share/apps/freesurfer-5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17083/1/ ./tmp.mri_nu_correct.mni.17083/nu1.mnc ./tmp.mri_nu_correct.mni.17083/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000979503 [twilliams@compute-0-1.local:/share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/] [2015-10-20 10:31:27] running: /share/apps/freesurfer-5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17083/nu1.mnc ./tmp.mri_nu_correct.mni.17083/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.17083/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17083/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17083/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17083/ones.mgz sysname Linux hostname compute-0-1.local machine x86_64 user twilliams input ./tmp.mri_nu_correct.mni.17083/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.17083/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.17083/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17083/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17083/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.17083/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17083/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17083/input.mean.dat sysname Linux hostname compute-0-1.local machine x86_64 user twilliams UseRobust 0 Loading ./tmp.mri_nu_correct.mni.17083/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.17083/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17083/ones.mgz --i ./tmp.mri_nu_correct.mni.17083/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17083/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17083/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.17083/ones.mgz --i ./tmp.mri_nu_correct.mni.17083/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17083/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17083/output.mean.dat sysname Linux hostname compute-0-1.local machine x86_64 user twilliams UseRobust 0 Loading ./tmp.mri_nu_correct.mni.17083/ones.mgz Loading ./tmp.mri_nu_correct.mni.17083/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.17083/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.17083/nu2.mnc ./tmp.mri_nu_correct.mni.17083/nu2.mnc mul .98442569500605742890 Saving result to './tmp.mri_nu_correct.mni.17083/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.17083/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.17083/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.17083/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.11759e-08, -5.58794e-08) j_ras = (-8.9407e-08, -1.40863e-08, -1) k_ras = (-8.56817e-08, 1, -9.42964e-09) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 13 seconds. mapping (10, 177) to ( 3, 110) Tue Oct 20 10:34:25 EDT 2015 mri_nu_correct.mni done mri_add_xform_to_header -c /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Oct 20 10:34:28 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.115 0.031 0.034 -4.191; -0.056 1.037 0.031 -32.102; -0.044 0.050 1.091 20.356; 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 = 21 Starting OpenSpline(): npoints = 21 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 65 (65), valley at 42 (42) csf peak at 32, setting threshold to 54 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 65 (65), valley at 30 (30) csf peak at 32, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 31 seconds. #-------------------------------------------- #@# Skull Stripping Tue Oct 20 10:37:01 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /share/apps/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.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=98 z=135 r=88 first estimation of the main basin volume: 2861614 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=148, y=81, z=97, Imax=255 CSF=13, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=25609129885 voxels, voxel volume =1.000 = 25609129885 mmm3 = 25609129.984 cm3 done. PostAnalyze...Basin Prior 22 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=128,y=101, z=127, r=9753 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=39 , nb = 44226 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=35 , nb = 3258 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 2736 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=38 , nb = 19098 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 18648 OTHER CSF_MIN=0, CSF_intensity=19, CSF_MAX=40 , nb = 486 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 39, 43, 46, 64 after analyzing : 39, 45, 46, 49 RIGHT_CER before analyzing : 35, 35, 36, 79 after analyzing : 20, 35, 36, 46 LEFT_CER before analyzing : 21, 30, 43, 70 after analyzing : 21, 38, 43, 46 RIGHT_BRAIN before analyzing : 38, 41, 44, 64 after analyzing : 38, 43, 44, 48 LEFT_BRAIN before analyzing : 38, 41, 44, 64 after analyzing : 38, 43, 44, 48 OTHER before analyzing : 40, 28, 19, 37 after analyzing : 25, 28, 28, 30 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.684, std = 7.062 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.61, sigma = 6.20 after rotation: sse = 4.61, sigma = 6.20 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.32, its var is 6.99 before Erosion-Dilatation 2.22% 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...50 iterations mri_strip_skull: done peeling brain Brain Size = 1605317 voxels, voxel volume = 1.000 mm3 = 1605317 mmm3 = 1605.317 cm3 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #------------------------------------- #@# EM Registration Tue Oct 20 10:37:44 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /share/apps/freesurfer-5.3.0/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 '/share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.9 skull bounding box = (64, 38, 43) --> (191, 154, 216) using (106, 77, 130) as brain centroid... mean wm in atlas = 107, using box (90,63,109) --> (121, 91,151) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.025071 @ (-9.091, 27.273, -27.273) max log p = -3.787479 @ (4.545, -4.545, 4.545) max log p = -3.766387 @ (2.273, -2.273, 2.273) max log p = -3.755645 @ (-1.136, -1.136, -1.136) max log p = -3.720972 @ (1.705, -0.568, -1.705) max log p = -3.720972 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 18.7, -23.3): log p = -3.721 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.7 (thresh=-3.7) 1.150 0.000 0.000 -20.982; 0.000 1.150 0.000 3.733; 0.000 0.000 1.000 -23.295; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4) 1.150 0.000 0.000 -20.982; 0.000 1.150 0.000 3.733; 0.000 0.000 1.000 -23.295; 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=-3.1, old_max_log_p =-3.4 (thresh=-3.4) 1.125 0.074 -0.034 -22.700; -0.074 1.167 -0.065 19.839; 0.041 0.077 1.015 -38.185; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.127 0.036 -0.033 -19.229; -0.035 1.170 -0.032 10.360; 0.043 0.038 0.998 -32.239; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.127 0.036 -0.033 -19.229; -0.035 1.170 -0.032 10.360; 0.043 0.038 0.998 -32.239; 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=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.125 0.026 -0.049 -15.419; -0.026 1.169 -0.033 8.848; 0.061 0.038 1.001 -35.560; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1) 1.125 0.026 -0.049 -15.419; -0.026 1.169 -0.033 8.848; 0.061 0.038 1.001 -35.560; 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 1.12464 0.02574 -0.04885 -15.41854; -0.02626 1.16925 -0.03276 8.84788; 0.06120 0.03830 1.00051 -35.56002; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.12464 0.02574 -0.04885 -15.41854; -0.02626 1.16925 -0.03276 8.84788; 0.06120 0.03830 1.00051 -35.56002; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.125 0.026 -0.049 -15.419; -0.026 1.169 -0.033 8.848; 0.061 0.038 1.001 -35.560; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.1 (old=-4.4) transform before final EM align: 1.125 0.026 -0.049 -15.419; -0.026 1.169 -0.033 8.848; 0.061 0.038 1.001 -35.560; 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 1.12464 0.02574 -0.04885 -15.41854; -0.02626 1.16925 -0.03276 8.84788; 0.06120 0.03830 1.00051 -35.56002; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.12464 0.02574 -0.04885 -15.41854; -0.02626 1.16925 -0.03276 8.84788; 0.06120 0.03830 1.00051 -35.56002; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 3.7 after pass:transform: ( 1.12, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 011: -log(p) = 3.7 after pass:transform: ( 1.12, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 012: -log(p) = 3.7 after pass:transform: ( 1.12, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 013: -log(p) = 3.7 after pass:transform: ( 1.12, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 014: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 015: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 016: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 017: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 018: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) dfp_em_step_func: 019: -log(p) = 3.7 after pass:transform: ( 1.13, 0.03, -0.05, -15.42) ( -0.03, 1.17, -0.03, 8.85) ( 0.06, 0.04, 1.00, -35.56) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 021: -log(p) = 3.7 tol 0.000000 final transform: 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 23 minutes and 10 seconds. #-------------------------------------- #@# CA Normalize Tue Oct 20 11:00:54 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=21.9 skull bounding box = (64, 38, 43) --> (191, 154, 216) using (106, 77, 130) as brain centroid... mean wm in atlas = 107, using box (90,63,109) --> (121, 91,151) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 244171 sample points... INFO: compute sample coordinates transform 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 43, 49) --> (187, 145, 217) Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 153.0 24 of 125 (19.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 43, 51) --> (131, 144, 218) Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 153.0 0 of 51 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 113, 69) --> (171, 151, 124) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 153.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 113, 69) --> (127, 150, 125) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 153.0 0 of 8 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 110, 103) --> (142, 168, 137) Brain_Stem: limiting intensities to 104.0 --> 153.0 5 of 10 (50.0%) samples deleted using 201 total control points for intensity normalization... bias field = 0.986 +- 0.063 0 of 172 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 43, 49) --> (187, 145, 217) Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 145.0 0 of 148 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 43, 51) --> (131, 144, 218) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 145.0 0 of 89 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 113, 69) --> (171, 151, 124) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 145.0 0 of 32 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 113, 69) --> (127, 150, 125) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 145.0 0 of 48 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 110, 103) --> (142, 168, 137) Brain_Stem: limiting intensities to 82.0 --> 145.0 0 of 94 (0.0%) samples deleted using 411 total control points for intensity normalization... bias field = 0.976 +- 0.069 0 of 411 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 43, 49) --> (187, 145, 217) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 146.0 0 of 263 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 43, 51) --> (131, 144, 218) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 146.0 0 of 194 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 113, 69) --> (171, 151, 124) Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 146.0 0 of 85 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (86, 113, 69) --> (127, 150, 125) Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 146.0 0 of 77 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 110, 103) --> (142, 168, 137) Brain_Stem: limiting intensities to 76.0 --> 146.0 0 of 127 (0.0%) samples deleted using 746 total control points for intensity normalization... bias field = 0.983 +- 0.047 1 of 746 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 46 seconds. #-------------------------------------- #@# CA Reg Tue Oct 20 11:02:40 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.32 (predicted orig area = 6.0) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.734, neg=0, invalid=96777 0001: dt=129.472000, rms=0.678 (7.633%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.665 (2.018%), neg=0, invalid=96777 0003: dt=369.920000, rms=0.654 (1.569%), neg=0, invalid=96777 0004: dt=110.976000, rms=0.649 (0.783%), neg=0, invalid=96777 0005: dt=369.920000, rms=0.645 (0.656%), neg=0, invalid=96777 0006: dt=92.480000, rms=0.642 (0.464%), neg=0, invalid=96777 0007: dt=1479.680000, rms=0.633 (1.424%), neg=0, invalid=96777 0008: dt=92.480000, rms=0.629 (0.567%), neg=0, invalid=96777 0009: dt=295.936000, rms=0.627 (0.277%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.627 (0.044%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.627 (0.045%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.626 (0.067%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.626 (0.107%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.625 (0.122%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.624 (0.154%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.623 (0.165%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.622 (0.163%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.621 (0.161%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.620 (0.165%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.619 (0.164%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.618 (0.152%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.617 (0.150%), neg=0, invalid=96777 0023: dt=73.984000, rms=0.616 (0.143%), neg=0, invalid=96777 0024: dt=73.984000, rms=0.615 (0.133%), neg=0, invalid=96777 0025: dt=73.984000, rms=0.614 (0.127%), neg=0, invalid=96777 0026: dt=73.984000, rms=0.614 (0.126%), neg=0, invalid=96777 0027: dt=73.984000, rms=0.613 (0.131%), neg=0, invalid=96777 0028: dt=73.984000, rms=0.612 (0.116%), neg=0, invalid=96777 0029: dt=73.984000, rms=0.612 (0.101%), neg=0, invalid=96777 0030: dt=443.904000, rms=0.611 (0.018%), neg=0, invalid=96777 0031: dt=443.904000, rms=0.611 (-0.021%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=96777 0032: dt=129.472000, rms=0.611 (0.055%), neg=0, invalid=96777 0033: dt=517.888000, rms=0.610 (0.180%), neg=0, invalid=96777 0034: dt=27.744000, rms=0.610 (0.004%), neg=0, invalid=96777 0035: dt=27.744000, rms=0.610 (0.003%), neg=0, invalid=96777 0036: dt=27.744000, rms=0.610 (-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=0.614, neg=0, invalid=96777 0037: dt=124.416000, rms=0.608 (0.976%), neg=0, invalid=96777 0038: dt=82.944000, rms=0.602 (0.989%), neg=0, invalid=96777 0039: dt=25.920000, rms=0.600 (0.330%), neg=0, invalid=96777 0040: dt=145.152000, rms=0.595 (0.831%), neg=0, invalid=96777 0041: dt=20.736000, rms=0.593 (0.272%), neg=0, invalid=96777 0042: dt=124.416000, rms=0.590 (0.594%), neg=0, invalid=96777 0043: dt=36.288000, rms=0.588 (0.272%), neg=0, invalid=96777 0044: dt=82.944000, rms=0.586 (0.338%), neg=0, invalid=96777 0045: dt=20.736000, rms=0.585 (0.154%), neg=0, invalid=96777 0046: dt=20.736000, rms=0.584 (0.122%), neg=0, invalid=96777 0047: dt=20.736000, rms=0.583 (0.161%), neg=0, invalid=96777 0048: dt=20.736000, rms=0.582 (0.209%), neg=0, invalid=96777 0049: dt=20.736000, rms=0.581 (0.260%), neg=0, invalid=96777 0050: dt=20.736000, rms=0.579 (0.303%), neg=0, invalid=96777 0051: dt=20.736000, rms=0.577 (0.326%), neg=0, invalid=96777 0052: dt=20.736000, rms=0.575 (0.337%), neg=0, invalid=96777 0053: dt=20.736000, rms=0.573 (0.338%), neg=0, invalid=96777 0054: dt=20.736000, rms=0.571 (0.327%), neg=0, invalid=96777 0055: dt=20.736000, rms=0.569 (0.322%), neg=0, invalid=96777 0056: dt=20.736000, rms=0.568 (0.309%), neg=0, invalid=96777 0057: dt=20.736000, rms=0.566 (0.312%), neg=0, invalid=96777 0058: dt=20.736000, rms=0.564 (0.294%), neg=0, invalid=96777 0059: dt=20.736000, rms=0.563 (0.264%), neg=0, invalid=96777 0060: dt=20.736000, rms=0.561 (0.233%), neg=0, invalid=96777 0061: dt=20.736000, rms=0.560 (0.213%), neg=0, invalid=96777 0062: dt=20.736000, rms=0.559 (0.201%), neg=0, invalid=96777 0063: dt=20.736000, rms=0.558 (0.192%), neg=0, invalid=96777 0064: dt=20.736000, rms=0.557 (0.165%), neg=0, invalid=96777 0065: dt=20.736000, rms=0.556 (0.149%), neg=0, invalid=96777 0066: dt=20.736000, rms=0.556 (0.122%), neg=0, invalid=96777 0067: dt=20.736000, rms=0.555 (0.116%), neg=0, invalid=96777 0068: dt=124.416000, rms=0.555 (0.055%), neg=0, invalid=96777 0069: dt=124.416000, rms=0.555 (-0.336%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=96777 0070: dt=36.288000, rms=0.554 (0.098%), neg=0, invalid=96777 0071: dt=103.680000, rms=0.553 (0.137%), neg=0, invalid=96777 0072: dt=20.736000, rms=0.553 (0.041%), neg=0, invalid=96777 0073: dt=20.736000, rms=0.553 (0.024%), neg=0, invalid=96777 0074: dt=20.736000, rms=0.553 (0.022%), neg=0, invalid=96777 0075: dt=20.736000, rms=0.553 (0.021%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 0076: dt=5.714286, rms=0.572 (0.046%), neg=0, invalid=96777 0077: dt=2.000000, rms=0.572 (0.004%), neg=0, invalid=96777 0078: dt=2.000000, rms=0.572 (0.000%), neg=0, invalid=96777 0079: dt=2.000000, rms=0.572 (-0.017%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 0080: dt=0.175000, rms=0.572 (0.000%), neg=0, invalid=96777 0081: dt=0.150000, rms=0.572 (0.001%), neg=0, invalid=96777 0082: dt=0.000000, rms=0.572 (0.001%), neg=0, invalid=96777 0083: dt=0.000000, rms=0.572 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.623, neg=0, invalid=96777 0084: dt=5.468041, rms=0.609 (2.243%), neg=0, invalid=96777 0085: dt=1.783133, rms=0.609 (0.048%), neg=0, invalid=96777 0086: dt=1.783133, rms=0.609 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=96777 0087: dt=0.000000, rms=0.609 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.663, neg=0, invalid=96777 0088: dt=1.087533, rms=0.660 (0.518%), neg=0, invalid=96777 0089: dt=2.248276, rms=0.654 (0.868%), neg=0, invalid=96777 0090: dt=0.486842, rms=0.653 (0.081%), neg=0, invalid=96777 0091: dt=0.486842, rms=0.653 (0.055%), neg=0, invalid=96777 0092: dt=0.486842, rms=0.653 (0.073%), neg=0, invalid=96777 0093: dt=0.486842, rms=0.652 (0.060%), neg=0, invalid=96777 0094: dt=0.486842, rms=0.652 (0.011%), neg=0, invalid=96777 0095: dt=1.792000, rms=0.652 (0.076%), neg=0, invalid=96777 0096: dt=0.256000, rms=0.652 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=96777 0097: dt=1.068966, rms=0.651 (0.110%), neg=0, invalid=96777 0098: dt=0.000050, rms=0.651 (0.000%), neg=0, invalid=96777 0099: dt=0.000050, rms=0.651 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.624, neg=0, invalid=96777 0100: dt=0.448000, rms=0.611 (2.176%), neg=0, invalid=96777 0101: dt=0.000000, rms=0.611 (0.005%), neg=0, invalid=96777 0102: dt=0.050000, rms=0.611 (-0.274%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.611, neg=0, invalid=96777 0103: dt=0.000000, rms=0.611 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.06288 (16) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1228 voxels, overlap=0.470) Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1228 voxels, peak = 13), gca=13.1 gca peak = 0.14022 (22) mri peak = 0.10084 (18) Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (587 voxels, overlap=0.185) Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (587 voxels, peak = 15), gca=15.3 gca peak = 0.24234 (100) mri peak = 0.13387 (101) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (488 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (488 voxels, peak = 102), gca=101.5 gca peak = 0.19192 (97) mri peak = 0.06268 (101) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (327 voxels, overlap=0.995) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (327 voxels, peak = 99), gca=99.4 gca peak = 0.24007 (63) mri peak = 0.08797 (67) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (811 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (811 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.08419 (64) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (846 voxels, overlap=0.993) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (846 voxels, peak = 63), gca=63.0 gca peak = 0.12541 (104) mri peak = 0.08746 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65753 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65753 voxels, peak = 110), gca=109.7 gca peak = 0.13686 (104) mri peak = 0.07674 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (67757 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (67757 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.03794 (62) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (29182 voxels, overlap=0.996) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (29182 voxels, peak = 62), gca=62.1 gca peak = 0.13270 (63) mri peak = 0.04143 (63) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (30965 voxels, overlap=0.997) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (30965 voxels, peak = 62), gca=62.1 gca peak = 0.15182 (70) mri peak = 0.09260 (77) Right_Caudate (50): linear fit = 1.08 x + 0.0 (595 voxels, overlap=0.788) Right_Caudate (50): linear fit = 1.08 x + 0.0 (595 voxels, peak = 75), gca=75.2 gca peak = 0.14251 (76) mri peak = 0.08276 (84) Left_Caudate (11): linear fit = 1.07 x + 0.0 (703 voxels, overlap=0.894) Left_Caudate (11): linear fit = 1.07 x + 0.0 (703 voxels, peak = 81), gca=80.9 gca peak = 0.12116 (60) mri peak = 0.04348 (63) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (22807 voxels, overlap=0.923) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (22807 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.04500 (67) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (24802 voxels, overlap=0.741) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (24802 voxels, peak = 67), gca=67.4 gca peak = 0.22684 (88) mri peak = 0.07986 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (8180 voxels, overlap=0.689) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (8180 voxels, peak = 92), gca=92.0 gca peak = 0.21067 (87) mri peak = 0.08266 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7699 voxels, overlap=0.732) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7699 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.07459 (62) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (370 voxels, overlap=0.996) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (370 voxels, peak = 62), gca=62.0 gca peak = 0.39668 (62) mri peak = 0.10496 (60) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (350 voxels, overlap=1.003) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (350 voxels, peak = 59), gca=59.2 gca peak = 0.10129 (93) mri peak = 0.05850 (100) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5078 voxels, overlap=0.613) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (5078 voxels, peak = 104), gca=103.7 gca peak = 0.12071 (89) mri peak = 0.06003 (97) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4135 voxels, overlap=0.783) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4135 voxels, peak = 96), gca=95.7 gca peak = 0.13716 (82) mri peak = 0.05371 (87) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2285 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2285 voxels, peak = 87), gca=86.5 gca peak = 0.15214 (84) mri peak = 0.05107 (83) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2324 voxels, overlap=1.001) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2324 voxels, peak = 82), gca=81.9 gca peak = 0.08983 (85) mri peak = 0.06644 (93) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11527 voxels, overlap=0.742) Brain_Stem (16): linear fit = 1.09 x + 0.0 (11527 voxels, peak = 92), gca=92.2 gca peak = 0.11809 (92) mri peak = 0.07171 (99) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (835 voxels, overlap=0.575) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (835 voxels, peak = 104), gca=103.5 gca peak = 0.12914 (94) mri peak = 0.07282 (104) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1183 voxels, overlap=0.613) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1183 voxels, peak = 104), gca=103.9 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.17887 (18) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (255 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (255 voxels, peak = 16), gca=16.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.62 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=0.645, neg=0, invalid=96777 0104: dt=129.472000, rms=0.638 (1.114%), neg=0, invalid=96777 0105: dt=221.952000, rms=0.634 (0.627%), neg=0, invalid=96777 0106: dt=129.472000, rms=0.632 (0.330%), neg=0, invalid=96777 0107: dt=92.480000, rms=0.631 (0.154%), neg=0, invalid=96777 0108: dt=221.952000, rms=0.629 (0.350%), neg=0, invalid=96777 0109: dt=32.368000, rms=0.628 (0.087%), neg=0, invalid=96777 0110: dt=92.480000, rms=0.628 (0.071%), neg=0, invalid=96777 0111: dt=295.936000, rms=0.626 (0.286%), neg=0, invalid=96777 0112: dt=32.368000, rms=0.625 (0.085%), neg=0, invalid=96777 0113: dt=55.488000, rms=0.625 (0.038%), neg=0, invalid=96777 0114: dt=55.488000, rms=0.625 (0.048%), neg=0, invalid=96777 0115: dt=55.488000, rms=0.624 (0.077%), neg=0, invalid=96777 0116: dt=55.488000, rms=0.624 (0.107%), neg=0, invalid=96777 0117: dt=55.488000, rms=0.623 (0.120%), neg=0, invalid=96777 0118: dt=55.488000, rms=0.622 (0.141%), neg=0, invalid=96777 0119: dt=55.488000, rms=0.621 (0.146%), neg=0, invalid=96777 0120: dt=55.488000, rms=0.620 (0.141%), neg=0, invalid=96777 0121: dt=55.488000, rms=0.619 (0.134%), neg=0, invalid=96777 0122: dt=55.488000, rms=0.619 (0.126%), neg=0, invalid=96777 0123: dt=55.488000, rms=0.618 (0.114%), neg=0, invalid=96777 0124: dt=55.488000, rms=0.617 (0.105%), neg=0, invalid=96777 0125: dt=55.488000, rms=0.617 (0.105%), neg=0, invalid=96777 0126: dt=55.488000, rms=0.616 (0.092%), neg=0, invalid=96777 0127: dt=55.488000, rms=0.616 (0.082%), neg=0, invalid=96777 0128: dt=55.488000, rms=0.615 (0.067%), neg=0, invalid=96777 0129: dt=55.488000, rms=0.615 (0.058%), neg=0, invalid=96777 0130: dt=55.488000, rms=0.614 (0.069%), neg=0, invalid=96777 0131: dt=55.488000, rms=0.614 (0.087%), neg=0, invalid=96777 0132: dt=55.488000, rms=0.613 (0.078%), neg=0, invalid=96777 0133: dt=55.488000, rms=0.613 (0.066%), neg=0, invalid=96777 0134: dt=55.488000, rms=0.613 (0.040%), neg=0, invalid=96777 0135: dt=55.488000, rms=0.612 (0.037%), neg=0, invalid=96777 0136: dt=55.488000, rms=0.612 (0.064%), neg=0, invalid=96777 0137: dt=55.488000, rms=0.612 (0.089%), neg=0, invalid=96777 0138: dt=55.488000, rms=0.611 (0.089%), neg=0, invalid=96777 0139: dt=55.488000, rms=0.611 (0.069%), neg=0, invalid=96777 0140: dt=55.488000, rms=0.610 (0.064%), neg=0, invalid=96777 0141: dt=55.488000, rms=0.610 (0.038%), neg=0, invalid=96777 0142: dt=55.488000, rms=0.610 (0.033%), neg=0, invalid=96777 0143: dt=55.488000, rms=0.609 (0.088%), neg=0, invalid=96777 0144: dt=55.488000, rms=0.609 (0.077%), neg=0, invalid=96777 0145: dt=55.488000, rms=0.608 (0.054%), neg=0, invalid=96777 0146: dt=55.488000, rms=0.608 (0.042%), neg=0, invalid=96777 0147: dt=55.488000, rms=0.608 (0.023%), neg=0, invalid=96777 0148: dt=55.488000, rms=0.608 (0.037%), neg=0, invalid=96777 0149: dt=55.488000, rms=0.607 (0.061%), neg=0, invalid=96777 0150: dt=55.488000, rms=0.607 (0.059%), neg=0, invalid=96777 0151: dt=55.488000, rms=0.607 (0.048%), neg=0, invalid=96777 0152: dt=55.488000, rms=0.607 (0.044%), neg=0, invalid=96777 0153: dt=55.488000, rms=0.606 (0.029%), neg=0, invalid=96777 0154: dt=55.488000, rms=0.606 (0.030%), neg=0, invalid=96777 0155: dt=55.488000, rms=0.606 (0.045%), neg=0, invalid=96777 0156: dt=55.488000, rms=0.606 (0.042%), neg=0, invalid=96777 0157: dt=55.488000, rms=0.605 (0.033%), neg=0, invalid=96777 0158: dt=55.488000, rms=0.605 (0.038%), neg=0, invalid=96777 0159: dt=55.488000, rms=0.605 (0.034%), neg=0, invalid=96777 0160: dt=55.488000, rms=0.605 (0.026%), neg=0, invalid=96777 0161: dt=55.488000, rms=0.605 (0.037%), neg=0, invalid=96777 0162: dt=55.488000, rms=0.604 (0.042%), neg=0, invalid=96777 0163: dt=55.488000, rms=0.604 (0.040%), neg=0, invalid=96777 0164: dt=55.488000, rms=0.604 (0.034%), neg=0, invalid=96777 0165: dt=55.488000, rms=0.604 (0.032%), neg=0, invalid=96777 0166: dt=55.488000, rms=0.604 (0.030%), neg=0, invalid=96777 0167: dt=55.488000, rms=0.603 (0.029%), neg=0, invalid=96777 0168: dt=55.488000, rms=0.603 (0.020%), neg=0, invalid=96777 0169: dt=55.488000, rms=0.603 (0.026%), neg=0, invalid=96777 0170: dt=55.488000, rms=0.603 (0.023%), neg=0, invalid=96777 0171: dt=55.488000, rms=0.603 (0.019%), neg=0, invalid=96777 0172: dt=295.936000, rms=0.603 (0.037%), neg=0, invalid=96777 0173: dt=18.496000, rms=0.603 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.603, neg=0, invalid=96777 0174: dt=32.368000, rms=0.602 (0.031%), neg=0, invalid=96777 0175: dt=92.480000, rms=0.602 (0.035%), neg=0, invalid=96777 0176: dt=369.920000, rms=0.602 (0.067%), neg=0, invalid=96777 0177: dt=92.480000, rms=0.602 (0.036%), neg=0, invalid=96777 0178: dt=92.480000, rms=0.601 (0.027%), neg=0, invalid=96777 0179: dt=92.480000, rms=0.601 (0.018%), neg=0, invalid=96777 0180: dt=92.480000, rms=0.601 (0.021%), neg=0, invalid=96777 0181: dt=92.480000, rms=0.601 (0.019%), neg=0, invalid=96777 0182: dt=129.472000, rms=0.601 (0.030%), neg=0, invalid=96777 0183: dt=32.368000, rms=0.601 (-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=0.602, neg=0, invalid=96777 0184: dt=82.944000, rms=0.599 (0.537%), neg=0, invalid=96777 0185: dt=82.944000, rms=0.593 (0.905%), neg=0, invalid=96777 0186: dt=36.288000, rms=0.591 (0.430%), neg=0, invalid=96777 0187: dt=331.776000, rms=0.583 (1.317%), neg=0, invalid=96777 0188: dt=21.160173, rms=0.578 (0.871%), neg=0, invalid=96777 0189: dt=36.288000, rms=0.576 (0.239%), neg=0, invalid=96777 0190: dt=145.152000, rms=0.573 (0.499%), neg=0, invalid=96777 0191: dt=20.736000, rms=0.572 (0.260%), neg=0, invalid=96777 0192: dt=497.664000, rms=0.564 (1.416%), neg=0, invalid=96777 0193: dt=20.736000, rms=0.563 (0.218%), neg=0, invalid=96777 0194: dt=124.416000, rms=0.561 (0.375%), neg=0, invalid=96777 0195: dt=31.104000, rms=0.560 (0.107%), neg=0, invalid=96777 0196: dt=103.680000, rms=0.559 (0.202%), neg=0, invalid=96777 0197: dt=20.736000, rms=0.558 (0.070%), neg=0, invalid=96777 0198: dt=145.152000, rms=0.557 (0.329%), neg=0, invalid=96777 0199: dt=25.920000, rms=0.556 (0.022%), neg=0, invalid=96777 0200: dt=25.920000, rms=0.556 (0.068%), neg=0, invalid=96777 0201: dt=25.920000, rms=0.556 (0.086%), neg=0, invalid=96777 0202: dt=25.920000, rms=0.556 (0.015%), neg=0, invalid=96777 0203: dt=12.960000, rms=0.555 (0.040%), neg=0, invalid=96777 0204: dt=3.240000, rms=0.555 (0.009%), neg=0, invalid=96777 0205: dt=1.620000, rms=0.555 (0.003%), neg=0, invalid=96777 0206: dt=0.141750, rms=0.555 (0.001%), neg=0, invalid=96777 0207: dt=0.000138, rms=0.555 (0.000%), neg=0, invalid=96777 0208: dt=0.000035, rms=0.555 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=96777 0209: dt=103.680000, rms=0.553 (0.436%), neg=0, invalid=96777 0210: dt=36.288000, rms=0.552 (0.228%), neg=0, invalid=96777 0211: dt=124.416000, rms=0.550 (0.253%), neg=0, invalid=96777 0212: dt=20.736000, rms=0.549 (0.126%), neg=0, invalid=96777 0213: dt=145.152000, rms=0.548 (0.185%), neg=0, invalid=96777 0214: dt=36.288000, rms=0.548 (0.165%), neg=0, invalid=96777 0215: dt=82.944000, rms=0.547 (0.060%), neg=0, invalid=96777 0216: dt=36.288000, rms=0.546 (0.134%), neg=0, invalid=96777 0217: dt=20.736000, rms=0.546 (0.019%), neg=0, invalid=96777 0218: dt=20.736000, rms=0.546 (0.038%), neg=0, invalid=96777 0219: dt=20.736000, rms=0.546 (0.052%), neg=0, invalid=96777 0220: dt=20.736000, rms=0.546 (0.070%), neg=0, invalid=96777 0221: dt=20.736000, rms=0.545 (0.093%), neg=0, invalid=96777 0222: dt=20.736000, rms=0.544 (0.108%), neg=0, invalid=96777 0223: dt=20.736000, rms=0.544 (0.029%), neg=0, invalid=96777 0224: dt=20.736000, rms=0.544 (0.043%), neg=0, invalid=96777 0225: dt=20.736000, rms=0.544 (0.024%), neg=0, invalid=96777 0226: dt=10.368000, rms=0.544 (0.010%), neg=0, invalid=96777 0227: dt=6.480000, rms=0.544 (0.010%), neg=0, invalid=96777 0228: dt=0.567000, rms=0.544 (-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=0.549, neg=0, invalid=96777 0229: dt=11.200000, rms=0.546 (0.641%), neg=0, invalid=96777 0230: dt=11.200000, rms=0.543 (0.567%), neg=0, invalid=96777 0231: dt=44.800000, rms=0.532 (1.884%), neg=0, invalid=96777 0232: dt=44.800000, rms=0.524 (1.527%), neg=0, invalid=96777 0233: dt=11.200000, rms=0.523 (0.261%), neg=0, invalid=96777 0234: dt=44.800000, rms=0.518 (0.900%), neg=0, invalid=96777 0235: dt=8.648649, rms=0.517 (0.223%), neg=0, invalid=96777 0236: dt=11.200000, rms=0.516 (0.281%), neg=0, invalid=96777 0237: dt=32.000000, rms=0.513 (0.424%), neg=0, invalid=96777 0238: dt=12.000000, rms=0.512 (0.255%), neg=0, invalid=96777 0239: dt=11.200000, rms=0.511 (0.132%), neg=0, invalid=96777 0240: dt=11.200000, rms=0.510 (0.207%), neg=0, invalid=96777 0241: dt=11.200000, rms=0.510 (0.102%), neg=0, invalid=96777 0242: dt=38.400000, rms=0.508 (0.305%), neg=0, invalid=96777 0243: dt=6.400000, rms=0.507 (0.194%), neg=0, invalid=96777 0244: dt=44.800000, rms=0.505 (0.492%), neg=0, invalid=96777 0245: dt=11.200000, rms=0.504 (0.112%), neg=0, invalid=96777 0246: dt=128.000000, rms=0.501 (0.531%), neg=0, invalid=96777 0247: dt=8.265060, rms=0.499 (0.403%), neg=0, invalid=96777 0248: dt=11.200000, rms=0.499 (0.168%), neg=0, invalid=96777 0249: dt=11.200000, rms=0.498 (0.083%), neg=0, invalid=96777 0250: dt=11.200000, rms=0.498 (0.049%), neg=0, invalid=96777 0251: dt=11.200000, rms=0.498 (0.076%), neg=0, invalid=96777 0252: dt=11.200000, rms=0.497 (0.102%), neg=0, invalid=96777 0253: dt=11.200000, rms=0.496 (0.134%), neg=0, invalid=96777 0254: dt=11.200000, rms=0.496 (0.178%), neg=0, invalid=96777 0255: dt=11.200000, rms=0.494 (0.215%), neg=0, invalid=96777 0256: dt=11.200000, rms=0.493 (0.216%), neg=0, invalid=96777 0257: dt=11.200000, rms=0.492 (0.226%), neg=0, invalid=96777 0258: dt=11.200000, rms=0.491 (0.241%), neg=0, invalid=96777 0259: dt=11.200000, rms=0.490 (0.239%), neg=0, invalid=96777 0260: dt=11.200000, rms=0.489 (0.224%), neg=0, invalid=96777 0261: dt=11.200000, rms=0.488 (0.225%), neg=0, invalid=96777 0262: dt=11.200000, rms=0.487 (0.212%), neg=0, invalid=96777 0263: dt=11.200000, rms=0.486 (0.197%), neg=0, invalid=96777 0264: dt=11.200000, rms=0.485 (0.168%), neg=0, invalid=96777 0265: dt=11.200000, rms=0.484 (0.159%), neg=0, invalid=96777 0266: dt=11.200000, rms=0.483 (0.142%), neg=0, invalid=96777 0267: dt=11.200000, rms=0.483 (0.138%), neg=0, invalid=96777 0268: dt=11.200000, rms=0.482 (0.110%), neg=0, invalid=96777 0269: dt=11.200000, rms=0.482 (0.109%), neg=0, invalid=96777 0270: dt=11.200000, rms=0.481 (0.108%), neg=0, invalid=96777 0271: dt=11.200000, rms=0.481 (0.098%), neg=0, invalid=96777 0272: dt=11.200000, rms=0.480 (0.091%), neg=0, invalid=96777 0273: dt=11.200000, rms=0.480 (0.077%), neg=0, invalid=96777 0274: dt=11.200000, rms=0.480 (0.065%), neg=0, invalid=96777 0275: dt=11.200000, rms=0.479 (0.070%), neg=0, invalid=96777 0276: dt=11.200000, rms=0.479 (0.081%), neg=0, invalid=96777 0277: dt=11.200000, rms=0.479 (0.059%), neg=0, invalid=96777 0278: dt=11.200000, rms=0.478 (0.051%), neg=0, invalid=96777 0279: dt=11.200000, rms=0.478 (0.046%), neg=0, invalid=96777 0280: dt=11.200000, rms=0.478 (0.053%), neg=0, invalid=96777 0281: dt=11.200000, rms=0.478 (0.058%), neg=0, invalid=96777 0282: dt=11.200000, rms=0.477 (0.038%), neg=0, invalid=96777 0283: dt=11.200000, rms=0.477 (0.057%), neg=0, invalid=96777 0284: dt=11.200000, rms=0.477 (0.052%), neg=0, invalid=96777 0285: dt=11.200000, rms=0.477 (0.038%), neg=0, invalid=96777 0286: dt=11.200000, rms=0.477 (0.024%), neg=0, invalid=96777 0287: dt=11.200000, rms=0.476 (0.038%), neg=0, invalid=96777 0288: dt=11.200000, rms=0.476 (0.057%), neg=0, invalid=96777 0289: dt=11.200000, rms=0.476 (0.046%), neg=0, invalid=96777 0290: dt=11.200000, rms=0.476 (0.030%), neg=0, invalid=96777 0291: dt=11.200000, rms=0.476 (0.022%), neg=0, invalid=96777 0292: dt=11.200000, rms=0.476 (0.036%), neg=0, invalid=96777 0293: dt=11.200000, rms=0.475 (0.035%), neg=0, invalid=96777 0294: dt=11.200000, rms=0.475 (0.027%), neg=0, invalid=96777 0295: dt=11.200000, rms=0.475 (0.032%), neg=0, invalid=96777 0296: dt=11.200000, rms=0.475 (0.028%), neg=0, invalid=96777 0297: dt=11.200000, rms=0.475 (0.037%), neg=0, invalid=96777 0298: dt=11.200000, rms=0.475 (0.018%), neg=0, invalid=96777 0299: dt=11.200000, rms=0.475 (0.022%), neg=0, invalid=96777 0300: dt=11.200000, rms=0.474 (0.027%), neg=0, invalid=96777 0301: dt=11.200000, rms=0.474 (0.025%), neg=0, invalid=96777 0302: dt=11.200000, rms=0.474 (0.016%), neg=0, invalid=96777 0303: dt=11.200000, rms=0.474 (0.005%), neg=0, invalid=96777 0304: dt=11.200000, rms=0.474 (0.010%), neg=0, invalid=96777 0305: dt=11.200000, rms=0.474 (0.004%), neg=0, invalid=96777 0306: dt=11.200000, rms=0.474 (0.008%), neg=0, invalid=96777 0307: dt=11.200000, rms=0.474 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=96777 0308: dt=32.000000, rms=0.472 (0.367%), neg=0, invalid=96777 0309: dt=11.200000, rms=0.472 (0.099%), neg=0, invalid=96777 0310: dt=32.000000, rms=0.471 (0.105%), neg=0, invalid=96777 0311: dt=6.400000, rms=0.471 (0.027%), neg=0, invalid=96777 0312: dt=6.400000, rms=0.471 (0.027%), neg=0, invalid=96777 0313: dt=6.400000, rms=0.471 (0.021%), neg=0, invalid=96777 0314: dt=6.400000, rms=0.471 (0.017%), neg=0, invalid=96777 0315: dt=44.800000, rms=0.471 (0.054%), neg=0, invalid=96777 0316: dt=6.400000, rms=0.471 (0.012%), neg=0, invalid=96777 0317: dt=6.400000, rms=0.471 (0.005%), neg=0, invalid=96777 0318: dt=6.400000, rms=0.471 (-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=0.495, neg=0, invalid=96777 0319: dt=0.000000, rms=0.495 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=96777 0320: dt=0.000000, rms=0.495 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.544, neg=0, invalid=96777 0321: dt=1.555556, rms=0.538 (1.150%), neg=0, invalid=96777 0322: dt=0.448000, rms=0.537 (0.040%), neg=0, invalid=96777 0323: dt=0.448000, rms=0.537 (-0.019%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.537, neg=0, invalid=96777 0324: dt=0.931034, rms=0.537 (0.147%), neg=0, invalid=96777 0325: dt=0.256000, rms=0.537 (0.006%), neg=0, invalid=96777 0326: dt=0.256000, rms=0.537 (-0.003%), 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=0.490, neg=0, invalid=96777 0327: dt=0.150330, rms=0.486 (0.954%), neg=0, invalid=96777 0328: dt=0.132386, rms=0.483 (0.605%), neg=0, invalid=96777 0329: dt=0.320000, rms=0.477 (1.110%), neg=0, invalid=96777 0330: dt=0.112000, rms=0.477 (0.192%), neg=0, invalid=96777 0331: dt=0.112000, rms=0.476 (0.168%), neg=0, invalid=96777 0332: dt=0.112000, rms=0.475 (0.145%), neg=0, invalid=96777 0333: dt=0.112000, rms=0.474 (0.125%), neg=0, invalid=96777 0334: dt=0.320000, rms=0.473 (0.319%), neg=0, invalid=96777 0335: dt=0.112000, rms=0.473 (0.075%), neg=0, invalid=96777 0336: dt=0.448000, rms=0.471 (0.276%), neg=0, invalid=96777 0337: dt=0.320000, rms=0.471 (0.135%), neg=0, invalid=96777 0338: dt=0.112000, rms=0.471 (0.037%), neg=0, invalid=96777 0339: dt=0.112000, rms=0.470 (0.039%), neg=0, invalid=96777 0340: dt=0.112000, rms=0.470 (0.066%), neg=0, invalid=96777 0341: dt=0.112000, rms=0.470 (0.029%), neg=0, invalid=96777 0342: dt=0.112000, rms=0.470 (0.058%), neg=0, invalid=96777 0343: dt=0.112000, rms=0.469 (0.024%), neg=0, invalid=96777 0344: dt=0.112000, rms=0.469 (0.027%), neg=0, invalid=96777 0345: dt=0.112000, rms=0.469 (0.040%), neg=0, invalid=96777 0346: dt=0.112000, rms=0.469 (0.068%), neg=0, invalid=96777 0347: dt=0.112000, rms=0.469 (0.073%), neg=0, invalid=96777 0348: dt=0.112000, rms=0.468 (0.078%), neg=0, invalid=96777 0349: dt=0.112000, rms=0.468 (0.085%), neg=0, invalid=96777 0350: dt=0.028000, rms=0.468 (0.006%), neg=0, invalid=96777 0351: dt=0.028000, rms=0.468 (0.003%), neg=0, invalid=96777 0352: dt=0.112000, rms=0.468 (0.005%), neg=0, invalid=96777 0353: dt=0.112000, rms=0.468 (0.011%), neg=0, invalid=96777 0354: dt=0.320000, rms=0.468 (0.020%), neg=0, invalid=96777 0355: dt=0.112000, rms=0.468 (0.008%), neg=0, invalid=96777 0356: dt=0.112000, rms=0.467 (0.009%), neg=0, invalid=96777 0357: dt=0.112000, rms=0.467 (0.014%), neg=0, invalid=96777 0358: dt=0.112000, rms=0.467 (0.016%), neg=0, invalid=96777 0359: dt=0.056000, rms=0.467 (0.002%), neg=0, invalid=96777 0360: dt=0.056000, rms=0.467 (0.007%), neg=0, invalid=96777 0361: dt=0.056000, rms=0.467 (0.007%), neg=0, invalid=96777 0362: dt=0.056000, rms=0.467 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=96777 0363: dt=0.112000, rms=0.466 (0.230%), neg=0, invalid=96777 0364: dt=0.112000, rms=0.465 (0.173%), neg=0, invalid=96777 0365: dt=0.112000, rms=0.465 (0.132%), neg=0, invalid=96777 0366: dt=0.448000, rms=0.463 (0.384%), neg=0, invalid=96777 0367: dt=0.028000, rms=0.463 (0.002%), neg=0, invalid=96777 0368: dt=0.028000, rms=0.463 (0.001%), neg=0, invalid=96777 0369: dt=0.028000, rms=0.463 (0.007%), neg=0, invalid=96777 0370: dt=0.028000, rms=0.463 (0.007%), neg=0, invalid=96777 0371: dt=0.028000, rms=0.463 (0.011%), neg=0, invalid=96777 0372: dt=0.028000, rms=0.463 (0.010%), neg=0, invalid=96777 0373: dt=0.112000, rms=0.463 (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=0.461, neg=0, invalid=96777 0374: dt=0.000000, rms=0.461 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.461, neg=0, invalid=96777 0375: dt=295.936000, rms=0.460 (0.109%), neg=0, invalid=96777 0376: dt=55.488000, rms=0.460 (0.029%), neg=0, invalid=96777 0377: dt=55.488000, rms=0.460 (0.019%), neg=0, invalid=96777 0378: dt=55.488000, rms=0.460 (0.015%), neg=0, invalid=96777 0379: dt=55.488000, rms=0.460 (0.017%), neg=0, invalid=96777 0380: dt=55.488000, rms=0.460 (0.033%), neg=0, invalid=96777 0381: dt=55.488000, rms=0.460 (0.031%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.460, neg=0, invalid=96777 0382: dt=36.288000, rms=0.459 (0.061%), neg=0, invalid=96777 0383: dt=82.944000, rms=0.459 (0.098%), neg=0, invalid=96777 0384: dt=62.208000, rms=0.458 (0.105%), neg=0, invalid=96777 0385: dt=25.920000, rms=0.458 (0.068%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0386: dt=25.920000, rms=0.458 (0.039%), neg=0, invalid=96777 0387: dt=25.920000, rms=0.458 (0.055%), neg=0, invalid=96777 0388: dt=25.920000, rms=0.457 (0.067%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0389: dt=25.920000, rms=0.457 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0390: dt=25.920000, rms=0.457 (0.032%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=96777 0391: dt=82.944000, rms=0.455 (0.416%), neg=0, invalid=96777 0392: dt=25.920000, rms=0.454 (0.139%), neg=0, invalid=96777 0393: dt=25.920000, rms=0.454 (0.074%), neg=0, invalid=96777 0394: dt=25.920000, rms=0.454 (0.090%), neg=0, invalid=96777 0395: dt=25.920000, rms=0.453 (0.105%), neg=0, invalid=96777 0396: dt=25.920000, rms=0.453 (0.102%), neg=0, invalid=96777 0397: dt=25.920000, rms=0.452 (0.123%), neg=0, invalid=96777 0398: dt=25.920000, rms=0.452 (0.109%), neg=0, invalid=96777 0399: dt=25.920000, rms=0.452 (0.018%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.452, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0400: dt=25.600000, rms=0.450 (0.355%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0401: dt=44.800000, rms=0.448 (0.534%), neg=0, invalid=96777 0402: dt=8.671329, rms=0.447 (0.223%), neg=0, invalid=96777 0403: dt=8.671329, rms=0.446 (0.124%), neg=0, invalid=96777 0404: dt=8.671329, rms=0.446 (0.124%), neg=0, invalid=96777 0405: dt=8.671329, rms=0.445 (0.223%), neg=0, invalid=96777 0406: dt=8.671329, rms=0.444 (0.245%), neg=0, invalid=96777 0407: dt=8.671329, rms=0.443 (0.269%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0408: dt=8.671329, rms=0.442 (0.237%), neg=0, invalid=96777 0409: dt=8.671329, rms=0.441 (0.220%), neg=0, invalid=96777 0410: dt=8.671329, rms=0.440 (0.209%), neg=0, invalid=96777 0411: dt=8.671329, rms=0.439 (0.171%), neg=0, invalid=96777 0412: dt=8.671329, rms=0.438 (0.160%), neg=0, invalid=96777 0413: dt=8.671329, rms=0.438 (0.150%), neg=0, invalid=96777 0414: dt=8.671329, rms=0.437 (0.160%), neg=0, invalid=96777 0415: dt=8.671329, rms=0.436 (0.162%), neg=0, invalid=96777 0416: dt=8.671329, rms=0.435 (0.155%), neg=0, invalid=96777 0417: dt=8.671329, rms=0.435 (0.142%), neg=0, invalid=96777 0418: dt=8.671329, rms=0.434 (0.119%), neg=0, invalid=96777 0419: dt=8.671329, rms=0.434 (0.108%), neg=0, invalid=96777 0420: dt=11.200000, rms=0.434 (0.020%), neg=0, invalid=96777 0421: dt=11.200000, rms=0.434 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=96777 0422: dt=38.400000, rms=0.431 (0.636%), neg=0, invalid=96777 0423: dt=9.600000, rms=0.430 (0.191%), neg=0, invalid=96777 0424: dt=9.600000, rms=0.430 (0.088%), neg=0, invalid=96777 0425: dt=9.600000, rms=0.429 (0.096%), neg=0, invalid=96777 0426: dt=9.600000, rms=0.429 (0.143%), neg=0, invalid=96777 0427: dt=9.600000, rms=0.428 (0.115%), neg=0, invalid=96777 0428: dt=9.600000, rms=0.428 (0.143%), neg=0, invalid=96777 0429: dt=9.600000, rms=0.427 (0.082%), neg=0, invalid=96777 0430: dt=9.600000, rms=0.427 (0.088%), neg=0, invalid=96777 0431: dt=9.600000, rms=0.427 (0.038%), neg=0, invalid=96777 0432: dt=6.400000, rms=0.427 (0.017%), neg=0, invalid=96777 0433: dt=6.400000, rms=0.427 (0.013%), neg=0, invalid=96777 0434: dt=6.400000, rms=0.427 (0.024%), neg=0, invalid=96777 0435: dt=6.400000, rms=0.427 (0.005%), neg=0, invalid=96777 0436: dt=6.400000, rms=0.426 (0.020%), neg=0, invalid=96777 0437: dt=6.400000, rms=0.426 (0.021%), neg=0, invalid=96777 0438: dt=6.400000, rms=0.426 (0.026%), neg=0, invalid=96777 0439: dt=6.400000, rms=0.426 (0.026%), neg=0, invalid=96777 0440: dt=6.400000, rms=0.426 (0.027%), neg=0, invalid=96777 0441: dt=6.400000, rms=0.426 (0.030%), neg=0, invalid=96777 0442: dt=6.400000, rms=0.426 (0.029%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.431, neg=0, invalid=96777 0443: dt=0.000000, rms=0.431 (0.001%), neg=0, invalid=96777 0444: dt=0.000000, rms=0.431 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.431, neg=0, invalid=96777 0445: dt=2.304000, rms=0.431 (0.021%), neg=0, invalid=96777 0446: dt=1.008000, rms=0.431 (0.005%), neg=0, invalid=96777 0447: dt=1.008000, rms=0.431 (0.007%), neg=0, invalid=96777 0448: dt=1.008000, rms=0.431 (-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=0.440, neg=0, invalid=96777 0449: dt=0.500000, rms=0.440 (0.044%), neg=0, invalid=96777 0450: dt=0.256000, rms=0.440 (0.006%), neg=0, invalid=96777 0451: dt=0.256000, rms=0.440 (-0.005%), 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 = 1 after 0 iterations, nbhd size=0, neg = 0 0452: dt=1.280000, rms=0.439 (0.149%), neg=0, invalid=96777 0453: dt=0.007000, rms=0.439 (0.000%), neg=0, invalid=96777 0454: dt=0.007000, rms=0.439 (-0.001%), 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=0.429, neg=0, invalid=96777 iter 0, gcam->neg = 491 after 21 iterations, nbhd size=2, neg = 0 0455: dt=1.695409, rms=0.402 (6.248%), neg=0, invalid=96777 0456: dt=0.000188, rms=0.402 (-0.003%), neg=0, invalid=96777 0457: dt=0.000188, rms=0.402 (0.000%), neg=0, invalid=96777 0458: dt=0.000188, rms=0.402 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.402, neg=0, invalid=96777 0459: dt=0.000438, rms=0.402 (0.000%), neg=0, invalid=96777 0460: dt=0.000000, rms=0.402 (0.001%), neg=0, invalid=96777 0461: dt=0.000000, rms=0.402 (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=0.391, neg=0, invalid=96777 0462: dt=0.000000, rms=0.392 (-0.254%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0463: dt=27.744000, rms=0.392 (0.002%), neg=0, invalid=96777 0464: dt=6.936000, rms=0.392 (0.000%), neg=0, invalid=96777 0465: dt=6.936000, rms=0.392 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0466: dt=0.000000, rms=0.392 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 0467: dt=36.288000, rms=0.392 (0.022%), neg=0, invalid=96777 0468: dt=36.288000, rms=0.392 (0.008%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0469: dt=36.288000, rms=0.392 (0.010%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0470: dt=36.288000, rms=0.392 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=2, neg = 0 0471: dt=8.000000, rms=0.392 (0.033%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0472: dt=2.800000, rms=0.392 (0.007%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 18 iterations, nbhd size=2, neg = 0 0473: dt=2.800000, rms=0.392 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 38 iterations, nbhd size=4, neg = 0 0474: dt=2.800000, rms=0.392 (-0.020%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=96777 iter 0, gcam->neg = 39 after 117 iterations, nbhd size=4, neg = 0 0475: dt=32.000000, rms=0.391 (0.336%), neg=0, invalid=96777 iter 0, gcam->neg = 22 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.003 (15.808%) 0476: dt=19.200000, rms=0.390 (0.146%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 33 iterations, nbhd size=4, neg = 0 0477: dt=19.200000, rms=0.390 (0.121%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 37 iterations, nbhd size=4, neg = 0 0478: dt=19.200000, rms=0.389 (0.123%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 18 iterations, nbhd size=2, neg = 0 0479: dt=19.200000, rms=0.389 (0.193%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 31 iterations, nbhd size=3, neg = 0 0480: dt=19.200000, rms=0.388 (0.191%), neg=0, invalid=96777 iter 0, gcam->neg = 31 after 49 iterations, nbhd size=4, neg = 0 0481: dt=19.200000, rms=0.387 (0.112%), neg=0, invalid=96777 iter 0, gcam->neg = 53 after 200 iterations, nbhd size=2, neg = 6 starting rms=0.004, neg=6, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 6, delta 6, rms=0.003 (21.731%) 0482: dt=19.200000, rms=0.387 (0.066%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 3, delta 3, rms=0.003 (13.466%) 0483: dt=11.200000, rms=0.387 (0.076%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 13 iterations, nbhd size=1, neg = 0 0484: dt=19.200000, rms=0.387 (0.081%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000188: new neg 0, old_neg 2, delta 2, rms=0.002 (41.275%) 0485: dt=38.400000, rms=0.386 (0.092%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 3 starting rms=0.003, neg=3, removing folds in lattice.... iter 1, dt=0.000039: new neg 0, old_neg 3, delta 3, rms=0.002 (25.158%) 0486: dt=38.400000, rms=0.386 (0.121%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000156: new neg 0, old_neg 2, delta 2, rms=0.002 (42.482%) 0487: dt=32.000000, rms=0.385 (0.058%), neg=0, invalid=96777 0488: dt=32.000000, rms=0.385 (0.042%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0489: dt=32.000000, rms=0.385 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 35 after 200 iterations, nbhd size=2, neg = 6 starting rms=0.005, neg=6, removing folds in lattice.... iter 1, dt=0.000039: new neg 0, old_neg 6, delta 6, rms=0.003 (49.959%) 0490: dt=32.000000, rms=0.385 (0.038%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 42 iterations, nbhd size=3, neg = 0 0491: dt=32.000000, rms=0.385 (0.019%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 2, delta 2, rms=0.002 (49.031%) 0492: dt=2.000000, rms=0.388 (0.015%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 23 iterations, nbhd size=4, neg = 0 0493: dt=1.008000, rms=0.388 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 32 iterations, nbhd size=4, neg = 0 0494: dt=1.008000, rms=0.388 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 23 iterations, nbhd size=3, neg = 0 0495: dt=1.008000, rms=0.388 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 35 iterations, nbhd size=4, neg = 0 0496: dt=1.008000, rms=0.388 (-0.022%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=96777 iter 0, gcam->neg = 18 after 9 iterations, nbhd size=1, neg = 0 0497: dt=11.520000, rms=0.386 (0.302%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 42 iterations, nbhd size=4, neg = 0 0498: dt=2.880000, rms=0.386 (0.056%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 28 iterations, nbhd size=3, neg = 0 0499: dt=2.880000, rms=0.386 (0.061%), neg=0, invalid=96777 iter 0, gcam->neg = 26 after 36 iterations, nbhd size=3, neg = 0 0500: dt=2.880000, rms=0.386 (0.079%), neg=0, invalid=96777 iter 0, gcam->neg = 35 after 41 iterations, nbhd size=4, neg = 0 0501: dt=2.880000, rms=0.385 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 38 after 50 iterations, nbhd size=4, neg = 0 0502: dt=2.880000, rms=0.385 (0.080%), neg=0, invalid=96777 iter 0, gcam->neg = 53 after 50 iterations, nbhd size=1, neg = 0 0503: dt=2.880000, rms=0.385 (0.084%), neg=0, invalid=96777 iter 0, gcam->neg = 53 after 64 iterations, nbhd size=2, neg = 0 0504: dt=2.880000, rms=0.384 (0.114%), neg=0, invalid=96777 iter 0, gcam->neg = 57 after 53 iterations, nbhd size=4, neg = 0 0505: dt=2.880000, rms=0.384 (0.105%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 17 iterations, nbhd size=2, neg = 0 0506: dt=3.456000, rms=0.384 (0.029%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 0507: dt=0.000000, rms=0.389 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=96777 0508: dt=0.000000, rms=0.389 (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=0.381, neg=0, invalid=96777 iter 0, gcam->neg = 336 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0509: dt=0.831800, 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 iter 0, gcam->neg = 583 after 24 iterations, nbhd size=2, neg = 0 0510: dt=1.024000, rms=0.364 (4.419%), neg=0, invalid=96777 0511: dt=0.000000, rms=0.364 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 83 after 7 iterations, nbhd size=1, neg = 0 0512: dt=0.050000, rms=0.364 (-0.224%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 3 hours, 18 minutes and 5 seconds. #-------------------------------------- #@# CA Reg Inv Tue Oct 20 14:20:46 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Tue Oct 20 14:22:09 EDT 2015 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11328081 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 30 seconds. #-------------------------------------- #@# SkullLTA Tue Oct 20 14:23:39 EDT 2015 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /share/apps/freesurfer-5.3.0/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 '/share/apps/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (51, 21, 36) --> (205, 199, 234) using (102, 80, 135) as brain centroid... mean wm in atlas = 126, using box (83,58,111) --> (120, 101,159) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 106, scaling input intensities by 1.189 scaling channel 0 by 1.18868 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.125 0.026 -0.048 -15.419; -0.028 1.257 -0.035 0.428; 0.066 0.041 1.076 -46.180; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.125 0.026 -0.048 -15.419; -0.028 1.257 -0.035 0.428; 0.066 0.041 1.076 -46.180; 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=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.125 0.071 -0.015 -24.287; -0.068 1.226 -0.105 19.659; 0.027 0.118 1.013 -40.832; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.125 0.071 -0.015 -24.287; -0.068 1.226 -0.105 19.659; 0.027 0.118 1.013 -40.832; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.123 0.083 0.000 -27.783; -0.077 1.227 -0.105 20.331; 0.009 0.117 1.014 -38.526; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.123 0.082 -0.008 -26.598; -0.077 1.227 -0.105 19.863; 0.018 0.118 1.011 -38.970; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12330 0.08215 -0.00781 -26.59829; -0.07717 1.22713 -0.10526 19.86253; 0.01776 0.11781 1.01146 -38.96956; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.12330 0.08215 -0.00781 -26.59829; -0.07717 1.22713 -0.10526 19.86253; 0.01776 0.11781 1.01146 -38.96956; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.123 0.082 -0.008 -26.598; -0.077 1.227 -0.105 19.863; 0.018 0.118 1.011 -38.970; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-3.9) transform before final EM align: 1.123 0.082 -0.008 -26.598; -0.077 1.227 -0.105 19.863; 0.018 0.118 1.011 -38.970; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.12330 0.08215 -0.00781 -26.59829; -0.07717 1.22713 -0.10526 19.86253; 0.01776 0.11781 1.01146 -38.96956; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.12330 0.08215 -0.00781 -26.59829; -0.07717 1.22713 -0.10526 19.86253; 0.01776 0.11781 1.01146 -38.96956; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.2 tol 0.000000 final transform: 1.123 0.082 -0.008 -26.598; -0.077 1.227 -0.105 19.863; 0.018 0.118 1.011 -38.970; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 24 minutes and 59 seconds. #-------------------------------------- #@# SubCort Seg Tue Oct 20 14:48:38 EDT 2015 mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz $Id: mri_seg_diff.c,v 1.5 2011/03/02 00:04:24 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname compute-0-1.local machine x86_64 user twilliams Seg1 aseg.auto.mgz Seg2 aseg.mgz Diff aseg.manedit.mgz InDiff (null) Merged (null) ForceDiff 0 Computing difference between segmentations No difference found. mri_ca_label -align norm.mgz transforms/talairach.m3z /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname compute-0-1.local machine x86_64 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /share/apps/freesurfer-5.3.0/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.09459 (17) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (295 voxels, overlap=0.733) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (295 voxels, peak = 18), gca=17.7 gca peak = 0.14982 (20) mri peak = 0.12979 (18) Right_Lateral_Ventricle (43): linear fit = 0.73 x + 0.0 (293 voxels, overlap=0.350) Right_Lateral_Ventricle (43): linear fit = 0.73 x + 0.0 (293 voxels, peak = 14), gca=14.5 gca peak = 0.28003 (97) mri peak = 0.13559 (101) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (295 voxels, overlap=0.972) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (295 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.13392 (104) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (341 voxels, overlap=0.730) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (341 voxels, peak = 100), gca=100.3 gca peak = 0.27536 (62) mri peak = 0.09703 (66) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (634 voxels, overlap=0.833) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (634 voxels, peak = 65), gca=64.8 gca peak = 0.32745 (63) mri peak = 0.08626 (64) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (659 voxels, overlap=1.010) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (659 voxels, peak = 63), gca=63.0 gca peak = 0.08597 (105) mri peak = 0.09879 (110) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (31933 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (31933 voxels, peak = 110), gca=109.7 gca peak = 0.09209 (106) mri peak = 0.08616 (110) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (35313 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (35313 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.04550 (62) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28117 voxels, overlap=0.894) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28117 voxels, peak = 62), gca=62.1 gca peak = 0.08598 (64) mri peak = 0.04446 (63) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (30013 voxels, overlap=0.902) Right_Cerebral_Cortex (42): linear fit = 0.96 x + 0.0 (30013 voxels, peak = 62), gca=61.8 gca peak = 0.24164 (71) mri peak = 0.11658 (81) Right_Caudate (50): linear fit = 1.11 x + 0.0 (609 voxels, overlap=0.602) Right_Caudate (50): linear fit = 1.11 x + 0.0 (609 voxels, peak = 78), gca=78.5 gca peak = 0.18227 (75) mri peak = 0.10822 (84) Left_Caudate (11): linear fit = 1.02 x + 0.0 (725 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.02 x + 0.0 (725 voxels, peak = 77), gca=76.9 gca peak = 0.10629 (62) mri peak = 0.05300 (65) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (20841 voxels, overlap=0.948) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (20841 voxels, peak = 67), gca=66.7 gca peak = 0.11668 (59) mri peak = 0.05284 (64) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (20925 voxels, overlap=0.812) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (20925 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.10493 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5613 voxels, overlap=0.815) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (5613 voxels, peak = 92), gca=92.0 gca peak = 0.16819 (86) mri peak = 0.09965 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4640 voxels, overlap=0.592) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4640 voxels, peak = 92), gca=91.6 gca peak = 0.41688 (64) mri peak = 0.07809 (69) Left_Amygdala (18): linear fit = 1.05 x + 0.0 (396 voxels, overlap=1.041) Left_Amygdala (18): linear fit = 1.05 x + 0.0 (396 voxels, peak = 68), gca=67.5 gca peak = 0.42394 (62) mri peak = 0.08540 (59) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (208 voxels, overlap=1.041) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (208 voxels, peak = 58), gca=58.0 gca peak = 0.10041 (96) mri peak = 0.07405 (100) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3699 voxels, overlap=0.715) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3699 voxels, peak = 98), gca=98.4 gca peak = 0.13978 (88) mri peak = 0.07095 (95) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3883 voxels, overlap=0.873) Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3883 voxels, peak = 94), gca=93.7 gca peak = 0.08514 (81) mri peak = 0.06872 (80) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1913 voxels, overlap=0.932) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1913 voxels, peak = 84), gca=83.8 gca peak = 0.09624 (82) mri peak = 0.06355 (80) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1571 voxels, overlap=0.979) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1571 voxels, peak = 82), gca=81.6 gca peak = 0.07543 (88) mri peak = 0.06917 (93) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11184 voxels, overlap=0.733) Brain_Stem (16): linear fit = 1.07 x + 0.0 (11184 voxels, peak = 94), gca=93.7 gca peak = 0.12757 (95) mri peak = 0.08799 (99) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (993 voxels, overlap=0.649) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (993 voxels, peak = 102), gca=102.1 gca peak = 0.17004 (92) mri peak = 0.07610 (107) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1001 voxels, overlap=0.702) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1001 voxels, peak = 101), gca=100.7 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.16180 (18) Fourth_Ventricle (15): linear fit = 0.64 x + 0.0 (115 voxels, overlap=0.018) Fourth_Ventricle (15): linear fit = 0.64 x + 0.0 (115 voxels, peak = 15), gca=14.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.69 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.21595 (18) mri peak = 0.09459 (17) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (295 voxels, overlap=0.973) Left_Lateral_Ventricle (4): linear fit = 0.99 x + 0.0 (295 voxels, peak = 18), gca=17.7 gca peak = 0.22747 (15) mri peak = 0.12979 (18) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (293 voxels, overlap=0.851) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (293 voxels, peak = 15), gca=15.4 gca peak = 0.30534 (100) mri peak = 0.13559 (101) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (295 voxels, overlap=0.821) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (295 voxels, peak = 100), gca=100.5 gca peak = 0.18300 (100) mri peak = 0.13392 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (341 voxels, overlap=0.885) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (341 voxels, peak = 100), gca=100.0 gca peak = 0.26329 (65) mri peak = 0.09703 (66) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (634 voxels, overlap=0.988) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (634 voxels, peak = 65), gca=65.0 gca peak = 0.31612 (63) mri peak = 0.08626 (64) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (659 voxels, overlap=1.012) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (659 voxels, peak = 63), gca=63.0 gca peak = 0.08168 (110) mri peak = 0.09879 (110) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31933 voxels, overlap=0.747) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31933 voxels, peak = 110), gca=110.0 gca peak = 0.08583 (111) mri peak = 0.08616 (110) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35313 voxels, overlap=0.753) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (35313 voxels, peak = 111), gca=111.0 gca peak = 0.07862 (62) mri peak = 0.04550 (62) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28117 voxels, overlap=0.930) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28117 voxels, peak = 61), gca=61.1 gca peak = 0.09119 (62) mri peak = 0.04446 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (30013 voxels, overlap=0.948) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (30013 voxels, peak = 64), gca=63.5 gca peak = 0.22081 (81) mri peak = 0.11658 (81) Right_Caudate (50): linear fit = 0.99 x + 0.0 (609 voxels, overlap=1.004) Right_Caudate (50): linear fit = 0.99 x + 0.0 (609 voxels, peak = 80), gca=79.8 gca peak = 0.18185 (77) mri peak = 0.10822 (84) Left_Caudate (11): linear fit = 1.00 x + 0.0 (725 voxels, overlap=1.002) Left_Caudate (11): linear fit = 1.00 x + 0.0 (725 voxels, peak = 77), gca=77.0 gca peak = 0.09845 (66) mri peak = 0.05300 (65) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (20841 voxels, overlap=0.998) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (20841 voxels, peak = 65), gca=65.0 gca peak = 0.12109 (64) mri peak = 0.05284 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20925 voxels, overlap=0.987) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (20925 voxels, peak = 66), gca=65.6 gca peak = 0.17465 (92) mri peak = 0.10493 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5613 voxels, overlap=0.976) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5613 voxels, peak = 92), gca=91.5 gca peak = 0.16064 (92) mri peak = 0.09965 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4640 voxels, overlap=0.975) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4640 voxels, peak = 92), gca=91.5 gca peak = 0.30715 (67) mri peak = 0.07809 (69) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (396 voxels, overlap=1.036) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (396 voxels, peak = 68), gca=68.0 gca peak = 0.42272 (58) mri peak = 0.08540 (59) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (208 voxels, overlap=1.027) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (208 voxels, peak = 58), gca=58.0 gca peak = 0.09900 (97) mri peak = 0.07405 (100) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3699 voxels, overlap=0.811) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3699 voxels, peak = 99), gca=99.4 gca peak = 0.09644 (91) mri peak = 0.07095 (95) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3883 voxels, overlap=0.950) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3883 voxels, peak = 91), gca=91.5 gca peak = 0.08482 (85) mri peak = 0.06872 (80) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1913 voxels, overlap=0.998) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1913 voxels, peak = 84), gca=83.7 gca peak = 0.10657 (82) mri peak = 0.06355 (80) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1571 voxels, overlap=0.987) Right_Putamen (51): linear fit = 0.99 x + 0.0 (1571 voxels, peak = 81), gca=80.8 gca peak = 0.06520 (88) mri peak = 0.06917 (93) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11184 voxels, overlap=0.854) Brain_Stem (16): linear fit = 0.99 x + 0.0 (11184 voxels, peak = 87), gca=86.7 gca peak = 0.12361 (98) mri peak = 0.08799 (99) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (993 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (993 voxels, peak = 98), gca=98.5 gca peak = 0.15683 (101) mri peak = 0.07610 (107) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1001 voxels, overlap=0.913) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1001 voxels, peak = 102), gca=101.5 gca peak = 0.25227 (26) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.32391 (16) mri peak = 0.16180 (18) Fourth_Ventricle (15): linear fit = 0.96 x + 0.0 (115 voxels, overlap=0.730) Fourth_Ventricle (15): linear fit = 0.96 x + 0.0 (115 voxels, peak = 15), gca=15.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.25227 (26) gca peak CSF = 0.21139 (27) gca peak Left_Accumbens_area = 0.37770 (71) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65202 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.32842 (33) gca peak Right_Accumbens_area = 0.26557 (79) gca peak Right_vessel = 0.80912 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (30) gca peak WM_hypointensities = 0.16549 (85) gca peak non_WM_hypointensities = 0.11940 (55) gca peak Optic_Chiasm = 0.34853 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 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 16350 gm and wm labels changed (%18 to gray, %82 to white out of all changed labels) 274 hippocampal voxels changed. 3 amygdala voxels changed. pass 1: 71200 changed. image ll: -2.149, PF=1.000 pass 2: 11173 changed. image ll: -2.147, PF=1.000 pass 3: 3575 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 22 minutes and 54 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/cc_up.lta af1021_recon will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/cc_up.lta reading aseg from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.auto_noCCseg.mgz reading norm from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/norm.mgz 32006 voxels in left wm, 84205 in right wm, xrange [120, 133] searching rotation angles z=[-9 5], y=[-10 4] searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 global minimum found at slice 129.0, rotations (-2.68, -2.57) final transformation (x=129.0, yr=-2.685, zr=-2.573): 0.998 0.045 -0.047 1.587; -0.045 0.999 0.002 47.595; 0.047 -0.000 0.999 -9.897; 0.000 0.000 0.000 1.000; updating x range to be [126, 131] in xformed coordinates best xformed slice 129 cc center is found at 129 155 168 eigenvectors: 0.000 -0.007 1.000; 0.205 -0.979 -0.007; 0.979 0.205 0.001; error in mid anterior detected - correcting... error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.0 minutes #-------------------------------------- #@# Merge ASeg Tue Oct 20 15:12:38 EDT 2015 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Oct 20 15:12:38 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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... 2842 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 68 (68), valley at 31 (31) csf peak at 10, setting threshold to 48 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 68 (68), valley at 31 (31) csf peak at 10, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 51 seconds. #-------------------------------------------- #@# Mask BFS Tue Oct 20 15:16:30 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1558913 voxels in mask (pct= 9.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Oct 20 15:16:32 EDT 2015 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-1.local machine x86_64 user twilliams input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-1.local machine x86_64 user twilliams input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 104.6 +- 6.2 [80.0 --> 125.0] GM (73.0) : 71.5 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 81.1 setting top of gray matter range to 90.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5040 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5172 filled 759 bright non-wm voxels segmented. 2815 diagonally connected voxels added... white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.62 minutes reading wm segmentation from wm.seg.mgz... 259 voxels added to wm to prevent paths from MTL structures to cortex 1780 additional wm voxels added 0 additional wm voxels added SEG EDIT: 35946 voxels turned on, 40715 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 8 found - 8 modified | TOTAL: 26 pass 2 (xy-): 0 found - 8 modified | TOTAL: 26 pass 1 (yz+): 24 found - 24 modified | TOTAL: 50 pass 2 (yz+): 0 found - 24 modified | TOTAL: 50 pass 1 (yz-): 31 found - 31 modified | TOTAL: 81 pass 2 (yz-): 0 found - 31 modified | TOTAL: 81 pass 1 (xz+): 11 found - 11 modified | TOTAL: 92 pass 2 (xz+): 0 found - 11 modified | TOTAL: 92 pass 1 (xz-): 15 found - 15 modified | TOTAL: 107 pass 2 (xz-): 0 found - 15 modified | TOTAL: 107 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 6 found - 6 modified | TOTAL: 10 pass 2 (+++): 0 found - 6 modified | TOTAL: 10 pass 1 (+++): 9 found - 9 modified | TOTAL: 19 pass 2 (+++): 0 found - 9 modified | TOTAL: 19 pass 1 (+++): 13 found - 13 modified | TOTAL: 32 pass 2 (+++): 0 found - 13 modified | TOTAL: 32 Iteration Number : 1 pass 1 (++): 63 found - 63 modified | TOTAL: 63 pass 2 (++): 0 found - 63 modified | TOTAL: 63 pass 1 (+-): 123 found - 123 modified | TOTAL: 186 pass 2 (+-): 0 found - 123 modified | TOTAL: 186 pass 1 (--): 108 found - 108 modified | TOTAL: 294 pass 2 (--): 0 found - 108 modified | TOTAL: 294 pass 1 (-+): 135 found - 135 modified | TOTAL: 429 pass 2 (-+): 0 found - 135 modified | TOTAL: 429 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 7 found - 7 modified | TOTAL: 9 pass 2 (yz+): 0 found - 7 modified | TOTAL: 9 pass 1 (yz-): 6 found - 6 modified | TOTAL: 15 pass 2 (yz-): 0 found - 6 modified | TOTAL: 15 pass 1 (xz+): 5 found - 5 modified | TOTAL: 20 pass 2 (xz+): 0 found - 5 modified | TOTAL: 20 pass 1 (xz-): 1 found - 1 modified | TOTAL: 21 pass 2 (xz-): 0 found - 1 modified | TOTAL: 21 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 2 found - 2 modified | TOTAL: 5 pass 2 (--): 0 found - 2 modified | TOTAL: 5 pass 1 (-+): 2 found - 2 modified | TOTAL: 7 pass 2 (-+): 0 found - 2 modified | TOTAL: 7 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 597 (out of 529595: 0.112728) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Tue Oct 20 15:19:06 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1362 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (126, 112, 88), TAL = (2.0, -40.0, 16.0) talairach voxel to voxel transform 0.886 -0.021 0.042 15.340; 0.018 0.854 0.029 -6.252; -0.055 -0.032 0.995 34.827; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 112, 88) --> (2.0, -40.0, 16.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (2.00, -40.00, 16.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -40.00, 16.00) SRC: (112.34, 93.87, 112.94) search lh wm seed point around talairach space (-16.00, -40.00, 16.00), SRC: (144.23, 94.52, 110.95) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Tue Oct 20 15:19:57 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 3 found - 3 modified | TOTAL: 11 pass 2 (xz+): 0 found - 3 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 254789: 0.005887) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 797 vertices, 889 faces slice 60: 5526 vertices, 5728 faces slice 70: 12871 vertices, 13135 faces slice 80: 21291 vertices, 21628 faces slice 90: 31254 vertices, 31595 faces slice 100: 41085 vertices, 41421 faces slice 110: 51073 vertices, 51413 faces slice 120: 62569 vertices, 62982 faces slice 130: 74831 vertices, 75282 faces slice 140: 86318 vertices, 86660 faces slice 150: 96554 vertices, 96931 faces slice 160: 106040 vertices, 106351 faces slice 170: 114009 vertices, 114302 faces slice 180: 121009 vertices, 121278 faces slice 190: 127640 vertices, 127884 faces slice 200: 132807 vertices, 133000 faces slice 210: 135887 vertices, 135989 faces slice 220: 136234 vertices, 136278 faces slice 230: 136234 vertices, 136278 faces slice 240: 136234 vertices, 136278 faces slice 250: 136234 vertices, 136278 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 136234 voxel in cpt #1: X=-44 [v=136234,e=408834,f=272556] located at (-26.273779, -3.643892, 33.029758) For the whole surface: X=-44 [v=136234,e=408834,f=272556] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Oct 20 15:20:04 EDT 2015 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Oct 20 15:20:07 EDT 2015 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts avg radius = 46.9 mm, total surface area = 71799 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Oct 20 15:20:34 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.58 (0.00-->6.87) (max @ vno 55345 --> 56522) face area 0.02 +- 0.03 (-0.21-->0.62) scaling brain by 0.302... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.289, avgs=0 005/300: dt: 0.9000, rms radial error=177.030, avgs=0 010/300: dt: 0.9000, rms radial error=176.476, avgs=0 015/300: dt: 0.9000, rms radial error=175.748, avgs=0 020/300: dt: 0.9000, rms radial error=174.917, avgs=0 025/300: dt: 0.9000, rms radial error=174.028, avgs=0 030/300: dt: 0.9000, rms radial error=173.106, avgs=0 035/300: dt: 0.9000, rms radial error=172.167, avgs=0 040/300: dt: 0.9000, rms radial error=171.221, avgs=0 045/300: dt: 0.9000, rms radial error=170.271, avgs=0 050/300: dt: 0.9000, rms radial error=169.322, avgs=0 055/300: dt: 0.9000, rms radial error=168.376, avgs=0 060/300: dt: 0.9000, rms radial error=167.433, avgs=0 065/300: dt: 0.9000, rms radial error=166.497, avgs=0 070/300: dt: 0.9000, rms radial error=165.565, avgs=0 075/300: dt: 0.9000, rms radial error=164.639, avgs=0 080/300: dt: 0.9000, rms radial error=163.717, avgs=0 085/300: dt: 0.9000, rms radial error=162.800, avgs=0 090/300: dt: 0.9000, rms radial error=161.888, avgs=0 095/300: dt: 0.9000, rms radial error=160.980, avgs=0 100/300: dt: 0.9000, rms radial error=160.078, avgs=0 105/300: dt: 0.9000, rms radial error=159.180, avgs=0 110/300: dt: 0.9000, rms radial error=158.288, avgs=0 115/300: dt: 0.9000, rms radial error=157.400, avgs=0 120/300: dt: 0.9000, rms radial error=156.517, avgs=0 125/300: dt: 0.9000, rms radial error=155.639, avgs=0 130/300: dt: 0.9000, rms radial error=154.766, avgs=0 135/300: dt: 0.9000, rms radial error=153.897, avgs=0 140/300: dt: 0.9000, rms radial error=153.033, avgs=0 145/300: dt: 0.9000, rms radial error=152.174, avgs=0 150/300: dt: 0.9000, rms radial error=151.319, avgs=0 155/300: dt: 0.9000, rms radial error=150.469, avgs=0 160/300: dt: 0.9000, rms radial error=149.624, avgs=0 165/300: dt: 0.9000, rms radial error=148.783, avgs=0 170/300: dt: 0.9000, rms radial error=147.947, avgs=0 175/300: dt: 0.9000, rms radial error=147.115, avgs=0 180/300: dt: 0.9000, rms radial error=146.288, avgs=0 185/300: dt: 0.9000, rms radial error=145.466, avgs=0 190/300: dt: 0.9000, rms radial error=144.647, avgs=0 195/300: dt: 0.9000, rms radial error=143.834, avgs=0 200/300: dt: 0.9000, rms radial error=143.025, avgs=0 205/300: dt: 0.9000, rms radial error=142.220, avgs=0 210/300: dt: 0.9000, rms radial error=141.419, avgs=0 215/300: dt: 0.9000, rms radial error=140.623, avgs=0 220/300: dt: 0.9000, rms radial error=139.832, avgs=0 225/300: dt: 0.9000, rms radial error=139.044, avgs=0 230/300: dt: 0.9000, rms radial error=138.262, avgs=0 235/300: dt: 0.9000, rms radial error=137.483, avgs=0 240/300: dt: 0.9000, rms radial error=136.709, avgs=0 245/300: dt: 0.9000, rms radial error=135.939, avgs=0 250/300: dt: 0.9000, rms radial error=135.173, avgs=0 255/300: dt: 0.9000, rms radial error=134.412, avgs=0 260/300: dt: 0.9000, rms radial error=133.654, avgs=0 265/300: dt: 0.9000, rms radial error=132.901, avgs=0 270/300: dt: 0.9000, rms radial error=132.153, avgs=0 275/300: dt: 0.9000, rms radial error=131.408, avgs=0 280/300: dt: 0.9000, rms radial error=130.668, avgs=0 285/300: dt: 0.9000, rms radial error=129.932, avgs=0 290/300: dt: 0.9000, rms radial error=129.199, avgs=0 295/300: dt: 0.9000, rms radial error=128.471, avgs=0 300/300: dt: 0.9000, rms radial error=127.747, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16087.29 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 = 2736.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 292.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00482 epoch 4 (K=640.0), pass 1, starting sse = 20.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00731 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue Oct 20 15:24:18 EDT 2015 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 af1021_recon lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-44 (nv=136234, nf=272556, ne=408834, g=23) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 3927 ambiguous faces found in tessellation segmenting defects... 28 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 28 defects to be corrected 0 vertices coincident reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2548 (-4.6274) -vertex loglikelihood: -6.1560 (-3.0780) -normal dot loglikelihood: -3.6201 (-3.6201) -quad curv loglikelihood: -6.3204 (-3.1602) Total Loglikelihood : -25.3512 CORRECTING DEFECT 0 (vertices=50, convex hull=98) After retessellation of defect 0, euler #=-22 (133881,400806,266903) : difference with theory (-25) = -3 CORRECTING DEFECT 1 (vertices=29, convex hull=86) After retessellation of defect 1, euler #=-21 (133890,400866,266955) : difference with theory (-24) = -3 CORRECTING DEFECT 2 (vertices=9, convex hull=27) After retessellation of defect 2, euler #=-20 (133891,400877,266966) : difference with theory (-23) = -3 CORRECTING DEFECT 3 (vertices=259, convex hull=205) After retessellation of defect 3, euler #=-19 (133940,401120,267161) : difference with theory (-22) = -3 CORRECTING DEFECT 4 (vertices=6, convex hull=16) After retessellation of defect 4, euler #=-18 (133941,401125,267166) : difference with theory (-21) = -3 CORRECTING DEFECT 5 (vertices=136, convex hull=145) After retessellation of defect 5, euler #=-17 (133985,401326,267324) : difference with theory (-20) = -3 CORRECTING DEFECT 6 (vertices=46, convex hull=67) After retessellation of defect 6, euler #=-16 (134012,401437,267409) : difference with theory (-19) = -3 CORRECTING DEFECT 7 (vertices=87, convex hull=95) After retessellation of defect 7, euler #=-17 (134064,401642,267561) : difference with theory (-18) = -1 CORRECTING DEFECT 8 (vertices=5, convex hull=20) After retessellation of defect 8, euler #=-16 (134064,401647,267567) : difference with theory (-17) = -1 CORRECTING DEFECT 9 (vertices=11, convex hull=10) After retessellation of defect 9, euler #=-15 (134064,401650,267571) : difference with theory (-16) = -1 CORRECTING DEFECT 10 (vertices=42, convex hull=70) After retessellation of defect 10, euler #=-14 (134090,401754,267650) : difference with theory (-15) = -1 CORRECTING DEFECT 11 (vertices=36, convex hull=27) After retessellation of defect 11, euler #=-13 (134096,401780,267671) : difference with theory (-14) = -1 CORRECTING DEFECT 12 (vertices=23, convex hull=20) After retessellation of defect 12, euler #=-12 (134099,401796,267685) : difference with theory (-13) = -1 CORRECTING DEFECT 13 (vertices=28, convex hull=44) After retessellation of defect 13, euler #=-11 (134108,401839,267720) : difference with theory (-12) = -1 CORRECTING DEFECT 14 (vertices=134, convex hull=112) After retessellation of defect 14, euler #=-10 (134163,402056,267883) : difference with theory (-11) = -1 CORRECTING DEFECT 15 (vertices=887, convex hull=214) After retessellation of defect 15, euler #=-9 (134225,402346,268112) : difference with theory (-10) = -1 CORRECTING DEFECT 16 (vertices=29, convex hull=51) After retessellation of defect 16, euler #=-9 (134239,402410,268162) : difference with theory (-9) = 0 CORRECTING DEFECT 17 (vertices=27, convex hull=74) After retessellation of defect 17, euler #=-8 (134255,402487,268224) : difference with theory (-8) = 0 CORRECTING DEFECT 18 (vertices=19, convex hull=50) After retessellation of defect 18, euler #=-7 (134264,402532,268261) : difference with theory (-7) = 0 CORRECTING DEFECT 19 (vertices=39, convex hull=45) After retessellation of defect 19, euler #=-6 (134269,402567,268292) : difference with theory (-6) = 0 CORRECTING DEFECT 20 (vertices=67, convex hull=66) After retessellation of defect 20, euler #=-5 (134287,402654,268362) : difference with theory (-5) = 0 CORRECTING DEFECT 21 (vertices=17, convex hull=30) After retessellation of defect 21, euler #=-4 (134291,402677,268382) : difference with theory (-4) = 0 CORRECTING DEFECT 22 (vertices=61, convex hull=95) After retessellation of defect 22, euler #=-3 (134321,402814,268490) : difference with theory (-3) = 0 CORRECTING DEFECT 23 (vertices=57, convex hull=58) After retessellation of defect 23, euler #=-2 (134337,402886,268547) : difference with theory (-2) = 0 CORRECTING DEFECT 24 (vertices=78, convex hull=95) After retessellation of defect 24, euler #=-1 (134358,402990,268631) : difference with theory (-1) = 0 CORRECTING DEFECT 25 (vertices=23, convex hull=49) After retessellation of defect 25, euler #=0 (134365,403028,268663) : difference with theory (0) = 0 CORRECTING DEFECT 26 (vertices=116, convex hull=100) normal vector of length zero at vertex 136109 with 4 faces After retessellation of defect 26, euler #=1 (134381,403122,268742) : difference with theory (1) = 0 CORRECTING DEFECT 27 (vertices=41, convex hull=36) After retessellation of defect 27, euler #=2 (134383,403143,268762) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.11-->7.44) (max @ vno 125519 --> 129730) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.11-->7.44) (max @ vno 125519 --> 129730) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 97 mutations (34.2%), 187 crossovers (65.8%), 249 vertices were eliminated building final representation... 1851 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134383, nf=268762, ne=403143, g=0) writing corrected surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 22.8 minutes 0 defective edges removing intersecting faces 000: 221 intersecting 001: 3 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 134383 - 403143 + 268762 = 2 --> 0 holes F =2V-4: 268762 = 268766-4 (0) 2E=3F: 806286 = 806286 (0) total defect index = 0 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 17 intersecting 001: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Tue Oct 20 15:47:14 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12571 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.88 3457 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.54 2734 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4892828.0, rms=9.92 001: dt: 0.5000, sse=5566344.5, rms=7.099 (0.000%) 002: dt: 0.5000, sse=5952963.5, rms=5.421 (0.000%) 003: dt: 0.5000, sse=6270257.5, rms=4.412 (0.000%) 004: dt: 0.5000, sse=6511372.5, rms=3.793 (0.000%) 005: dt: 0.5000, sse=6646172.5, rms=3.482 (0.000%) 006: dt: 0.5000, sse=6745737.0, rms=3.293 (0.000%) 007: dt: 0.5000, sse=6787876.0, rms=3.217 (0.000%) 008: dt: 0.5000, sse=6808347.0, rms=3.145 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6803474.0, rms=3.126 (0.000%) 010: dt: 0.2500, sse=4088440.0, rms=2.113 (0.000%) 011: dt: 0.2500, sse=3761433.0, rms=1.869 (0.000%) 012: dt: 0.2500, sse=3615080.2, rms=1.813 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3566575.0, rms=1.783 (0.000%) rms = 1.75, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3509653.8, rms=1.752 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.8, 41 (6) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.3 (%26.2))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.03-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.40) mean absolute distance = 0.25 +- 0.37 3083 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4100091.8, rms=4.66 015: dt: 0.5000, sse=4396954.0, rms=2.790 (0.000%) rms = 2.79, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4865183.0, rms=2.785 (0.000%) 017: dt: 0.2500, sse=4087599.5, rms=1.708 (0.000%) 018: dt: 0.2500, sse=3957018.2, rms=1.512 (0.000%) rms = 1.47, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3845835.0, rms=1.475 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3799473.8, rms=1.433 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.2, 21 (3) missing vertices, mean dist -0.1 [0.3 (%71.9)->0.2 (%28.1))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.50) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3251 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4001116.2, rms=3.27 021: dt: 0.5000, sse=4304313.5, rms=2.448 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4040074.0, rms=1.739 (0.000%) 023: dt: 0.2500, sse=3963482.8, rms=1.400 (0.000%) 024: dt: 0.2500, sse=3935912.5, rms=1.316 (0.000%) rms = 1.32, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3913786.8, rms=1.301 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.0, 29 (2) missing vertices, mean dist -0.0 [0.2 (%56.4)->0.2 (%43.6))] %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3929055.0, rms=1.62 rms = 1.67, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=3991274.2, rms=1.215 (0.000%) 027: dt: 0.2500, sse=4167403.5, rms=0.985 (0.000%) rms = 0.99, time step reduction 2 of 3 to 0.125... rms = 0.98, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4168569.0, rms=0.984 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 23 non-cortical segments detected only using segment with 2182 vertices erasing segment 1 (vno[0] = 57470) erasing segment 2 (vno[0] = 77359) erasing segment 3 (vno[0] = 78446) erasing segment 4 (vno[0] = 82313) erasing segment 5 (vno[0] = 83246) erasing segment 6 (vno[0] = 89295) erasing segment 7 (vno[0] = 93408) erasing segment 8 (vno[0] = 95380) erasing segment 9 (vno[0] = 97413) erasing segment 10 (vno[0] = 97437) erasing segment 11 (vno[0] = 97489) erasing segment 12 (vno[0] = 98344) erasing segment 13 (vno[0] = 98353) erasing segment 14 (vno[0] = 98456) erasing segment 15 (vno[0] = 99252) erasing segment 16 (vno[0] = 99310) erasing segment 17 (vno[0] = 100095) erasing segment 18 (vno[0] = 101770) erasing segment 19 (vno[0] = 101844) erasing segment 20 (vno[0] = 105977) erasing segment 21 (vno[0] = 106623) erasing segment 22 (vno[0] = 134247) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv writing smoothed area to lh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area vertex spacing 0.89 +- 0.25 (0.07-->6.52) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.26) refinement took 4.9 minutes #-------------------------------------------- #@# Smooth2 lh Tue Oct 20 15:52:10 EDT 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Oct 20 15:52:13 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.0 mm, total surface area = 81870 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 141 vertices thresholded to be in k1 ~ [-0.27 0.32], k2 ~ [-0.11 0.08] total integrated curvature = 0.533*4pi (6.694) --> 0 handles ICI = 1.6, FI = 9.9, variation=171.870 118 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 129 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Tue Oct 20 15:54:04 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 257 ] Gb_filter = 0 WARN: S lookup min: -0.486032 WARN: S explicit min: 0.000000 vertex = 245 #-------------------------------------------- #@# Sphere lh Tue Oct 20 15:54:11 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.282... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %19.78 pass 1: epoch 2 of 3 starting distance error %19.78 unfolding complete - removing small folds... starting distance error %19.73 removing remaining folds... final distance error %19.74 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.69 hours #-------------------------------------------- #@# Surf Reg lh Tue Oct 20 16:35:48 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_register -curv ../surf/lh.sphere /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, 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 = 0.578 curvature mean = 0.039, std = 0.935 curvature mean = 0.022, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 337229.2, tmin=0.9515 d=32.00 min @ (0.00, -8.00, 0.00) sse = 281077.2, tmin=1.9097 d=16.00 min @ (4.00, 0.00, -4.00) sse = 254592.3, tmin=2.8689 d=8.00 min @ (0.00, 2.00, 2.00) sse = 252122.2, tmin=3.9127 d=4.00 min @ (0.00, 0.00, -1.00) sse = 251389.0, tmin=5.0332 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 250911.2, tmin=6.1665 d=1.00 min @ (0.25, 0.00, 0.00) sse = 250884.6, tmin=7.2972 d=0.50 min @ (-0.12, -0.12, 0.00) sse = 250849.5, tmin=8.4251 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.43 min curvature mean = 0.014, std = 0.962 curvature mean = 0.010, std = 0.940 curvature mean = 0.012, std = 0.974 curvature mean = 0.004, std = 0.973 curvature mean = 0.009, std = 0.975 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.028, std = 0.295 curvature mean = 0.003, std = 0.067 curvature mean = 0.066, std = 0.342 curvature mean = 0.003, std = 0.080 curvature mean = 0.032, std = 0.527 curvature mean = 0.003, std = 0.086 curvature mean = 0.017, std = 0.669 curvature mean = 0.003, std = 0.088 curvature mean = 0.007, std = 0.776 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Tue Oct 20 17:00:15 EDT 2015 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Oct 20 17:00:24 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Oct 20 17:00:31 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1080 labels changed using aseg relabeling using gibbs priors... 000: 2998 changed, 134383 examined... 001: 687 changed, 12813 examined... 002: 158 changed, 3844 examined... 003: 54 changed, 949 examined... 004: 20 changed, 327 examined... 005: 10 changed, 130 examined... 006: 6 changed, 57 examined... 007: 4 changed, 36 examined... 008: 2 changed, 28 examined... 009: 1 changed, 15 examined... 010: 0 changed, 6 examined... 221 labels changed using aseg 000: 102 total segments, 59 labels (226 vertices) changed 001: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 39 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1230 vertices marked for relabeling... 1230 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 46 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Oct 20 17:01:23 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12571 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.89 3533 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 58 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 4 with 589 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 20 points - only 0.00% unknown mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.55 2833 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4906516.0, rms=9.91 001: dt: 0.5000, sse=5584919.0, rms=7.087 (0.000%) 002: dt: 0.5000, sse=5971842.0, rms=5.412 (0.000%) 003: dt: 0.5000, sse=6295095.5, rms=4.407 (0.000%) 004: dt: 0.5000, sse=6537852.5, rms=3.792 (0.000%) 005: dt: 0.5000, sse=6681860.0, rms=3.482 (0.000%) 006: dt: 0.5000, sse=6780486.5, rms=3.292 (0.000%) 007: dt: 0.5000, sse=6830326.5, rms=3.216 (0.000%) 008: dt: 0.5000, sse=6847692.5, rms=3.144 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6848157.5, rms=3.126 (0.000%) 010: dt: 0.2500, sse=4112707.0, rms=2.115 (0.000%) 011: dt: 0.2500, sse=3785237.8, rms=1.871 (0.000%) 012: dt: 0.2500, sse=3640015.2, rms=1.816 (0.000%) rms = 1.79, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3591487.2, rms=1.786 (0.000%) rms = 1.76, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3534378.5, rms=1.756 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 141 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 5 with 502 points - only 0.00% unknown deleting segment 9 with 13 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown mean border=83.8, 44 (9) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.3 (%26.3))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.03-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.39) mean absolute distance = 0.26 +- 0.38 3165 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4128960.2, rms=4.65 015: dt: 0.5000, sse=4428448.0, rms=2.790 (0.000%) rms = 2.79, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4907061.5, rms=2.785 (0.000%) 017: dt: 0.2500, sse=4118854.8, rms=1.714 (0.000%) 018: dt: 0.2500, sse=3989801.5, rms=1.519 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3879248.2, rms=1.482 (0.000%) rms = 1.44, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3831904.5, rms=1.441 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 535 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 47 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown mean border=86.2, 34 (5) missing vertices, mean dist -0.1 [0.3 (%71.8)->0.2 (%28.2))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.50) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3329 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4035464.2, rms=3.27 021: dt: 0.5000, sse=4342159.0, rms=2.452 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4076464.0, rms=1.749 (0.000%) 023: dt: 0.2500, sse=4000122.5, rms=1.416 (0.000%) 024: dt: 0.2500, sse=3970749.2, rms=1.332 (0.000%) rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.32, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3948572.0, rms=1.317 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 540 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 15 points - only 0.00% unknown mean border=87.0, 44 (4) missing vertices, mean dist -0.0 [0.2 (%56.3)->0.2 (%43.7))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=3964720.0, rms=1.63 rms = 1.67, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4029283.2, rms=1.228 (0.000%) 027: dt: 0.2500, sse=4209924.5, rms=1.001 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4211571.0, rms=0.999 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.1, 61 (61) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.5 (%100.0))] %19 local maxima, %48 large gradients and %29 min vals, 2550 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21194238.0, rms=26.91 001: dt: 0.5000, sse=16177710.0, rms=22.987 (0.000%) 002: dt: 0.5000, sse=12511884.0, rms=19.660 (0.000%) 003: dt: 0.5000, sse=9935601.0, rms=16.892 (0.000%) 004: dt: 0.5000, sse=8271835.0, rms=14.595 (0.000%) 005: dt: 0.5000, sse=7201807.5, rms=12.715 (0.000%) 006: dt: 0.5000, sse=6564423.0, rms=11.197 (0.000%) 007: dt: 0.5000, sse=6195552.5, rms=9.892 (0.000%) 008: dt: 0.5000, sse=5944976.5, rms=8.753 (0.000%) 009: dt: 0.5000, sse=5813457.5, rms=7.736 (0.000%) 010: dt: 0.5000, sse=5740933.0, rms=6.837 (0.000%) 011: dt: 0.5000, sse=5759568.0, rms=6.034 (0.000%) 012: dt: 0.5000, sse=5744825.0, rms=5.300 (0.000%) 013: dt: 0.5000, sse=5830524.5, rms=4.707 (0.000%) 014: dt: 0.5000, sse=5884602.5, rms=4.272 (0.000%) 015: dt: 0.5000, sse=5996652.5, rms=3.978 (0.000%) 016: dt: 0.5000, sse=6030062.0, rms=3.778 (0.000%) 017: dt: 0.5000, sse=6088289.0, rms=3.652 (0.000%) 018: dt: 0.5000, sse=6084106.0, rms=3.556 (0.000%) 019: dt: 0.5000, sse=6118176.0, rms=3.493 (0.000%) 020: dt: 0.5000, sse=6138362.0, rms=3.442 (0.000%) rms = 3.41, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=6133908.5, rms=3.410 (0.000%) 022: dt: 0.2500, sse=4409242.5, rms=2.794 (0.000%) 023: dt: 0.2500, sse=4266424.5, rms=2.634 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=4153288.2, rms=2.616 (0.000%) 025: dt: 0.1250, sse=4016203.5, rms=2.546 (0.000%) rms = 2.54, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3998913.8, rms=2.540 (0.000%) positioning took 2.6 minutes mean border=57.8, 972 (24) missing vertices, mean dist 0.2 [0.2 (%44.9)->0.6 (%55.1))] %39 local maxima, %33 large gradients and %23 min vals, 1002 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4627678.0, rms=4.69 027: dt: 0.5000, sse=4770570.5, rms=3.666 (0.000%) 028: dt: 0.5000, sse=6037900.0, rms=3.553 (0.000%) rms = 3.55, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=5907187.5, rms=3.553 (0.000%) 030: dt: 0.2500, sse=4851860.0, rms=2.808 (0.000%) 031: dt: 0.2500, sse=4736925.5, rms=2.609 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4666506.5, rms=2.577 (0.000%) 033: dt: 0.1250, sse=4528337.5, rms=2.472 (0.000%) rms = 2.45, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=4520418.0, rms=2.452 (0.000%) positioning took 0.8 minutes mean border=56.1, 1173 (20) missing vertices, mean dist 0.1 [0.2 (%38.1)->0.4 (%61.9))] %55 local maxima, %17 large gradients and %23 min vals, 1161 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4670800.5, rms=3.31 rms = 3.27, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=4854815.5, rms=3.274 (0.000%) 036: dt: 0.2500, sse=4860777.5, rms=2.608 (0.000%) 037: dt: 0.2500, sse=4851694.0, rms=2.465 (0.000%) rms = 2.45, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4837670.0, rms=2.453 (0.000%) 039: dt: 0.1250, sse=4716520.5, rms=2.329 (0.000%) rms = 2.31, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4717036.5, rms=2.314 (0.000%) positioning took 0.6 minutes mean border=55.3, 2461 (17) missing vertices, mean dist 0.0 [0.2 (%44.6)->0.3 (%55.4))] %58 local maxima, %14 large gradients and %22 min vals, 909 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4740523.0, rms=2.51 rms = 2.90, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4649935.5, rms=2.347 (0.000%) rms = 2.30, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4802499.5, rms=2.302 (0.000%) 043: dt: 0.1250, sse=4712826.5, rms=2.250 (0.000%) rms = 2.23, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4740258.0, rms=2.234 (0.000%) positioning took 0.5 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.06-->8.04) (max @ vno 92642 --> 92643) face area 0.41 +- 0.32 (0.00-->11.66) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 714:1242 truncations. 27368 vertices at 0 distance 86933 vertices at 1 distance 84333 vertices at 2 distance 39033 vertices at 3 distance 12967 vertices at 4 distance 3966 vertices at 5 distance 1355 vertices at 6 distance 478 vertices at 7 distance 174 vertices at 8 distance 91 vertices at 9 distance 55 vertices at 10 distance 40 vertices at 11 distance 27 vertices at 12 distance 18 vertices at 13 distance 20 vertices at 14 distance 20 vertices at 15 distance 10 vertices at 16 distance 8 vertices at 17 distance 7 vertices at 18 distance 15 vertices at 19 distance 16 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.thickness positioning took 10.7 minutes #-------------------------------------------- #@# Surf Volume lh Tue Oct 20 17:12:05 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Tue Oct 20 17:12:05 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts pctsurfcon --s af1021_recon --lh-only Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts/pctsurfcon.log Tue Oct 20 17:12:05 EDT 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-1.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.9456/lh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 73830 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.9456/lh.wm.mgh Dim: 134383 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.9456/lh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 87912 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.9456/lh.gm.mgh Dim: 134383 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.9456/lh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.9456/lh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-1.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh Vertex Area is 0.663955 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1569 1086.962 2 1002 caudalanteriorcingulate 814 522.250 3 1003 caudalmiddlefrontal 2764 1864.563 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 1883 1217.582 6 1006 entorhinal 629 417.842 7 1007 fusiform 4799 3219.453 8 1008 inferiorparietal 6854 4603.135 9 1009 inferiortemporal 4719 3154.068 10 1010 isthmuscingulate 1422 922.708 11 1011 lateraloccipital 8366 5390.013 12 1012 lateralorbitofrontal 3788 2557.312 13 1013 lingual 5325 3458.724 14 1014 medialorbitofrontal 2410 1593.298 15 1015 middletemporal 4533 3092.269 16 1016 parahippocampal 1136 726.788 17 1017 paracentral 1942 1265.307 18 1018 parsopercularis 2937 2028.785 19 1019 parsorbitalis 925 609.904 20 1020 parstriangularis 1947 1316.733 21 1021 pericalcarine 2184 1389.921 22 1022 postcentral 6527 4170.566 23 1023 posteriorcingulate 1726 1180.100 24 1024 precentral 7435 4766.086 25 1025 precuneus 5912 4054.477 26 1026 rostralanteriorcingulate 1079 697.362 27 1027 rostralmiddlefrontal 8007 5515.635 28 1028 superiorfrontal 9959 6792.604 29 1029 superiorparietal 7689 5110.637 30 1030 superiortemporal 6200 4140.839 31 1031 supramarginal 5569 3709.949 32 1032 frontalpole 276 193.698 33 1033 temporalpole 656 457.104 34 1034 transversetemporal 842 513.617 35 1035 insula 3107 2035.490 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Tue Oct 20 17:12:13 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1569 1087 2846 2.470 0.540 0.111 0.029 12 1.9 bankssts 814 522 1559 2.657 0.511 0.147 0.039 13 1.3 caudalanteriorcingulate 2764 1865 5278 2.590 0.605 0.136 0.065 52 8.5 caudalmiddlefrontal 1883 1218 2578 1.945 0.462 0.164 0.063 34 4.8 cuneus 629 418 1608 3.005 0.670 0.123 0.047 6 1.1 entorhinal 4799 3219 10709 2.888 0.620 0.158 0.084 105 13.2 fusiform 6854 4603 13088 2.536 0.549 0.143 0.058 117 14.7 inferiorparietal 4719 3154 10526 2.879 0.821 0.146 0.074 96 12.7 inferiortemporal 1422 923 2608 2.632 0.682 0.152 0.066 34 3.6 isthmuscingulate 8366 5390 12445 2.104 0.543 0.147 0.051 122 17.4 lateraloccipital 3788 2557 7888 2.761 0.732 0.149 0.064 71 9.7 lateralorbitofrontal 5325 3459 8278 2.196 0.571 0.159 0.066 97 13.5 lingual 2410 1593 4399 2.420 0.716 0.157 0.126 120 10.9 medialorbitofrontal 4533 3092 11432 2.911 0.733 0.138 0.048 72 8.4 middletemporal 1136 727 2152 2.531 0.618 0.117 0.038 10 1.8 parahippocampal 1942 1265 3245 2.339 0.465 0.132 0.077 99 7.9 paracentral 2937 2029 6285 2.714 0.437 0.131 0.043 41 5.4 parsopercularis 925 610 2379 2.896 0.587 0.161 0.097 26 3.7 parsorbitalis 1947 1317 4111 2.709 0.597 0.133 0.045 26 3.3 parstriangularis 2184 1390 2455 1.864 0.460 0.131 0.064 32 5.8 pericalcarine 6527 4171 10629 2.256 0.706 0.132 0.045 87 12.6 postcentral 1726 1180 3384 2.703 0.618 0.158 0.056 33 4.0 posteriorcingulate 7435 4766 13528 2.580 0.615 0.136 0.055 100 17.0 precentral 5912 4054 10262 2.340 0.554 0.141 0.047 93 11.5 precuneus 1079 697 2505 3.053 0.797 0.162 0.058 22 2.4 rostralanteriorcingulate 8007 5516 16686 2.540 0.652 0.158 0.065 158 20.4 rostralmiddlefrontal 9959 6793 23602 2.971 0.637 0.148 0.061 162 23.7 superiorfrontal 7689 5111 12720 2.221 0.556 0.141 0.056 303 14.4 superiorparietal 6200 4141 14442 2.932 0.637 0.127 0.045 86 12.0 superiortemporal 5569 3710 11797 2.797 0.595 0.142 0.058 133 13.1 supramarginal 276 194 794 3.001 0.443 0.251 0.169 14 1.9 frontalpole 656 457 2583 3.475 0.840 0.187 0.093 19 2.7 temporalpole 842 514 1541 2.532 0.532 0.136 0.067 13 2.5 transversetemporal 3107 2035 6910 3.267 0.828 0.115 0.052 34 5.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Oct 20 17:12:27 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 179 labels changed using aseg relabeling using gibbs priors... 000: 9263 changed, 134383 examined... 001: 2241 changed, 35608 examined... 002: 713 changed, 11519 examined... 003: 297 changed, 4013 examined... 004: 158 changed, 1678 examined... 005: 79 changed, 867 examined... 006: 30 changed, 433 examined... 007: 18 changed, 185 examined... 008: 20 changed, 114 examined... 009: 6 changed, 89 examined... 010: 2 changed, 37 examined... 011: 2 changed, 12 examined... 012: 0 changed, 8 examined... 83 labels changed using aseg 000: 295 total segments, 214 labels (2830 vertices) changed 001: 94 total segments, 13 labels (124 vertices) changed 002: 83 total segments, 2 labels (2 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 114 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 539 vertices marked for relabeling... 539 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Oct 20 17:13:14 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1044 704 2096 2.370 0.735 0.179 0.081 28 3.5 G_and_S_frontomargin 1688 1144 2994 2.335 0.514 0.158 0.099 37 3.5 G_and_S_occipital_inf 1472 894 2367 2.186 0.499 0.136 0.066 92 4.3 G_and_S_paracentral 1587 1041 3502 2.903 0.618 0.158 0.065 30 4.0 G_and_S_subcentral 663 455 1664 2.513 0.705 0.218 0.129 28 2.9 G_and_S_transv_frontopol 1976 1323 4356 3.077 0.733 0.154 0.053 33 4.1 G_and_S_cingul-Ant 1112 754 2209 2.684 0.556 0.123 0.033 10 1.5 G_and_S_cingul-Mid-Ant 1276 897 2484 2.655 0.533 0.143 0.048 17 2.6 G_and_S_cingul-Mid-Post 499 338 1286 3.134 0.581 0.169 0.061 11 1.2 G_cingul-Post-dorsal 283 163 457 2.356 0.791 0.160 0.103 8 1.2 G_cingul-Post-ventral 1654 1038 2207 1.878 0.429 0.167 0.070 33 4.8 G_cuneus 1528 1070 4089 2.897 0.386 0.150 0.058 33 4.0 G_front_inf-Opercular 410 262 1120 3.172 0.420 0.183 0.166 19 2.5 G_front_inf-Orbital 1299 876 3374 2.836 0.522 0.148 0.048 21 2.6 G_front_inf-Triangul 4000 2727 10188 2.890 0.593 0.173 0.088 111 14.8 G_front_middle 7440 5014 19252 3.058 0.608 0.160 0.078 151 24.0 G_front_sup 535 343 1404 3.611 0.772 0.114 0.076 6 0.9 G_Ins_lg_and_S_cent_ins 631 402 2180 3.971 0.728 0.133 0.074 13 2.2 G_insular_short 2945 1862 6553 2.636 0.539 0.159 0.056 59 6.5 G_occipital_middle 1516 971 2603 2.173 0.556 0.160 0.060 28 3.6 G_occipital_sup 1895 1262 4711 2.914 0.541 0.169 0.067 43 5.5 G_oc-temp_lat-fusifor 3719 2357 6067 2.167 0.612 0.168 0.081 83 10.8 G_oc-temp_med-Lingual 1284 806 2923 2.948 0.757 0.119 0.044 12 2.4 G_oc-temp_med-Parahip 2602 1768 6810 2.853 0.722 0.168 0.083 65 8.5 G_orbital 2245 1491 4933 2.650 0.594 0.159 0.087 59 6.4 G_pariet_inf-Angular 3257 2163 8092 2.971 0.565 0.149 0.065 104 9.2 G_pariet_inf-Supramar 2706 1804 5389 2.333 0.651 0.140 0.050 39 5.3 G_parietal_sup 2617 1582 4881 2.413 0.638 0.138 0.052 43 5.9 G_postcentral 3048 1777 6360 2.821 0.551 0.138 0.063 49 8.5 G_precentral 2656 1817 5675 2.464 0.545 0.159 0.062 61 7.1 G_precuneus 999 678 2286 2.524 0.667 0.177 0.087 30 3.7 G_rectus 455 265 613 2.246 0.853 0.180 0.399 81 6.0 G_subcallosal 678 404 1384 2.701 0.621 0.155 0.084 13 2.5 G_temp_sup-G_T_transv 2426 1583 7578 3.248 0.656 0.149 0.064 55 6.9 G_temp_sup-Lateral 472 300 1165 3.386 0.704 0.140 0.073 9 1.4 G_temp_sup-Plan_polar 1035 733 2165 2.605 0.519 0.105 0.025 7 1.0 G_temp_sup-Plan_tempo 2200 1477 6192 3.104 0.781 0.165 0.098 53 6.6 G_temporal_inf 2671 1810 7865 3.119 0.710 0.153 0.059 54 6.1 G_temporal_middle 336 219 471 2.630 0.609 0.106 0.027 2 0.3 Lat_Fis-ant-Horizont 335 228 489 2.542 0.390 0.101 0.024 1 0.3 Lat_Fis-ant-Vertical 1339 887 1831 2.608 0.530 0.118 0.037 12 2.0 Lat_Fis-post 2543 1542 3017 1.778 0.469 0.145 0.058 40 6.3 Pole_occipital 1821 1237 6082 3.416 0.828 0.180 0.098 49 6.6 Pole_temporal 3040 2002 3962 2.090 0.526 0.131 0.050 39 6.5 S_calcarine 3197 2176 3438 1.791 0.518 0.133 0.046 32 5.8 S_central 887 631 1369 2.269 0.495 0.127 0.039 9 1.4 S_cingul-Marginalis 443 296 771 2.963 0.515 0.108 0.030 3 0.6 S_circular_insula_ant 1433 957 2440 2.720 0.653 0.083 0.018 5 1.1 S_circular_insula_inf 1741 1170 2689 2.718 0.485 0.108 0.028 11 2.1 S_circular_insula_sup 1179 797 2515 3.040 0.701 0.145 0.067 21 2.8 S_collat_transv_ant 449 298 528 2.255 0.397 0.138 0.042 4 0.8 S_collat_transv_post 2543 1729 3928 2.308 0.476 0.121 0.034 22 3.6 S_front_inf 1454 1017 2437 2.405 0.499 0.133 0.038 14 2.5 S_front_middle 2382 1646 3991 2.454 0.481 0.119 0.044 23 3.9 S_front_sup 265 180 662 3.024 0.574 0.167 0.059 5 0.7 S_interm_prim-Jensen 3328 2241 4676 2.197 0.469 0.131 0.044 37 5.2 S_intrapariet_and_P_trans 1417 933 1584 1.908 0.376 0.139 0.041 16 2.4 S_oc_middle_and_Lunatus 1294 845 1645 2.023 0.381 0.127 0.081 212 1.7 S_oc_sup_and_transversal 1256 861 1655 2.247 0.368 0.138 0.053 22 3.2 S_occipital_ant 767 527 1093 2.424 0.380 0.109 0.026 5 0.8 S_oc-temp_lat 2026 1414 3093 2.454 0.521 0.133 0.040 20 3.4 S_oc-temp_med_and_Lingual 295 200 396 2.142 0.409 0.118 0.033 2 0.4 S_orbital_lateral 758 511 1028 2.279 0.685 0.108 0.022 5 0.6 S_orbital_med-olfact 1192 802 2190 2.744 0.742 0.140 0.054 20 2.6 S_orbital-H_Shaped 2585 1762 3493 2.160 0.573 0.129 0.035 25 3.9 S_parieto_occipital 899 577 1088 2.445 0.593 0.166 0.056 25 2.0 S_pericallosal 2287 1540 3313 2.368 0.432 0.122 0.035 21 3.4 S_postcentral 1848 1286 2967 2.418 0.475 0.117 0.030 13 2.3 S_precentral-inf-part 708 512 1073 2.437 0.409 0.117 0.027 4 0.9 S_precentral-sup-part 610 421 970 2.538 0.712 0.137 0.037 6 0.9 S_suborbital 902 607 1504 2.444 0.551 0.131 0.042 10 1.5 S_subparietal 1506 1018 2327 2.393 0.703 0.124 0.047 20 3.6 S_temporal_inf 5987 4106 10562 2.571 0.485 0.120 0.036 55 8.8 S_temporal_sup 355 249 502 2.456 0.397 0.130 0.034 3 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Oct 20 17:13:28 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1246 labels changed using aseg relabeling using gibbs priors... 000: 2899 changed, 134383 examined... 001: 703 changed, 12164 examined... 002: 174 changed, 3786 examined... 003: 80 changed, 984 examined... 004: 31 changed, 481 examined... 005: 20 changed, 188 examined... 006: 19 changed, 104 examined... 007: 15 changed, 97 examined... 008: 9 changed, 79 examined... 009: 8 changed, 51 examined... 010: 7 changed, 43 examined... 011: 2 changed, 40 examined... 012: 3 changed, 12 examined... 013: 1 changed, 13 examined... 014: 2 changed, 7 examined... 015: 0 changed, 11 examined... 270 labels changed using aseg 000: 75 total segments, 42 labels (284 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 559 vertices marked for relabeling... 559 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Oct 20 17:14:09 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1574 1020 3075 2.771 0.615 0.137 0.038 21 2.6 caudalanteriorcingulate 2790 1889 5344 2.588 0.604 0.136 0.065 53 8.5 caudalmiddlefrontal 3021 1949 4183 1.987 0.491 0.153 0.055 49 6.8 cuneus 558 368 1483 3.026 0.714 0.123 0.044 5 1.0 entorhinal 4232 2860 8916 2.793 0.549 0.153 0.062 77 10.4 fusiform 6608 4440 12747 2.537 0.556 0.144 0.058 115 14.4 inferiorparietal 4968 3307 11929 2.988 0.839 0.152 0.077 100 13.7 inferiortemporal 1407 915 2553 2.616 0.684 0.152 0.065 33 3.5 isthmuscingulate 8664 5564 12876 2.096 0.544 0.148 0.063 149 19.5 lateraloccipital 3858 2621 8587 2.805 0.797 0.159 0.073 89 11.2 lateralorbitofrontal 5325 3467 8286 2.194 0.574 0.158 0.066 97 13.4 lingual 2045 1355 3818 2.418 0.700 0.146 0.067 43 5.5 medialorbitofrontal 6012 4085 13762 2.799 0.729 0.133 0.044 83 10.6 middletemporal 1153 736 2192 2.540 0.626 0.119 0.038 10 1.9 parahippocampal 2324 1519 3959 2.403 0.502 0.131 0.070 84 8.5 paracentral 2484 1726 5249 2.697 0.412 0.129 0.042 36 4.4 parsopercularis 1044 703 2499 2.938 0.535 0.137 0.082 23 3.1 parsorbitalis 2501 1674 5268 2.659 0.610 0.136 0.045 32 4.6 parstriangularis 2132 1360 2408 1.874 0.459 0.132 0.065 31 5.7 pericalcarine 7110 4600 11730 2.272 0.693 0.133 0.045 94 13.4 postcentral 1828 1248 3517 2.706 0.602 0.156 0.055 34 4.2 posteriorcingulate 7573 4836 13641 2.585 0.614 0.137 0.055 121 17.5 precentral 5628 3866 9871 2.325 0.574 0.142 0.048 91 11.3 precuneus 1486 977 3186 2.911 0.844 0.176 0.155 99 7.8 rostralanteriorcingulate 5507 3770 11640 2.593 0.637 0.156 0.058 96 12.8 rostralmiddlefrontal 11109 7601 25989 2.871 0.663 0.155 0.070 211 29.9 superiorfrontal 6092 4053 10336 2.283 0.545 0.142 0.059 283 11.3 superiorparietal 8066 5437 19340 2.938 0.675 0.131 0.049 117 16.6 superiortemporal 5253 3495 10948 2.793 0.592 0.141 0.058 127 12.4 supramarginal 829 505 1516 2.526 0.527 0.137 0.068 13 2.5 transversetemporal 2749 1829 6403 3.266 0.819 0.110 0.047 27 4.7 insula #-------------------------------------------- #@# Tessellate rh Tue Oct 20 17:14:22 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 254379: 0.001572) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 60: 1433 vertices, 1540 faces slice 70: 6181 vertices, 6407 faces slice 80: 13052 vertices, 13308 faces slice 90: 21514 vertices, 21856 faces slice 100: 31864 vertices, 32228 faces slice 110: 42481 vertices, 42864 faces slice 120: 54336 vertices, 54740 faces slice 130: 67248 vertices, 67687 faces slice 140: 79843 vertices, 80285 faces slice 150: 91429 vertices, 91817 faces slice 160: 101695 vertices, 102034 faces slice 170: 109545 vertices, 109817 faces slice 180: 117416 vertices, 117726 faces slice 190: 124512 vertices, 124785 faces slice 200: 130623 vertices, 130864 faces slice 210: 135029 vertices, 135167 faces slice 220: 135960 vertices, 135992 faces slice 230: 135960 vertices, 135992 faces slice 240: 135960 vertices, 135992 faces slice 250: 135960 vertices, 135992 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 135960 voxel in cpt #1: X=-32 [v=135960,e=407976,f=271984] located at (25.719248, 2.998522, 35.666489) For the whole surface: X=-32 [v=135960,e=407976,f=271984] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Tue Oct 20 17:14:29 EDT 2015 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Tue Oct 20 17:14:33 EDT 2015 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts avg radius = 45.7 mm, total surface area = 70897 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Tue Oct 20 17:15:00 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.56 (0.00-->6.85) (max @ vno 45690 --> 46760) face area 0.03 +- 0.03 (-0.09-->0.76) scaling brain by 0.311... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.055, avgs=0 005/300: dt: 0.9000, rms radial error=176.795, avgs=0 010/300: dt: 0.9000, rms radial error=176.236, avgs=0 015/300: dt: 0.9000, rms radial error=175.501, avgs=0 020/300: dt: 0.9000, rms radial error=174.671, avgs=0 025/300: dt: 0.9000, rms radial error=173.782, avgs=0 030/300: dt: 0.9000, rms radial error=172.860, avgs=0 035/300: dt: 0.9000, rms radial error=171.922, avgs=0 040/300: dt: 0.9000, rms radial error=170.976, avgs=0 045/300: dt: 0.9000, rms radial error=170.028, avgs=0 050/300: dt: 0.9000, rms radial error=169.081, avgs=0 055/300: dt: 0.9000, rms radial error=168.137, avgs=0 060/300: dt: 0.9000, rms radial error=167.196, avgs=0 065/300: dt: 0.9000, rms radial error=166.260, avgs=0 070/300: dt: 0.9000, rms radial error=165.328, avgs=0 075/300: dt: 0.9000, rms radial error=164.400, avgs=0 080/300: dt: 0.9000, rms radial error=163.478, avgs=0 085/300: dt: 0.9000, rms radial error=162.561, avgs=0 090/300: dt: 0.9000, rms radial error=161.649, avgs=0 095/300: dt: 0.9000, rms radial error=160.741, avgs=0 100/300: dt: 0.9000, rms radial error=159.838, avgs=0 105/300: dt: 0.9000, rms radial error=158.940, avgs=0 110/300: dt: 0.9000, rms radial error=158.047, avgs=0 115/300: dt: 0.9000, rms radial error=157.159, avgs=0 120/300: dt: 0.9000, rms radial error=156.276, avgs=0 125/300: dt: 0.9000, rms radial error=155.398, avgs=0 130/300: dt: 0.9000, rms radial error=154.524, avgs=0 135/300: dt: 0.9000, rms radial error=153.656, avgs=0 140/300: dt: 0.9000, rms radial error=152.792, avgs=0 145/300: dt: 0.9000, rms radial error=151.932, avgs=0 150/300: dt: 0.9000, rms radial error=151.078, avgs=0 155/300: dt: 0.9000, rms radial error=150.228, avgs=0 160/300: dt: 0.9000, rms radial error=149.383, avgs=0 165/300: dt: 0.9000, rms radial error=148.543, avgs=0 170/300: dt: 0.9000, rms radial error=147.707, avgs=0 175/300: dt: 0.9000, rms radial error=146.875, avgs=0 180/300: dt: 0.9000, rms radial error=146.049, avgs=0 185/300: dt: 0.9000, rms radial error=145.227, avgs=0 190/300: dt: 0.9000, rms radial error=144.410, avgs=0 195/300: dt: 0.9000, rms radial error=143.598, avgs=0 200/300: dt: 0.9000, rms radial error=142.790, avgs=0 205/300: dt: 0.9000, rms radial error=141.986, avgs=0 210/300: dt: 0.9000, rms radial error=141.187, avgs=0 215/300: dt: 0.9000, rms radial error=140.392, avgs=0 220/300: dt: 0.9000, rms radial error=139.602, avgs=0 225/300: dt: 0.9000, rms radial error=138.816, avgs=0 230/300: dt: 0.9000, rms radial error=138.035, avgs=0 235/300: dt: 0.9000, rms radial error=137.257, avgs=0 240/300: dt: 0.9000, rms radial error=136.484, avgs=0 245/300: dt: 0.9000, rms radial error=135.716, avgs=0 250/300: dt: 0.9000, rms radial error=134.951, avgs=0 255/300: dt: 0.9000, rms radial error=134.191, avgs=0 260/300: dt: 0.9000, rms radial error=133.436, avgs=0 265/300: dt: 0.9000, rms radial error=132.684, avgs=0 270/300: dt: 0.9000, rms radial error=131.937, avgs=0 275/300: dt: 0.9000, rms radial error=131.193, avgs=0 280/300: dt: 0.9000, rms radial error=130.454, avgs=0 285/300: dt: 0.9000, rms radial error=129.719, avgs=0 290/300: dt: 0.9000, rms radial error=128.988, avgs=0 295/300: dt: 0.9000, rms radial error=128.262, avgs=0 300/300: dt: 0.9000, rms radial error=127.539, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15904.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 2638.92 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 = 268.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00631 epoch 4 (K=640.0), pass 1, starting sse = 15.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/13 = 0.00492 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Tue Oct 20 17:18:59 EDT 2015 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 af1021_recon rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-32 (nv=135960, nf=271984, ne=407976, g=17) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 2506 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 11 24 defects to be corrected 0 vertices coincident reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2556 (-4.6278) -vertex loglikelihood: -6.1765 (-3.0883) -normal dot loglikelihood: -3.6583 (-3.6583) -quad curv loglikelihood: -6.5684 (-3.2842) Total Loglikelihood : -25.6589 CORRECTING DEFECT 0 (vertices=31, convex hull=61) After retessellation of defect 0, euler #=-22 (134430,402642,268190) : difference with theory (-21) = 1 CORRECTING DEFECT 1 (vertices=29, convex hull=82) After retessellation of defect 1, euler #=-21 (134444,402716,268251) : difference with theory (-20) = 1 CORRECTING DEFECT 2 (vertices=23, convex hull=70) After retessellation of defect 2, euler #=-20 (134461,402794,268313) : difference with theory (-19) = 1 CORRECTING DEFECT 3 (vertices=6, convex hull=14) After retessellation of defect 3, euler #=-19 (134462,402801,268320) : difference with theory (-18) = 1 CORRECTING DEFECT 4 (vertices=42, convex hull=70) After retessellation of defect 4, euler #=-18 (134489,402912,268405) : difference with theory (-17) = 1 CORRECTING DEFECT 5 (vertices=30, convex hull=83) After retessellation of defect 5, euler #=-17 (134506,402998,268475) : difference with theory (-16) = 1 CORRECTING DEFECT 6 (vertices=54, convex hull=37) After retessellation of defect 6, euler #=-16 (134512,403026,268498) : difference with theory (-15) = 1 CORRECTING DEFECT 7 (vertices=121, convex hull=132) After retessellation of defect 7, euler #=-15 (134549,403197,268633) : difference with theory (-14) = 1 CORRECTING DEFECT 8 (vertices=159, convex hull=78) After retessellation of defect 8, euler #=-14 (134579,403327,268734) : difference with theory (-13) = 1 CORRECTING DEFECT 9 (vertices=47, convex hull=87) After retessellation of defect 9, euler #=-13 (134601,403433,268819) : difference with theory (-12) = 1 CORRECTING DEFECT 10 (vertices=6, convex hull=22) After retessellation of defect 10, euler #=-12 (134602,403442,268828) : difference with theory (-11) = 1 CORRECTING DEFECT 11 (vertices=113, convex hull=118) After retessellation of defect 11, euler #=-10 (134645,403628,268973) : difference with theory (-10) = 0 CORRECTING DEFECT 12 (vertices=28, convex hull=62) After retessellation of defect 12, euler #=-9 (134656,403684,269019) : difference with theory (-9) = 0 CORRECTING DEFECT 13 (vertices=219, convex hull=70) After retessellation of defect 13, euler #=-8 (134669,403754,269077) : difference with theory (-8) = 0 CORRECTING DEFECT 14 (vertices=198, convex hull=101) After retessellation of defect 14, euler #=-7 (134705,403905,269193) : difference with theory (-7) = 0 CORRECTING DEFECT 15 (vertices=25, convex hull=31) After retessellation of defect 15, euler #=-6 (134708,403923,269209) : difference with theory (-6) = 0 CORRECTING DEFECT 16 (vertices=87, convex hull=122) After retessellation of defect 16, euler #=-5 (134741,404073,269327) : difference with theory (-5) = 0 CORRECTING DEFECT 17 (vertices=23, convex hull=54) After retessellation of defect 17, euler #=-4 (134751,404126,269371) : difference with theory (-4) = 0 CORRECTING DEFECT 18 (vertices=15, convex hull=23) After retessellation of defect 18, euler #=-3 (134754,404142,269385) : difference with theory (-3) = 0 CORRECTING DEFECT 19 (vertices=16, convex hull=15) After retessellation of defect 19, euler #=-2 (134754,404146,269390) : difference with theory (-2) = 0 CORRECTING DEFECT 20 (vertices=19, convex hull=51) After retessellation of defect 20, euler #=-1 (134766,404200,269433) : difference with theory (-1) = 0 CORRECTING DEFECT 21 (vertices=118, convex hull=65) After retessellation of defect 21, euler #=0 (134777,404262,269485) : difference with theory (0) = 0 CORRECTING DEFECT 22 (vertices=105, convex hull=95) After retessellation of defect 22, euler #=1 (134796,404361,269566) : difference with theory (1) = 0 CORRECTING DEFECT 23 (vertices=33, convex hull=60) After retessellation of defect 23, euler #=2 (134806,404412,269608) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.10-->8.46) (max @ vno 51160 --> 56118) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.10-->8.46) (max @ vno 51160 --> 56118) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (37.2%), 137 crossovers (62.8%), 85 vertices were eliminated building final representation... 1154 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134806, nf=269608, ne=404412, g=0) writing corrected surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 12.1 minutes 0 defective edges removing intersecting faces 000: 171 intersecting 001: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 134806 - 404412 + 269608 = 2 --> 0 holes F =2V-4: 269608 = 269612-4 (0) 2E=3F: 808824 = 808824 (0) total defect index = 0 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 43 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Tue Oct 20 17:31:10 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 7.9 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.72 +- 0.91 3825 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=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.8, 20 (20) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.33) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2614 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5028703.0, rms=9.93 001: dt: 0.5000, sse=5798095.0, rms=7.145 (0.000%) 002: dt: 0.5000, sse=6203343.0, rms=5.512 (0.000%) 003: dt: 0.5000, sse=6482051.5, rms=4.508 (0.000%) 004: dt: 0.5000, sse=6737260.0, rms=3.876 (0.000%) 005: dt: 0.5000, sse=6852365.5, rms=3.535 (0.000%) 006: dt: 0.5000, sse=6976557.5, rms=3.322 (0.000%) 007: dt: 0.5000, sse=7006738.0, rms=3.233 (0.000%) 008: dt: 0.5000, sse=7047161.5, rms=3.151 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7017312.0, rms=3.132 (0.000%) 010: dt: 0.2500, sse=4336957.5, rms=2.129 (0.000%) 011: dt: 0.2500, sse=4010876.8, rms=1.885 (0.000%) 012: dt: 0.2500, sse=3853105.2, rms=1.832 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3813539.0, rms=1.801 (0.000%) rms = 1.76, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3750707.5, rms=1.764 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.7, 51 (5) missing vertices, mean dist -0.2 [0.4 (%72.0)->0.3 (%28.0))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.59) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.38 3687 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4287212.5, rms=4.33 015: dt: 0.5000, sse=4680078.5, rms=2.730 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4372707.5, rms=2.168 (0.000%) 017: dt: 0.2500, sse=4217287.5, rms=1.751 (0.000%) 018: dt: 0.2500, sse=4125774.8, rms=1.579 (0.000%) 019: dt: 0.2500, sse=4071074.8, rms=1.525 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4054175.8, rms=1.503 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4010530.0, rms=1.472 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.0, 39 (3) missing vertices, mean dist -0.1 [0.3 (%71.2)->0.2 (%28.8))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->4.66) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.90) mean absolute distance = 0.22 +- 0.31 3608 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4208390.0, rms=3.25 022: dt: 0.5000, sse=4531338.0, rms=2.426 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4266951.5, rms=1.765 (0.000%) 024: dt: 0.2500, sse=4186573.8, rms=1.436 (0.000%) 025: dt: 0.2500, sse=4155218.8, rms=1.354 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4130778.0, rms=1.353 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4097113.2, rms=1.324 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.8, 53 (1) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4112361.8, rms=1.66 rms = 1.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=5244013.0, rms=1.628 (0.000%) 029: dt: 0.2500, sse=4485060.5, rms=1.269 (0.000%) 030: dt: 0.2500, sse=4692758.0, rms=1.096 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.06, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4654068.0, rms=1.065 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 15 non-cortical segments detected only using segment with 2313 vertices erasing segment 1 (vno[0] = 45502) erasing segment 2 (vno[0] = 50090) erasing segment 3 (vno[0] = 83943) erasing segment 4 (vno[0] = 94873) erasing segment 5 (vno[0] = 94892) erasing segment 6 (vno[0] = 94904) erasing segment 7 (vno[0] = 95880) erasing segment 8 (vno[0] = 96851) erasing segment 9 (vno[0] = 99617) erasing segment 10 (vno[0] = 101371) erasing segment 11 (vno[0] = 102196) erasing segment 12 (vno[0] = 102270) erasing segment 13 (vno[0] = 103084) erasing segment 14 (vno[0] = 103867) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv writing smoothed area to rh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area vertex spacing 0.89 +- 0.25 (0.02-->4.59) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.87) refinement took 5.3 minutes #-------------------------------------------- #@# Smooth2 rh Tue Oct 20 17:36:28 EDT 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Tue Oct 20 17:36:32 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 45.8 mm, total surface area = 81367 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.117 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 146 vertices thresholded to be in k1 ~ [-0.35 0.34], k2 ~ [-0.11 0.09] total integrated curvature = 0.562*4pi (7.061) --> 0 handles ICI = 1.4, FI = 8.6, variation=149.296 113 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 131 vertices thresholded to be in [-0.14 0.17] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats rh Tue Oct 20 17:38:24 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 247 ] Gb_filter = 0 WARN: S lookup min: -0.713181 WARN: S explicit min: 0.000000 vertex = 427 #-------------------------------------------- #@# Sphere rh Tue Oct 20 17:38:30 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.290... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %20.08 pass 1: epoch 2 of 3 starting distance error %20.00 unfolding complete - removing small folds... starting distance error %19.91 removing remaining folds... final distance error %19.93 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.69 hours #-------------------------------------------- #@# Surf Reg rh Tue Oct 20 18:20:07 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_register -curv ../surf/rh.sphere /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, 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 = 0.590 curvature mean = 0.038, std = 0.931 curvature mean = 0.022, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 16.00) sse = 377629.5, tmin=0.9699 d=32.00 min @ (0.00, 8.00, 0.00) sse = 333386.8, tmin=1.9537 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 314571.8, tmin=2.9449 d=8.00 min @ (0.00, 2.00, -2.00) sse = 313948.2, tmin=3.9726 d=4.00 min @ (0.00, -1.00, 1.00) sse = 312803.1, tmin=5.0241 d=2.00 min @ (0.00, 0.00, -0.50) sse = 312781.5, tmin=6.0705 d=1.00 min @ (0.00, 0.00, 0.25) sse = 312736.7, tmin=7.0966 d=0.50 min @ (0.00, -0.12, 0.00) sse = 312731.5, tmin=8.1122 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.11 min curvature mean = 0.024, std = 0.960 curvature mean = 0.007, std = 0.938 curvature mean = 0.021, std = 0.970 curvature mean = 0.004, std = 0.972 curvature mean = 0.020, std = 0.970 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.028, std = 0.391 curvature mean = 0.006, std = 0.070 curvature mean = 0.049, std = 0.262 curvature mean = 0.006, std = 0.083 curvature mean = 0.023, std = 0.409 curvature mean = 0.006, std = 0.089 curvature mean = 0.013, std = 0.517 curvature mean = 0.007, std = 0.092 curvature mean = 0.004, std = 0.605 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Oct 20 18:43:42 EDT 2015 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Oct 20 18:43:44 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Oct 20 18:43:45 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1183 labels changed using aseg relabeling using gibbs priors... 000: 3078 changed, 134806 examined... 001: 690 changed, 13166 examined... 002: 181 changed, 3798 examined... 003: 67 changed, 1081 examined... 004: 28 changed, 395 examined... 005: 9 changed, 155 examined... 006: 8 changed, 65 examined... 007: 5 changed, 43 examined... 008: 1 changed, 21 examined... 009: 0 changed, 7 examined... 153 labels changed using aseg 000: 96 total segments, 57 labels (478 vertices) changed 001: 40 total segments, 2 labels (2 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1134 vertices marked for relabeling... 1134 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 42 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Oct 20 18:44:28 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 7.9 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.73 +- 0.92 3426 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 384 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=80.8, 25 (24) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.33) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2648 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5038844.0, rms=9.92 001: dt: 0.5000, sse=5814627.5, rms=7.139 (0.000%) 002: dt: 0.5000, sse=6222935.5, rms=5.509 (0.000%) 003: dt: 0.5000, sse=6502243.5, rms=4.506 (0.000%) 004: dt: 0.5000, sse=6758716.5, rms=3.876 (0.000%) 005: dt: 0.5000, sse=6871853.0, rms=3.535 (0.000%) 006: dt: 0.5000, sse=6998138.5, rms=3.322 (0.000%) 007: dt: 0.5000, sse=7027588.5, rms=3.234 (0.000%) 008: dt: 0.5000, sse=7068909.0, rms=3.152 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7037584.5, rms=3.133 (0.000%) 010: dt: 0.2500, sse=4353948.5, rms=2.132 (0.000%) 011: dt: 0.2500, sse=4026537.0, rms=1.889 (0.000%) 012: dt: 0.2500, sse=3868687.5, rms=1.836 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3828527.0, rms=1.805 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3765107.0, rms=1.768 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 297 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 22 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown mean border=83.7, 55 (6) missing vertices, mean dist -0.2 [0.4 (%71.9)->0.3 (%28.1))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.59) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.39 3727 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4305371.5, rms=4.33 015: dt: 0.5000, sse=4697748.0, rms=2.730 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4391852.0, rms=2.169 (0.000%) 017: dt: 0.2500, sse=4239539.5, rms=1.753 (0.000%) 018: dt: 0.2500, sse=4146410.0, rms=1.581 (0.000%) 019: dt: 0.2500, sse=4091415.0, rms=1.528 (0.000%) rms = 1.51, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4074417.2, rms=1.506 (0.000%) rms = 1.48, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4030618.8, rms=1.475 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 300 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=86.0, 40 (3) missing vertices, mean dist -0.1 [0.3 (%71.1)->0.2 (%28.9))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->4.66) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.90) mean absolute distance = 0.22 +- 0.31 2768 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4228552.0, rms=3.25 022: dt: 0.5000, sse=4553882.5, rms=2.425 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4287966.5, rms=1.766 (0.000%) 024: dt: 0.2500, sse=4205730.0, rms=1.439 (0.000%) 025: dt: 0.2500, sse=4176810.0, rms=1.357 (0.000%) rms = 1.36, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4150228.8, rms=1.357 (0.000%) rms = 1.33, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4117656.2, rms=1.327 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 304 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=86.8, 54 (1) missing vertices, mean dist -0.0 [0.2 (%57.2)->0.2 (%42.8))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4133005.5, rms=1.67 rms = 1.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=5277291.5, rms=1.628 (0.000%) 029: dt: 0.2500, sse=4514169.5, rms=1.271 (0.000%) 030: dt: 0.2500, sse=4722153.5, rms=1.099 (0.000%) rms = 1.16, time step reduction 2 of 3 to 0.125... rms = 1.07, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4683113.5, rms=1.068 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group smoothing surface for 5 iterations... mean border=60.2, 49 (49) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.6 (%100.0))] %19 local maxima, %45 large gradients and %32 min vals, 2376 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21254276.0, rms=26.82 001: dt: 0.5000, sse=16363014.0, rms=23.004 (0.000%) 002: dt: 0.5000, sse=12765346.0, rms=19.767 (0.000%) 003: dt: 0.5000, sse=10241108.0, rms=17.081 (0.000%) 004: dt: 0.5000, sse=8602027.0, rms=14.855 (0.000%) 005: dt: 0.5000, sse=7530341.0, rms=13.020 (0.000%) 006: dt: 0.5000, sse=6845582.0, rms=11.543 (0.000%) 007: dt: 0.5000, sse=6417503.0, rms=10.267 (0.000%) 008: dt: 0.5000, sse=6131376.5, rms=9.129 (0.000%) 009: dt: 0.5000, sse=5967624.0, rms=8.078 (0.000%) 010: dt: 0.5000, sse=5861806.0, rms=7.133 (0.000%) 011: dt: 0.5000, sse=5848593.0, rms=6.277 (0.000%) 012: dt: 0.5000, sse=5832226.5, rms=5.527 (0.000%) 013: dt: 0.5000, sse=5939219.5, rms=4.900 (0.000%) 014: dt: 0.5000, sse=5983240.5, rms=4.446 (0.000%) 015: dt: 0.5000, sse=6110336.0, rms=4.119 (0.000%) 016: dt: 0.5000, sse=6144840.5, rms=3.911 (0.000%) 017: dt: 0.5000, sse=6209216.0, rms=3.767 (0.000%) 018: dt: 0.5000, sse=6223545.5, rms=3.676 (0.000%) 019: dt: 0.5000, sse=6279600.0, rms=3.602 (0.000%) rms = 3.56, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6271217.5, rms=3.560 (0.000%) 021: dt: 0.2500, sse=4564613.0, rms=2.979 (0.000%) 022: dt: 0.2500, sse=4422597.5, rms=2.819 (0.000%) rms = 2.80, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4324017.0, rms=2.795 (0.000%) 024: dt: 0.1250, sse=4158617.8, rms=2.716 (0.000%) rms = 2.71, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4138553.0, rms=2.705 (0.000%) positioning took 2.7 minutes mean border=58.0, 1051 (3) missing vertices, mean dist 0.2 [0.2 (%44.6)->0.6 (%55.4))] %38 local maxima, %31 large gradients and %26 min vals, 876 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4744649.0, rms=4.66 026: dt: 0.5000, sse=4932263.5, rms=3.755 (0.000%) 027: dt: 0.5000, sse=6193329.5, rms=3.613 (0.000%) rms = 3.60, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=6060425.5, rms=3.598 (0.000%) 029: dt: 0.2500, sse=5033093.5, rms=2.879 (0.000%) 030: dt: 0.2500, sse=4903777.0, rms=2.686 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4841873.5, rms=2.672 (0.000%) 032: dt: 0.1250, sse=4692738.0, rms=2.562 (0.000%) rms = 2.54, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4682554.5, rms=2.544 (0.000%) positioning took 0.9 minutes mean border=56.5, 1317 (2) missing vertices, mean dist 0.1 [0.2 (%39.1)->0.4 (%60.9))] %52 local maxima, %18 large gradients and %25 min vals, 951 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4820253.0, rms=3.30 rms = 3.35, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4659440.5, rms=2.937 (0.000%) 035: dt: 0.2500, sse=4677714.0, rms=2.701 (0.000%) 036: dt: 0.2500, sse=4850115.0, rms=2.628 (0.000%) rms = 2.60, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4909077.0, rms=2.601 (0.000%) 038: dt: 0.1250, sse=4805551.5, rms=2.527 (0.000%) rms = 2.51, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4821908.5, rms=2.510 (0.000%) positioning took 0.7 minutes mean border=55.8, 2795 (2) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.3 (%55.4))] %55 local maxima, %14 large gradients and %25 min vals, 833 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4845860.5, rms=2.70 rms = 3.04, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4771183.0, rms=2.552 (0.000%) 041: dt: 0.2500, sse=4952673.0, rms=2.493 (0.000%) rms = 2.47, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5020869.0, rms=2.470 (0.000%) 043: dt: 0.1250, sse=4939721.0, rms=2.406 (0.000%) rms = 2.39, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4966083.0, rms=2.389 (0.000%) positioning took 0.6 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area.pial vertex spacing 1.01 +- 0.44 (0.05-->7.36) (max @ vno 101451 --> 134658) face area 0.40 +- 0.31 (0.00-->5.11) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 817:1388 truncations. 25712 vertices at 0 distance 83583 vertices at 1 distance 85081 vertices at 2 distance 42066 vertices at 3 distance 14483 vertices at 4 distance 4522 vertices at 5 distance 1434 vertices at 6 distance 510 vertices at 7 distance 240 vertices at 8 distance 129 vertices at 9 distance 62 vertices at 10 distance 49 vertices at 11 distance 41 vertices at 12 distance 55 vertices at 13 distance 25 vertices at 14 distance 15 vertices at 15 distance 11 vertices at 16 distance 16 vertices at 17 distance 6 vertices at 18 distance 6 vertices at 19 distance 6 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.thickness positioning took 11.5 minutes #-------------------------------------------- #@# Surf Volume rh Tue Oct 20 18:56:00 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Tue Oct 20 18:56:00 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts pctsurfcon --s af1021_recon --rh-only Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts/pctsurfcon.log Tue Oct 20 18:56:00 EDT 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-1.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.15164/rh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 73363 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.15164/rh.wm.mgh Dim: 134806 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.15164/rh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 87880 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.15164/rh.gm.mgh Dim: 134806 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.15164/rh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.15164/rh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-1.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh Vertex Area is 0.661523 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1561 1094.279 2 2002 caudalanteriorcingulate 1237 808.057 3 2003 caudalmiddlefrontal 2992 2066.130 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2205 1402.712 6 2006 entorhinal 634 426.316 7 2007 fusiform 5330 3566.980 8 2008 inferiorparietal 8292 5603.694 9 2009 inferiortemporal 4337 2926.609 10 2010 isthmuscingulate 1237 797.656 11 2011 lateraloccipital 7249 4645.855 12 2012 lateralorbitofrontal 3685 2487.292 13 2013 lingual 5101 3366.425 14 2014 medialorbitofrontal 2789 1878.021 15 2015 middletemporal 4389 3011.584 16 2016 parahippocampal 1269 805.625 17 2017 paracentral 2191 1352.664 18 2018 parsopercularis 2339 1549.661 19 2019 parsorbitalis 1100 797.024 20 2020 parstriangularis 2143 1427.397 21 2021 pericalcarine 2366 1577.206 22 2022 postcentral 5734 3554.974 23 2023 posteriorcingulate 1898 1275.721 24 2024 precentral 7196 4670.821 25 2025 precuneus 6268 4230.708 26 2026 rostralanteriorcingulate 744 478.121 27 2027 rostralmiddlefrontal 8736 5933.263 28 2028 superiorfrontal 9154 6337.103 29 2029 superiorparietal 7347 4721.856 30 2030 superiortemporal 5905 3912.371 31 2031 supramarginal 6011 3964.572 32 2032 frontalpole 442 293.571 33 2033 temporalpole 533 364.143 34 2034 transversetemporal 700 410.010 35 2035 insula 3150 2052.494 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Tue Oct 20 18:56:08 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1561 1094 3002 2.678 0.485 0.130 0.035 19 2.4 bankssts 1237 808 2367 2.551 0.785 0.166 0.061 25 3.0 caudalanteriorcingulate 2992 2066 6062 2.585 0.499 0.137 0.046 38 5.9 caudalmiddlefrontal 2205 1403 3387 2.051 0.517 0.169 0.086 49 9.2 cuneus 634 426 1927 3.126 0.819 0.170 0.086 12 2.2 entorhinal 5330 3567 12008 2.899 0.695 0.153 0.068 105 14.5 fusiform 8292 5604 15300 2.399 0.581 0.155 0.121 246 21.1 inferiorparietal 4337 2927 9814 2.877 0.759 0.156 0.079 129 15.6 inferiortemporal 1237 798 2164 2.590 0.689 0.154 0.064 23 3.0 isthmuscingulate 7249 4646 11880 2.292 0.556 0.155 0.061 126 19.1 lateraloccipital 3685 2487 7638 2.612 0.796 0.170 0.081 96 12.3 lateralorbitofrontal 5101 3366 7867 2.227 0.600 0.168 0.074 179 16.0 lingual 2789 1878 5572 2.502 0.836 0.164 0.082 77 9.4 medialorbitofrontal 4389 3012 11288 3.047 0.663 0.154 0.094 116 11.5 middletemporal 1269 806 2365 2.560 0.570 0.114 0.042 11 2.4 parahippocampal 2191 1353 3558 2.496 0.525 0.129 0.089 66 4.0 paracentral 2339 1550 4616 2.769 0.453 0.132 0.053 31 4.9 parsopercularis 1100 797 3032 2.804 0.762 0.183 0.085 24 3.8 parsorbitalis 2143 1427 4207 2.505 0.567 0.141 0.053 31 4.3 parstriangularis 2366 1577 2810 1.917 0.542 0.157 0.071 41 7.1 pericalcarine 5734 3555 8484 2.120 0.694 0.129 0.051 73 13.2 postcentral 1898 1276 3714 2.598 0.800 0.172 0.066 40 5.1 posteriorcingulate 7196 4671 12734 2.528 0.630 0.140 1.530 436 15.2 precentral 6268 4231 11187 2.497 0.576 0.151 0.055 105 14.0 precuneus 744 478 1623 2.703 0.966 0.152 0.061 13 1.9 rostralanteriorcingulate 8736 5933 16125 2.265 0.678 0.166 0.089 328 30.7 rostralmiddlefrontal 9154 6337 21312 2.865 0.688 0.149 0.059 145 21.0 superiorfrontal 7347 4722 11901 2.222 0.549 0.141 0.051 102 15.6 superiorparietal 5905 3912 14316 3.092 0.761 0.143 0.064 112 13.4 superiortemporal 6011 3965 11381 2.675 0.591 0.138 0.053 91 12.0 supramarginal 442 294 1025 2.457 0.870 0.211 0.099 19 1.8 frontalpole 533 364 1986 3.610 1.126 0.198 0.122 20 2.2 temporalpole 700 410 1223 2.508 0.372 0.132 0.073 11 1.4 transversetemporal 3150 2052 6867 3.245 0.861 0.133 0.109 89 18.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Oct 20 18:56:22 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 14 labels changed using aseg relabeling using gibbs priors... 000: 9872 changed, 134806 examined... 001: 2371 changed, 37485 examined... 002: 750 changed, 11992 examined... 003: 325 changed, 4245 examined... 004: 164 changed, 1795 examined... 005: 78 changed, 888 examined... 006: 32 changed, 429 examined... 007: 15 changed, 184 examined... 008: 6 changed, 91 examined... 009: 5 changed, 32 examined... 010: 2 changed, 24 examined... 011: 0 changed, 12 examined... 13 labels changed using aseg 000: 304 total segments, 216 labels (2977 vertices) changed 001: 102 total segments, 14 labels (41 vertices) changed 002: 88 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 183 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 603 vertices marked for relabeling... 603 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 49 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Oct 20 18:57:11 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1163 800 2042 2.012 0.761 0.177 0.071 27 3.4 G_and_S_frontomargin 1251 835 2755 2.819 0.508 0.158 0.054 20 2.8 G_and_S_occipital_inf 1356 737 2063 2.331 0.480 0.133 0.130 62 3.3 G_and_S_paracentral 1501 1007 3314 2.933 0.554 0.165 0.060 28 3.6 G_and_S_subcentral 782 527 2033 2.685 0.732 0.228 0.130 94 4.5 G_and_S_transv_frontopol 2350 1592 4837 2.825 0.773 0.151 0.068 43 6.1 G_and_S_cingul-Ant 1401 973 3008 2.850 0.553 0.152 0.052 23 3.0 G_and_S_cingul-Mid-Ant 1421 960 2709 2.673 0.511 0.146 0.054 22 2.9 G_and_S_cingul-Mid-Post 471 315 1242 3.117 0.748 0.211 0.103 14 2.1 G_cingul-Post-dorsal 304 181 571 2.691 0.527 0.167 0.094 8 1.2 G_cingul-Post-ventral 1881 1212 2632 1.893 0.495 0.171 0.094 44 8.8 G_cuneus 1462 965 3383 2.858 0.429 0.158 0.075 32 4.3 G_front_inf-Opercular 323 215 849 2.839 0.616 0.172 0.076 8 0.9 G_front_inf-Orbital 1064 709 2498 2.675 0.563 0.150 0.056 18 2.1 G_front_inf-Triangul 3653 2521 8798 2.637 0.646 0.174 0.111 132 16.5 G_front_middle 6709 4532 17152 2.986 0.693 0.164 0.069 136 18.3 G_front_sup 451 302 1293 3.915 0.967 0.133 0.366 43 11.4 G_Ins_lg_and_S_cent_ins 639 401 2034 3.861 0.730 0.142 0.076 15 1.9 G_insular_short 2060 1295 4462 2.587 0.459 0.158 0.061 41 5.0 G_occipital_middle 1892 1174 3280 2.283 0.581 0.146 0.050 27 4.2 G_occipital_sup 2040 1306 4855 2.979 0.621 0.165 0.080 54 5.9 G_oc-temp_lat-fusifor 3192 2075 5344 2.293 0.624 0.179 0.089 68 11.8 G_oc-temp_med-Lingual 1663 1044 4542 3.124 0.790 0.153 0.078 36 5.2 G_oc-temp_med-Parahip 2806 1911 7753 2.907 0.785 0.202 0.115 139 13.3 G_orbital 2777 1871 6397 2.678 0.695 0.176 0.084 111 9.5 G_pariet_inf-Angular 2733 1750 5996 2.902 0.568 0.148 0.059 52 6.1 G_pariet_inf-Supramar 2272 1486 4318 2.343 0.532 0.149 0.058 35 5.7 G_parietal_sup 2264 1255 3443 2.176 0.631 0.123 0.060 32 6.9 G_postcentral 2603 1566 5283 2.671 0.605 0.135 4.131 373 5.5 G_precentral 2905 1977 6145 2.478 0.524 0.160 0.061 59 7.2 G_precuneus 798 514 2067 2.836 0.559 0.180 0.078 27 2.6 G_rectus 329 224 413 1.692 0.808 0.125 0.109 9 1.2 G_subcallosal 500 292 973 2.511 0.415 0.144 0.088 9 1.3 G_temp_sup-G_T_transv 2215 1464 7183 3.533 0.693 0.174 0.075 49 6.6 G_temp_sup-Lateral 635 418 1822 3.608 0.731 0.158 0.091 13 2.0 G_temp_sup-Plan_polar 915 615 1816 2.606 0.499 0.122 0.058 14 1.8 G_temp_sup-Plan_tempo 2136 1437 5775 3.092 0.864 0.171 0.089 62 8.3 G_temporal_inf 2544 1739 7644 3.187 0.593 0.169 0.090 72 7.9 G_temporal_middle 344 232 556 2.292 0.471 0.128 0.041 4 0.6 Lat_Fis-ant-Horizont 139 94 258 2.540 0.293 0.085 0.020 1 0.1 Lat_Fis-ant-Vertical 1959 1307 2908 2.591 0.463 0.125 0.038 19 3.0 Lat_Fis-post 3298 2062 5023 2.086 0.582 0.174 0.089 86 12.8 Pole_occipital 1763 1222 6098 3.305 0.956 0.194 0.126 92 9.1 Pole_temporal 2839 1892 3519 2.043 0.553 0.153 0.058 125 6.9 S_calcarine 2760 1918 2905 1.726 0.478 0.136 0.054 30 5.3 S_central 1377 940 2170 2.469 0.513 0.136 0.044 17 2.4 S_cingul-Marginalis 627 439 1000 2.741 0.410 0.116 0.034 4 1.0 S_circular_insula_ant 1396 887 2181 2.664 0.584 0.095 0.033 8 1.7 S_circular_insula_inf 1454 970 2330 2.768 0.622 0.121 0.046 14 3.0 S_circular_insula_sup 925 612 2177 3.197 0.784 0.152 0.078 16 3.4 S_collat_transv_ant 796 532 924 2.075 0.472 0.155 0.057 10 1.8 S_collat_transv_post 2741 1827 4526 2.421 0.532 0.130 0.041 27 4.8 S_front_inf 2270 1513 3386 2.015 0.562 0.155 0.070 43 5.4 S_front_middle 2366 1656 3856 2.318 0.489 0.117 0.037 21 3.7 S_front_sup 509 342 685 2.248 0.500 0.130 0.056 7 0.9 S_interm_prim-Jensen 3052 2026 4138 2.091 0.510 0.140 0.047 38 5.9 S_intrapariet_and_P_trans 1209 811 1624 2.072 0.435 0.136 0.046 13 2.3 S_oc_middle_and_Lunatus 1088 714 1286 1.990 0.360 0.131 0.043 11 1.8 S_oc_sup_and_transversal 924 620 1295 2.443 0.308 0.125 0.036 8 1.4 S_occipital_ant 1239 877 2009 2.535 0.383 0.134 0.043 15 2.2 S_oc-temp_lat 2261 1550 3372 2.452 0.446 0.117 0.033 16 3.1 S_oc-temp_med_and_Lingual 476 334 638 2.083 0.480 0.127 0.042 4 0.8 S_orbital_lateral 767 556 1110 1.862 0.586 0.116 0.032 6 1.1 S_orbital_med-olfact 1325 896 2304 2.359 0.709 0.161 0.067 25 3.5 S_orbital-H_Shaped 2691 1777 3908 2.428 0.629 0.140 0.043 31 4.9 S_parieto_occipital 1593 997 1596 1.969 0.732 0.156 0.056 28 3.6 S_pericallosal 2179 1449 2732 2.012 0.426 0.114 0.033 17 3.1 S_postcentral 1973 1375 3582 2.580 0.519 0.125 0.039 19 3.0 S_precentral-inf-part 796 540 1133 2.456 0.511 0.125 0.037 6 1.3 S_precentral-sup-part 174 128 329 2.768 0.867 0.153 0.040 2 0.3 S_suborbital 958 650 1788 2.641 0.487 0.141 0.049 11 1.9 S_subparietal 1097 736 1770 2.640 0.547 0.139 0.140 32 2.5 S_temporal_inf 7134 4904 12511 2.548 0.537 0.134 0.119 166 13.0 S_temporal_sup 304 208 390 2.361 0.215 0.129 0.031 3 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Tue Oct 20 18:57:26 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1166 labels changed using aseg relabeling using gibbs priors... 000: 2638 changed, 134806 examined... 001: 614 changed, 11352 examined... 002: 165 changed, 3301 examined... 003: 83 changed, 1023 examined... 004: 30 changed, 457 examined... 005: 15 changed, 180 examined... 006: 4 changed, 84 examined... 007: 1 changed, 25 examined... 008: 1 changed, 7 examined... 009: 1 changed, 7 examined... 010: 1 changed, 7 examined... 011: 1 changed, 7 examined... 012: 1 changed, 7 examined... 013: 1 changed, 7 examined... 014: 1 changed, 7 examined... 015: 0 changed, 8 examined... 119 labels changed using aseg 000: 59 total segments, 26 labels (123 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 57 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 724 vertices marked for relabeling... 724 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 41 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Tue Oct 20 18:58:07 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1205 788 2343 2.587 0.767 0.166 0.060 25 2.9 caudalanteriorcingulate 3010 2070 6052 2.594 0.501 0.137 0.046 39 5.9 caudalmiddlefrontal 2707 1748 4104 2.075 0.512 0.163 0.068 53 8.4 cuneus 634 429 1922 3.128 0.829 0.168 0.086 12 2.2 entorhinal 4675 3113 10129 2.891 0.694 0.149 0.066 87 12.1 fusiform 7762 5232 14182 2.395 0.591 0.156 0.127 238 20.1 inferiorparietal 4988 3372 11604 2.876 0.751 0.157 0.078 143 17.3 inferiortemporal 1255 806 2180 2.589 0.685 0.153 0.064 23 3.0 isthmuscingulate 7508 4803 12412 2.294 0.560 0.156 0.062 134 19.9 lateraloccipital 4239 2871 9044 2.518 0.841 0.181 0.088 158 15.4 lateralorbitofrontal 5145 3397 7890 2.225 0.597 0.168 0.072 173 16.0 lingual 2179 1461 4686 2.582 0.806 0.167 0.081 62 7.6 medialorbitofrontal 5350 3681 13176 2.986 0.646 0.151 0.087 128 13.5 middletemporal 1201 766 2255 2.562 0.566 0.114 0.043 11 2.3 parahippocampal 2234 1388 3653 2.502 0.530 0.129 0.088 67 4.0 paracentral 2416 1596 4714 2.757 0.449 0.132 0.052 33 4.9 parsopercularis 1216 832 2845 2.734 0.734 0.156 0.072 20 3.2 parsorbitalis 2299 1539 4517 2.477 0.582 0.139 0.049 33 4.4 parstriangularis 2441 1605 2858 1.898 0.538 0.159 0.087 51 9.4 pericalcarine 6148 3839 9026 2.113 0.683 0.130 0.050 77 14.0 postcentral 1989 1331 3872 2.595 0.802 0.172 0.067 42 5.5 posteriorcingulate 7051 4583 12463 2.525 0.631 0.141 1.561 435 15.2 precentral 6302 4234 11461 2.507 0.569 0.152 0.056 109 14.4 precuneus 890 572 1873 2.709 0.928 0.148 0.058 14 2.1 rostralanteriorcingulate 5955 4085 11609 2.349 0.665 0.165 0.094 170 21.8 rostralmiddlefrontal 12021 8260 26064 2.694 0.761 0.154 0.064 276 30.6 superiorfrontal 6248 4036 10278 2.238 0.555 0.139 0.050 84 12.9 superiorparietal 7757 5185 18912 3.077 0.795 0.148 0.066 159 18.6 superiortemporal 5807 3836 10950 2.669 0.580 0.137 0.052 87 11.4 supramarginal 705 415 1233 2.509 0.373 0.131 0.072 11 1.4 transversetemporal 2927 1917 6435 3.253 0.846 0.126 0.104 76 16.9 insula #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Tue Oct 20 18:58:21 EDT 2015 bbregister --s af1021_recon --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz --lta /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.lta --init-fsl --T2 Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat.log Tue Oct 20 18:58:21 EDT 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/bbregister --s af1021_recon --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz --lta /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux compute-0-1.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz... TR=6000.00, TE=475.00, TI=2100.00, flip angle=120.00 i_ras = (0.0313814, -0.959852, 0.278747) j_ras = (0.0851089, -0.275305, -0.957582) k_ras = (-0.995877, -0.053774, -0.0730522) writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii... fslregister --s af1021_recon --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii --reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister --dof 6 --fsvol brainmask.mgz Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat.fslregister.log Tue Oct 20 18:58:22 EDT 2015 --s af1021_recon --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii --reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ compute-0-1.local Linux compute-0-1.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brainmask.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/refvol.fslregister.nii mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brainmask.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brainmask.mgz... TR=2530.00, TE=3.32, TI=1100.00, flip angle=7.00 i_ras = (-1, 1.11759e-08, -5.58794e-08) j_ras = (-8.9407e-08, -1.40863e-08, -1) k_ras = (-8.56817e-08, 1, -9.42964e-09) writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/refvol.fslregister.nii... -------------------------------------- /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/movvol.fslregister.nii --frame 0 mri_convert /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii... TR=6000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0313814, -0.959852, 0.278747) j_ras = (0.0851089, -0.275305, -0.957582) k_ras = (-0.995877, -0.053774, -0.0730522) keeping frame 0 writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/movvol.fslregister.nii... Mov determinant is -1 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts tkregister2_cmdl --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/movvol.fslregister.nii --reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/reg0.15456.dat --regheader --fslregout /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat.fsl.mat0 --s af1021_recon --noedit tkregister_tcl /share/apps/freesurfer-5.3.0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/movvol.fslregister.nii reg file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/reg0.15456.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -88.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -0.031 0.960 -0.279 0.717; -0.996 -0.054 -0.073 -0.937; -0.085 0.275 0.958 4.193; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.031 0.960 -0.279 0.717; -0.996 -0.054 -0.073 -0.937; -0.085 0.275 0.958 4.193; 0.000 0.000 0.000 1.000; Determinant 1 subject = af1021_recon RegMat --------------------------- -0.031 0.960 -0.279 0.717; -0.996 -0.054 -0.073 -0.937; -0.085 0.275 0.958 4.193; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1, ref det = -1 Tue Oct 20 18:58:26 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts flirt.fsl -ref /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/refvol.fslregister.nii -in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/fslmat0.trans.mat -schedule /share/apps/fsl-5.0.8/etc/flirtsch/xyztrans.sch -init /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat.fsl.mat0 Tue Oct 20 19:00:34 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts flirt.fsl -ref /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/refvol.fslregister.nii -in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat.fsl.mat -init /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/fslregister/fslmat0.trans.mat -schedule /share/apps/freesurfer-5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s af1021_recon --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii --reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat --fslreg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat.fsl.mat --noedit tkregister_tcl /share/apps/freesurfer-5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- -0.026 -0.074 0.997 52.965; -0.306 0.950 0.063 45.541; -0.952 -0.303 -0.048 291.374; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii reg file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -88.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -1, ref det = -1 ---- Input registration matrix (computed) -------- -0.026 0.952 -0.306 -0.280; -0.997 -0.048 -0.063 -0.215; -0.074 0.303 0.950 5.694; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.026 0.952 -0.306 -0.280; -0.997 -0.048 -0.063 -0.215; -0.074 0.303 0.950 5.694; 0.000 0.000 0.000 1.000; Determinant 1 subject = af1021_recon RegMat --------------------------- -0.026 0.952 -0.306 -0.280; -0.997 -0.048 -0.063 -0.215; -0.074 0.303 0.950 5.694; 0.000 0.000 0.000 1.000; Started at Tue Oct 20 18:58:22 EDT 2015 Ended at Tue Oct 20 19:02:41 EDT 2015 fslregister Done To check results, run: tkregister2 --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii --reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat --surf orig mri_segreg --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii --init-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat --out-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mri_segreg --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii --init-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat --out-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname compute-0-1.local machine x86_64 user twilliams movvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii regfile /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.init.dat subject af1021_recon dof 6 outregfile /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1446240114 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.026 0.952 -0.306 -0.280; -0.997 -0.048 -0.063 -0.215; -0.074 0.303 0.950 5.694; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.039097 1 -25.0 -25.0 25.0 1.014352 2 -25.0 25.0 -25.0 1.012813 3 -25.0 25.0 25.0 1.061509 4 25.0 -25.0 -25.0 0.983432 5 25.0 -25.0 25.0 1.039872 6 25.0 25.0 -25.0 1.063661 7 25.0 25.0 25.0 0.999577 REL: 8 0.227636 8.214314 1.026789 rel = 0.221697 Initial costs ---------------- Number of surface hits 2520 WM Intensity 86.1020 +/- 10.7768 Ctx Intensity 98.4920 +/- 12.4782 Pct Contrast 13.3150 +/- 12.1962 Cost 0.2276 RelCost 0.2217 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0461 1.0461 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0298 1.0298 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9841 0.9841 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9760 0.9760 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9564 0.9564 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.9479 0.9479 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9103 0.9103 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.8771 0.8771 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.8663 0.8663 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.8569 0.8569 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.8397 0.8397 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.8166 0.8166 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2276 0.2276 0.0 Brute Force -------------------------- Min cost was 0.227636 Number of iterations 729 Search time 2.155000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 -0.270 0.000 0.000 0.000 0.000 0.000 0.2134632668 9 -0.230 0.000 0.000 0.000 0.000 0.000 0.2130165035 12 -0.232 0.000 0.000 0.000 0.000 0.000 0.2130143452 21 -0.232 -0.042 0.000 0.000 0.000 0.000 0.2119155859 23 -0.232 -0.056 0.000 0.000 0.000 0.000 0.2118509627 24 -0.232 -0.054 0.000 0.000 0.000 0.000 0.2118488807 25 -0.232 -0.053 0.000 0.000 0.000 0.000 0.2118486736 35 -0.232 -0.053 -0.075 0.000 0.000 0.000 0.2115978901 37 -0.232 -0.053 -0.040 0.000 0.000 0.000 0.2110612253 40 -0.232 -0.053 -0.034 0.000 0.000 0.000 0.2110335647 42 -0.232 -0.053 -0.035 0.000 0.000 0.000 0.2110331535 50 -0.232 -0.053 -0.035 0.005 0.000 0.000 0.2109511732 52 -0.232 -0.053 -0.035 0.021 0.000 0.000 0.2108525624 53 -0.232 -0.053 -0.035 0.018 0.000 0.000 0.2108463704 62 -0.232 -0.053 -0.035 0.018 -0.210 0.000 0.1966791002 63 -0.232 -0.053 -0.035 0.018 -0.232 0.000 0.1959778444 66 -0.232 -0.053 -0.035 0.018 -0.246 0.000 0.1958763926 67 -0.232 -0.053 -0.035 0.018 -0.245 0.000 0.1958741061 68 -0.232 -0.053 -0.035 0.018 -0.244 0.000 0.1958724655 80 -0.232 -0.053 -0.035 0.018 -0.244 0.006 0.1958509769 82 -0.232 -0.053 -0.035 0.018 -0.244 0.005 0.1958503548 92 -0.059 -0.053 -0.035 0.018 -0.244 0.005 0.1929470592 93 -0.064 -0.053 -0.035 0.018 -0.244 0.005 0.1929182047 94 -0.083 -0.053 -0.035 0.018 -0.244 0.005 0.1928464480 96 -0.098 -0.053 -0.035 0.018 -0.244 0.005 0.1928227991 97 -0.102 -0.053 -0.035 0.018 -0.244 0.005 0.1928226328 98 -0.100 -0.053 -0.035 0.018 -0.244 0.005 0.1928223180 106 -0.100 -0.029 -0.035 0.018 -0.244 0.005 0.1926031751 108 -0.100 -0.028 -0.035 0.018 -0.244 0.005 0.1926019551 109 -0.100 -0.027 -0.035 0.018 -0.244 0.005 0.1926016530 110 -0.100 -0.026 -0.035 0.018 -0.244 0.005 0.1926014512 120 -0.100 -0.026 -0.043 0.018 -0.244 0.005 0.1925793184 121 -0.100 -0.026 -0.045 0.018 -0.244 0.005 0.1925713733 123 -0.100 -0.026 -0.050 0.018 -0.244 0.005 0.1925622274 132 -0.100 -0.026 -0.050 0.030 -0.244 0.005 0.1923005742 133 -0.100 -0.026 -0.050 0.074 -0.244 0.005 0.1917372765 136 -0.100 -0.026 -0.050 0.076 -0.244 0.005 0.1917329479 137 -0.100 -0.026 -0.050 0.078 -0.244 0.005 0.1917315954 145 -0.100 -0.026 -0.050 0.078 -0.305 0.005 0.1907760295 146 -0.100 -0.026 -0.050 0.078 -0.307 0.005 0.1907604747 147 -0.100 -0.026 -0.050 0.078 -0.329 0.005 0.1907067787 149 -0.100 -0.026 -0.050 0.078 -0.325 0.005 0.1906992702 152 -0.100 -0.026 -0.050 0.078 -0.324 0.005 0.1906989637 160 -0.100 -0.026 -0.050 0.078 -0.324 -0.008 0.1906292235 161 -0.100 -0.026 -0.050 0.078 -0.324 -0.012 0.1906254096 164 0.032 0.002 -0.065 0.139 -0.405 -0.029 0.1899055249 170 -0.019 -0.008 -0.059 0.116 -0.374 -0.023 0.1894419605 171 -0.020 -0.008 -0.059 0.115 -0.373 -0.023 0.1894395710 172 -0.029 -0.010 -0.058 0.111 -0.368 -0.021 0.1894352505 174 -0.025 -0.010 -0.058 0.113 -0.370 -0.022 0.1894292782 176 -0.026 -0.010 -0.058 0.112 -0.370 -0.022 0.1894286726 177 -0.027 -0.010 -0.058 0.112 -0.369 -0.022 0.1894286653 178 -0.026 -0.010 -0.058 0.112 -0.369 -0.022 0.1894279961 179 -0.026 -0.010 -0.058 0.112 -0.369 -0.022 0.1894277986 189 -0.026 -0.010 -0.058 0.112 -0.369 -0.010 0.1893950236 190 -0.026 -0.010 -0.058 0.112 -0.369 -0.011 0.1893928620 191 -0.026 -0.010 -0.058 0.112 -0.369 -0.013 0.1893907227 193 -0.026 -0.010 -0.058 0.112 -0.369 -0.014 0.1893899485 203 -0.026 -0.011 -0.058 0.112 -0.369 -0.014 0.1893821485 205 -0.026 -0.016 -0.058 0.112 -0.369 -0.014 0.1893587284 206 -0.026 -0.017 -0.058 0.112 -0.369 -0.014 0.1893579671 214 -0.026 -0.017 -0.054 0.112 -0.369 -0.014 0.1892030576 216 -0.026 -0.017 -0.032 0.112 -0.369 -0.014 0.1887982638 217 -0.026 -0.017 -0.027 0.112 -0.369 -0.014 0.1887870549 228 -0.026 -0.017 -0.027 0.126 -0.369 -0.014 0.1887119116 229 -0.026 -0.017 -0.027 0.127 -0.369 -0.014 0.1887108821 230 -0.026 -0.017 -0.027 0.128 -0.369 -0.014 0.1887107320 239 -0.026 -0.017 -0.027 0.128 -0.362 -0.014 0.1885813740 240 -0.026 -0.017 -0.027 0.128 -0.335 -0.014 0.1884551181 242 -0.026 -0.017 -0.027 0.128 -0.342 -0.014 0.1884438081 250 0.024 -0.006 -0.032 0.151 -0.373 -0.021 0.1876067637 252 0.027 -0.006 -0.033 0.152 -0.375 -0.021 0.1876006356 253 0.029 -0.005 -0.033 0.153 -0.376 -0.021 0.1875989929 254 0.030 -0.005 -0.033 0.154 -0.377 -0.021 0.1875986830 255 0.030 -0.005 -0.033 0.154 -0.376 -0.021 0.1875985061 256 0.030 -0.005 -0.033 0.153 -0.376 -0.021 0.1875983422 269 0.030 -0.005 -0.033 0.153 -0.376 -0.018 0.1875807813 270 0.030 -0.005 -0.033 0.153 -0.376 -0.016 0.1875721033 272 0.030 -0.005 -0.033 0.153 -0.376 -0.014 0.1875713144 284 0.030 -0.004 -0.033 0.153 -0.376 -0.014 0.1875680638 285 0.030 -0.003 -0.033 0.153 -0.376 -0.014 0.1875674994 295 0.030 -0.003 -0.022 0.153 -0.376 -0.014 0.1875188311 296 0.030 -0.003 -0.021 0.153 -0.376 -0.014 0.1875139019 297 0.030 -0.003 -0.014 0.153 -0.376 -0.014 0.1875055288 298 0.030 -0.003 -0.016 0.153 -0.376 -0.014 0.1875032986 307 0.030 -0.003 -0.016 0.156 -0.376 -0.014 0.1874977901 318 0.030 -0.003 -0.016 0.156 -0.353 -0.014 0.1874009788 319 0.030 -0.003 -0.016 0.156 -0.359 -0.014 0.1873942665 320 0.030 -0.003 -0.016 0.156 -0.358 -0.014 0.1873925532 328 0.045 0.001 -0.018 0.164 -0.367 -0.016 0.1873143608 330 0.045 0.001 -0.018 0.163 -0.367 -0.016 0.1873138463 336 0.045 0.001 -0.018 0.163 -0.367 -0.016 0.1873137641 347 0.045 0.001 -0.018 0.163 -0.367 -0.020 0.1873136051 348 0.045 0.001 -0.018 0.163 -0.367 -0.018 0.1873102266 358 0.045 0.017 -0.018 0.163 -0.367 -0.018 0.1873090528 359 0.045 0.009 -0.018 0.163 -0.367 -0.018 0.1872965149 369 0.045 0.009 -0.011 0.163 -0.367 -0.018 0.1872873397 370 0.045 0.009 -0.012 0.163 -0.367 -0.018 0.1872857850 371 0.045 0.009 -0.013 0.163 -0.367 -0.018 0.1872852423 382 0.045 0.009 -0.013 0.169 -0.367 -0.018 0.1872761781 383 0.045 0.009 -0.013 0.168 -0.367 -0.018 0.1872754707 384 0.045 0.009 -0.013 0.167 -0.367 -0.018 0.1872754272 393 0.045 0.009 -0.013 0.167 -0.358 -0.018 0.1872653300 397 0.045 0.009 -0.013 0.167 -0.357 -0.018 0.1872651751 404 0.049 0.010 -0.014 0.169 -0.360 -0.019 0.1872620044 405 0.048 0.010 -0.013 0.169 -0.359 -0.019 0.1872618906 406 0.048 0.010 -0.013 0.169 -0.359 -0.019 0.1872617636 409 0.048 0.010 -0.013 0.169 -0.359 -0.019 0.1872615055 420 0.048 0.010 -0.013 0.169 -0.359 -0.016 0.1872460303 421 0.048 0.010 -0.013 0.169 -0.359 -0.013 0.1872429960 431 0.048 0.037 -0.013 0.169 -0.359 -0.013 0.1871838332 432 0.048 0.036 -0.013 0.169 -0.359 -0.013 0.1871827995 434 0.048 0.035 -0.013 0.169 -0.359 -0.013 0.1871827408 442 0.048 0.035 -0.018 0.169 -0.359 -0.013 0.1871769250 453 0.048 0.035 -0.018 0.181 -0.359 -0.013 0.1871394376 457 0.048 0.035 -0.018 0.182 -0.359 -0.013 0.1871357283 458 0.048 0.035 -0.018 0.189 -0.359 -0.013 0.1871346624 459 0.048 0.035 -0.018 0.185 -0.359 -0.013 0.1871285388 469 0.048 0.035 -0.018 0.185 -0.357 -0.013 0.1871225625 470 0.048 0.035 -0.018 0.185 -0.352 -0.013 0.1871219751 472 0.048 0.035 -0.018 0.185 -0.354 -0.013 0.1871193382 484 0.049 0.035 -0.018 0.186 -0.355 -0.013 0.1871189530 487 0.049 0.060 -0.023 0.202 -0.350 -0.008 0.1869592021 492 0.049 0.075 -0.026 0.213 -0.347 -0.004 0.1869007939 493 0.049 0.084 -0.028 0.219 -0.346 -0.002 0.1868991452 494 0.049 0.080 -0.027 0.216 -0.347 -0.003 0.1868967644 495 0.049 0.080 -0.027 0.216 -0.347 -0.003 0.1868964997 509 0.049 0.080 -0.027 0.216 -0.347 0.030 0.1868303563 510 0.049 0.080 -0.027 0.216 -0.347 0.017 0.1867223576 511 0.049 0.080 -0.027 0.216 -0.347 0.015 0.1867212648 518 0.100 0.091 -0.033 0.239 -0.377 0.009 0.1866714879 519 0.076 0.086 -0.030 0.228 -0.363 0.012 0.1865312109 520 0.077 0.086 -0.030 0.229 -0.363 0.012 0.1865310122 522 0.077 0.086 -0.030 0.229 -0.364 0.012 0.1865308002 523 0.078 0.086 -0.030 0.229 -0.364 0.012 0.1865307908 524 0.078 0.086 -0.030 0.229 -0.364 0.012 0.1865305985 535 0.078 0.086 -0.035 0.229 -0.364 0.012 0.1865276723 537 0.078 0.086 -0.033 0.229 -0.364 0.012 0.1865261941 548 0.078 0.086 -0.033 0.215 -0.364 0.012 0.1864896062 549 0.078 0.086 -0.033 0.216 -0.364 0.012 0.1864881157 550 0.078 0.086 -0.033 0.218 -0.364 0.012 0.1864849176 552 0.078 0.086 -0.033 0.219 -0.364 0.012 0.1864825357 562 0.078 0.086 -0.033 0.219 -0.371 0.012 0.1864591242 563 0.078 0.086 -0.033 0.219 -0.370 0.012 0.1864590550 570 0.078 0.096 -0.035 0.226 -0.368 0.014 0.1864464074 571 0.078 0.093 -0.035 0.224 -0.368 0.013 0.1864439759 587 0.078 0.093 -0.035 0.224 -0.368 0.027 0.1863498518 588 0.078 0.093 -0.035 0.224 -0.368 0.028 0.1863495020 598 0.076 0.093 -0.034 0.223 -0.368 0.028 0.1863488203 599 0.076 0.093 -0.034 0.223 -0.367 0.028 0.1863487754 600 0.076 0.093 -0.034 0.223 -0.367 0.028 0.1863487259 612 0.076 0.093 -0.028 0.223 -0.367 0.028 0.1863437075 613 0.076 0.093 -0.030 0.223 -0.367 0.028 0.1863411938 622 0.076 0.093 -0.030 0.179 -0.367 0.028 0.1863138983 623 0.076 0.093 -0.030 0.182 -0.367 0.028 0.1862989382 624 0.076 0.093 -0.030 0.199 -0.367 0.028 0.1862401803 627 0.076 0.093 -0.030 0.198 -0.367 0.028 0.1862378059 629 0.076 0.093 -0.030 0.196 -0.367 0.028 0.1862364456 631 0.076 0.093 -0.030 0.197 -0.367 0.028 0.1862364124 640 0.076 0.093 -0.030 0.197 -0.373 0.028 0.1862108741 641 0.076 0.093 -0.030 0.197 -0.374 0.028 0.1862106996 644 0.076 0.118 -0.034 0.214 -0.370 0.034 0.1860891981 648 0.076 0.108 -0.033 0.207 -0.372 0.032 0.1860888321 649 0.076 0.113 -0.034 0.210 -0.371 0.033 0.1860815847 650 0.076 0.113 -0.034 0.210 -0.371 0.033 0.1860815155 654 0.076 0.113 -0.034 0.210 -0.371 0.033 0.1860814711 657 0.074 0.132 -0.032 0.197 -0.373 0.052 0.1858629306 660 0.072 0.163 -0.031 0.174 -0.377 0.084 0.1850335317 661 0.067 0.214 -0.028 0.138 -0.383 0.135 0.1848837120 681 0.071 0.169 -0.030 0.170 -0.378 0.135 0.1844786116 683 0.071 0.169 -0.030 0.170 -0.378 0.143 0.1844460528 688 0.071 0.169 -0.030 0.170 -0.378 0.145 0.1844451911 689 0.071 0.169 -0.030 0.170 -0.378 0.146 0.1844449608 696 0.121 0.180 -0.036 0.193 -0.408 0.139 0.1839269668 700 0.122 0.180 -0.036 0.193 -0.408 0.139 0.1839269614 701 0.122 0.180 -0.036 0.193 -0.409 0.139 0.1839268903 702 0.122 0.180 -0.036 0.193 -0.409 0.139 0.1839266650 710 0.122 0.180 -0.025 0.193 -0.409 0.139 0.1837512631 711 0.122 0.180 0.005 0.193 -0.409 0.139 0.1834669112 713 0.122 0.180 0.016 0.193 -0.409 0.139 0.1834328812 715 0.122 0.180 0.018 0.193 -0.409 0.139 0.1834315284 725 0.122 0.180 0.018 0.176 -0.409 0.139 0.1833251299 726 0.122 0.180 0.018 0.174 -0.409 0.139 0.1833197701 728 0.122 0.180 0.018 0.172 -0.409 0.139 0.1833169340 738 0.122 0.180 0.018 0.172 -0.420 0.139 0.1832122133 740 0.122 0.180 0.018 0.172 -0.422 0.139 0.1832105065 743 0.120 0.200 0.019 0.158 -0.424 0.159 0.1823210854 746 0.119 0.212 0.020 0.149 -0.425 0.171 0.1822682118 748 0.120 0.207 0.020 0.153 -0.425 0.166 0.1822019171 749 0.120 0.206 0.020 0.153 -0.425 0.165 0.1822019001 750 0.120 0.206 0.020 0.153 -0.425 0.165 0.1822016046 753 0.120 0.206 0.020 0.153 -0.425 0.165 0.1822015823 754 0.120 0.206 0.020 0.153 -0.425 0.165 0.1822013796 756 0.120 0.206 0.020 0.153 -0.425 0.165 0.1822013385 757 0.120 0.206 0.020 0.153 -0.425 0.165 0.1822013243 768 0.120 0.206 0.020 0.153 -0.425 0.187 0.1820860432 769 0.120 0.206 0.020 0.153 -0.425 0.183 0.1820523011 770 0.120 0.206 0.020 0.153 -0.425 0.180 0.1820450161 779 0.137 0.210 0.018 0.161 -0.435 0.177 0.1819895268 780 0.135 0.209 0.018 0.161 -0.434 0.178 0.1819862036 781 0.133 0.209 0.018 0.160 -0.433 0.178 0.1819818643 783 0.132 0.209 0.018 0.159 -0.432 0.178 0.1819803464 786 0.132 0.209 0.018 0.159 -0.432 0.178 0.1819799073 796 0.132 0.209 0.047 0.159 -0.432 0.178 0.1818848771 797 0.132 0.209 0.037 0.159 -0.432 0.178 0.1818497939 799 0.132 0.209 0.038 0.159 -0.432 0.178 0.1818497419 810 0.132 0.209 0.038 0.184 -0.432 0.178 0.1813296993 811 0.132 0.209 0.038 0.186 -0.432 0.178 0.1813217820 820 0.132 0.209 0.038 0.186 -0.472 0.178 0.1813154286 821 0.132 0.209 0.038 0.186 -0.452 0.178 0.1811061333 822 0.132 0.209 0.038 0.186 -0.451 0.178 0.1811038981 826 0.131 0.228 0.040 0.173 -0.454 0.197 0.1810922341 830 0.131 0.221 0.039 0.178 -0.453 0.190 0.1808551963 831 0.131 0.220 0.039 0.179 -0.453 0.189 0.1808496745 832 0.131 0.219 0.039 0.179 -0.453 0.189 0.1808490957 848 0.131 0.219 0.039 0.179 -0.453 0.190 0.1808482339 856 0.140 0.221 0.038 0.183 -0.458 0.189 0.1808444910 857 0.136 0.220 0.038 0.181 -0.456 0.189 0.1808427236 858 0.137 0.221 0.038 0.181 -0.456 0.189 0.1808425782 861 0.137 0.221 0.038 0.181 -0.456 0.189 0.1808425222 870 0.137 0.221 0.040 0.181 -0.456 0.189 0.1808408535 880 0.137 0.221 0.040 0.198 -0.456 0.189 0.1805992889 881 0.137 0.221 0.040 0.199 -0.456 0.189 0.1805981548 890 0.137 0.221 0.040 0.199 -0.457 0.189 0.1805949771 891 0.137 0.221 0.040 0.199 -0.460 0.189 0.1805893940 894 0.137 0.221 0.040 0.199 -0.461 0.189 0.1805886923 901 0.136 0.228 0.041 0.194 -0.462 0.197 0.1804151572 903 0.136 0.228 0.041 0.194 -0.462 0.197 0.1804140332 904 0.136 0.228 0.041 0.193 -0.462 0.197 0.1804139707 909 0.136 0.228 0.041 0.193 -0.462 0.197 0.1804138147 912 0.141 0.238 0.042 0.208 -0.471 0.205 0.1802358117 919 0.142 0.240 0.043 0.211 -0.473 0.207 0.1802290268 920 0.142 0.240 0.043 0.211 -0.473 0.207 0.1802284679 924 0.142 0.240 0.043 0.211 -0.473 0.207 0.1802282741 937 0.142 0.240 0.043 0.211 -0.473 0.182 0.1800926327 938 0.142 0.240 0.043 0.211 -0.473 0.189 0.1800187728 939 0.142 0.240 0.043 0.211 -0.473 0.191 0.1800126321 948 0.132 0.238 0.044 0.207 -0.467 0.193 0.1799949248 950 0.131 0.237 0.044 0.206 -0.466 0.193 0.1799948827 951 0.131 0.237 0.044 0.207 -0.466 0.193 0.1799946354 961 0.131 0.237 0.045 0.207 -0.466 0.193 0.1799907316 962 0.131 0.237 0.047 0.207 -0.466 0.193 0.1799859937 964 0.131 0.237 0.048 0.207 -0.466 0.193 0.1799854936 972 0.131 0.239 0.048 0.205 -0.467 0.194 0.1799766981 973 0.131 0.239 0.048 0.205 -0.467 0.195 0.1799754334 975 0.131 0.240 0.048 0.205 -0.467 0.195 0.1799741574 978 0.131 0.240 0.048 0.205 -0.467 0.195 0.1799741391 991 0.131 0.240 0.048 0.205 -0.463 0.195 0.1799596999 992 0.131 0.240 0.048 0.205 -0.462 0.195 0.1799586661 995 0.136 0.249 0.050 0.219 -0.471 0.204 0.1798271713 1000 0.136 0.250 0.050 0.221 -0.472 0.205 0.1798250385 1006 0.136 0.250 0.050 0.221 -0.472 0.205 0.1798249659 1010 0.137 0.272 0.060 0.248 -0.483 0.212 0.1797486576 1016 0.137 0.264 0.056 0.238 -0.479 0.209 0.1797267274 1017 0.137 0.265 0.057 0.240 -0.480 0.210 0.1797228766 1029 0.134 0.260 0.056 0.231 -0.474 0.205 0.1796599848 1030 0.132 0.256 0.055 0.226 -0.471 0.202 0.1796556358 1031 0.132 0.257 0.056 0.227 -0.472 0.203 0.1796524875 1032 0.133 0.258 0.056 0.228 -0.472 0.203 0.1796519398 1037 0.133 0.258 0.056 0.228 -0.472 0.203 0.1796519189 1057 0.133 0.258 0.048 0.228 -0.472 0.203 0.1796381414 1058 0.133 0.258 0.051 0.228 -0.472 0.203 0.1796320489 1067 0.133 0.256 0.050 0.229 -0.472 0.202 0.1796217117 1069 0.133 0.256 0.050 0.229 -0.472 0.201 0.1796197043 1070 0.133 0.256 0.050 0.229 -0.472 0.201 0.1796194702 1082 0.133 0.256 0.050 0.229 -0.469 0.201 0.1796194063 1084 0.133 0.256 0.050 0.229 -0.470 0.201 0.1796183987 1090 0.133 0.264 0.054 0.240 -0.474 0.204 0.1795776228 1091 0.133 0.264 0.054 0.239 -0.474 0.204 0.1795775002 1092 0.133 0.264 0.054 0.239 -0.474 0.204 0.1795774356 1095 0.133 0.263 0.054 0.238 -0.474 0.204 0.1795774096 1096 0.133 0.263 0.054 0.239 -0.474 0.204 0.1795772478 1104 0.130 0.258 0.053 0.230 -0.468 0.199 0.1795585047 1106 0.131 0.259 0.053 0.233 -0.470 0.200 0.1795533679 1110 0.131 0.259 0.053 0.232 -0.470 0.200 0.1795532692 1122 0.136 0.260 0.052 0.235 -0.473 0.199 0.1795496271 1124 0.134 0.260 0.053 0.234 -0.472 0.200 0.1795453246 1136 0.134 0.260 0.052 0.234 -0.472 0.200 0.1795448668 1145 0.134 0.260 0.052 0.234 -0.472 0.200 0.1795448034 1147 0.134 0.260 0.052 0.234 -0.472 0.200 0.1795446135 1166 0.134 0.269 0.055 0.244 -0.476 0.203 0.1795372498 1167 0.134 0.265 0.054 0.240 -0.474 0.202 0.1795281297 1172 0.134 0.265 0.054 0.240 -0.474 0.202 0.1795280813 1175 0.135 0.267 0.054 0.241 -0.475 0.200 0.1794907688 1178 0.137 0.270 0.054 0.242 -0.476 0.197 0.1794529424 1179 0.138 0.273 0.054 0.243 -0.476 0.194 0.1794445132 1180 0.138 0.273 0.054 0.243 -0.476 0.195 0.1794443896 1183 0.138 0.272 0.054 0.243 -0.476 0.195 0.1794442559 1184 0.138 0.272 0.054 0.243 -0.476 0.195 0.1794440286 1211 0.133 0.271 0.054 0.241 -0.473 0.195 0.1794306446 1213 0.134 0.272 0.054 0.241 -0.474 0.195 0.1794302668 1216 0.135 0.272 0.054 0.241 -0.474 0.195 0.1794301650 1218 0.135 0.272 0.054 0.242 -0.474 0.195 0.1794301468 1230 0.135 0.272 0.053 0.242 -0.474 0.195 0.1794297424 1237 0.135 0.271 0.053 0.242 -0.474 0.194 0.1794262380 1238 0.135 0.271 0.053 0.242 -0.474 0.194 0.1794257830 1241 0.135 0.271 0.053 0.242 -0.474 0.194 0.1794256547 1244 0.135 0.271 0.053 0.242 -0.474 0.194 0.1794256501 1245 0.135 0.271 0.053 0.242 -0.474 0.194 0.1794256364 1261 0.135 0.271 0.053 0.243 -0.474 0.193 0.1794251899 1263 0.135 0.271 0.053 0.243 -0.474 0.193 0.1794251069 1266 0.135 0.271 0.053 0.243 -0.474 0.193 0.1794249381 1267 0.135 0.272 0.053 0.243 -0.474 0.193 0.1794249283 1279 0.135 0.272 0.054 0.244 -0.474 0.194 0.1794247683 1296 0.132 0.272 0.054 0.242 -0.473 0.194 0.1794214020 1310 0.132 0.272 0.052 0.242 -0.473 0.194 0.1794207538 1346 0.132 0.272 0.052 0.242 -0.473 0.194 0.1794205320 Powell done niters = 15 Computing relative cost 0 -25.0 -25.0 -25.0 1.029869 1 -25.0 -25.0 25.0 1.003389 2 -25.0 25.0 -25.0 1.003119 3 -25.0 25.0 25.0 1.053427 4 25.0 -25.0 -25.0 0.978478 5 25.0 -25.0 25.0 1.027536 6 25.0 25.0 -25.0 1.070558 7 25.0 25.0 25.0 1.015058 REL: 8 0.179421 8.181434 1.022679 rel = 0.175442 Number of iterations 15 Min cost was 0.179421 Number of FunctionCalls 1354 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 3.916000 sec Parameters at optimum (transmm) 0.13240 0.27168 0.05211 Parameters at optimum (rotdeg) 0.24228 -0.47256 0.19380 Final costs ---------------- Number of surface hits 2520 WM Intensity 86.0297 +/- 10.7290 Ctx Intensity 98.7761 +/- 12.2944 Pct Contrast 13.7113 +/- 12.0102 Cost 0.1794 RelCost 0.2217 Reg at min cost was -0.022 0.949 -0.314 -0.194; -0.997 -0.046 -0.068 0.031; -0.079 0.311 0.947 5.743; 0.000 0.000 0.000 1.000; Writing optimal reg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/bbr.pass1.dat, type = 14 Original Reg -0.026 0.952 -0.306 -0.280; -0.997 -0.048 -0.063 -0.215; -0.074 0.303 0.950 5.694; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.004 0.002 0.008 -0.086; -0.000 -0.002 0.005 -0.246; 0.004 -0.008 0.003 -0.049; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.472788 Computing change in rh position Surface RMS Diff (mm) 0.452685 0.866500 mri_segreg done mri_segreg --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii --init-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/bbr.pass1.dat --out-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mri_segreg --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii --init-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/bbr.pass1.dat --out-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname compute-0-1.local machine x86_64 user twilliams movvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/template.nii regfile /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/tmp.bbregister.15416/bbr.pass1.dat subject af1021_recon dof 6 outregfile /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1445640253 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.022 0.949 -0.314 -0.194; -0.997 -0.046 -0.068 0.031; -0.079 0.311 0.947 5.743; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.024760 1 -25.0 -25.0 25.0 1.037819 2 -25.0 25.0 -25.0 1.033642 3 -25.0 25.0 25.0 1.032312 4 25.0 -25.0 -25.0 1.026415 5 25.0 -25.0 25.0 1.024327 6 25.0 25.0 -25.0 1.029810 7 25.0 25.0 25.0 1.022019 REL: 8 0.211948 8.231103 1.028888 rel = 0.205997 Initial costs ---------------- Number of surface hits 252194 WM Intensity 86.2706 +/- 10.8035 Ctx Intensity 98.8475 +/- 12.2414 Pct Contrast 13.5322 +/- 11.6096 Cost 0.2119 RelCost 0.2060 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.2035 0.2035 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1990 0.1990 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1907 0.1907 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1863 0.1863 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1861 0.1861 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1856 0.1856 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1848 0.1848 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1818 0.1818 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1794 0.1794 0.0 Brute Force -------------------------- Min cost was 0.179421 Number of iterations 729 Search time 2.119000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 8 -0.011 0.000 0.000 0.000 0.000 0.000 0.2119339477 17 -0.011 -0.065 0.000 0.000 0.000 0.000 0.2115297115 18 -0.011 -0.057 0.000 0.000 0.000 0.000 0.2115062919 19 -0.011 -0.052 0.000 0.000 0.000 0.000 0.2115026491 28 -0.011 -0.052 0.022 0.000 0.000 0.000 0.2114395186 29 -0.011 -0.052 0.021 0.000 0.000 0.000 0.2114394360 37 -0.011 -0.052 0.021 -0.073 0.000 0.000 0.2106156684 47 -0.011 -0.052 0.021 -0.072 0.027 0.000 0.2105429960 48 -0.011 -0.052 0.021 -0.072 0.020 0.000 0.2105362123 49 -0.011 -0.052 0.021 -0.072 0.021 0.000 0.2105360040 57 -0.011 -0.052 0.021 -0.072 0.021 -0.227 0.2051524679 58 -0.011 -0.052 0.021 -0.072 0.021 -0.220 0.2051297671 59 -0.011 -0.052 0.021 -0.072 0.021 -0.211 0.2051175027 60 -0.011 -0.052 0.021 -0.072 0.021 -0.209 0.2051174850 69 -0.012 -0.060 0.024 -0.083 0.024 -0.239 0.2049989918 70 -0.012 -0.060 0.025 -0.083 0.024 -0.240 0.2049984717 71 -0.012 -0.061 0.025 -0.085 0.025 -0.245 0.2049971775 73 -0.012 -0.061 0.025 -0.084 0.025 -0.243 0.2049968034 74 -0.012 -0.061 0.025 -0.084 0.025 -0.243 0.2049967241 83 -0.010 -0.061 0.025 -0.084 0.025 -0.243 0.2049922816 84 -0.004 -0.061 0.025 -0.084 0.025 -0.243 0.2049877690 86 -0.002 -0.061 0.025 -0.084 0.025 -0.243 0.2049872890 94 -0.002 -0.199 0.025 -0.084 0.025 -0.243 0.2025775177 97 -0.002 -0.198 0.025 -0.084 0.025 -0.243 0.2025773221 104 -0.002 -0.198 0.008 -0.084 0.025 -0.243 0.2025718932 105 -0.002 -0.198 0.015 -0.084 0.025 -0.243 0.2025621033 106 -0.002 -0.198 0.016 -0.084 0.025 -0.243 0.2025619800 114 -0.002 -0.198 0.016 -0.149 0.025 -0.243 0.2020030848 116 -0.002 -0.198 0.016 -0.152 0.025 -0.243 0.2020024015 126 -0.002 -0.198 0.016 -0.152 0.041 -0.243 0.2019114895 127 -0.002 -0.198 0.016 -0.152 0.046 -0.243 0.2019059624 136 -0.004 -0.203 0.018 -0.159 0.048 -0.264 0.2018583419 137 -0.004 -0.203 0.018 -0.159 0.048 -0.263 0.2018577614 138 -0.003 -0.203 0.018 -0.158 0.047 -0.262 0.2018574009 144 0.004 -0.353 0.015 -0.244 0.074 -0.314 0.2014472277 150 0.001 -0.296 0.016 -0.211 0.064 -0.294 0.2013031545 151 0.001 -0.302 0.016 -0.215 0.065 -0.296 0.2013002940 152 0.001 -0.303 0.016 -0.215 0.065 -0.297 0.2013002024 163 -0.036 -0.303 0.016 -0.215 0.065 -0.297 0.2011494706 164 -0.034 -0.303 0.016 -0.215 0.065 -0.297 0.2011486617 172 -0.033 -0.301 0.015 -0.212 0.064 -0.288 0.2011470930 173 -0.033 -0.302 0.015 -0.213 0.064 -0.292 0.2011465080 174 -0.033 -0.302 0.015 -0.213 0.064 -0.291 0.2011463944 175 -0.033 -0.301 0.015 -0.213 0.064 -0.290 0.2011462811 177 -0.033 -0.301 0.015 -0.213 0.064 -0.290 0.2011462679 178 -0.033 -0.301 0.015 -0.213 0.064 -0.290 0.2011462304 186 -0.033 -0.301 -0.012 -0.213 0.064 -0.290 0.2010382137 187 -0.033 -0.301 -0.013 -0.213 0.064 -0.290 0.2010381312 195 -0.033 -0.301 -0.013 -0.215 0.064 -0.290 0.2010331369 196 -0.033 -0.301 -0.013 -0.222 0.064 -0.290 0.2010290068 197 -0.033 -0.301 -0.013 -0.220 0.064 -0.290 0.2010287056 205 -0.033 -0.301 -0.013 -0.220 0.070 -0.290 0.2010105151 206 -0.033 -0.301 -0.013 -0.220 0.074 -0.290 0.2010066051 215 -0.032 -0.321 -0.014 -0.232 0.078 -0.297 0.2009802236 216 -0.032 -0.322 -0.014 -0.232 0.078 -0.297 0.2009799556 217 -0.032 -0.324 -0.014 -0.233 0.078 -0.298 0.2009796664 218 -0.032 -0.324 -0.014 -0.233 0.078 -0.298 0.2009796572 219 -0.032 -0.324 -0.014 -0.233 0.078 -0.298 0.2009795516 221 -0.032 -0.324 -0.014 -0.233 0.078 -0.298 0.2009795364 230 -0.046 -0.324 -0.014 -0.233 0.078 -0.298 0.2009733195 231 -0.041 -0.324 -0.014 -0.233 0.078 -0.298 0.2009705351 240 -0.041 -0.323 -0.014 -0.232 0.078 -0.295 0.2009693199 241 -0.041 -0.323 -0.014 -0.232 0.078 -0.294 0.2009692102 245 -0.041 -0.323 -0.014 -0.232 0.078 -0.294 0.2009691929 253 -0.041 -0.323 -0.018 -0.232 0.078 -0.294 0.2009664509 254 -0.041 -0.323 -0.019 -0.232 0.078 -0.294 0.2009662519 263 -0.041 -0.323 -0.019 -0.235 0.078 -0.294 0.2009645075 264 -0.041 -0.323 -0.019 -0.236 0.078 -0.294 0.2009644073 273 -0.041 -0.323 -0.019 -0.236 0.080 -0.294 0.2009623878 277 -0.041 -0.323 -0.019 -0.236 0.081 -0.294 0.2009621997 284 -0.041 -0.324 -0.019 -0.237 0.081 -0.295 0.2009609857 285 -0.040 -0.329 -0.019 -0.240 0.082 -0.296 0.2009597381 288 -0.040 -0.328 -0.019 -0.239 0.082 -0.296 0.2009596042 291 -0.048 -0.333 -0.024 -0.246 0.086 -0.294 0.2009594085 299 -0.043 -0.328 -0.019 -0.239 0.082 -0.296 0.2009588411 317 -0.043 -0.328 -0.020 -0.239 0.082 -0.296 0.2009583103 318 -0.043 -0.328 -0.022 -0.239 0.082 -0.296 0.2009580829 328 -0.043 -0.328 -0.022 -0.241 0.082 -0.296 0.2009580713 337 -0.043 -0.328 -0.022 -0.241 0.083 -0.296 0.2009579416 346 -0.043 -0.331 -0.022 -0.242 0.083 -0.297 0.2009579076 348 -0.043 -0.329 -0.022 -0.242 0.083 -0.296 0.2009578139 350 -0.043 -0.329 -0.022 -0.241 0.083 -0.296 0.2009578045 351 -0.043 -0.329 -0.022 -0.241 0.083 -0.296 0.2009577402 361 -0.044 -0.329 -0.022 -0.241 0.083 -0.296 0.2009576255 369 -0.044 -0.329 -0.022 -0.241 0.083 -0.295 0.2009574471 370 -0.044 -0.328 -0.022 -0.241 0.083 -0.294 0.2009573731 412 -0.044 -0.330 -0.022 -0.242 0.083 -0.295 0.2009572108 413 -0.044 -0.330 -0.022 -0.242 0.083 -0.295 0.2009572103 414 -0.044 -0.330 -0.022 -0.242 0.083 -0.295 0.2009571498 434 -0.044 -0.330 -0.022 -0.242 0.083 -0.295 0.2009571431 435 -0.044 -0.330 -0.022 -0.242 0.083 -0.294 0.2009570605 479 -0.044 -0.329 -0.022 -0.241 0.083 -0.294 0.2009570495 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.024924 1 -25.0 -25.0 25.0 1.039081 2 -25.0 25.0 -25.0 1.034766 3 -25.0 25.0 25.0 1.034139 4 25.0 -25.0 -25.0 1.023477 5 25.0 -25.0 25.0 1.025428 6 25.0 25.0 -25.0 1.029199 7 25.0 25.0 25.0 1.022217 REL: 8 0.200957 8.233232 1.029154 rel = 0.195264 Number of iterations 7 Min cost was 0.200957 Number of FunctionCalls 543 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 63.672000 sec Parameters at optimum (transmm) -0.04408 -0.32924 -0.02208 Parameters at optimum (rotdeg) -0.24109 0.08309 -0.29377 Final costs ---------------- Number of surface hits 252194 WM Intensity 86.1863 +/- 10.7977 Ctx Intensity 99.0045 +/- 12.2267 Pct Contrast 13.7927 +/- 11.5930 Cost 0.2010 RelCost 0.2060 Reg at min cost was -0.027 0.950 -0.313 -0.230; -0.997 -0.049 -0.062 -0.273; -0.075 0.310 0.948 5.721; 0.000 0.000 0.000 1.000; Writing optimal reg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat, type = 14 Original Reg -0.022 0.949 -0.314 -0.194; -0.997 -0.046 -0.068 0.031; -0.079 0.311 0.947 5.743; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.005 -0.000 -0.001 0.035; 0.000 0.004 -0.006 0.304; -0.004 0.001 -0.001 0.022; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.279537 Computing change in rh position Surface RMS Diff (mm) 0.285903 0.595307 mri_segreg done tkregister2_cmdl --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz --reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat --noedit --ltaout /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.lta tkregister_tcl /share/apps/freesurfer-5.3.0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz reg file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.027 0.950 -0.313 -0.230; -0.997 -0.049 -0.062 -0.273; -0.075 0.310 0.948 5.721; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -88.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.027 0.950 -0.313 -0.230; -0.997 -0.049 -0.062 -0.273; -0.075 0.310 0.948 5.721; 0.000 0.000 0.000 1.000; Determinant 1 subject = af1021_recon RegMat --------------------------- -0.027 0.950 -0.313 -0.230; -0.997 -0.049 -0.062 -0.273; -0.075 0.310 0.948 5.721; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 0.007 0.009 1.033; -0.007 0.999 0.036 1.884; -0.009 -0.036 0.999 -1.336; 0.000 0.000 0.000 1.000; transformed matrix: -0.027 -0.075 0.997 53.202; -0.313 0.948 0.062 46.695; -0.950 -0.310 -0.049 291.969; 0.000 0.000 0.000 1.000; Cleaning up Started at Tue Oct 20 18:58:21 EDT 2015 Ended at Tue Oct 20 19:04:15 EDT 2015 BBR-Run-Time-Sec 354 bbregister Done To check results, run: tkregister2 --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz --reg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.dat --surf mri_convert -at /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.lta -rl /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/FLAIR.mgz mri_convert -at /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.lta -rl /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/FLAIR.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig/FLAIRraw.mgz... TR=6000.00, TE=475.00, TI=2100.00, flip angle=120.00 i_ras = (0.0313814, -0.959852, 0.278747) j_ras = (0.0851089, -0.275305, -0.957582) k_ras = (-0.995877, -0.053774, -0.0730522) INFO: Reading transformation from file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.lta... Reading transform with LTAreadEx() reading extra input line subject af1021_recon reading extra input line fscale 0.150000 reading template info from volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz... INFO: Applying transformation from file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/transforms/FLAIRraw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 0.007 0.009 1.033; -0.007 0.999 0.036 1.884; -0.009 -0.036 0.999 -1.336; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/FLAIR.mgz... mri_normalize -aseg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz -sigma 4 -surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white identity.nofile -surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white identity.nofile /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/FLAIR.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/FLAIR.mgz using segmentation for initial intensity normalization using Gaussian smoothing of bias field, sigma=4.000 reading from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/FLAIR.mgz... computing distance transform computing distance transform computing nonmaximum suppression 8623 non wm control points removed building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field writing normalized volume to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/FLAIR.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts cp -v /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.woFLAIR.pial `/share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial' -> `/share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.woFLAIR.pial' mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12571 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.26 (0.04-->6.52) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.23) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 593 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.10-->6.52) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.23) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4155848.8, rms=0.00 rms = 0.92, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4155848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 593 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.10-->6.52) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.23) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4155848.8, rms=0.00 rms = 0.92, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4155848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 593 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=compu, 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 (0.10-->6.52) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.23) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4155848.8, rms=0.00 rms = 0.92, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4155848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 593 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=compu, 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=4155848.8, rms=0.00 rms = 0.92, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4155848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [92.20 173.80], gm=133.00+-13.60, and vertices in regions > 126.2 14549 surface locations found to contain inconsistent values (14294 in, 255 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=472019.3, rms=0.21 001: dt: 0.5000, sse=443995.3, rms=0.205 (0.000%) 002: dt: 0.5000, sse=421604.5, rms=0.194 (0.000%) 003: dt: 0.5000, sse=407608.6, rms=0.185 (0.000%) 004: dt: 0.5000, sse=396586.2, rms=0.176 (0.000%) 005: dt: 0.5000, sse=388565.8, rms=0.168 (0.000%) 006: dt: 0.5000, sse=381724.2, rms=0.160 (0.000%) 007: dt: 0.5000, sse=376102.9, rms=0.153 (0.000%) 008: dt: 0.5000, sse=371469.2, rms=0.147 (0.000%) 009: dt: 0.5000, sse=367481.3, rms=0.142 (0.000%) 010: dt: 0.5000, sse=363803.3, rms=0.137 (0.000%) 011: dt: 0.5000, sse=360719.7, rms=0.132 (0.000%) 012: dt: 0.5000, sse=358128.8, rms=0.128 (0.000%) 013: dt: 0.5000, sse=355649.8, rms=0.125 (0.000%) 014: dt: 0.5000, sse=353241.8, rms=0.121 (0.000%) 015: dt: 0.5000, sse=351249.2, rms=0.119 (0.000%) 016: dt: 0.5000, sse=349420.7, rms=0.116 (0.000%) 017: dt: 0.5000, sse=347352.2, rms=0.114 (0.000%) 018: dt: 0.5000, sse=345751.4, rms=0.112 (0.000%) 019: dt: 0.5000, sse=344234.4, rms=0.111 (0.000%) 020: dt: 0.5000, sse=342637.4, rms=0.109 (0.000%) 021: dt: 0.5000, sse=341105.9, rms=0.108 (0.000%) 022: dt: 0.5000, sse=339873.5, rms=0.107 (0.000%) 023: dt: 0.5000, sse=338623.2, rms=0.106 (0.000%) 024: dt: 0.5000, sse=337218.2, rms=0.106 (0.000%) 025: dt: 0.5000, sse=335958.8, rms=0.105 (0.000%) 026: dt: 0.5000, sse=334976.4, rms=0.105 (0.000%) 027: dt: 0.5000, sse=334092.5, rms=0.104 (0.000%) 028: dt: 0.5000, sse=332976.8, rms=0.104 (0.000%) 029: dt: 0.5000, sse=332235.7, rms=0.104 (0.000%) 030: dt: 0.5000, sse=331161.1, rms=0.104 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [93.40 172.60], gm=133.00+-13.20, and vertices in regions > 126.4 6535 surface locations found to contain inconsistent values (6268 in, 267 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=33382.0, rms=0.08 031: dt: 0.5000, sse=33259.6, rms=0.074 (0.000%) 032: dt: 0.5000, sse=33327.3, rms=0.068 (0.000%) 033: dt: 0.5000, sse=33454.2, rms=0.065 (0.000%) 034: dt: 0.5000, sse=33573.7, rms=0.061 (0.000%) 035: dt: 0.5000, sse=33689.1, rms=0.059 (0.000%) 036: dt: 0.5000, sse=33772.5, rms=0.056 (0.000%) 037: dt: 0.5000, sse=33827.9, rms=0.054 (0.000%) 038: dt: 0.5000, sse=33889.0, rms=0.052 (0.000%) 039: dt: 0.5000, sse=33957.4, rms=0.050 (0.000%) 040: dt: 0.5000, sse=34027.8, rms=0.048 (0.000%) 041: dt: 0.5000, sse=34106.3, rms=0.046 (0.000%) 042: dt: 0.5000, sse=34173.4, rms=0.045 (0.000%) 043: dt: 0.5000, sse=34218.1, rms=0.043 (0.000%) 044: dt: 0.5000, sse=34262.2, rms=0.042 (0.000%) 045: dt: 0.5000, sse=34331.9, rms=0.040 (0.000%) 046: dt: 0.5000, sse=34371.5, rms=0.039 (0.000%) 047: dt: 0.5000, sse=34405.5, rms=0.038 (0.000%) 048: dt: 0.5000, sse=34451.5, rms=0.037 (0.000%) 049: dt: 0.5000, sse=34497.2, rms=0.036 (0.000%) 050: dt: 0.5000, sse=34531.4, rms=0.035 (0.000%) 051: dt: 0.5000, sse=34576.1, rms=0.034 (0.000%) 052: dt: 0.5000, sse=34597.0, rms=0.033 (0.000%) 053: dt: 0.5000, sse=34618.6, rms=0.032 (0.000%) 054: dt: 0.5000, sse=34661.4, rms=0.031 (0.000%) 055: dt: 0.5000, sse=34692.6, rms=0.030 (0.000%) 056: dt: 0.5000, sse=34706.8, rms=0.030 (0.000%) 057: dt: 0.5000, sse=34733.8, rms=0.029 (0.000%) 058: dt: 0.5000, sse=34766.1, rms=0.028 (0.000%) 059: dt: 0.5000, sse=34789.7, rms=0.028 (0.000%) 060: dt: 0.5000, sse=34795.6, rms=0.027 (0.000%) positioning took 3.0 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [93.70 172.30], gm=133.00+-13.10, and vertices in regions > 126.4 1670 surface locations found to contain inconsistent values (1425 in, 245 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3593.6, rms=0.03 061: dt: 0.5000, sse=3591.1, rms=0.031 (0.000%) 062: dt: 0.5000, sse=3588.6, rms=0.029 (0.000%) 063: dt: 0.5000, sse=3588.2, rms=0.028 (0.000%) 064: dt: 0.5000, sse=3587.4, rms=0.027 (0.000%) 065: dt: 0.5000, sse=3587.9, rms=0.026 (0.000%) 066: dt: 0.5000, sse=3588.3, rms=0.025 (0.000%) 067: dt: 0.5000, sse=3586.1, rms=0.025 (0.000%) 068: dt: 0.5000, sse=3584.3, rms=0.024 (0.000%) 069: dt: 0.5000, sse=3585.8, rms=0.024 (0.000%) 070: dt: 0.5000, sse=3586.9, rms=0.023 (0.000%) 071: dt: 0.5000, sse=3586.0, rms=0.023 (0.000%) 072: dt: 0.5000, sse=3586.5, rms=0.022 (0.000%) 073: dt: 0.5000, sse=3586.2, rms=0.022 (0.000%) 074: dt: 0.5000, sse=3586.8, rms=0.022 (0.000%) 075: dt: 0.5000, sse=3586.7, rms=0.022 (0.000%) 076: dt: 0.5000, sse=3586.3, rms=0.021 (0.000%) 077: dt: 0.5000, sse=3584.7, rms=0.021 (0.000%) 078: dt: 0.5000, sse=3585.8, rms=0.021 (0.000%) 079: dt: 0.5000, sse=3585.8, rms=0.020 (0.000%) 080: dt: 0.5000, sse=3586.2, rms=0.020 (0.000%) 081: dt: 0.5000, sse=3586.4, rms=0.020 (0.000%) 082: dt: 0.5000, sse=3588.0, rms=0.020 (0.000%) 083: dt: 0.5000, sse=3588.8, rms=0.020 (0.000%) 084: dt: 0.5000, sse=3589.9, rms=0.020 (0.000%) 085: dt: 0.5000, sse=3590.6, rms=0.020 (0.000%) 086: dt: 0.5000, sse=3591.4, rms=0.019 (0.000%) 087: dt: 0.5000, sse=3591.8, rms=0.019 (0.000%) 088: dt: 0.5000, sse=3591.3, rms=0.019 (0.000%) 089: dt: 0.5000, sse=3593.4, rms=0.019 (0.000%) 090: dt: 0.5000, sse=3593.1, rms=0.019 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 250 surface locations found to contain inconsistent values (28 in, 222 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=396.7, rms=0.02 091: dt: 0.5000, sse=396.8, rms=0.018 (0.000%) 092: dt: 0.5000, sse=395.0, rms=0.018 (0.000%) 093: dt: 0.5000, sse=394.1, rms=0.017 (0.000%) 094: dt: 0.5000, sse=393.3, rms=0.017 (0.000%) 095: dt: 0.5000, sse=392.2, rms=0.017 (0.000%) 096: dt: 0.5000, sse=391.5, rms=0.017 (0.000%) 097: dt: 0.5000, sse=391.1, rms=0.017 (0.000%) 098: dt: 0.5000, sse=390.8, rms=0.016 (0.000%) 099: dt: 0.5000, sse=390.7, rms=0.016 (0.000%) 100: dt: 0.5000, sse=390.7, rms=0.016 (0.000%) 101: dt: 0.5000, sse=390.4, rms=0.016 (0.000%) 102: dt: 0.5000, sse=390.3, rms=0.016 (0.000%) 103: dt: 0.5000, sse=390.3, rms=0.016 (0.000%) 104: dt: 0.5000, sse=389.9, rms=0.016 (0.000%) 105: dt: 0.5000, sse=390.0, rms=0.016 (0.000%) 106: dt: 0.5000, sse=389.9, rms=0.016 (0.000%) 107: dt: 0.5000, sse=389.8, rms=0.016 (0.000%) 108: dt: 0.5000, sse=389.8, rms=0.016 (0.000%) 109: dt: 0.5000, sse=389.5, rms=0.016 (0.000%) 110: dt: 0.5000, sse=389.5, rms=0.016 (0.000%) 111: dt: 0.5000, sse=389.5, rms=0.016 (0.000%) 112: dt: 0.5000, sse=389.6, rms=0.016 (0.000%) 113: dt: 0.5000, sse=389.6, rms=0.016 (0.000%) 114: dt: 0.5000, sse=390.0, rms=0.016 (0.000%) 115: dt: 0.5000, sse=389.8, rms=0.016 (0.000%) 116: dt: 0.5000, sse=389.7, rms=0.016 (0.000%) 117: dt: 0.5000, sse=389.6, rms=0.016 (0.000%) 118: dt: 0.5000, sse=389.5, rms=0.016 (0.000%) 119: dt: 0.5000, sse=389.5, rms=0.016 (0.000%) 120: dt: 0.5000, sse=389.5, rms=0.016 (0.000%) positioning took 3.0 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area.pial vertex spacing 1.00 +- 0.43 (0.08-->8.04) (max @ vno 92642 --> 92643) face area 0.39 +- 0.30 (0.00-->11.45) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 597:965 truncations. 28994 vertices at 0 distance 88955 vertices at 1 distance 83737 vertices at 2 distance 37654 vertices at 3 distance 11940 vertices at 4 distance 3682 vertices at 5 distance 1208 vertices at 6 distance 429 vertices at 7 distance 138 vertices at 8 distance 64 vertices at 9 distance 48 vertices at 10 distance 32 vertices at 11 distance 18 vertices at 12 distance 17 vertices at 13 distance 13 vertices at 14 distance 11 vertices at 15 distance 12 vertices at 16 distance 10 vertices at 17 distance 9 vertices at 18 distance 9 vertices at 19 distance 16 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.thickness positioning took 15.3 minutes /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts cp -v /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.woFLAIR.pial `/share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial' -> `/share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.woFLAIR.pial' mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 7.9 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->4.59) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown deleting segment 4 with 380 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown deleting segment 7 with 11 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.02-->4.59) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4635191.5, rms=0.00 rms = 0.88, time step reduction 1 of 3 to 0.250... rms = 0.23, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4635191.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 380 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.02-->4.59) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4635191.5, rms=0.00 rms = 0.92, time step reduction 1 of 3 to 0.250... rms = 0.23, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4635191.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 380 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=compu, 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 (0.02-->4.59) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4635191.5, rms=0.00 rms = 0.88, time step reduction 1 of 3 to 0.250... rms = 0.23, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4635191.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 380 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=compu, 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=4635191.5, rms=0.00 rms = 0.92, time step reduction 1 of 3 to 0.250... rms = 0.23, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4635191.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 13521 surface locations found to contain inconsistent values (13344 in, 177 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=489007.4, rms=0.21 001: dt: 0.5000, sse=457569.6, rms=0.199 (0.000%) 002: dt: 0.5000, sse=433955.9, rms=0.188 (0.000%) 003: dt: 0.5000, sse=419256.8, rms=0.180 (0.000%) 004: dt: 0.5000, sse=407981.2, rms=0.171 (0.000%) 005: dt: 0.5000, sse=399403.4, rms=0.164 (0.000%) 006: dt: 0.5000, sse=392157.3, rms=0.157 (0.000%) 007: dt: 0.5000, sse=386270.9, rms=0.151 (0.000%) 008: dt: 0.5000, sse=381203.8, rms=0.145 (0.000%) 009: dt: 0.5000, sse=376873.5, rms=0.140 (0.000%) 010: dt: 0.5000, sse=372788.0, rms=0.135 (0.000%) 011: dt: 0.5000, sse=369455.7, rms=0.131 (0.000%) 012: dt: 0.5000, sse=366247.4, rms=0.127 (0.000%) 013: dt: 0.5000, sse=363323.8, rms=0.124 (0.000%) 014: dt: 0.5000, sse=360769.5, rms=0.121 (0.000%) 015: dt: 0.5000, sse=358402.8, rms=0.118 (0.000%) 016: dt: 0.5000, sse=356288.3, rms=0.116 (0.000%) 017: dt: 0.5000, sse=354195.4, rms=0.113 (0.000%) 018: dt: 0.5000, sse=352405.2, rms=0.112 (0.000%) 019: dt: 0.5000, sse=350507.8, rms=0.110 (0.000%) 020: dt: 0.5000, sse=348740.7, rms=0.108 (0.000%) 021: dt: 0.5000, sse=347164.6, rms=0.107 (0.000%) 022: dt: 0.5000, sse=345701.8, rms=0.106 (0.000%) 023: dt: 0.5000, sse=344518.1, rms=0.105 (0.000%) 024: dt: 0.5000, sse=343204.2, rms=0.104 (0.000%) 025: dt: 0.5000, sse=341952.2, rms=0.103 (0.000%) 026: dt: 0.5000, sse=340805.7, rms=0.102 (0.000%) 027: dt: 0.5000, sse=339622.8, rms=0.102 (0.000%) 028: dt: 0.5000, sse=338466.2, rms=0.102 (0.000%) 029: dt: 0.5000, sse=337480.1, rms=0.101 (0.000%) 030: dt: 0.5000, sse=336482.3, rms=0.101 (0.000%) positioning took 3.3 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 4115 surface locations found to contain inconsistent values (3943 in, 172 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=33751.6, rms=0.07 031: dt: 0.5000, sse=33598.5, rms=0.066 (0.000%) 032: dt: 0.5000, sse=33629.5, rms=0.061 (0.000%) 033: dt: 0.5000, sse=33701.4, rms=0.058 (0.000%) 034: dt: 0.5000, sse=33772.2, rms=0.055 (0.000%) 035: dt: 0.5000, sse=33819.0, rms=0.052 (0.000%) 036: dt: 0.5000, sse=33882.5, rms=0.050 (0.000%) 037: dt: 0.5000, sse=33922.3, rms=0.048 (0.000%) 038: dt: 0.5000, sse=33978.0, rms=0.046 (0.000%) 039: dt: 0.5000, sse=34007.9, rms=0.044 (0.000%) 040: dt: 0.5000, sse=34040.9, rms=0.042 (0.000%) 041: dt: 0.5000, sse=34073.1, rms=0.040 (0.000%) 042: dt: 0.5000, sse=34104.7, rms=0.039 (0.000%) 043: dt: 0.5000, sse=34137.3, rms=0.037 (0.000%) 044: dt: 0.5000, sse=34170.9, rms=0.036 (0.000%) 045: dt: 0.5000, sse=34193.6, rms=0.035 (0.000%) 046: dt: 0.5000, sse=34227.0, rms=0.034 (0.000%) 047: dt: 0.5000, sse=34246.8, rms=0.033 (0.000%) 048: dt: 0.5000, sse=34276.1, rms=0.031 (0.000%) 049: dt: 0.5000, sse=34298.1, rms=0.030 (0.000%) 050: dt: 0.5000, sse=34332.6, rms=0.030 (0.000%) 051: dt: 0.5000, sse=34340.5, rms=0.029 (0.000%) 052: dt: 0.5000, sse=34359.4, rms=0.028 (0.000%) 053: dt: 0.5000, sse=34373.1, rms=0.028 (0.000%) 054: dt: 0.5000, sse=34386.4, rms=0.027 (0.000%) 055: dt: 0.5000, sse=34399.2, rms=0.026 (0.000%) 056: dt: 0.5000, sse=34406.0, rms=0.026 (0.000%) 057: dt: 0.5000, sse=34428.7, rms=0.026 (0.000%) 058: dt: 0.5000, sse=34435.9, rms=0.025 (0.000%) 059: dt: 0.5000, sse=34443.3, rms=0.025 (0.000%) 060: dt: 0.5000, sse=34447.0, rms=0.024 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 769 surface locations found to contain inconsistent values (603 in, 166 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3506.0, rms=0.02 061: dt: 0.5000, sse=3507.2, rms=0.023 (0.000%) 062: dt: 0.5000, sse=3508.0, rms=0.022 (0.000%) 063: dt: 0.5000, sse=3509.6, rms=0.022 (0.000%) 064: dt: 0.5000, sse=3512.6, rms=0.021 (0.000%) 065: dt: 0.5000, sse=3511.7, rms=0.021 (0.000%) 066: dt: 0.5000, sse=3510.9, rms=0.020 (0.000%) 067: dt: 0.5000, sse=3510.2, rms=0.020 (0.000%) 068: dt: 0.5000, sse=3509.6, rms=0.020 (0.000%) 069: dt: 0.5000, sse=3510.2, rms=0.019 (0.000%) 070: dt: 0.5000, sse=3509.7, rms=0.019 (0.000%) 071: dt: 0.5000, sse=3510.5, rms=0.019 (0.000%) 072: dt: 0.5000, sse=3510.3, rms=0.019 (0.000%) 073: dt: 0.5000, sse=3511.2, rms=0.019 (0.000%) 074: dt: 0.5000, sse=3512.4, rms=0.019 (0.000%) 075: dt: 0.5000, sse=3513.7, rms=0.019 (0.000%) 076: dt: 0.5000, sse=3513.1, rms=0.019 (0.000%) 077: dt: 0.5000, sse=3512.8, rms=0.018 (0.000%) 078: dt: 0.5000, sse=3511.8, rms=0.018 (0.000%) 079: dt: 0.5000, sse=3511.4, rms=0.018 (0.000%) 080: dt: 0.5000, sse=3512.6, rms=0.018 (0.000%) 081: dt: 0.5000, sse=3512.8, rms=0.018 (0.000%) 082: dt: 0.5000, sse=3513.0, rms=0.018 (0.000%) 083: dt: 0.5000, sse=3514.3, rms=0.018 (0.000%) 084: dt: 0.5000, sse=3514.6, rms=0.018 (0.000%) 085: dt: 0.5000, sse=3514.9, rms=0.018 (0.000%) 086: dt: 0.5000, sse=3514.0, rms=0.018 (0.000%) 087: dt: 0.5000, sse=3515.7, rms=0.018 (0.000%) 088: dt: 0.5000, sse=3515.7, rms=0.018 (0.000%) 089: dt: 0.5000, sse=3515.7, rms=0.018 (0.000%) 090: dt: 0.5000, sse=3516.1, rms=0.018 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 234 surface locations found to contain inconsistent values (73 in, 161 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=384.8, rms=0.02 091: dt: 0.5000, sse=387.8, rms=0.018 (0.000%) 092: dt: 0.5000, sse=386.8, rms=0.017 (0.000%) 093: dt: 0.5000, sse=385.7, rms=0.017 (0.000%) 094: dt: 0.5000, sse=386.1, rms=0.017 (0.000%) 095: dt: 0.5000, sse=385.5, rms=0.017 (0.000%) 096: dt: 0.5000, sse=385.3, rms=0.017 (0.000%) 097: dt: 0.5000, sse=384.5, rms=0.017 (0.000%) 098: dt: 0.5000, sse=384.2, rms=0.017 (0.000%) 099: dt: 0.5000, sse=384.4, rms=0.017 (0.000%) 100: dt: 0.5000, sse=385.3, rms=0.017 (0.000%) 101: dt: 0.5000, sse=384.6, rms=0.017 (0.000%) 102: dt: 0.5000, sse=384.5, rms=0.017 (0.000%) 103: dt: 0.5000, sse=384.8, rms=0.017 (0.000%) 104: dt: 0.5000, sse=385.0, rms=0.017 (0.000%) 105: dt: 0.5000, sse=385.5, rms=0.017 (0.000%) 106: dt: 0.5000, sse=384.8, rms=0.017 (0.000%) 107: dt: 0.5000, sse=384.1, rms=0.017 (0.000%) 108: dt: 0.5000, sse=383.5, rms=0.017 (0.000%) 109: dt: 0.5000, sse=383.7, rms=0.017 (0.000%) 110: dt: 0.5000, sse=383.9, rms=0.017 (0.000%) 111: dt: 0.5000, sse=383.9, rms=0.017 (0.000%) 112: dt: 0.5000, sse=384.1, rms=0.017 (0.000%) 113: dt: 0.5000, sse=384.2, rms=0.017 (0.000%) 114: dt: 0.5000, sse=384.5, rms=0.017 (0.000%) 115: dt: 0.5000, sse=384.3, rms=0.017 (0.000%) 116: dt: 0.5000, sse=383.6, rms=0.017 (0.000%) 117: dt: 0.5000, sse=383.2, rms=0.017 (0.000%) 118: dt: 0.5000, sse=383.1, rms=0.016 (0.000%) 119: dt: 0.5000, sse=383.1, rms=0.016 (0.000%) 120: dt: 0.5000, sse=384.2, rms=0.017 (0.000%) positioning took 3.0 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area.pial vertex spacing 0.99 +- 0.43 (0.05-->7.35) (max @ vno 101451 --> 134658) face area 0.39 +- 0.30 (0.00-->5.06) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 760:1146 truncations. 26951 vertices at 0 distance 85670 vertices at 1 distance 84055 vertices at 2 distance 40954 vertices at 3 distance 13752 vertices at 4 distance 4259 vertices at 5 distance 1391 vertices at 6 distance 476 vertices at 7 distance 221 vertices at 8 distance 121 vertices at 9 distance 58 vertices at 10 distance 46 vertices at 11 distance 46 vertices at 12 distance 49 vertices at 13 distance 23 vertices at 14 distance 10 vertices at 15 distance 13 vertices at 16 distance 8 vertices at 17 distance 8 vertices at 18 distance 7 vertices at 19 distance 4 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.thickness positioning took 16.1 minutes #-------------------------------------------- #@# Surf Volume lh Tue Oct 20 19:37:22 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Surf Volume rh Tue Oct 20 19:37:23 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Cortical ribbon mask Tue Oct 20 19:37:23 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon af1021_recon SUBJECTS_DIR is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 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 = 147 writing volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue Oct 20 19:53:01 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon 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 /share/apps/freesurfer-5.3.0/ASegStatsLUT.txt --subject af1021_recon $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 /share/apps/freesurfer-5.3.0/ASegStatsLUT.txt --subject af1021_recon sysname Linux hostname compute-0-1.local machine x86_64 user twilliams UseRobust 0 atlas_icv (eTIV) = 1541622 mm^3 (det: 1.263673 ) Computing euler number orig.nofix lheno = -44, rheno = -32 orig.nofix lhholes = 23, rhholes = 17 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 238472.746 238567.000 diff= -94.3 pctdiff=-0.040 rhCtxGM: 236843.593 236578.000 diff= 265.6 pctdiff= 0.112 lhCtxWM: 219121.061 218842.000 diff= 279.1 pctdiff= 0.127 rhCtxWM: 220291.314 220716.000 diff= -424.7 pctdiff=-0.193 SubCortGMVol 62225.000 SupraTentVol 989021.714 (987957.000) diff=1064.714 pctdiff=0.108 SupraTentVolNotVent 978152.714 (977088.000) diff=1064.714 pctdiff=0.109 BrainSegVol 1120336.000 (1118352.000) diff=1984.000 pctdiff=0.177 BrainSegVolNotVent 1106453.000 (1106327.714) diff=125.286 pctdiff=0.011 BrainSegVolNotVent 1106453.000 CerebellumVol 129214.000 VentChorVol 10869.000 3rd4th5thCSF 3014.000 CSFVol 1046.000, OptChiasmVol 135.000 MaskVol 1600589.000 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 4657 4657.085 4 5 Left-Inf-Lat-Vent 147 147.216 5 7 Left-Cerebellum-White-Matter 15131 15130.936 6 8 Left-Cerebellum-Cortex 49465 49464.539 7 10 Left-Thalamus-Proper 8027 8026.642 8 11 Left-Caudate 3803 3803.185 9 12 Left-Putamen 6337 6336.562 10 13 Left-Pallidum 1648 1648.023 11 14 3rd-Ventricle 739 739.349 12 15 4th-Ventricle 1501 1501.291 13 16 Brain-Stem 21351 21351.275 14 17 Left-Hippocampus 4730 4730.166 15 18 Left-Amygdala 1888 1887.705 16 24 CSF 1110 1110.174 17 26 Left-Accumbens-area 749 748.657 18 28 Left-VentralDC 3769 3768.568 19 30 Left-vessel 85 85.161 20 31 Left-choroid-plexus 1057 1056.964 23 43 Right-Lateral-Ventricle 3857 3856.684 24 44 Right-Inf-Lat-Vent 108 107.650 25 46 Right-Cerebellum-White-Matter 14819 14818.603 26 47 Right-Cerebellum-Cortex 51367 51367.012 27 49 Right-Thalamus-Proper 7432 7432.446 28 50 Right-Caudate 4211 4210.721 29 51 Right-Putamen 5637 5636.977 30 52 Right-Pallidum 1575 1575.200 31 53 Right-Hippocampus 4560 4560.470 32 54 Right-Amygdala 1372 1371.704 33 58 Right-Accumbens-area 760 759.631 34 60 Right-VentralDC 3998 3997.655 35 62 Right-vessel 74 74.438 36 63 Right-choroid-plexus 1407 1406.849 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1237 1237.188 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 17 17.220 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 133 132.774 45 251 CC_Posterior 858 858.164 46 252 CC_Mid_Posterior 539 539.010 47 253 CC_Central 505 505.136 48 254 CC_Mid_Anterior 426 425.545 49 255 CC_Anterior 784 783.820 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Tue Oct 20 19:57:01 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --volmask SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 472911 Used brute-force search on 0 voxels Writing output aseg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --volmask --a2009s SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 472911 Used brute-force search on 0 voxels Writing output aseg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue Oct 20 20:00:26 EDT 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/ribbon.mgz Loading filled from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8453 vertices from left hemi Ripped 8542 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz Loading Ctx Seg File /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 911455 Used brute-force search on 60 voxels Fixing Parahip LH WM Found 9 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 3.000000 7 k 27.000000 8 k 1712.000000 Fixing Parahip RH WM Found 10 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 2050.000000 Writing output aseg to mri/wmparc.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon 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 af1021_recon --surf-wm-vol --ctab /share/apps/freesurfer-5.3.0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject af1021_recon --surf-wm-vol --ctab /share/apps/freesurfer-5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-1.local machine x86_64 user twilliams UseRobust 0 atlas_icv (eTIV) = 1541622 mm^3 (det: 1.263673 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 238472.746 238567.000 diff= -94.3 pctdiff=-0.040 rhCtxGM: 236843.593 236578.000 diff= 265.6 pctdiff= 0.112 lhCtxWM: 219121.061 218842.000 diff= 279.1 pctdiff= 0.127 rhCtxWM: 220291.314 220716.000 diff= -424.7 pctdiff=-0.193 SubCortGMVol 62225.000 SupraTentVol 989021.714 (987957.000) diff=1064.714 pctdiff=0.108 SupraTentVolNotVent 978152.714 (977088.000) diff=1064.714 pctdiff=0.109 BrainSegVol 1120336.000 (1118352.000) diff=1984.000 pctdiff=0.177 BrainSegVolNotVent 1106453.000 (1106327.714) diff=125.286 pctdiff=0.011 BrainSegVolNotVent 1106453.000 CerebellumVol 129214.000 VentChorVol 10869.000 3rd4th5thCSF 3014.000 CSFVol 1046.000, OptChiasmVol 135.000 MaskVol 1600589.000 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 2348 2348.002 2 3002 wm-lh-caudalanteriorcingulate 2357 2357.339 3 3003 wm-lh-caudalmiddlefrontal 5327 5327.235 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 1976 1976.147 6 3006 wm-lh-entorhinal 1148 1148.231 7 3007 wm-lh-fusiform 5875 5875.175 8 3008 wm-lh-inferiorparietal 9901 9901.043 9 3009 wm-lh-inferiortemporal 6017 6017.053 10 3010 wm-lh-isthmuscingulate 3257 3256.546 11 3011 wm-lh-lateraloccipital 10274 10274.278 12 3012 wm-lh-lateralorbitofrontal 6228 6227.683 13 3013 wm-lh-lingual 6544 6543.639 14 3014 wm-lh-medialorbitofrontal 2714 2714.264 15 3015 wm-lh-middletemporal 5275 5274.743 16 3016 wm-lh-parahippocampal 1750 1750.281 17 3017 wm-lh-paracentral 3451 3451.271 18 3018 wm-lh-parsopercularis 4565 4565.379 19 3019 wm-lh-parsorbitalis 777 777.317 20 3020 wm-lh-parstriangularis 3141 3141.210 21 3021 wm-lh-pericalcarine 3486 3486.120 22 3022 wm-lh-postcentral 7573 7572.563 23 3023 wm-lh-posteriorcingulate 4263 4263.073 24 3024 wm-lh-precentral 12939 12938.585 25 3025 wm-lh-precuneus 9843 9842.609 26 3026 wm-lh-rostralanteriorcingulate 2488 2487.622 27 3027 wm-lh-rostralmiddlefrontal 11493 11493.447 28 3028 wm-lh-superiorfrontal 17208 17208.365 29 3029 wm-lh-superiorparietal 10795 10795.265 30 3030 wm-lh-superiortemporal 8632 8632.018 31 3031 wm-lh-supramarginal 8306 8305.808 32 3032 wm-lh-frontalpole 173 173.119 33 3033 wm-lh-temporalpole 559 558.694 34 3034 wm-lh-transversetemporal 746 746.460 35 3035 wm-lh-insula 8328 8327.700 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 2785 2784.752 120 4002 wm-rh-caudalanteriorcingulate 3512 3512.333 121 4003 wm-rh-caudalmiddlefrontal 4922 4921.562 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2059 2058.750 124 4006 wm-rh-entorhinal 821 821.294 125 4007 wm-rh-fusiform 6125 6125.485 126 4008 wm-rh-inferiorparietal 11185 11185.028 127 4009 wm-rh-inferiortemporal 5570 5569.789 128 4010 wm-rh-isthmuscingulate 2889 2888.626 129 4011 wm-rh-lateraloccipital 8933 8932.891 130 4012 wm-rh-lateralorbitofrontal 6284 6284.309 131 4013 wm-rh-lingual 6459 6458.981 132 4014 wm-rh-medialorbitofrontal 3344 3344.058 133 4015 wm-rh-middletemporal 5153 5152.666 134 4016 wm-rh-parahippocampal 2058 2057.921 135 4017 wm-rh-paracentral 4206 4206.260 136 4018 wm-rh-parsopercularis 3883 3882.978 137 4019 wm-rh-parsorbitalis 1065 1064.602 138 4020 wm-rh-parstriangularis 3073 3073.127 139 4021 wm-rh-pericalcarine 3732 3731.792 140 4022 wm-rh-postcentral 6846 6845.507 141 4023 wm-rh-posteriorcingulate 4332 4331.604 142 4024 wm-rh-precentral 12796 12795.932 143 4025 wm-rh-precuneus 10363 10362.959 144 4026 wm-rh-rostralanteriorcingulate 1891 1890.899 145 4027 wm-rh-rostralmiddlefrontal 12639 12639.312 146 4028 wm-rh-superiorfrontal 15456 15456.269 147 4029 wm-rh-superiorparietal 8850 8850.392 148 4030 wm-rh-superiortemporal 7872 7871.803 149 4031 wm-rh-supramarginal 8955 8955.332 150 4032 wm-rh-frontalpole 361 361.071 151 4033 wm-rh-temporalpole 486 485.529 152 4034 wm-rh-transversetemporal 629 628.685 153 4035 wm-rh-insula 8698 8698.138 154 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 28524 28523.795 237 5002 Right-UnsegmentedWhiteMatter 29840 29840.057 238 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label #-------------------------------------------- #@# BA Labels lh Tue Oct 20 20:12:37 EDT 2015 mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.label --trgsubject af1021_recon --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./lh.BA1.label 4441 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.label --trgsubject af1021_recon --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./lh.BA2.label 8259 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.label --trgsubject af1021_recon --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.label --trgsubject af1021_recon --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 450 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6433 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.label --trgsubject af1021_recon --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 399 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6183 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.label --trgsubject af1021_recon --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 227 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4297 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.label --trgsubject af1021_recon --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1056 Checking for and removing duplicates Writing label file ./lh.BA6.label 14645 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.label --trgsubject af1021_recon --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 717 Checking for and removing duplicates Writing label file ./lh.BA44.label 4898 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.label --trgsubject af1021_recon --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 857 Checking for and removing duplicates Writing label file ./lh.BA45.label 4279 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.label --trgsubject af1021_recon --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1642 Checking for and removing duplicates Writing label file ./lh.V1.label 6283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.label --trgsubject af1021_recon --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 3385 Checking for and removing duplicates Writing label file ./lh.V2.label 11499 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.label --trgsubject af1021_recon --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 789 Checking for and removing duplicates Writing label file ./lh.MT.label 2807 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.perirhinal.label --trgsubject af1021_recon --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 184 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1383 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1087 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 135 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2227 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1528 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 201 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2197 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2539 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1630 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 437 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7472 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2279 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 433 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1584 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.thresh.label --trgsubject af1021_recon --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1168 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4573 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.thresh.label --trgsubject af1021_recon --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1506 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4840 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.thresh.label --trgsubject af1021_recon --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 230 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 743 mri_label2label: Done mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-1.local machine x86_64 user twilliams subject af1021_recon hemi lh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 92420 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.BA.annot mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-1.local machine x86_64 user twilliams subject af1021_recon hemi lh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 109619 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab af1021_recon lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1111 631 2023 2.414 0.503 0.148 0.056 19 2.4 BA1 3343 2199 5850 2.504 0.491 0.126 0.042 42 6.0 BA2 992 681 884 1.789 0.481 0.158 0.053 11 2.3 BA3a 2599 1682 3562 1.895 0.675 0.132 0.044 32 5.0 BA3b 1655 949 2707 2.532 0.477 0.133 0.092 101 8.5 BA4a 1352 878 1941 2.259 0.562 0.131 0.054 17 2.7 BA4p 8399 5578 18772 2.897 0.561 0.139 0.060 130 22.3 BA6 2752 1918 5935 2.691 0.458 0.136 0.047 43 5.4 BA44 3249 2209 6785 2.623 0.526 0.137 0.049 46 6.1 BA45 3858 2478 4344 1.770 0.460 0.143 0.063 62 10.3 V1 8982 5709 12371 2.043 0.524 0.157 0.063 159 21.8 V2 2576 1752 4541 2.382 0.498 0.147 0.057 47 6.4 MT 1095 700 2290 2.694 0.680 0.130 0.051 14 2.4 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab af1021_recon lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 727 399 1361 2.494 0.421 0.144 0.059 12 1.6 BA1 1490 973 2842 2.539 0.500 0.126 0.047 23 3.3 BA2 756 527 615 1.681 0.381 0.165 0.055 9 1.7 BA3a 1668 1093 1867 1.592 0.458 0.123 0.038 15 2.7 BA3b 1676 937 2729 2.566 0.432 0.129 0.088 50 7.9 BA4a 1083 736 1404 2.089 0.497 0.134 0.055 14 2.1 BA4p 4702 3066 10337 2.864 0.559 0.139 0.060 69 12.2 BA6 1902 1345 4167 2.692 0.358 0.141 0.050 34 4.1 BA44 1455 981 3425 2.720 0.462 0.152 0.052 24 3.2 BA45 4100 2636 4699 1.772 0.465 0.142 0.062 63 10.3 V1 4494 2785 5770 1.927 0.506 0.161 0.071 91 12.3 V2 711 479 1002 2.140 0.350 0.127 0.031 7 1.1 MT #-------------------------------------------- #@# BA Labels rh Tue Oct 20 20:16:17 EDT 2015 mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.label --trgsubject af1021_recon --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 281 Checking for and removing duplicates Writing label file ./rh.BA1.label 4243 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.label --trgsubject af1021_recon --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 306 Checking for and removing duplicates Writing label file ./rh.BA2.label 6993 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.label --trgsubject af1021_recon --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 123 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4103 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.label --trgsubject af1021_recon --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 345 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4867 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.label --trgsubject af1021_recon --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6097 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.label --trgsubject af1021_recon --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4658 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.label --trgsubject af1021_recon --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 706 Checking for and removing duplicates Writing label file ./rh.BA6.label 12962 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.label --trgsubject af1021_recon --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1441 Checking for and removing duplicates Writing label file ./rh.BA44.label 8353 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.label --trgsubject af1021_recon --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1272 Checking for and removing duplicates Writing label file ./rh.BA45.label 6627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.label --trgsubject af1021_recon --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1846 Checking for and removing duplicates Writing label file ./rh.V1.label 6573 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.label --trgsubject af1021_recon --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 3084 Checking for and removing duplicates Writing label file ./rh.V2.label 11100 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.label --trgsubject af1021_recon --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 535 Checking for and removing duplicates Writing label file ./rh.MT.label 2467 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.perirhinal.label --trgsubject af1021_recon --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 147 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 899 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 89 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 965 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2733 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1733 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 195 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2378 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 86 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1474 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 38 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1527 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 263 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7222 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1225 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 237 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1415 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.thresh.label --trgsubject af1021_recon --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1332 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4564 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.thresh.label --trgsubject af1021_recon --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1463 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4900 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.thresh.label --trgsubject af1021_recon --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 75 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 343 mri_label2label: Done mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-1.local machine x86_64 user twilliams subject af1021_recon hemi rh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 94227 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.BA.annot mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-1.local machine x86_64 user twilliams subject af1021_recon hemi rh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 113257 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab af1021_recon rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 860 419 1444 2.465 0.379 0.133 0.092 20 4.2 BA1 2677 1735 3829 2.139 0.519 0.109 0.032 18 3.4 BA2 972 632 794 1.641 0.379 0.145 0.049 11 2.0 BA3a 2111 1316 2616 1.735 0.521 0.130 0.091 65 4.1 BA3b 1522 868 2495 2.518 0.496 0.121 0.050 15 3.4 BA4a 1027 732 1329 1.986 0.506 0.147 0.052 11 2.4 BA4p 6607 4378 13967 2.808 0.564 0.140 1.661 429 13.7 BA6 4482 3037 8623 2.732 0.490 0.137 0.051 61 9.2 BA44 4508 3036 9113 2.510 0.567 0.149 0.074 76 14.6 BA45 4377 2869 5135 1.809 0.510 0.169 0.096 106 19.2 V1 8530 5501 11907 2.116 0.518 0.166 0.067 235 24.0 V2 2145 1442 3382 2.385 0.375 0.140 0.044 26 4.1 MT 761 500 1902 2.891 0.599 0.154 0.073 12 2.3 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab af1021_recon rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 593 260 959 2.495 0.364 0.135 0.101 17 3.2 BA1 1433 937 2077 2.130 0.550 0.105 0.031 9 1.8 BA2 832 535 624 1.642 0.357 0.152 0.052 10 1.8 BA3a 1675 1111 1835 1.547 0.398 0.119 0.036 13 2.6 BA3b 888 464 1504 2.639 0.434 0.118 0.050 10 2.0 BA4a 813 624 1057 1.916 0.536 0.153 0.052 7 1.9 BA4p 4147 2688 8491 2.765 0.530 0.138 2.610 389 8.5 BA6 985 678 2144 2.773 0.388 0.146 0.072 19 2.5 BA44 1124 745 2483 2.614 0.469 0.147 0.059 18 2.5 BA45 4212 2761 4875 1.805 0.506 0.166 0.093 100 18.3 V1 4526 2903 6117 2.028 0.568 0.176 0.078 175 15.3 V2 321 213 655 2.447 0.278 0.121 0.037 3 0.5 MT /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Tue Oct 20 20:20:01 EDT 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o af1021_recon label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject af1021_recon. processing subject lh.EC_average... reading output surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 993 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label af1021_recon lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 374 211 860 2.769 0.691 0.153 0.128 15 1.9 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Tue Oct 20 20:20:14 EDT 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o af1021_recon label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject af1021_recon. processing subject rh.EC_average... reading output surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 947 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label af1021_recon rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 351 224 943 2.872 0.692 0.199 0.148 11 2.1 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Tue Oct 20 10:20:25 EDT 2015 Ended at Tue Oct 20 20:20:28 EDT 2015 #@#%# recon-all-run-time-hours 10.001 recon-all -s af1021_recon finished without error at Tue Oct 20 20:20:28 EDT 2015 New invocation of recon-all Wed Nov 18 15:57:12 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon /share/apps/freesurfer-5.3.0/bin/recon-all -subjid af1021_recon -FLAIRpial -autorecon-pial -no-isrunning subjid af1021_recon setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /share/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux compute-0-20.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 41943040 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 401408 total used free shared buffers cached Mem: 49449168 43634128 5815040 0 235644 40673120 -/+ buffers/cache: 2725364 46723804 Swap: 1020116 0 1020116 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 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: 2015/11/18-20:57:12-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/11/18-20:57:12-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/11/18-20:57:12-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:12-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:12-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:12-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:13-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:14-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/11/18-20:57:15-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/11/18-20:57:15-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:15-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:15-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:15-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/11/18-20:57:15-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: twilliams Machine: compute-0-20.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /share/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /share/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Mask BFS Wed Nov 18 15:57:15 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1558106 voxels in mask (pct= 9.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# Make White Surf lh Wed Nov 18 15:57:17 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.88 3435 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.54 2744 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4895479.5, rms=9.93 001: dt: 0.5000, sse=5563255.0, rms=7.101 (0.000%) 002: dt: 0.5000, sse=5950070.0, rms=5.421 (0.000%) 003: dt: 0.5000, sse=6270018.0, rms=4.412 (0.000%) 004: dt: 0.5000, sse=6508964.0, rms=3.792 (0.000%) 005: dt: 0.5000, sse=6643423.0, rms=3.481 (0.000%) 006: dt: 0.5000, sse=6742135.0, rms=3.291 (0.000%) 007: dt: 0.5000, sse=6790056.0, rms=3.216 (0.000%) 008: dt: 0.5000, sse=6807864.0, rms=3.143 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6803028.0, rms=3.125 (0.000%) 010: dt: 0.2500, sse=4088114.0, rms=2.112 (0.000%) 011: dt: 0.2500, sse=3760371.5, rms=1.869 (0.000%) 012: dt: 0.2500, sse=3613746.8, rms=1.813 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3566466.2, rms=1.783 (0.000%) rms = 1.75, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3509115.8, rms=1.752 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.8, 40 (7) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.3 (%26.2))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.40) mean absolute distance = 0.25 +- 0.37 3098 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4100148.5, rms=4.66 015: dt: 0.5000, sse=4398513.5, rms=2.790 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4864968.5, rms=2.784 (0.000%) 017: dt: 0.2500, sse=4087508.5, rms=1.707 (0.000%) 018: dt: 0.2500, sse=3955543.5, rms=1.511 (0.000%) rms = 1.47, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3846167.8, rms=1.474 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3800323.0, rms=1.432 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.2, 21 (3) missing vertices, mean dist -0.1 [0.3 (%72.0)->0.2 (%28.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.53) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3167 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4003219.2, rms=3.28 021: dt: 0.5000, sse=4305613.5, rms=2.452 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4040969.5, rms=1.742 (0.000%) 023: dt: 0.2500, sse=3963460.0, rms=1.401 (0.000%) 024: dt: 0.2500, sse=3935674.0, rms=1.316 (0.000%) rms = 1.32, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3906902.0, rms=1.316 (0.000%) rms = 1.29, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3874962.5, rms=1.290 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.0, 26 (2) missing vertices, mean dist -0.0 [0.2 (%56.8)->0.2 (%43.2))] %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3889749.0, rms=1.61 rms = 1.61, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=4959261.5, rms=1.605 (0.000%) 028: dt: 0.2500, sse=4232694.5, rms=1.227 (0.000%) 029: dt: 0.2500, sse=4419370.0, rms=1.057 (0.000%) rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.03, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4386916.0, rms=1.031 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 23 non-cortical segments detected only using segment with 2186 vertices erasing segment 1 (vno[0] = 57470) erasing segment 2 (vno[0] = 77359) erasing segment 3 (vno[0] = 78446) erasing segment 4 (vno[0] = 82313) erasing segment 5 (vno[0] = 83246) erasing segment 6 (vno[0] = 89295) erasing segment 7 (vno[0] = 93408) erasing segment 8 (vno[0] = 95389) erasing segment 9 (vno[0] = 97402) erasing segment 10 (vno[0] = 97413) erasing segment 11 (vno[0] = 97437) erasing segment 12 (vno[0] = 97489) erasing segment 13 (vno[0] = 98353) erasing segment 14 (vno[0] = 98456) erasing segment 15 (vno[0] = 99252) erasing segment 16 (vno[0] = 99310) erasing segment 17 (vno[0] = 100095) erasing segment 18 (vno[0] = 101770) erasing segment 19 (vno[0] = 101844) erasing segment 20 (vno[0] = 105977) erasing segment 21 (vno[0] = 106623) erasing segment 22 (vno[0] = 134247) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv writing smoothed area to lh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.22) refinement took 5.2 minutes #-------------------------------------------- #@# Smooth2 lh Wed Nov 18 16:02:27 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Nov 18 16:02:31 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.0 mm, total surface area = 81449 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 137 vertices thresholded to be in k1 ~ [-0.21 0.37], k2 ~ [-0.11 0.23] total integrated curvature = 0.530*4pi (6.656) --> 0 handles ICI = 1.6, FI = 9.9, variation=172.323 103 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 143 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Wed Nov 18 16:04:26 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 264 ] Gb_filter = 0 WARN: S lookup min: -0.500392 WARN: S explicit min: 0.000000 vertex = 245 #-------------------------------------------- #@# Sphere lh Wed Nov 18 16:04:33 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.283... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %19.75 pass 1: epoch 2 of 3 starting distance error %19.72 unfolding complete - removing small folds... starting distance error %19.69 removing remaining folds... final distance error %19.71 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.77 hours #-------------------------------------------- #@# Surf Reg lh Wed Nov 18 16:50:59 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_register -curv ../surf/lh.sphere /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 0.577 curvature mean = 0.040, std = 0.936 curvature mean = 0.023, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 343481.7, tmin=0.9715 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 279147.0, tmin=1.9465 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 252608.6, tmin=2.9347 d=8.00 min @ (0.00, 2.00, 0.00) sse = 251924.4, tmin=3.9347 d=4.00 min @ (1.00, -1.00, -1.00) sse = 250820.9, tmin=4.9390 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 250138.2, tmin=5.9497 d=1.00 min @ (0.00, 0.25, 0.00) sse = 250049.8, tmin=6.9631 d=0.50 min @ (0.00, 0.00, -0.12) sse = 250048.6, tmin=7.9871 tol=1.0e+00, sigma=0.5, host=compu, 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 7.99 min curvature mean = 0.014, std = 0.962 curvature mean = 0.010, std = 0.940 curvature mean = 0.011, std = 0.974 curvature mean = 0.005, std = 0.973 curvature mean = 0.009, std = 0.976 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.029, std = 0.296 curvature mean = 0.003, std = 0.067 curvature mean = 0.066, std = 0.343 curvature mean = 0.003, std = 0.080 curvature mean = 0.032, std = 0.529 curvature mean = 0.003, std = 0.086 curvature mean = 0.017, std = 0.670 curvature mean = 0.003, std = 0.089 curvature mean = 0.007, std = 0.778 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Wed Nov 18 17:14:30 EST 2015 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Wed Nov 18 17:14:32 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Nov 18 17:14:34 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1056 labels changed using aseg relabeling using gibbs priors... 000: 3103 changed, 134383 examined... 001: 682 changed, 13015 examined... 002: 173 changed, 3852 examined... 003: 54 changed, 1023 examined... 004: 21 changed, 325 examined... 005: 7 changed, 127 examined... 006: 6 changed, 38 examined... 007: 6 changed, 37 examined... 008: 1 changed, 21 examined... 009: 0 changed, 7 examined... 262 labels changed using aseg 000: 103 total segments, 59 labels (174 vertices) changed 001: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1314 vertices marked for relabeling... 1314 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 41 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Nov 18 17:15:15 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.90 3528 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 58 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 4 with 589 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 20 points - only 0.00% unknown mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.55 2842 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4910133.5, rms=9.91 001: dt: 0.5000, sse=5581897.0, rms=7.091 (0.000%) 002: dt: 0.5000, sse=5969936.5, rms=5.414 (0.000%) 003: dt: 0.5000, sse=6294036.0, rms=4.408 (0.000%) 004: dt: 0.5000, sse=6537145.5, rms=3.792 (0.000%) 005: dt: 0.5000, sse=6679090.0, rms=3.482 (0.000%) 006: dt: 0.5000, sse=6778039.0, rms=3.292 (0.000%) 007: dt: 0.5000, sse=6831903.5, rms=3.217 (0.000%) 008: dt: 0.5000, sse=6847970.5, rms=3.144 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6847041.0, rms=3.127 (0.000%) 010: dt: 0.2500, sse=4111519.8, rms=2.116 (0.000%) 011: dt: 0.2500, sse=3782389.5, rms=1.872 (0.000%) 012: dt: 0.2500, sse=3636471.2, rms=1.817 (0.000%) rms = 1.79, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3588702.2, rms=1.787 (0.000%) rms = 1.76, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3530796.0, rms=1.757 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 141 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 5 with 503 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown deleting segment 10 with 13 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown deleting segment 14 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 6 points - only 0.00% unknown mean border=83.8, 43 (10) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.3 (%26.3))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.39) mean absolute distance = 0.26 +- 0.38 3194 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4126274.5, rms=4.65 015: dt: 0.5000, sse=4428417.5, rms=2.790 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4903927.0, rms=2.784 (0.000%) 017: dt: 0.2500, sse=4116609.8, rms=1.714 (0.000%) 018: dt: 0.2500, sse=3986968.5, rms=1.519 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3878579.5, rms=1.482 (0.000%) rms = 1.44, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3831825.8, rms=1.441 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 519 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 47 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown mean border=86.2, 34 (5) missing vertices, mean dist -0.1 [0.3 (%71.9)->0.2 (%28.1))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.50) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3358 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4036701.0, rms=3.28 021: dt: 0.5000, sse=4342123.5, rms=2.455 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4076523.0, rms=1.751 (0.000%) 023: dt: 0.2500, sse=4000223.8, rms=1.417 (0.000%) 024: dt: 0.2500, sse=3971807.5, rms=1.332 (0.000%) rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.32, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3949862.0, rms=1.318 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 542 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 15 points - only 0.00% unknown mean border=87.0, 45 (4) missing vertices, mean dist -0.0 [0.2 (%56.3)->0.2 (%43.7))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=3965833.5, rms=1.63 rms = 1.67, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4030579.2, rms=1.226 (0.000%) 027: dt: 0.2500, sse=4210250.0, rms=1.000 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4211942.0, rms=0.998 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.1, 63 (63) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.5 (%100.0))] %19 local maxima, %48 large gradients and %29 min vals, 2536 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21210330.0, rms=26.92 001: dt: 0.5000, sse=16190595.0, rms=22.998 (0.000%) 002: dt: 0.5000, sse=12521362.0, rms=19.671 (0.000%) 003: dt: 0.5000, sse=9938165.0, rms=16.901 (0.000%) 004: dt: 0.5000, sse=8274347.5, rms=14.603 (0.000%) 005: dt: 0.5000, sse=7200233.0, rms=12.720 (0.000%) 006: dt: 0.5000, sse=6567840.5, rms=11.201 (0.000%) 007: dt: 0.5000, sse=6195436.0, rms=9.893 (0.000%) 008: dt: 0.5000, sse=5953478.5, rms=8.748 (0.000%) 009: dt: 0.5000, sse=5823097.5, rms=7.723 (0.000%) 010: dt: 0.5000, sse=5755740.0, rms=6.818 (0.000%) 011: dt: 0.5000, sse=5771526.0, rms=6.010 (0.000%) 012: dt: 0.5000, sse=5770032.5, rms=5.284 (0.000%) 013: dt: 0.5000, sse=5831664.5, rms=4.697 (0.000%) 014: dt: 0.5000, sse=5903816.5, rms=4.271 (0.000%) 015: dt: 0.5000, sse=5991542.0, rms=3.985 (0.000%) 016: dt: 0.5000, sse=6059026.0, rms=3.792 (0.000%) 017: dt: 0.5000, sse=6113671.0, rms=3.670 (0.000%) 018: dt: 0.5000, sse=6117787.5, rms=3.576 (0.000%) 019: dt: 0.5000, sse=6162662.5, rms=3.519 (0.000%) rms = 3.47, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6164091.5, rms=3.470 (0.000%) 021: dt: 0.2500, sse=4430887.5, rms=2.863 (0.000%) 022: dt: 0.2500, sse=4274107.5, rms=2.709 (0.000%) rms = 2.69, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4183480.0, rms=2.687 (0.000%) 024: dt: 0.1250, sse=4032809.5, rms=2.613 (0.000%) rms = 2.61, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4015818.5, rms=2.607 (0.000%) positioning took 2.6 minutes mean border=57.7, 970 (29) missing vertices, mean dist 0.2 [0.2 (%45.0)->0.6 (%55.0))] %39 local maxima, %33 large gradients and %23 min vals, 968 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4649037.5, rms=4.74 026: dt: 0.5000, sse=4787437.5, rms=3.735 (0.000%) 027: dt: 0.5000, sse=6092889.0, rms=3.602 (0.000%) rms = 3.61, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5127987.5, rms=3.032 (0.000%) 029: dt: 0.2500, sse=4703083.0, rms=2.790 (0.000%) 030: dt: 0.2500, sse=4684753.0, rms=2.723 (0.000%) rms = 2.70, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4651405.5, rms=2.696 (0.000%) 032: dt: 0.1250, sse=4534031.5, rms=2.606 (0.000%) rms = 2.59, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4528865.5, rms=2.588 (0.000%) positioning took 0.9 minutes mean border=56.1, 1194 (26) missing vertices, mean dist 0.1 [0.2 (%38.2)->0.4 (%61.8))] %55 local maxima, %17 large gradients and %23 min vals, 1145 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4680251.5, rms=3.42 rms = 3.38, time step reduction 1 of 3 to 0.250... 034: dt: 0.5000, sse=4928660.0, rms=3.378 (0.000%) 035: dt: 0.2500, sse=4913630.5, rms=2.724 (0.000%) 036: dt: 0.2500, sse=4936017.0, rms=2.582 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4913444.0, rms=2.578 (0.000%) 038: dt: 0.1250, sse=4789696.0, rms=2.449 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4791635.5, rms=2.431 (0.000%) positioning took 0.6 minutes mean border=55.3, 2550 (26) missing vertices, mean dist 0.0 [0.2 (%44.6)->0.3 (%55.4))] %58 local maxima, %14 large gradients and %22 min vals, 909 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4815846.5, rms=2.61 rms = 3.00, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4723632.5, rms=2.451 (0.000%) rms = 2.40, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=4868891.5, rms=2.403 (0.000%) 042: dt: 0.1250, sse=4780392.0, rms=2.348 (0.000%) rms = 2.33, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4807761.0, rms=2.330 (0.000%) positioning took 0.5 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.06-->7.83) (max @ vno 48431 --> 47310) face area 0.41 +- 0.32 (0.00-->9.57) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 614:1142 truncations. 27931 vertices at 0 distance 88109 vertices at 1 distance 84334 vertices at 2 distance 38319 vertices at 3 distance 12427 vertices at 4 distance 3739 vertices at 5 distance 1252 vertices at 6 distance 382 vertices at 7 distance 138 vertices at 8 distance 63 vertices at 9 distance 59 vertices at 10 distance 39 vertices at 11 distance 26 vertices at 12 distance 23 vertices at 13 distance 16 vertices at 14 distance 21 vertices at 15 distance 12 vertices at 16 distance 10 vertices at 17 distance 8 vertices at 18 distance 14 vertices at 19 distance 12 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.thickness positioning took 11.1 minutes #-------------------------------------------- #@# Surf Volume lh Wed Nov 18 17:26:19 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Make White Surf rh Wed Nov 18 17:26:19 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.73 +- 0.91 3383 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=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.8, 20 (20) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.34) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2632 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5030457.5, rms=9.93 001: dt: 0.5000, sse=5796978.0, rms=7.147 (0.000%) 002: dt: 0.5000, sse=6204708.5, rms=5.513 (0.000%) 003: dt: 0.5000, sse=6478530.5, rms=4.508 (0.000%) 004: dt: 0.5000, sse=6741257.0, rms=3.876 (0.000%) 005: dt: 0.5000, sse=6849746.5, rms=3.534 (0.000%) 006: dt: 0.5000, sse=6977133.5, rms=3.321 (0.000%) 007: dt: 0.5000, sse=7007491.0, rms=3.232 (0.000%) 008: dt: 0.5000, sse=7045294.5, rms=3.150 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7019629.5, rms=3.130 (0.000%) 010: dt: 0.2500, sse=4337829.5, rms=2.129 (0.000%) 011: dt: 0.2500, sse=4012794.8, rms=1.885 (0.000%) 012: dt: 0.2500, sse=3854614.8, rms=1.833 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3814733.5, rms=1.803 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3753020.5, rms=1.766 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.7, 50 (5) missing vertices, mean dist -0.2 [0.4 (%72.0)->0.3 (%28.0))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.50) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.38 3705 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4290996.5, rms=4.34 015: dt: 0.5000, sse=4682878.0, rms=2.732 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4366005.0, rms=2.170 (0.000%) 017: dt: 0.2500, sse=4221162.5, rms=1.753 (0.000%) 018: dt: 0.2500, sse=4126458.0, rms=1.580 (0.000%) 019: dt: 0.2500, sse=4073992.0, rms=1.524 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4057223.8, rms=1.501 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4011195.2, rms=1.471 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.0, 37 (3) missing vertices, mean dist -0.1 [0.3 (%71.2)->0.2 (%28.8))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 (0.10-->4.55) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.89) mean absolute distance = 0.22 +- 0.31 2829 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4209697.5, rms=3.26 022: dt: 0.5000, sse=4551017.0, rms=2.427 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4264880.0, rms=1.765 (0.000%) 024: dt: 0.2500, sse=4191594.2, rms=1.437 (0.000%) 025: dt: 0.2500, sse=4152948.5, rms=1.352 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... rms = 1.34, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4130497.8, rms=1.336 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.8, 45 (2) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4145720.2, rms=1.68 rms = 1.69, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4214452.0, rms=1.265 (0.000%) 028: dt: 0.2500, sse=4405054.5, rms=1.016 (0.000%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4404326.0, rms=1.012 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 14 non-cortical segments detected only using segment with 2295 vertices erasing segment 1 (vno[0] = 45502) erasing segment 2 (vno[0] = 83943) erasing segment 3 (vno[0] = 94873) erasing segment 4 (vno[0] = 94892) erasing segment 5 (vno[0] = 94904) erasing segment 6 (vno[0] = 95880) erasing segment 7 (vno[0] = 96851) erasing segment 8 (vno[0] = 99617) erasing segment 9 (vno[0] = 101371) erasing segment 10 (vno[0] = 102196) erasing segment 11 (vno[0] = 102270) erasing segment 12 (vno[0] = 103084) erasing segment 13 (vno[0] = 103867) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv writing smoothed area to rh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.86) refinement took 5.3 minutes #-------------------------------------------- #@# Smooth2 rh Wed Nov 18 17:31:40 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Wed Nov 18 17:31:44 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 45.8 mm, total surface area = 81849 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.118 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 148 vertices thresholded to be in k1 ~ [-0.33 0.35], k2 ~ [-0.11 0.09] total integrated curvature = 0.565*4pi (7.094) --> 0 handles ICI = 1.4, FI = 8.6, variation=148.924 113 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 133 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats rh Wed Nov 18 17:33:47 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 245 ] Gb_filter = 0 WARN: S lookup min: -0.817811 WARN: S explicit min: 0.000000 vertex = 427 #-------------------------------------------- #@# Sphere rh Wed Nov 18 17:33:54 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %20.14 pass 1: epoch 2 of 3 starting distance error %20.07 unfolding complete - removing small folds... starting distance error %19.94 removing remaining folds... final distance error %19.96 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.84 hours #-------------------------------------------- #@# Surf Reg rh Wed Nov 18 18:24:01 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_register -curv ../surf/rh.sphere /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, 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 = 0.591 curvature mean = 0.043, std = 0.931 curvature mean = 0.021, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 16.00) sse = 361095.2, tmin=1.0658 d=32.00 min @ (0.00, 8.00, 0.00) sse = 327242.8, tmin=2.1312 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 305767.9, tmin=3.2033 d=4.00 min @ (1.00, 0.00, 1.00) sse = 304760.8, tmin=5.4243 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 304666.7, tmin=6.5495 d=1.00 min @ (0.25, 0.25, 0.00) sse = 304561.9, tmin=7.6573 d=0.50 min @ (-0.12, 0.00, -0.12) sse = 304536.6, tmin=8.7742 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.77 min curvature mean = 0.029, std = 0.960 curvature mean = 0.007, std = 0.938 curvature mean = 0.026, std = 0.969 curvature mean = 0.004, std = 0.971 curvature mean = 0.024, std = 0.969 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.026, std = 0.388 curvature mean = 0.006, std = 0.069 curvature mean = 0.048, std = 0.263 curvature mean = 0.006, std = 0.083 curvature mean = 0.024, std = 0.410 curvature mean = 0.007, std = 0.089 curvature mean = 0.014, std = 0.517 curvature mean = 0.007, std = 0.091 curvature mean = 0.005, std = 0.613 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Wed Nov 18 18:50:00 EST 2015 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Wed Nov 18 18:50:02 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Wed Nov 18 18:50:04 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1202 labels changed using aseg relabeling using gibbs priors... 000: 3050 changed, 134806 examined... 001: 715 changed, 13277 examined... 002: 174 changed, 3906 examined... 003: 75 changed, 1057 examined... 004: 34 changed, 433 examined... 005: 17 changed, 206 examined... 006: 8 changed, 100 examined... 007: 4 changed, 41 examined... 008: 4 changed, 26 examined... 009: 1 changed, 22 examined... 010: 1 changed, 8 examined... 011: 2 changed, 8 examined... 012: 1 changed, 10 examined... 013: 0 changed, 7 examined... 159 labels changed using aseg 000: 95 total segments, 57 labels (335 vertices) changed 001: 41 total segments, 3 labels (4 vertices) changed 002: 38 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... 1082 vertices marked for relabeling... 1082 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 41 seconds. #-------------------------------------------- #@# Make Pial Surf rh Wed Nov 18 18:50:45 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.73 +- 0.92 3430 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 384 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=80.8, 25 (24) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.34) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2670 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5040671.0, rms=9.92 001: dt: 0.5000, sse=5813598.0, rms=7.141 (0.000%) 002: dt: 0.5000, sse=6224298.5, rms=5.510 (0.000%) 003: dt: 0.5000, sse=6498853.5, rms=4.506 (0.000%) 004: dt: 0.5000, sse=6762585.5, rms=3.875 (0.000%) 005: dt: 0.5000, sse=6869478.0, rms=3.534 (0.000%) 006: dt: 0.5000, sse=6998033.0, rms=3.321 (0.000%) 007: dt: 0.5000, sse=7028486.0, rms=3.233 (0.000%) 008: dt: 0.5000, sse=7066930.0, rms=3.151 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7039925.0, rms=3.131 (0.000%) 010: dt: 0.2500, sse=4354474.0, rms=2.132 (0.000%) 011: dt: 0.2500, sse=4028360.5, rms=1.889 (0.000%) 012: dt: 0.2500, sse=3870135.0, rms=1.837 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3829512.0, rms=1.807 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3767567.2, rms=1.770 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 299 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 22 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown mean border=83.7, 54 (6) missing vertices, mean dist -0.2 [0.4 (%71.9)->0.3 (%28.1))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.50) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.39 3758 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4309256.5, rms=4.33 015: dt: 0.5000, sse=4700820.5, rms=2.732 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4385123.5, rms=2.172 (0.000%) 017: dt: 0.2500, sse=4242888.0, rms=1.755 (0.000%) 018: dt: 0.2500, sse=4147145.0, rms=1.583 (0.000%) 019: dt: 0.2500, sse=4094185.8, rms=1.528 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4076906.5, rms=1.504 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4030592.8, rms=1.474 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 303 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=86.0, 38 (3) missing vertices, mean dist -0.1 [0.3 (%71.1)->0.2 (%28.9))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 (0.10-->4.55) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.89) mean absolute distance = 0.22 +- 0.32 2871 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4229315.5, rms=3.25 022: dt: 0.5000, sse=4573934.5, rms=2.426 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4286142.5, rms=1.767 (0.000%) 024: dt: 0.2500, sse=4210874.5, rms=1.440 (0.000%) 025: dt: 0.2500, sse=4174444.5, rms=1.356 (0.000%) rms = 1.36, time step reduction 2 of 3 to 0.125... rms = 1.34, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4151896.8, rms=1.340 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 311 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=86.8, 47 (2) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4167169.2, rms=1.69 rms = 1.69, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4237478.0, rms=1.268 (0.000%) 028: dt: 0.2500, sse=4432497.0, rms=1.019 (0.000%) rms = 1.03, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4431764.5, rms=1.016 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=60.2, 52 (52) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.6 (%100.0))] %19 local maxima, %44 large gradients and %32 min vals, 2330 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21095174.0, rms=26.68 001: dt: 0.5000, sse=16219415.0, rms=22.858 (0.000%) 002: dt: 0.5000, sse=12634789.0, rms=19.614 (0.000%) 003: dt: 0.5000, sse=10127611.0, rms=16.925 (0.000%) 004: dt: 0.5000, sse=8511865.0, rms=14.699 (0.000%) 005: dt: 0.5000, sse=7457957.5, rms=12.869 (0.000%) 006: dt: 0.5000, sse=6784133.0, rms=11.402 (0.000%) 007: dt: 0.5000, sse=6385647.5, rms=10.144 (0.000%) 008: dt: 0.5000, sse=6107506.0, rms=9.027 (0.000%) 009: dt: 0.5000, sse=5971715.0, rms=7.991 (0.000%) 010: dt: 0.5000, sse=5883049.0, rms=7.059 (0.000%) 011: dt: 0.5000, sse=5875117.5, rms=6.211 (0.000%) 012: dt: 0.5000, sse=5878926.0, rms=5.469 (0.000%) 013: dt: 0.5000, sse=5950857.0, rms=4.853 (0.000%) 014: dt: 0.5000, sse=6024235.5, rms=4.415 (0.000%) 015: dt: 0.5000, sse=6134776.5, rms=4.094 (0.000%) 016: dt: 0.5000, sse=6184613.5, rms=3.893 (0.000%) 017: dt: 0.5000, sse=6226774.5, rms=3.746 (0.000%) 018: dt: 0.5000, sse=6247221.0, rms=3.669 (0.000%) 019: dt: 0.5000, sse=6298535.5, rms=3.597 (0.000%) rms = 3.56, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6292106.0, rms=3.561 (0.000%) 021: dt: 0.2500, sse=4602540.5, rms=2.967 (0.000%) 022: dt: 0.2500, sse=4443622.5, rms=2.815 (0.000%) rms = 2.79, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4347487.5, rms=2.789 (0.000%) 024: dt: 0.1250, sse=4178397.2, rms=2.706 (0.000%) rms = 2.70, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4153944.8, rms=2.698 (0.000%) positioning took 2.6 minutes mean border=58.0, 1075 (3) missing vertices, mean dist 0.2 [0.2 (%44.5)->0.6 (%55.5))] %38 local maxima, %31 large gradients and %25 min vals, 861 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4762497.5, rms=4.68 026: dt: 0.5000, sse=4969183.5, rms=3.783 (0.000%) 027: dt: 0.5000, sse=6246533.0, rms=3.640 (0.000%) rms = 3.64, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=6107095.5, rms=3.635 (0.000%) 029: dt: 0.2500, sse=5066130.5, rms=2.924 (0.000%) 030: dt: 0.2500, sse=4962338.0, rms=2.729 (0.000%) rms = 2.72, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4899494.0, rms=2.721 (0.000%) 032: dt: 0.1250, sse=4743177.5, rms=2.613 (0.000%) rms = 2.60, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4731522.5, rms=2.598 (0.000%) positioning took 0.9 minutes mean border=56.5, 1297 (2) missing vertices, mean dist 0.1 [0.2 (%39.1)->0.4 (%60.9))] %52 local maxima, %18 large gradients and %25 min vals, 965 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4869240.0, rms=3.34 rms = 3.42, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4704507.0, rms=2.982 (0.000%) 035: dt: 0.2500, sse=4726097.0, rms=2.761 (0.000%) 036: dt: 0.2500, sse=4896541.5, rms=2.690 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4960427.5, rms=2.668 (0.000%) 038: dt: 0.1250, sse=4843940.5, rms=2.586 (0.000%) rms = 2.57, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4865271.5, rms=2.570 (0.000%) positioning took 0.7 minutes mean border=55.8, 2773 (2) missing vertices, mean dist 0.1 [0.2 (%44.5)->0.3 (%55.5))] %55 local maxima, %14 large gradients and %25 min vals, 843 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4889507.0, rms=2.76 rms = 3.10, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4818572.5, rms=2.609 (0.000%) 041: dt: 0.2500, sse=5004985.5, rms=2.554 (0.000%) rms = 2.53, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5068982.0, rms=2.535 (0.000%) 043: dt: 0.1250, sse=4985673.0, rms=2.457 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5013903.0, rms=2.440 (0.000%) positioning took 0.6 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area.pial vertex spacing 1.01 +- 0.44 (0.04-->6.99) (max @ vno 101451 --> 134658) face area 0.40 +- 0.31 (0.00-->4.95) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 784:1305 truncations. 25877 vertices at 0 distance 84621 vertices at 1 distance 85363 vertices at 2 distance 41293 vertices at 3 distance 14079 vertices at 4 distance 4337 vertices at 5 distance 1349 vertices at 6 distance 484 vertices at 7 distance 202 vertices at 8 distance 107 vertices at 9 distance 64 vertices at 10 distance 54 vertices at 11 distance 47 vertices at 12 distance 40 vertices at 13 distance 26 vertices at 14 distance 22 vertices at 15 distance 11 vertices at 16 distance 10 vertices at 17 distance 20 vertices at 18 distance 9 vertices at 19 distance 3 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.thickness positioning took 11.3 minutes #-------------------------------------------- #@# Surf Volume rh Wed Nov 18 19:02:04 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Wed Nov 18 19:02:05 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.04-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 602 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=compu, 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 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=compu, 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=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [92.20 173.80], gm=133.00+-13.60, and vertices in regions > 126.2 14552 surface locations found to contain inconsistent values (14297 in, 255 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=472305.5, rms=0.21 001: dt: 0.5000, sse=444260.5, rms=0.205 (0.000%) 002: dt: 0.5000, sse=421809.5, rms=0.194 (0.000%) 003: dt: 0.5000, sse=407687.8, rms=0.185 (0.000%) 004: dt: 0.5000, sse=396863.3, rms=0.176 (0.000%) 005: dt: 0.5000, sse=388843.9, rms=0.168 (0.000%) 006: dt: 0.5000, sse=381906.5, rms=0.160 (0.000%) 007: dt: 0.5000, sse=376432.4, rms=0.154 (0.000%) 008: dt: 0.5000, sse=371905.8, rms=0.148 (0.000%) 009: dt: 0.5000, sse=367695.6, rms=0.142 (0.000%) 010: dt: 0.5000, sse=364125.8, rms=0.137 (0.000%) 011: dt: 0.5000, sse=361083.9, rms=0.133 (0.000%) 012: dt: 0.5000, sse=358422.6, rms=0.129 (0.000%) 013: dt: 0.5000, sse=356064.7, rms=0.125 (0.000%) 014: dt: 0.5000, sse=353791.0, rms=0.122 (0.000%) 015: dt: 0.5000, sse=351691.0, rms=0.119 (0.000%) 016: dt: 0.5000, sse=349777.4, rms=0.117 (0.000%) 017: dt: 0.5000, sse=348005.8, rms=0.115 (0.000%) 018: dt: 0.5000, sse=346400.8, rms=0.113 (0.000%) 019: dt: 0.5000, sse=344816.1, rms=0.112 (0.000%) 020: dt: 0.5000, sse=343302.3, rms=0.110 (0.000%) 021: dt: 0.5000, sse=341740.5, rms=0.109 (0.000%) 022: dt: 0.5000, sse=340381.9, rms=0.108 (0.000%) 023: dt: 0.5000, sse=339083.9, rms=0.108 (0.000%) 024: dt: 0.5000, sse=337783.5, rms=0.107 (0.000%) 025: dt: 0.5000, sse=336731.9, rms=0.107 (0.000%) 026: dt: 0.5000, sse=335736.1, rms=0.106 (0.000%) 027: dt: 0.5000, sse=334848.0, rms=0.106 (0.000%) 028: dt: 0.5000, sse=333960.9, rms=0.106 (0.000%) 029: dt: 0.5000, sse=332960.8, rms=0.106 (0.000%) 030: dt: 0.5000, sse=332064.1, rms=0.106 (0.000%) positioning took 3.5 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 2866 surface locations found to contain inconsistent values (2659 in, 207 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=33232.4, rms=0.06 031: dt: 0.5000, sse=33124.9, rms=0.061 (0.000%) 032: dt: 0.5000, sse=33098.5, rms=0.057 (0.000%) 033: dt: 0.5000, sse=33131.1, rms=0.054 (0.000%) 034: dt: 0.5000, sse=33163.9, rms=0.052 (0.000%) 035: dt: 0.5000, sse=33191.3, rms=0.049 (0.000%) 036: dt: 0.5000, sse=33245.7, rms=0.047 (0.000%) 037: dt: 0.5000, sse=33280.5, rms=0.045 (0.000%) 038: dt: 0.5000, sse=33320.0, rms=0.044 (0.000%) 039: dt: 0.5000, sse=33365.9, rms=0.042 (0.000%) 040: dt: 0.5000, sse=33402.3, rms=0.040 (0.000%) 041: dt: 0.5000, sse=33440.8, rms=0.039 (0.000%) 042: dt: 0.5000, sse=33469.8, rms=0.037 (0.000%) 043: dt: 0.5000, sse=33489.4, rms=0.036 (0.000%) 044: dt: 0.5000, sse=33524.6, rms=0.035 (0.000%) 045: dt: 0.5000, sse=33544.5, rms=0.034 (0.000%) 046: dt: 0.5000, sse=33567.3, rms=0.032 (0.000%) 047: dt: 0.5000, sse=33609.8, rms=0.031 (0.000%) 048: dt: 0.5000, sse=33634.9, rms=0.030 (0.000%) 049: dt: 0.5000, sse=33649.1, rms=0.029 (0.000%) 050: dt: 0.5000, sse=33673.5, rms=0.029 (0.000%) 051: dt: 0.5000, sse=33697.0, rms=0.028 (0.000%) 052: dt: 0.5000, sse=33719.1, rms=0.027 (0.000%) 053: dt: 0.5000, sse=33735.4, rms=0.026 (0.000%) 054: dt: 0.5000, sse=33745.0, rms=0.026 (0.000%) 055: dt: 0.5000, sse=33772.2, rms=0.025 (0.000%) 056: dt: 0.5000, sse=33776.5, rms=0.024 (0.000%) 057: dt: 0.5000, sse=33785.8, rms=0.024 (0.000%) 058: dt: 0.5000, sse=33795.3, rms=0.023 (0.000%) 059: dt: 0.5000, sse=33814.4, rms=0.023 (0.000%) 060: dt: 0.5000, sse=33814.1, rms=0.022 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 727 surface locations found to contain inconsistent values (529 in, 198 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3440.5, rms=0.02 061: dt: 0.5000, sse=3437.9, rms=0.022 (0.000%) 062: dt: 0.5000, sse=3437.1, rms=0.021 (0.000%) 063: dt: 0.5000, sse=3436.7, rms=0.020 (0.000%) 064: dt: 0.5000, sse=3436.0, rms=0.019 (0.000%) 065: dt: 0.5000, sse=3435.9, rms=0.019 (0.000%) 066: dt: 0.5000, sse=3436.4, rms=0.018 (0.000%) 067: dt: 0.5000, sse=3434.9, rms=0.018 (0.000%) 068: dt: 0.5000, sse=3434.3, rms=0.017 (0.000%) 069: dt: 0.5000, sse=3433.9, rms=0.017 (0.000%) 070: dt: 0.5000, sse=3434.3, rms=0.017 (0.000%) 071: dt: 0.5000, sse=3434.3, rms=0.016 (0.000%) 072: dt: 0.5000, sse=3434.1, rms=0.016 (0.000%) 073: dt: 0.5000, sse=3434.4, rms=0.016 (0.000%) 074: dt: 0.5000, sse=3434.1, rms=0.016 (0.000%) 075: dt: 0.5000, sse=3434.8, rms=0.016 (0.000%) 076: dt: 0.5000, sse=3434.8, rms=0.015 (0.000%) 077: dt: 0.5000, sse=3435.2, rms=0.015 (0.000%) 078: dt: 0.5000, sse=3435.1, rms=0.015 (0.000%) 079: dt: 0.5000, sse=3435.0, rms=0.015 (0.000%) 080: dt: 0.5000, sse=3435.4, rms=0.015 (0.000%) 081: dt: 0.5000, sse=3435.3, rms=0.015 (0.000%) 082: dt: 0.5000, sse=3435.1, rms=0.015 (0.000%) 083: dt: 0.5000, sse=3435.8, rms=0.015 (0.000%) 084: dt: 0.5000, sse=3435.8, rms=0.014 (0.000%) 085: dt: 0.5000, sse=3436.1, rms=0.014 (0.000%) 086: dt: 0.5000, sse=3436.3, rms=0.014 (0.000%) 087: dt: 0.5000, sse=3436.6, rms=0.014 (0.000%) 088: dt: 0.5000, sse=3436.4, rms=0.014 (0.000%) 089: dt: 0.5000, sse=3436.2, rms=0.014 (0.000%) 090: dt: 0.5000, sse=3436.9, rms=0.014 (0.000%) positioning took 3.4 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 262 surface locations found to contain inconsistent values (63 in, 199 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=366.2, rms=0.01 091: dt: 0.5000, sse=366.2, rms=0.014 (0.000%) 092: dt: 0.5000, sse=365.8, rms=0.014 (0.000%) 093: dt: 0.5000, sse=365.5, rms=0.014 (0.000%) 094: dt: 0.5000, sse=365.3, rms=0.014 (0.000%) 095: dt: 0.5000, sse=365.2, rms=0.014 (0.000%) 096: dt: 0.5000, sse=365.1, rms=0.014 (0.000%) 097: dt: 0.5000, sse=365.0, rms=0.014 (0.000%) 098: dt: 0.5000, sse=364.9, rms=0.014 (0.000%) 099: dt: 0.5000, sse=364.9, rms=0.014 (0.000%) 100: dt: 0.5000, sse=364.8, rms=0.014 (0.000%) 101: dt: 0.5000, sse=364.8, rms=0.013 (0.000%) 102: dt: 0.5000, sse=364.7, rms=0.013 (0.000%) 103: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 104: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 105: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 106: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 107: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 108: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 109: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 110: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 111: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 112: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 113: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 114: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 115: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 116: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 117: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 118: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 119: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 120: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) positioning took 3.4 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area.pial vertex spacing 1.00 +- 0.43 (0.04-->8.03) (max @ vno 92642 --> 92643) face area 0.39 +- 0.30 (0.00-->10.95) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 600:981 truncations. 28508 vertices at 0 distance 88163 vertices at 1 distance 83783 vertices at 2 distance 38396 vertices at 3 distance 12342 vertices at 4 distance 3767 vertices at 5 distance 1244 vertices at 6 distance 425 vertices at 7 distance 141 vertices at 8 distance 72 vertices at 9 distance 43 vertices at 10 distance 40 vertices at 11 distance 20 vertices at 12 distance 16 vertices at 13 distance 12 vertices at 14 distance 13 vertices at 15 distance 11 vertices at 16 distance 7 vertices at 17 distance 8 vertices at 18 distance 8 vertices at 19 distance 15 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.thickness positioning took 16.9 minutes /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 380 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.00, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.02, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=compu, 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 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.00, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=compu, 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=4390928.5, rms=0.00 rms = 1.02, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 13521 surface locations found to contain inconsistent values (13344 in, 177 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=489117.8, rms=0.21 001: dt: 0.5000, sse=457629.3, rms=0.199 (0.000%) 002: dt: 0.5000, sse=434001.4, rms=0.188 (0.000%) 003: dt: 0.5000, sse=419565.2, rms=0.180 (0.000%) 004: dt: 0.5000, sse=407977.9, rms=0.171 (0.000%) 005: dt: 0.5000, sse=399536.7, rms=0.164 (0.000%) 006: dt: 0.5000, sse=392343.6, rms=0.157 (0.000%) 007: dt: 0.5000, sse=386541.2, rms=0.151 (0.000%) 008: dt: 0.5000, sse=381371.6, rms=0.145 (0.000%) 009: dt: 0.5000, sse=377076.8, rms=0.140 (0.000%) 010: dt: 0.5000, sse=373152.3, rms=0.135 (0.000%) 011: dt: 0.5000, sse=369700.8, rms=0.131 (0.000%) 012: dt: 0.5000, sse=366605.1, rms=0.128 (0.000%) 013: dt: 0.5000, sse=363736.5, rms=0.124 (0.000%) 014: dt: 0.5000, sse=360975.4, rms=0.121 (0.000%) 015: dt: 0.5000, sse=358703.4, rms=0.118 (0.000%) 016: dt: 0.5000, sse=356400.9, rms=0.116 (0.000%) 017: dt: 0.5000, sse=354514.8, rms=0.114 (0.000%) 018: dt: 0.5000, sse=352853.1, rms=0.112 (0.000%) 019: dt: 0.5000, sse=350970.0, rms=0.110 (0.000%) 020: dt: 0.5000, sse=349133.9, rms=0.109 (0.000%) 021: dt: 0.5000, sse=347413.0, rms=0.107 (0.000%) 022: dt: 0.5000, sse=346105.8, rms=0.106 (0.000%) 023: dt: 0.5000, sse=344796.4, rms=0.105 (0.000%) 024: dt: 0.5000, sse=343241.6, rms=0.104 (0.000%) 025: dt: 0.5000, sse=342058.9, rms=0.104 (0.000%) 026: dt: 0.5000, sse=340694.0, rms=0.103 (0.000%) 027: dt: 0.5000, sse=339543.8, rms=0.102 (0.000%) 028: dt: 0.5000, sse=338511.8, rms=0.102 (0.000%) 029: dt: 0.5000, sse=337478.8, rms=0.102 (0.000%) 030: dt: 0.5000, sse=336519.2, rms=0.102 (0.000%) positioning took 3.4 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 4103 surface locations found to contain inconsistent values (3938 in, 165 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=33749.7, rms=0.07 031: dt: 0.5000, sse=33605.8, rms=0.065 (0.000%) 032: dt: 0.5000, sse=33624.2, rms=0.061 (0.000%) 033: dt: 0.5000, sse=33699.0, rms=0.057 (0.000%) 034: dt: 0.5000, sse=33759.0, rms=0.054 (0.000%) 035: dt: 0.5000, sse=33808.3, rms=0.052 (0.000%) 036: dt: 0.5000, sse=33860.1, rms=0.049 (0.000%) 037: dt: 0.5000, sse=33900.6, rms=0.047 (0.000%) 038: dt: 0.5000, sse=33953.3, rms=0.045 (0.000%) 039: dt: 0.5000, sse=33991.1, rms=0.043 (0.000%) 040: dt: 0.5000, sse=34026.4, rms=0.041 (0.000%) 041: dt: 0.5000, sse=34062.4, rms=0.040 (0.000%) 042: dt: 0.5000, sse=34083.4, rms=0.038 (0.000%) 043: dt: 0.5000, sse=34114.1, rms=0.037 (0.000%) 044: dt: 0.5000, sse=34145.6, rms=0.035 (0.000%) 045: dt: 0.5000, sse=34177.8, rms=0.034 (0.000%) 046: dt: 0.5000, sse=34198.5, rms=0.033 (0.000%) 047: dt: 0.5000, sse=34226.3, rms=0.031 (0.000%) 048: dt: 0.5000, sse=34249.0, rms=0.030 (0.000%) 049: dt: 0.5000, sse=34279.6, rms=0.029 (0.000%) 050: dt: 0.5000, sse=34301.8, rms=0.029 (0.000%) 051: dt: 0.5000, sse=34317.2, rms=0.028 (0.000%) 052: dt: 0.5000, sse=34330.8, rms=0.027 (0.000%) 053: dt: 0.5000, sse=34351.1, rms=0.026 (0.000%) 054: dt: 0.5000, sse=34369.1, rms=0.026 (0.000%) 055: dt: 0.5000, sse=34373.8, rms=0.025 (0.000%) 056: dt: 0.5000, sse=34383.5, rms=0.024 (0.000%) 057: dt: 0.5000, sse=34392.1, rms=0.024 (0.000%) 058: dt: 0.5000, sse=34404.5, rms=0.023 (0.000%) 059: dt: 0.5000, sse=34414.8, rms=0.023 (0.000%) 060: dt: 0.5000, sse=34432.2, rms=0.023 (0.000%) positioning took 3.4 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 755 surface locations found to contain inconsistent values (597 in, 158 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3496.5, rms=0.02 061: dt: 0.5000, sse=3495.3, rms=0.021 (0.000%) 062: dt: 0.5000, sse=3496.2, rms=0.020 (0.000%) 063: dt: 0.5000, sse=3497.6, rms=0.019 (0.000%) 064: dt: 0.5000, sse=3499.3, rms=0.019 (0.000%) 065: dt: 0.5000, sse=3500.1, rms=0.019 (0.000%) 066: dt: 0.5000, sse=3500.1, rms=0.018 (0.000%) 067: dt: 0.5000, sse=3499.9, rms=0.018 (0.000%) 068: dt: 0.5000, sse=3500.0, rms=0.018 (0.000%) 069: dt: 0.5000, sse=3499.6, rms=0.017 (0.000%) 070: dt: 0.5000, sse=3500.5, rms=0.017 (0.000%) 071: dt: 0.5000, sse=3499.0, rms=0.017 (0.000%) 072: dt: 0.5000, sse=3499.3, rms=0.017 (0.000%) 073: dt: 0.5000, sse=3499.9, rms=0.017 (0.000%) 074: dt: 0.5000, sse=3500.2, rms=0.016 (0.000%) 075: dt: 0.5000, sse=3499.7, rms=0.016 (0.000%) 076: dt: 0.5000, sse=3499.8, rms=0.016 (0.000%) 077: dt: 0.5000, sse=3500.0, rms=0.016 (0.000%) 078: dt: 0.5000, sse=3500.3, rms=0.016 (0.000%) 079: dt: 0.5000, sse=3500.5, rms=0.016 (0.000%) 080: dt: 0.5000, sse=3500.7, rms=0.016 (0.000%) 081: dt: 0.5000, sse=3501.3, rms=0.016 (0.000%) 082: dt: 0.5000, sse=3502.6, rms=0.016 (0.000%) 083: dt: 0.5000, sse=3502.9, rms=0.016 (0.000%) 084: dt: 0.5000, sse=3503.0, rms=0.016 (0.000%) 085: dt: 0.5000, sse=3503.2, rms=0.016 (0.000%) 086: dt: 0.5000, sse=3503.1, rms=0.016 (0.000%) 087: dt: 0.5000, sse=3504.2, rms=0.016 (0.000%) 088: dt: 0.5000, sse=3504.4, rms=0.016 (0.000%) 089: dt: 0.5000, sse=3504.1, rms=0.016 (0.000%) 090: dt: 0.5000, sse=3504.0, rms=0.016 (0.000%) positioning took 3.2 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 228 surface locations found to contain inconsistent values (75 in, 153 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=377.5, rms=0.02 091: dt: 0.5000, sse=378.6, rms=0.016 (0.000%) 092: dt: 0.5000, sse=378.0, rms=0.015 (0.000%) 093: dt: 0.5000, sse=378.4, rms=0.015 (0.000%) 094: dt: 0.5000, sse=377.9, rms=0.015 (0.000%) 095: dt: 0.5000, sse=377.5, rms=0.015 (0.000%) 096: dt: 0.5000, sse=377.1, rms=0.015 (0.000%) 097: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 098: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 099: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 100: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 101: dt: 0.5000, sse=377.6, rms=0.015 (0.000%) 102: dt: 0.5000, sse=377.9, rms=0.015 (0.000%) 103: dt: 0.5000, sse=377.5, rms=0.015 (0.000%) 104: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 105: dt: 0.5000, sse=377.4, rms=0.015 (0.000%) 106: dt: 0.5000, sse=377.3, rms=0.015 (0.000%) 107: dt: 0.5000, sse=377.1, rms=0.015 (0.000%) 108: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 109: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 110: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 111: dt: 0.5000, sse=377.7, rms=0.015 (0.000%) 112: dt: 0.5000, sse=377.6, rms=0.015 (0.000%) 113: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 114: dt: 0.5000, sse=376.9, rms=0.015 (0.000%) 115: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 116: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 117: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 118: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 119: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 120: dt: 0.5000, sse=376.7, rms=0.015 (0.000%) positioning took 3.2 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area.pial vertex spacing 0.99 +- 0.43 (0.05-->7.35) (max @ vno 101451 --> 134658) face area 0.39 +- 0.30 (0.00-->5.06) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 778:1103 truncations. 27462 vertices at 0 distance 86290 vertices at 1 distance 84109 vertices at 2 distance 40276 vertices at 3 distance 13389 vertices at 4 distance 4172 vertices at 5 distance 1366 vertices at 6 distance 465 vertices at 7 distance 229 vertices at 8 distance 115 vertices at 9 distance 58 vertices at 10 distance 37 vertices at 11 distance 51 vertices at 12 distance 49 vertices at 13 distance 21 vertices at 14 distance 8 vertices at 15 distance 13 vertices at 16 distance 9 vertices at 17 distance 7 vertices at 18 distance 7 vertices at 19 distance 3 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.thickness positioning took 16.8 minutes #-------------------------------------------- #@# Surf Volume lh Wed Nov 18 19:35:59 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Surf Volume rh Wed Nov 18 19:36:00 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Wed Nov 18 19:36:00 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1584 1096 2875 2.489 0.530 0.114 0.032 12 2.2 bankssts 789 507 1495 2.661 0.477 0.152 0.044 14 1.6 caudalanteriorcingulate 2765 1859 5182 2.593 0.570 0.140 0.067 167 8.6 caudalmiddlefrontal 1917 1225 2555 1.949 0.422 0.165 0.068 36 5.2 cuneus 622 410 1341 2.764 0.564 0.128 0.049 7 1.2 entorhinal 4867 3257 10270 2.835 0.561 0.162 0.071 103 14.5 fusiform 6836 4574 12418 2.499 0.486 0.145 0.055 113 15.5 inferiorparietal 4680 3132 10037 2.856 0.759 0.152 0.096 95 11.5 inferiortemporal 1431 927 2491 2.593 0.674 0.156 0.064 33 3.5 isthmuscingulate 8254 5273 11527 2.054 0.512 0.149 0.056 137 20.0 lateraloccipital 3790 2560 7678 2.731 0.683 0.153 0.067 70 10.7 lateralorbitofrontal 5400 3475 8106 2.183 0.558 0.159 0.064 91 14.0 lingual 2479 1635 4419 2.398 0.685 0.163 0.096 126 9.7 medialorbitofrontal 4545 3086 10932 2.876 0.668 0.142 0.052 77 9.5 middletemporal 1146 731 1953 2.407 0.561 0.121 0.039 10 2.0 parahippocampal 2004 1283 3370 2.399 0.476 0.130 0.112 89 10.2 paracentral 2911 2005 6138 2.715 0.416 0.134 0.046 39 5.4 parsopercularis 933 614 2243 2.827 0.529 0.169 0.153 61 8.6 parsorbitalis 1982 1338 4111 2.718 0.543 0.137 0.045 29 3.6 parstriangularis 2156 1370 2449 1.917 0.455 0.130 0.058 27 4.8 pericalcarine 6459 4112 10363 2.256 0.683 0.133 0.048 94 13.5 postcentral 1744 1188 3384 2.702 0.619 0.164 0.062 38 4.2 posteriorcingulate 7497 4785 13586 2.612 0.589 0.138 0.060 105 18.6 precentral 5881 4013 10123 2.358 0.548 0.145 0.068 99 11.7 precuneus 1067 686 2451 3.079 0.782 0.163 0.061 22 2.5 rostralanteriorcingulate 7995 5492 16389 2.553 0.628 0.162 0.070 162 22.1 rostralmiddlefrontal 9871 6735 23089 2.984 0.609 0.151 0.063 172 27.7 superiorfrontal 7763 5131 12315 2.194 0.506 0.144 0.064 396 16.2 superiorparietal 6185 4127 13956 2.914 0.607 0.129 0.051 79 12.3 superiortemporal 5512 3663 11335 2.782 0.548 0.144 0.058 100 12.6 supramarginal 280 192 765 2.981 0.448 0.260 0.176 16 2.1 frontalpole 620 433 2312 3.461 0.849 0.194 0.103 19 3.0 temporalpole 866 518 1557 2.562 0.544 0.134 0.105 16 4.9 transversetemporal 3115 2040 6764 3.227 0.793 0.118 0.048 38 6.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Nov 18 19:36:14 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 180 labels changed using aseg relabeling using gibbs priors... 000: 9295 changed, 134383 examined... 001: 2265 changed, 35617 examined... 002: 701 changed, 11469 examined... 003: 273 changed, 3914 examined... 004: 121 changed, 1548 examined... 005: 53 changed, 686 examined... 006: 34 changed, 324 examined... 007: 17 changed, 185 examined... 008: 13 changed, 85 examined... 009: 11 changed, 66 examined... 010: 5 changed, 64 examined... 011: 3 changed, 30 examined... 012: 1 changed, 15 examined... 013: 0 changed, 7 examined... 94 labels changed using aseg 000: 304 total segments, 224 labels (3092 vertices) changed 001: 96 total segments, 17 labels (152 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 123 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 567 vertices marked for relabeling... 567 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 48 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Nov 18 19:37:02 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1059 718 2124 2.409 0.714 0.185 0.091 27 3.9 G_and_S_frontomargin 1520 1033 2481 2.232 0.462 0.161 0.051 26 3.3 G_and_S_occipital_inf 1504 902 2436 2.243 0.480 0.131 0.100 80 9.4 G_and_S_paracentral 1564 1018 3374 2.905 0.584 0.161 0.067 32 4.1 G_and_S_subcentral 687 468 1759 2.610 0.694 0.225 0.132 29 3.5 G_and_S_transv_frontopol 2103 1400 4568 3.086 0.723 0.158 0.056 38 4.7 G_and_S_cingul-Ant 1068 723 2114 2.686 0.530 0.132 0.039 12 1.8 G_and_S_cingul-Mid-Ant 1302 914 2513 2.656 0.520 0.146 0.056 19 2.7 G_and_S_cingul-Mid-Post 516 342 1282 3.130 0.578 0.178 0.066 14 1.3 G_cingul-Post-dorsal 347 209 551 2.306 0.690 0.156 0.074 10 0.9 G_cingul-Post-ventral 1684 1029 2205 1.899 0.416 0.168 0.074 35 5.1 G_cuneus 1543 1077 4051 2.899 0.370 0.153 0.060 30 4.0 G_front_inf-Opercular 376 237 994 3.137 0.413 0.201 0.295 53 7.2 G_front_inf-Orbital 1332 892 3289 2.793 0.452 0.148 0.051 22 2.8 G_front_inf-Triangul 3939 2663 9777 2.889 0.548 0.179 0.091 224 15.2 G_front_middle 7353 4937 18691 3.066 0.576 0.162 0.083 160 24.7 G_front_sup 508 329 1250 3.470 0.768 0.120 0.049 6 0.9 G_Ins_lg_and_S_cent_ins 651 415 2213 3.936 0.742 0.137 0.077 16 2.4 G_insular_short 2876 1805 5803 2.518 0.460 0.163 0.059 58 6.6 G_occipital_middle 1469 933 2205 2.025 0.425 0.163 0.069 41 4.2 G_occipital_sup 1902 1258 4410 2.835 0.458 0.171 0.067 46 5.6 G_oc-temp_lat-fusifor 3696 2320 5802 2.156 0.576 0.168 0.074 71 10.7 G_oc-temp_med-Lingual 1341 837 2572 2.667 0.669 0.122 0.047 14 2.6 G_oc-temp_med-Parahip 2590 1753 6424 2.782 0.653 0.174 0.084 65 9.2 G_orbital 2191 1455 4520 2.584 0.514 0.163 0.078 52 7.1 G_pariet_inf-Angular 3224 2128 7698 2.941 0.516 0.151 0.067 72 8.5 G_pariet_inf-Supramar 2781 1841 5288 2.300 0.569 0.141 0.066 43 5.7 G_parietal_sup 2661 1594 4838 2.398 0.607 0.140 0.055 51 6.8 G_postcentral 3103 1793 6385 2.830 0.536 0.138 0.067 49 7.6 G_precentral 2675 1817 5617 2.472 0.537 0.162 0.062 60 6.6 G_precuneus 979 666 2196 2.510 0.659 0.184 0.097 34 4.0 G_rectus 485 284 630 2.195 0.769 0.169 0.192 78 3.8 G_subcallosal 674 392 1330 2.692 0.614 0.152 0.133 16 4.8 G_temp_sup-G_T_transv 2643 1720 7570 3.169 0.625 0.149 0.068 50 6.8 G_temp_sup-Lateral 467 296 1047 3.240 0.884 0.139 0.079 8 1.5 G_temp_sup-Plan_polar 1128 795 2309 2.630 0.509 0.108 0.026 7 1.3 G_temp_sup-Plan_tempo 2190 1467 5857 3.030 0.711 0.170 0.137 59 6.9 G_temporal_inf 2666 1800 7522 3.070 0.616 0.161 0.068 61 7.3 G_temporal_middle 308 203 447 2.720 0.582 0.115 0.031 2 0.4 Lat_Fis-ant-Horizont 318 218 466 2.537 0.401 0.099 0.026 1 0.3 Lat_Fis-ant-Vertical 1326 884 1819 2.636 0.514 0.121 0.039 12 2.1 Lat_Fis-post 2532 1503 2728 1.701 0.436 0.146 0.060 44 6.4 Pole_occipital 1857 1258 5737 3.377 0.791 0.188 0.106 52 8.0 Pole_temporal 3041 2002 3934 2.094 0.518 0.132 0.084 45 5.9 S_calcarine 3115 2130 3377 1.830 0.532 0.134 0.053 34 7.8 S_central 870 619 1301 2.260 0.484 0.126 0.036 8 1.4 S_cingul-Marginalis 469 316 832 2.983 0.508 0.108 0.031 3 0.7 S_circular_insula_ant 1463 972 2454 2.689 0.610 0.086 0.020 5 1.3 S_circular_insula_inf 1777 1193 2746 2.751 0.494 0.110 0.030 11 2.3 S_circular_insula_sup 1223 822 2414 2.933 0.670 0.152 0.103 27 3.4 S_collat_transv_ant 439 290 498 2.262 0.428 0.139 0.045 4 0.9 S_collat_transv_post 2518 1716 3879 2.324 0.463 0.124 0.038 24 3.9 S_front_inf 1512 1061 2544 2.429 0.504 0.136 0.050 18 2.8 S_front_middle 2386 1647 3970 2.464 0.463 0.122 0.040 25 4.0 S_front_sup 288 188 677 2.953 0.441 0.166 0.060 6 0.7 S_interm_prim-Jensen 3275 2201 4588 2.215 0.466 0.134 0.042 37 5.7 S_intrapariet_and_P_trans 1442 958 1635 1.931 0.378 0.140 0.043 16 2.7 S_oc_middle_and_Lunatus 1264 821 1581 2.038 0.369 0.133 0.088 285 2.0 S_oc_sup_and_transversal 1515 1017 2159 2.328 0.392 0.140 0.067 30 5.1 S_occipital_ant 755 519 1079 2.439 0.363 0.112 0.028 5 0.9 S_oc-temp_lat 2029 1418 3087 2.483 0.510 0.136 0.043 21 3.8 S_oc-temp_med_and_Lingual 291 198 390 2.175 0.395 0.121 0.037 2 0.5 S_orbital_lateral 741 503 992 2.291 0.675 0.112 0.026 5 0.8 S_orbital_med-olfact 1197 806 2188 2.765 0.721 0.147 0.063 22 2.9 S_orbital-H_Shaped 2562 1746 3463 2.186 0.571 0.130 0.037 25 4.1 S_parieto_occipital 846 540 968 2.421 0.604 0.175 0.062 25 2.1 S_pericallosal 2271 1530 3264 2.384 0.417 0.124 0.038 21 3.6 S_postcentral 1842 1285 2955 2.434 0.465 0.119 0.032 13 2.5 S_precentral-inf-part 723 523 1113 2.466 0.402 0.117 0.028 5 0.9 S_precentral-sup-part 603 412 956 2.544 0.646 0.148 0.052 8 1.3 S_suborbital 880 591 1466 2.487 0.553 0.137 0.048 10 1.7 S_subparietal 1458 983 2173 2.416 0.686 0.128 0.042 20 2.4 S_temporal_inf 5705 3919 9972 2.578 0.458 0.121 0.037 54 8.8 S_temporal_sup 308 218 429 2.446 0.386 0.130 0.036 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Nov 18 19:37:17 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1245 labels changed using aseg relabeling using gibbs priors... 000: 2823 changed, 134383 examined... 001: 714 changed, 11751 examined... 002: 195 changed, 3818 examined... 003: 78 changed, 1129 examined... 004: 29 changed, 473 examined... 005: 19 changed, 171 examined... 006: 19 changed, 105 examined... 007: 11 changed, 94 examined... 008: 8 changed, 62 examined... 009: 3 changed, 40 examined... 010: 3 changed, 16 examined... 011: 2 changed, 20 examined... 012: 3 changed, 12 examined... 013: 1 changed, 13 examined... 014: 2 changed, 7 examined... 015: 0 changed, 11 examined... 268 labels changed using aseg 000: 68 total segments, 35 labels (229 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 578 vertices marked for relabeling... 578 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 44 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Nov 18 19:38:01 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1491 967 2875 2.779 0.595 0.141 0.042 22 2.8 caudalanteriorcingulate 2798 1885 5279 2.596 0.568 0.140 0.067 167 8.7 caudalmiddlefrontal 3022 1927 4081 1.999 0.450 0.156 0.062 65 7.9 cuneus 583 385 1300 2.783 0.609 0.127 0.046 6 1.2 entorhinal 4214 2829 8391 2.747 0.491 0.157 0.066 85 11.5 fusiform 6577 4401 11978 2.496 0.487 0.147 0.056 112 15.4 inferiorparietal 4831 3206 11046 2.949 0.771 0.159 0.103 109 13.6 inferiortemporal 1435 926 2478 2.587 0.675 0.157 0.064 33 3.5 isthmuscingulate 8537 5447 11910 2.042 0.509 0.148 0.055 141 20.5 lateraloccipital 3855 2619 8316 2.762 0.735 0.163 0.076 83 12.1 lateralorbitofrontal 5382 3469 8094 2.182 0.556 0.158 0.064 90 13.9 lingual 2057 1363 3747 2.411 0.674 0.153 0.074 49 6.3 medialorbitofrontal 6086 4134 13353 2.772 0.676 0.137 0.049 90 11.9 middletemporal 1157 741 1985 2.414 0.565 0.122 0.039 11 2.0 parahippocampal 2336 1508 3980 2.445 0.501 0.130 0.103 92 10.8 paracentral 2491 1724 5212 2.704 0.400 0.132 0.044 33 4.4 parsopercularis 1015 682 2320 2.893 0.494 0.145 0.129 58 7.8 parsorbitalis 2474 1653 5097 2.658 0.564 0.139 0.048 32 4.9 parstriangularis 2141 1361 2434 1.920 0.457 0.131 0.060 27 5.0 pericalcarine 7052 4524 11432 2.277 0.671 0.134 0.047 102 14.6 postcentral 1841 1253 3491 2.701 0.605 0.161 0.061 38 4.3 posteriorcingulate 7527 4807 13485 2.610 0.590 0.138 0.060 105 18.8 precentral 5594 3834 9709 2.332 0.570 0.145 0.069 96 11.2 precuneus 1514 989 3193 2.902 0.840 0.177 0.098 98 6.0 rostralanteriorcingulate 5628 3835 11676 2.607 0.604 0.161 0.064 109 14.8 rostralmiddlefrontal 11130 7605 25636 2.882 0.635 0.158 0.072 223 34.2 superiorfrontal 6080 4033 9955 2.256 0.494 0.145 0.067 361 12.2 superiorparietal 8208 5522 19038 2.925 0.648 0.135 0.054 115 18.0 superiortemporal 5290 3507 10720 2.781 0.548 0.143 0.058 95 12.0 supramarginal 838 501 1497 2.529 0.510 0.133 0.107 16 4.8 transversetemporal 2762 1837 6269 3.243 0.792 0.112 0.042 31 5.0 insula #----------------------------------------- #@# WM/GM Contrast lh Wed Nov 18 19:38:15 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts pctsurfcon --s af1021_recon --lh-only Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts/pctsurfcon.log Wed Nov 18 19:38:15 EST 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-20.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.31904/lh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 73420 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.31904/lh.wm.mgh Dim: 134383 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.31904/lh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 87295 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.31904/lh.gm.mgh Dim: 134383 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.31904/lh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.31904/lh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-20.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh Vertex Area is 0.661663 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1584 1095.910 2 1002 caudalanteriorcingulate 789 506.564 3 1003 caudalmiddlefrontal 2765 1858.920 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 1917 1225.443 6 1006 entorhinal 622 409.929 7 1007 fusiform 4867 3257.278 8 1008 inferiorparietal 6836 4573.844 9 1009 inferiortemporal 4680 3131.517 10 1010 isthmuscingulate 1431 927.172 11 1011 lateraloccipital 8254 5273.195 12 1012 lateralorbitofrontal 3790 2559.588 13 1013 lingual 5400 3475.210 14 1014 medialorbitofrontal 2479 1635.068 15 1015 middletemporal 4545 3085.708 16 1016 parahippocampal 1146 731.078 17 1017 paracentral 2004 1283.079 18 1018 parsopercularis 2911 2005.479 19 1019 parsorbitalis 933 614.015 20 1020 parstriangularis 1982 1337.828 21 1021 pericalcarine 2156 1369.830 22 1022 postcentral 6459 4112.391 23 1023 posteriorcingulate 1744 1187.680 24 1024 precentral 7497 4785.458 25 1025 precuneus 5881 4012.888 26 1026 rostralanteriorcingulate 1067 686.341 27 1027 rostralmiddlefrontal 7995 5492.088 28 1028 superiorfrontal 9871 6735.381 29 1029 superiorparietal 7763 5130.734 30 1030 superiortemporal 6185 4126.916 31 1031 supramarginal 5512 3662.862 32 1032 frontalpole 280 191.547 33 1033 temporalpole 620 432.797 34 1034 transversetemporal 866 517.973 35 1035 insula 3115 2039.750 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Wed Nov 18 19:38:24 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1593 1109 3015 2.682 0.457 0.130 0.034 20 2.4 bankssts 1197 786 2345 2.626 0.751 0.153 0.052 22 2.2 caudalanteriorcingulate 3380 2338 6702 2.581 0.464 0.133 0.043 40 6.2 caudalmiddlefrontal 2179 1407 2986 1.922 0.475 0.168 0.077 51 7.5 cuneus 589 396 1566 2.976 0.716 0.168 0.091 12 1.8 entorhinal 5442 3646 11546 2.834 0.613 0.150 0.097 157 13.3 fusiform 8167 5545 14263 2.348 0.503 0.152 0.079 212 32.1 inferiorparietal 4320 2929 9483 2.858 0.725 0.152 0.080 89 11.4 inferiortemporal 1285 824 2162 2.568 0.679 0.147 0.062 22 2.9 isthmuscingulate 7233 4662 10989 2.190 0.516 0.154 0.067 142 18.6 lateraloccipital 3685 2495 7466 2.624 0.776 0.165 0.076 85 10.7 lateralorbitofrontal 5135 3408 7248 2.131 0.581 0.165 0.068 118 15.1 lingual 2768 1867 5430 2.512 0.830 0.157 0.083 77 9.3 medialorbitofrontal 4406 3036 10881 3.006 0.591 0.148 0.060 89 10.5 middletemporal 1247 797 2097 2.437 0.432 0.110 0.036 10 1.9 parahippocampal 2205 1371 3496 2.458 0.513 0.126 0.048 30 4.5 paracentral 2109 1406 4176 2.782 0.441 0.129 0.048 27 4.3 parsopercularis 1084 789 2817 2.747 0.665 0.188 0.331 287 3.4 parsorbitalis 2159 1445 4093 2.478 0.521 0.138 0.046 30 3.8 parstriangularis 2365 1581 2680 1.868 0.524 0.156 0.058 37 5.6 pericalcarine 5742 3591 8275 2.088 0.670 0.129 0.050 81 11.4 postcentral 1953 1314 3713 2.596 0.791 0.167 0.062 41 4.6 posteriorcingulate 7239 4713 12460 2.496 0.596 0.140 0.088 88 33.6 precentral 6267 4256 11047 2.501 0.561 0.147 0.052 99 12.7 precuneus 752 487 1602 2.699 0.958 0.143 0.063 12 1.6 rostralanteriorcingulate 8460 5766 15268 2.251 0.635 0.161 0.080 197 25.1 rostralmiddlefrontal 9201 6382 21012 2.862 0.663 0.146 0.055 139 19.8 superiorfrontal 7356 4758 11489 2.187 0.483 0.140 0.049 101 14.3 superiorparietal 5857 3902 13807 3.056 0.718 0.138 0.060 95 14.4 superiortemporal 6006 3985 11151 2.653 0.561 0.135 0.048 85 10.8 supramarginal 437 288 982 2.480 0.836 0.205 0.089 17 1.7 frontalpole 570 397 2015 3.578 1.067 0.204 0.325 36 3.5 temporalpole 720 426 1246 2.482 0.374 0.129 0.051 9 1.3 transversetemporal 3153 2056 6767 3.278 0.914 0.130 0.106 85 17.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Wed Nov 18 19:38:38 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 17 labels changed using aseg relabeling using gibbs priors... 000: 9780 changed, 134806 examined... 001: 2387 changed, 37288 examined... 002: 747 changed, 12158 examined... 003: 358 changed, 4168 examined... 004: 166 changed, 1995 examined... 005: 89 changed, 938 examined... 006: 44 changed, 485 examined... 007: 25 changed, 251 examined... 008: 7 changed, 160 examined... 009: 6 changed, 38 examined... 010: 6 changed, 40 examined... 011: 3 changed, 27 examined... 012: 2 changed, 19 examined... 013: 1 changed, 12 examined... 014: 0 changed, 8 examined... 10 labels changed using aseg 000: 319 total segments, 232 labels (2779 vertices) changed 001: 100 total segments, 15 labels (415 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 142 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 592 vertices marked for relabeling... 592 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 52 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Wed Nov 18 19:39:31 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1172 794 2040 2.075 0.737 0.179 0.074 29 4.0 G_and_S_frontomargin 1268 848 2580 2.712 0.432 0.153 0.050 20 2.7 G_and_S_occipital_inf 1375 764 2034 2.265 0.462 0.133 0.064 30 3.7 G_and_S_paracentral 1515 1018 3247 2.914 0.541 0.163 0.058 27 3.5 G_and_S_subcentral 738 508 1830 2.572 0.707 0.194 0.097 27 2.7 G_and_S_transv_frontopol 2530 1708 5175 2.828 0.751 0.150 0.067 46 6.1 G_and_S_cingul-Ant 1346 953 2891 2.867 0.551 0.142 0.048 19 2.4 G_and_S_cingul-Mid-Ant 1554 1040 2912 2.698 0.509 0.147 0.055 25 3.2 G_and_S_cingul-Mid-Post 469 322 1212 3.079 0.786 0.199 0.098 13 1.7 G_cingul-Post-dorsal 304 183 549 2.639 0.539 0.170 0.092 11 1.0 G_cingul-Post-ventral 1829 1192 2375 1.811 0.468 0.172 0.082 47 6.8 G_cuneus 1366 918 3160 2.843 0.424 0.152 0.062 26 3.4 G_front_inf-Opercular 313 211 774 2.762 0.548 0.171 0.071 8 0.8 G_front_inf-Orbital 1040 697 2383 2.651 0.489 0.149 0.048 17 2.0 G_front_inf-Triangul 3767 2631 8798 2.597 0.591 0.170 0.095 104 12.9 G_front_middle 6507 4428 16398 2.978 0.673 0.158 0.063 117 15.8 G_front_sup 389 262 1100 3.966 1.062 0.136 0.422 43 11.1 G_Ins_lg_and_S_cent_ins 589 373 1860 4.004 0.759 0.135 0.068 12 1.5 G_insular_short 2017 1282 4131 2.517 0.405 0.153 0.063 38 4.5 G_occipital_middle 1909 1196 3018 2.181 0.469 0.145 0.049 29 4.0 G_occipital_sup 2054 1333 4532 2.851 0.542 0.165 0.154 105 5.5 G_oc-temp_lat-fusifor 3335 2183 5036 2.163 0.583 0.175 0.077 67 10.5 G_oc-temp_med-Lingual 1701 1072 4086 2.939 0.766 0.146 0.076 32 4.6 G_oc-temp_med-Parahip 2739 1882 7222 2.882 0.755 0.198 0.207 356 11.4 G_orbital 2792 1905 5854 2.552 0.594 0.171 0.083 109 10.7 G_pariet_inf-Angular 2637 1683 5607 2.860 0.532 0.144 0.056 47 5.4 G_pariet_inf-Supramar 2263 1494 4210 2.313 0.453 0.148 0.057 34 5.2 G_parietal_sup 2223 1247 3241 2.073 0.576 0.123 0.060 41 5.3 G_postcentral 2737 1670 5254 2.599 0.544 0.141 0.144 31 22.9 G_precentral 2950 2026 6083 2.473 0.497 0.156 0.060 55 6.7 G_precuneus 813 525 2040 2.808 0.570 0.174 0.113 34 4.1 G_rectus 280 189 323 1.617 0.731 0.127 0.094 7 1.0 G_subcallosal 499 295 956 2.477 0.414 0.140 0.060 7 1.1 G_temp_sup-G_T_transv 2268 1512 7028 3.447 0.645 0.171 0.073 51 6.1 G_temp_sup-Lateral 596 389 1656 3.561 0.725 0.158 0.126 27 1.9 G_temp_sup-Plan_polar 959 657 1875 2.590 0.472 0.119 0.091 17 4.0 G_temp_sup-Plan_tempo 2295 1558 5995 3.056 0.815 0.163 0.077 57 7.1 G_temporal_inf 2554 1758 7329 3.131 0.523 0.163 0.075 68 7.4 G_temporal_middle 375 253 614 2.334 0.462 0.128 0.042 4 0.7 Lat_Fis-ant-Horizont 135 89 236 2.469 0.354 0.084 0.019 1 0.1 Lat_Fis-ant-Vertical 1988 1329 2931 2.591 0.447 0.125 0.038 19 3.0 Lat_Fis-post 3339 2116 4113 1.822 0.478 0.172 0.090 91 11.4 Pole_occipital 1805 1253 5748 3.226 0.894 0.187 0.188 57 8.0 Pole_temporal 2857 1909 3524 2.059 0.559 0.151 0.054 70 7.0 S_calcarine 2746 1906 2838 1.718 0.460 0.135 0.043 23 5.1 S_central 1337 912 2095 2.489 0.497 0.134 0.045 15 2.4 S_cingul-Marginalis 621 429 990 2.779 0.387 0.113 0.033 4 1.0 S_circular_insula_ant 1387 884 2188 2.669 0.628 0.093 0.033 9 1.4 S_circular_insula_inf 1530 1016 2554 2.846 0.656 0.119 0.043 14 2.9 S_circular_insula_sup 931 617 2000 3.080 0.718 0.145 0.080 15 2.0 S_collat_transv_ant 795 536 923 2.093 0.468 0.156 0.055 10 1.8 S_collat_transv_post 2634 1758 4386 2.430 0.510 0.130 0.040 27 4.6 S_front_inf 2106 1385 3029 2.022 0.551 0.149 0.063 37 4.7 S_front_middle 2417 1694 3868 2.302 0.475 0.116 0.033 19 3.4 S_front_sup 555 373 771 2.317 0.575 0.130 0.035 6 0.9 S_interm_prim-Jensen 3059 2042 4128 2.097 0.496 0.138 0.044 37 5.3 S_intrapariet_and_P_trans 1207 811 1634 2.085 0.403 0.133 0.044 13 2.0 S_oc_middle_and_Lunatus 1101 720 1302 2.006 0.344 0.130 0.053 16 2.7 S_oc_sup_and_transversal 1011 671 1489 2.480 0.311 0.128 0.042 11 1.6 S_occipital_ant 1243 875 1960 2.539 0.341 0.128 0.039 13 2.0 S_oc-temp_lat 2214 1517 3253 2.464 0.443 0.114 0.030 15 2.7 S_oc-temp_med_and_Lingual 509 353 673 2.102 0.460 0.127 0.038 4 0.8 S_orbital_lateral 760 551 1071 1.866 0.591 0.108 0.021 5 0.6 S_orbital_med-olfact 1359 921 2374 2.395 0.684 0.156 0.066 25 3.3 S_orbital-H_Shaped 2605 1713 3746 2.441 0.611 0.137 0.041 29 4.4 S_parieto_occipital 1569 985 1524 1.992 0.702 0.139 0.041 23 2.3 S_pericallosal 2138 1420 2628 2.022 0.425 0.111 0.030 15 2.7 S_postcentral 2059 1428 3664 2.586 0.489 0.123 0.052 22 5.1 S_precentral-inf-part 816 553 1169 2.472 0.501 0.122 0.033 6 1.2 S_precentral-sup-part 196 137 429 3.132 0.692 0.217 0.119 10 0.7 S_suborbital 946 638 1763 2.660 0.476 0.139 0.045 12 1.7 S_subparietal 843 568 1177 2.609 0.530 0.130 0.046 12 1.7 S_temporal_inf 7073 4882 12306 2.552 0.524 0.131 0.062 117 22.7 S_temporal_sup 303 205 382 2.370 0.228 0.128 0.029 2 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Wed Nov 18 19:39:46 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1169 labels changed using aseg relabeling using gibbs priors... 000: 2644 changed, 134806 examined... 001: 657 changed, 11528 examined... 002: 174 changed, 3541 examined... 003: 76 changed, 1035 examined... 004: 30 changed, 428 examined... 005: 17 changed, 157 examined... 006: 7 changed, 98 examined... 007: 5 changed, 45 examined... 008: 4 changed, 30 examined... 009: 4 changed, 22 examined... 010: 4 changed, 23 examined... 011: 6 changed, 28 examined... 012: 4 changed, 28 examined... 013: 6 changed, 24 examined... 014: 5 changed, 34 examined... 015: 6 changed, 34 examined... 016: 2 changed, 23 examined... 017: 1 changed, 12 examined... 018: 1 changed, 7 examined... 019: 0 changed, 7 examined... 154 labels changed using aseg 000: 57 total segments, 24 labels (104 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 669 vertices marked for relabeling... 669 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 41 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Wed Nov 18 19:40:27 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1185 777 2297 2.615 0.750 0.153 0.052 21 2.2 caudalanteriorcingulate 3339 2298 6590 2.597 0.459 0.134 0.044 41 6.2 caudalmiddlefrontal 2698 1754 3657 1.960 0.468 0.162 0.063 54 6.9 cuneus 632 430 1706 2.985 0.728 0.166 0.090 12 1.9 entorhinal 4727 3172 9720 2.829 0.618 0.147 0.099 137 10.6 fusiform 7720 5232 13354 2.345 0.510 0.154 0.081 204 31.4 inferiorparietal 5025 3394 11193 2.851 0.713 0.154 0.096 109 13.8 inferiortemporal 1288 829 2170 2.571 0.682 0.148 0.062 22 2.9 isthmuscingulate 7512 4841 11526 2.194 0.520 0.154 0.067 149 19.5 lateraloccipital 4220 2867 8781 2.530 0.825 0.174 0.081 110 13.6 lateralorbitofrontal 5152 3422 7267 2.135 0.578 0.165 0.068 117 15.0 lingual 2150 1446 4555 2.583 0.809 0.159 0.086 64 7.8 medialorbitofrontal 5317 3680 12593 2.946 0.576 0.144 0.055 99 11.7 middletemporal 1247 794 2072 2.437 0.430 0.109 0.035 10 1.8 parahippocampal 2254 1410 3589 2.465 0.524 0.125 0.048 30 4.5 paracentral 2268 1513 4389 2.753 0.444 0.128 0.047 28 4.4 parsopercularis 1200 826 2599 2.668 0.638 0.151 0.064 18 2.8 parsorbitalis 2243 1496 4260 2.458 0.529 0.138 0.045 32 4.2 parstriangularis 2438 1613 2739 1.852 0.519 0.157 0.069 45 7.6 pericalcarine 6136 3859 8925 2.095 0.662 0.130 0.050 87 12.1 postcentral 2075 1396 3972 2.616 0.768 0.167 0.063 43 5.1 posteriorcingulate 7111 4638 12173 2.491 0.601 0.141 0.089 87 33.4 precentral 6211 4206 11191 2.514 0.551 0.149 0.053 102 13.0 precuneus 882 572 1853 2.725 0.929 0.141 0.060 13 1.8 rostralanteriorcingulate 5759 3975 11015 2.331 0.620 0.162 0.131 401 17.2 rostralmiddlefrontal 11984 8253 25555 2.696 0.735 0.150 0.059 203 27.6 superiorfrontal 6337 4112 9949 2.196 0.486 0.136 0.047 83 11.9 superiorparietal 7802 5236 18462 3.044 0.757 0.144 0.068 155 20.7 superiortemporal 5722 3783 10504 2.642 0.552 0.133 0.048 80 10.3 supramarginal 718 425 1239 2.483 0.374 0.128 0.051 9 1.3 transversetemporal 2909 1910 6380 3.305 0.889 0.124 0.104 76 16.3 insula #----------------------------------------- #@# WM/GM Contrast rh Wed Nov 18 19:40:41 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts pctsurfcon --s af1021_recon --rh-only Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts/pctsurfcon.log Wed Nov 18 19:40:41 EST 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-20.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.32164/rh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 73821 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.32164/rh.wm.mgh Dim: 134806 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.32164/rh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 87789 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.32164/rh.gm.mgh Dim: 134806 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.32164/rh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.32164/rh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-20.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh Vertex Area is 0.664253 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1593 1108.692 2 2002 caudalanteriorcingulate 1197 785.953 3 2003 caudalmiddlefrontal 3380 2338.266 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2179 1407.114 6 2006 entorhinal 589 396.363 7 2007 fusiform 5442 3645.660 8 2008 inferiorparietal 8167 5544.499 9 2009 inferiortemporal 4320 2929.486 10 2010 isthmuscingulate 1285 823.827 11 2011 lateraloccipital 7233 4662.327 12 2012 lateralorbitofrontal 3685 2494.787 13 2013 lingual 5135 3408.429 14 2014 medialorbitofrontal 2768 1866.921 15 2015 middletemporal 4406 3035.524 16 2016 parahippocampal 1247 797.235 17 2017 paracentral 2205 1371.040 18 2018 parsopercularis 2109 1406.215 19 2019 parsorbitalis 1084 789.439 20 2020 parstriangularis 2159 1444.928 21 2021 pericalcarine 2365 1580.832 22 2022 postcentral 5742 3590.525 23 2023 posteriorcingulate 1953 1313.774 24 2024 precentral 7239 4713.337 25 2025 precuneus 6267 4255.853 26 2026 rostralanteriorcingulate 752 486.565 27 2027 rostralmiddlefrontal 8460 5765.568 28 2028 superiorfrontal 9201 6381.974 29 2029 superiorparietal 7356 4757.753 30 2030 superiortemporal 5857 3902.342 31 2031 supramarginal 6006 3985.072 32 2032 frontalpole 437 288.075 33 2033 temporalpole 570 397.121 34 2034 transversetemporal 720 426.451 35 2035 insula 3153 2055.899 Reporting on 34 segmentations mri_segstats done Cleaning up #-------------------------------------------- #@# Cortical ribbon mask Wed Nov 18 19:40:50 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon af1021_recon SUBJECTS_DIR is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 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 = 141 writing volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Wed Nov 18 19:55:33 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon 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 /share/apps/freesurfer-5.3.0/ASegStatsLUT.txt --subject af1021_recon $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 /share/apps/freesurfer-5.3.0/ASegStatsLUT.txt --subject af1021_recon sysname Linux hostname compute-0-20.local machine x86_64 user twilliams UseRobust 0 atlas_icv (eTIV) = 1541622 mm^3 (det: 1.263673 ) Computing euler number orig.nofix lheno = -44, rheno = -32 orig.nofix lhholes = 23, rhholes = 17 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 239785.689 239722.000 diff= 63.7 pctdiff= 0.027 rhCtxGM: 236017.021 235804.000 diff= 213.0 pctdiff= 0.090 lhCtxWM: 218340.398 218144.000 diff= 196.4 pctdiff= 0.090 rhCtxWM: 221137.567 221480.000 diff= -342.4 pctdiff=-0.155 SubCortGMVol 62225.000 SupraTentVol 989576.675 (988404.000) diff=1172.675 pctdiff=0.119 SupraTentVolNotVent 978707.675 (977535.000) diff=1172.675 pctdiff=0.120 BrainSegVol 1120783.000 (1118799.000) diff=1984.000 pctdiff=0.177 BrainSegVolNotVent 1106900.000 (1106879.675) diff=20.325 pctdiff=0.002 BrainSegVolNotVent 1106900.000 CerebellumVol 129214.000 VentChorVol 10869.000 3rd4th5thCSF 3014.000 CSFVol 1046.000, OptChiasmVol 135.000 MaskVol 1600589.000 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 4657 4657.085 4 5 Left-Inf-Lat-Vent 147 147.216 5 7 Left-Cerebellum-White-Matter 15131 15130.936 6 8 Left-Cerebellum-Cortex 49465 49464.539 7 10 Left-Thalamus-Proper 8027 8026.642 8 11 Left-Caudate 3803 3803.185 9 12 Left-Putamen 6337 6336.562 10 13 Left-Pallidum 1648 1648.023 11 14 3rd-Ventricle 739 739.349 12 15 4th-Ventricle 1501 1501.291 13 16 Brain-Stem 21351 21351.275 14 17 Left-Hippocampus 4730 4730.166 15 18 Left-Amygdala 1888 1887.705 16 24 CSF 1110 1110.174 17 26 Left-Accumbens-area 749 748.657 18 28 Left-VentralDC 3769 3768.568 19 30 Left-vessel 85 85.161 20 31 Left-choroid-plexus 1057 1056.964 23 43 Right-Lateral-Ventricle 3857 3856.684 24 44 Right-Inf-Lat-Vent 108 107.650 25 46 Right-Cerebellum-White-Matter 14819 14818.603 26 47 Right-Cerebellum-Cortex 51367 51367.012 27 49 Right-Thalamus-Proper 7432 7432.446 28 50 Right-Caudate 4211 4210.721 29 51 Right-Putamen 5637 5636.977 30 52 Right-Pallidum 1575 1575.200 31 53 Right-Hippocampus 4560 4560.470 32 54 Right-Amygdala 1372 1371.704 33 58 Right-Accumbens-area 760 759.631 34 60 Right-VentralDC 3998 3997.655 35 62 Right-vessel 74 74.438 36 63 Right-choroid-plexus 1407 1406.849 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1237 1237.188 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 17 17.220 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 133 132.774 45 251 CC_Posterior 858 858.164 46 252 CC_Mid_Posterior 539 539.010 47 253 CC_Central 505 505.136 48 254 CC_Mid_Anterior 426 425.545 49 255 CC_Anterior 784 783.820 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Wed Nov 18 19:59:22 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --volmask SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 473290 Used brute-force search on 0 voxels Writing output aseg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --volmask --a2009s SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 473290 Used brute-force search on 0 voxels Writing output aseg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Wed Nov 18 20:03:06 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/ribbon.mgz Loading filled from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8437 vertices from left hemi Ripped 8545 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz Loading Ctx Seg File /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 911902 Used brute-force search on 43 voxels Fixing Parahip LH WM Found 9 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 3.000000 7 k 27.000000 8 k 1744.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1.000000 1 k 2065.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon 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 af1021_recon --surf-wm-vol --ctab /share/apps/freesurfer-5.3.0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject af1021_recon --surf-wm-vol --ctab /share/apps/freesurfer-5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-20.local machine x86_64 user twilliams UseRobust 0 atlas_icv (eTIV) = 1541622 mm^3 (det: 1.263673 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 239785.689 239722.000 diff= 63.7 pctdiff= 0.027 rhCtxGM: 236017.021 235804.000 diff= 213.0 pctdiff= 0.090 lhCtxWM: 218340.398 218144.000 diff= 196.4 pctdiff= 0.090 rhCtxWM: 221137.567 221480.000 diff= -342.4 pctdiff=-0.155 SubCortGMVol 62225.000 SupraTentVol 989576.675 (988404.000) diff=1172.675 pctdiff=0.119 SupraTentVolNotVent 978707.675 (977535.000) diff=1172.675 pctdiff=0.120 BrainSegVol 1120783.000 (1118799.000) diff=1984.000 pctdiff=0.177 BrainSegVolNotVent 1106900.000 (1106879.675) diff=20.325 pctdiff=0.002 BrainSegVolNotVent 1106900.000 CerebellumVol 129214.000 VentChorVol 10869.000 3rd4th5thCSF 3014.000 CSFVol 1046.000, OptChiasmVol 135.000 MaskVol 1600589.000 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 2344 2344.273 2 3002 wm-lh-caudalanteriorcingulate 2311 2311.051 3 3003 wm-lh-caudalmiddlefrontal 5321 5321.469 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 1997 1996.924 6 3006 wm-lh-entorhinal 1106 1105.882 7 3007 wm-lh-fusiform 5888 5888.177 8 3008 wm-lh-inferiorparietal 9937 9936.673 9 3009 wm-lh-inferiortemporal 6002 6002.427 10 3010 wm-lh-isthmuscingulate 3303 3302.840 11 3011 wm-lh-lateraloccipital 10050 10049.559 12 3012 wm-lh-lateralorbitofrontal 6212 6211.568 13 3013 wm-lh-lingual 6587 6586.856 14 3014 wm-lh-medialorbitofrontal 2839 2838.649 15 3015 wm-lh-middletemporal 5309 5309.288 16 3016 wm-lh-parahippocampal 1788 1787.837 17 3017 wm-lh-paracentral 3497 3497.255 18 3018 wm-lh-parsopercularis 4557 4557.250 19 3019 wm-lh-parsorbitalis 788 788.333 20 3020 wm-lh-parstriangularis 3174 3173.637 21 3021 wm-lh-pericalcarine 3449 3449.457 22 3022 wm-lh-postcentral 7535 7534.977 23 3023 wm-lh-posteriorcingulate 4296 4295.991 24 3024 wm-lh-precentral 12936 12936.485 25 3025 wm-lh-precuneus 9754 9754.364 26 3026 wm-lh-rostralanteriorcingulate 2415 2414.948 27 3027 wm-lh-rostralmiddlefrontal 11447 11447.485 28 3028 wm-lh-superiorfrontal 17092 17091.590 29 3029 wm-lh-superiorparietal 10885 10884.594 30 3030 wm-lh-superiortemporal 8594 8594.010 31 3031 wm-lh-supramarginal 8152 8152.295 32 3032 wm-lh-frontalpole 174 174.381 33 3033 wm-lh-temporalpole 558 557.755 34 3034 wm-lh-transversetemporal 771 771.418 35 3035 wm-lh-insula 8244 8244.409 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 2745 2745.338 120 4002 wm-rh-caudalanteriorcingulate 3277 3277.310 121 4003 wm-rh-caudalmiddlefrontal 5680 5680.276 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2076 2075.569 124 4006 wm-rh-entorhinal 756 755.761 125 4007 wm-rh-fusiform 6202 6202.351 126 4008 wm-rh-inferiorparietal 11103 11103.320 127 4009 wm-rh-inferiortemporal 5543 5543.002 128 4010 wm-rh-isthmuscingulate 2980 2980.250 129 4011 wm-rh-lateraloccipital 8910 8909.699 130 4012 wm-rh-lateralorbitofrontal 6387 6387.220 131 4013 wm-rh-lingual 6584 6583.537 132 4014 wm-rh-medialorbitofrontal 3336 3335.857 133 4015 wm-rh-middletemporal 5246 5246.438 134 4016 wm-rh-parahippocampal 2072 2071.721 135 4017 wm-rh-paracentral 4321 4321.378 136 4018 wm-rh-parsopercularis 3431 3431.199 137 4019 wm-rh-parsorbitalis 1059 1059.295 138 4020 wm-rh-parstriangularis 3135 3135.126 139 4021 wm-rh-pericalcarine 3741 3741.461 140 4022 wm-rh-postcentral 6895 6894.644 141 4023 wm-rh-posteriorcingulate 4600 4599.785 142 4024 wm-rh-precentral 12945 12945.029 143 4025 wm-rh-precuneus 10324 10324.216 144 4026 wm-rh-rostralanteriorcingulate 1900 1900.417 145 4027 wm-rh-rostralmiddlefrontal 11919 11919.202 146 4028 wm-rh-superiorfrontal 15647 15646.612 147 4029 wm-rh-superiorparietal 8818 8817.864 148 4030 wm-rh-superiortemporal 7913 7912.903 149 4031 wm-rh-supramarginal 8952 8952.393 150 4032 wm-rh-frontalpole 354 353.875 151 4033 wm-rh-temporalpole 544 544.304 152 4034 wm-rh-transversetemporal 643 642.564 153 4035 wm-rh-insula 8754 8754.361 154 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 28574 28574.098 237 5002 Right-UnsegmentedWhiteMatter 29781 29781.430 238 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label #-------------------------------------------- #@# BA Labels lh Wed Nov 18 20:14:32 EST 2015 mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.label --trgsubject af1021_recon --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 323 Checking for and removing duplicates Writing label file ./lh.BA1.label 4452 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.label --trgsubject af1021_recon --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./lh.BA2.label 8276 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.label --trgsubject af1021_recon --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.label --trgsubject af1021_recon --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 432 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6415 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.label --trgsubject af1021_recon --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 411 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6195 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.label --trgsubject af1021_recon --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.label --trgsubject af1021_recon --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1084 Checking for and removing duplicates Writing label file ./lh.BA6.label 14673 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.label --trgsubject af1021_recon --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 687 Checking for and removing duplicates Writing label file ./lh.BA44.label 4868 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.label --trgsubject af1021_recon --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 856 Checking for and removing duplicates Writing label file ./lh.BA45.label 4278 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.label --trgsubject af1021_recon --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1634 Checking for and removing duplicates Writing label file ./lh.V1.label 6275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.label --trgsubject af1021_recon --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 3389 Checking for and removing duplicates Writing label file ./lh.V2.label 11503 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.label --trgsubject af1021_recon --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 784 Checking for and removing duplicates Writing label file ./lh.MT.label 2802 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.perirhinal.label --trgsubject af1021_recon --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1081 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2230 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2211 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 467 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 352 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2264 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 421 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1572 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.thresh.label --trgsubject af1021_recon --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1147 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.thresh.label --trgsubject af1021_recon --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1520 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4854 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.thresh.label --trgsubject af1021_recon --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 736 mri_label2label: Done mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-20.local machine x86_64 user twilliams subject af1021_recon hemi lh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 92465 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.BA.annot mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-20.local machine x86_64 user twilliams subject af1021_recon hemi lh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 109651 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab af1021_recon lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1104 617 2022 2.446 0.498 0.144 0.054 18 2.4 BA1 3348 2200 5882 2.513 0.497 0.130 0.046 49 6.9 BA2 967 661 829 1.762 0.454 0.158 0.055 11 2.3 BA3a 2566 1647 3532 1.911 0.676 0.133 0.046 33 5.2 BA3b 1694 959 2837 2.602 0.473 0.124 0.096 27 3.6 BA4a 1322 871 1911 2.289 0.552 0.135 0.072 25 4.8 BA4p 8466 5596 19000 2.915 0.561 0.142 0.074 317 30.9 BA6 2744 1914 5943 2.698 0.472 0.138 0.049 40 5.5 BA44 3246 2203 6806 2.635 0.526 0.141 0.051 49 6.6 BA45 3830 2445 4376 1.802 0.470 0.142 0.061 57 9.0 V1 8960 5631 12455 2.072 0.519 0.158 0.076 174 23.4 V2 2557 1727 4523 2.392 0.503 0.150 0.063 52 7.5 MT 1114 712 2314 2.711 0.666 0.133 0.052 14 2.6 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab af1021_recon lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 723 394 1405 2.563 0.407 0.145 0.054 12 1.6 BA1 1489 975 2846 2.549 0.500 0.130 0.054 29 4.0 BA2 748 525 616 1.687 0.386 0.166 0.057 8 1.8 BA3a 1679 1087 1884 1.612 0.463 0.122 0.041 15 2.9 BA3b 1694 932 2803 2.638 0.437 0.122 0.085 30 3.7 BA4a 1062 727 1391 2.114 0.493 0.137 0.076 17 4.3 BA4p 4749 3079 10498 2.886 0.560 0.142 0.081 140 20.2 BA6 1881 1328 4132 2.698 0.366 0.144 0.050 30 4.1 BA44 1446 973 3419 2.735 0.465 0.156 0.058 24 3.4 BA45 4078 2601 4746 1.805 0.474 0.141 0.058 58 9.2 V1 4483 2745 5827 1.963 0.505 0.161 0.097 94 13.2 V2 700 475 1005 2.148 0.351 0.127 0.033 7 1.1 MT #-------------------------------------------- #@# BA Labels rh Wed Nov 18 20:19:22 EST 2015 mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.label --trgsubject af1021_recon --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./rh.BA1.label 4256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.label --trgsubject af1021_recon --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./rh.BA2.label 6999 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.label --trgsubject af1021_recon --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4093 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.label --trgsubject af1021_recon --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4850 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.label --trgsubject af1021_recon --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 326 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6073 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.label --trgsubject af1021_recon --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4638 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.label --trgsubject af1021_recon --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 732 Checking for and removing duplicates Writing label file ./rh.BA6.label 12988 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.label --trgsubject af1021_recon --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1343 Checking for and removing duplicates Writing label file ./rh.BA44.label 8255 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.label --trgsubject af1021_recon --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1143 Checking for and removing duplicates Writing label file ./rh.BA45.label 6498 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.label --trgsubject af1021_recon --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1819 Checking for and removing duplicates Writing label file ./rh.V1.label 6546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.label --trgsubject af1021_recon --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 3038 Checking for and removing duplicates Writing label file ./rh.V2.label 11054 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.label --trgsubject af1021_recon --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 500 Checking for and removing duplicates Writing label file ./rh.MT.label 2432 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.perirhinal.label --trgsubject af1021_recon --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 872 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 972 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2736 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1737 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2349 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1458 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1524 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 329 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7288 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1194 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1402 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.thresh.label --trgsubject af1021_recon --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1301 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4533 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.thresh.label --trgsubject af1021_recon --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1436 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4873 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.thresh.label --trgsubject af1021_recon --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 341 mri_label2label: Done mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-20.local machine x86_64 user twilliams subject af1021_recon hemi rh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 94394 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.BA.annot mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-20.local machine x86_64 user twilliams subject af1021_recon hemi rh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 113207 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab af1021_recon rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 913 458 1502 2.392 0.392 0.134 0.089 29 2.9 BA1 2655 1727 3775 2.124 0.518 0.109 0.029 18 3.1 BA2 979 642 801 1.639 0.365 0.146 0.049 11 1.9 BA3a 2049 1291 2488 1.687 0.500 0.128 0.044 24 3.9 BA3b 1524 870 2435 2.465 0.505 0.125 0.059 33 4.1 BA4a 1027 728 1301 1.953 0.506 0.143 0.048 9 2.2 BA4p 6912 4610 14506 2.787 0.563 0.140 0.083 67 30.2 BA6 4237 2873 8206 2.733 0.498 0.135 0.053 56 9.9 BA44 4395 2972 8863 2.505 0.564 0.147 0.061 73 11.0 BA45 4364 2894 5043 1.771 0.506 0.167 0.088 112 15.2 V1 8492 5513 11751 2.091 0.521 0.164 0.064 177 22.6 V2 2140 1448 3397 2.380 0.374 0.139 0.044 26 3.8 MT 725 484 1770 2.844 0.601 0.142 0.061 10 1.8 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab af1021_recon rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 616 284 976 2.407 0.388 0.135 0.105 26 2.1 BA1 1438 945 2080 2.116 0.547 0.105 0.029 9 1.7 BA2 835 539 628 1.640 0.341 0.152 0.051 10 1.8 BA3a 1612 1080 1719 1.502 0.359 0.119 0.035 13 2.5 BA3b 890 471 1474 2.574 0.451 0.126 0.065 28 2.7 BA4a 823 626 1041 1.883 0.525 0.147 0.049 7 1.8 BA4p 4347 2825 8733 2.736 0.532 0.138 0.094 31 24.9 BA6 918 633 1993 2.750 0.391 0.145 0.067 17 2.3 BA44 1101 730 2429 2.611 0.460 0.144 0.050 17 2.3 BA45 4207 2784 4782 1.764 0.499 0.166 0.088 108 14.8 V1 4497 2922 6025 1.995 0.572 0.173 0.073 115 13.9 V2 315 212 635 2.414 0.266 0.117 0.033 3 0.5 MT /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Wed Nov 18 20:23:01 EST 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o af1021_recon label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject af1021_recon. processing subject lh.EC_average... reading output surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1020 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label af1021_recon lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 385 218 877 2.767 0.674 0.147 0.104 11 1.8 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Wed Nov 18 20:23:14 EST 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o af1021_recon label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject af1021_recon. processing subject rh.EC_average... reading output surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 906 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label af1021_recon rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 325 203 882 2.977 0.494 0.174 0.084 7 1.2 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Wed Nov 18 15:57:12 EST 2015 Ended at Wed Nov 18 20:23:28 EST 2015 #@#%# recon-all-run-time-hours 4.438 recon-all -s af1021_recon finished without error at Wed Nov 18 20:23:28 EST 2015 New invocation of recon-all Tue Dec 1 17:22:02 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon /share/apps/freesurfer-5.3.0/bin/recon-all -subjid af1021_recon -FLAIRpial -autorecon-pial -no-isrunning subjid af1021_recon setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /share/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux compute-0-0.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 41943040 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 401408 total used free shared buffers cached Mem: 49449548 48542240 907308 0 246812 47252100 -/+ buffers/cache: 1043328 48406220 Swap: 1020116 244 1019872 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 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: 2015/12/01-22:22:02-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/01-22:22:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/01-22:22:09-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:12-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:15-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:17-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:22-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:30-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:34-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:37-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:40-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:44-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:50-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:52-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:22:59-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:03-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:09-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:12-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:16-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:23-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:26-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:29-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:32-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/01-22:23:36-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/01-22:23:39-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:42-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:44-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/01-22:23:47-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: twilliams Machine: compute-0-0.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /share/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /share/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Mask BFS Tue Dec 1 17:23:47 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1558106 voxels in mask (pct= 9.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# Make White Surf lh Tue Dec 1 17:23:53 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.88 3435 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.54 2744 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4895479.5, rms=9.93 001: dt: 0.5000, sse=5563255.0, rms=7.101 (0.000%) 002: dt: 0.5000, sse=5950070.0, rms=5.421 (0.000%) 003: dt: 0.5000, sse=6270018.0, rms=4.412 (0.000%) 004: dt: 0.5000, sse=6508964.0, rms=3.792 (0.000%) 005: dt: 0.5000, sse=6643423.0, rms=3.481 (0.000%) 006: dt: 0.5000, sse=6742135.0, rms=3.291 (0.000%) 007: dt: 0.5000, sse=6790056.0, rms=3.216 (0.000%) 008: dt: 0.5000, sse=6807864.0, rms=3.143 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6803028.0, rms=3.125 (0.000%) 010: dt: 0.2500, sse=4088114.0, rms=2.112 (0.000%) 011: dt: 0.2500, sse=3760371.5, rms=1.869 (0.000%) 012: dt: 0.2500, sse=3613746.8, rms=1.813 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3566466.2, rms=1.783 (0.000%) rms = 1.75, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3509115.8, rms=1.752 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.8, 40 (7) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.3 (%26.2))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.40) mean absolute distance = 0.25 +- 0.37 3098 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4100148.5, rms=4.66 015: dt: 0.5000, sse=4398513.5, rms=2.790 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4864968.5, rms=2.784 (0.000%) 017: dt: 0.2500, sse=4087508.5, rms=1.707 (0.000%) 018: dt: 0.2500, sse=3955543.5, rms=1.511 (0.000%) rms = 1.47, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3846167.8, rms=1.474 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3800323.0, rms=1.432 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.2, 21 (3) missing vertices, mean dist -0.1 [0.3 (%72.0)->0.2 (%28.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.53) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3167 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4003219.2, rms=3.28 021: dt: 0.5000, sse=4305613.5, rms=2.452 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4040969.5, rms=1.742 (0.000%) 023: dt: 0.2500, sse=3963460.0, rms=1.401 (0.000%) 024: dt: 0.2500, sse=3935674.0, rms=1.316 (0.000%) rms = 1.32, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3906902.0, rms=1.316 (0.000%) rms = 1.29, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3874962.5, rms=1.290 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.0, 26 (2) missing vertices, mean dist -0.0 [0.2 (%56.8)->0.2 (%43.2))] %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3889749.0, rms=1.61 rms = 1.61, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=4959261.5, rms=1.605 (0.000%) 028: dt: 0.2500, sse=4232694.5, rms=1.227 (0.000%) 029: dt: 0.2500, sse=4419370.0, rms=1.057 (0.000%) rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.03, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4386916.0, rms=1.031 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 23 non-cortical segments detected only using segment with 2186 vertices erasing segment 1 (vno[0] = 57470) erasing segment 2 (vno[0] = 77359) erasing segment 3 (vno[0] = 78446) erasing segment 4 (vno[0] = 82313) erasing segment 5 (vno[0] = 83246) erasing segment 6 (vno[0] = 89295) erasing segment 7 (vno[0] = 93408) erasing segment 8 (vno[0] = 95389) erasing segment 9 (vno[0] = 97402) erasing segment 10 (vno[0] = 97413) erasing segment 11 (vno[0] = 97437) erasing segment 12 (vno[0] = 97489) erasing segment 13 (vno[0] = 98353) erasing segment 14 (vno[0] = 98456) erasing segment 15 (vno[0] = 99252) erasing segment 16 (vno[0] = 99310) erasing segment 17 (vno[0] = 100095) erasing segment 18 (vno[0] = 101770) erasing segment 19 (vno[0] = 101844) erasing segment 20 (vno[0] = 105977) erasing segment 21 (vno[0] = 106623) erasing segment 22 (vno[0] = 134247) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv writing smoothed area to lh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.22) refinement took 4.9 minutes #-------------------------------------------- #@# Smooth2 lh Tue Dec 1 17:28:48 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Tue Dec 1 17:28:51 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.0 mm, total surface area = 81449 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 142 vertices thresholded to be in k1 ~ [-0.23 0.34], k2 ~ [-0.11 0.16] total integrated curvature = 0.531*4pi (6.672) --> 0 handles ICI = 1.6, FI = 9.9, variation=172.204 108 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 140 vertices thresholded to be in [-0.13 0.17] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Tue Dec 1 17:30:43 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 264 ] Gb_filter = 0 WARN: S lookup min: -0.500392 WARN: S explicit min: 0.000000 vertex = 245 #-------------------------------------------- #@# Sphere lh Tue Dec 1 17:30:50 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.283... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %19.75 pass 1: epoch 2 of 3 starting distance error %19.72 unfolding complete - removing small folds... starting distance error %19.69 removing remaining folds... final distance error %19.71 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.72 hours #-------------------------------------------- #@# Surf Reg lh Tue Dec 1 18:13:55 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_register -curv ../surf/lh.sphere /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 0.577 curvature mean = 0.040, std = 0.936 curvature mean = 0.023, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 343481.7, tmin=1.0483 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 279147.0, tmin=2.1109 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 252608.6, tmin=3.1803 d=8.00 min @ (0.00, 2.00, 0.00) sse = 251924.4, tmin=4.2566 d=4.00 min @ (1.00, -1.00, -1.00) sse = 250820.9, tmin=5.3370 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 250138.2, tmin=6.4259 d=1.00 min @ (0.00, 0.25, 0.00) sse = 250049.8, tmin=7.5225 d=0.50 min @ (0.00, 0.00, -0.12) sse = 250048.6, tmin=8.6261 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.63 min curvature mean = 0.014, std = 0.962 curvature mean = 0.010, std = 0.940 curvature mean = 0.011, std = 0.974 curvature mean = 0.005, std = 0.973 curvature mean = 0.009, std = 0.976 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.029, std = 0.296 curvature mean = 0.003, std = 0.067 curvature mean = 0.066, std = 0.343 curvature mean = 0.003, std = 0.080 curvature mean = 0.032, std = 0.529 curvature mean = 0.003, std = 0.086 curvature mean = 0.017, std = 0.670 curvature mean = 0.003, std = 0.089 curvature mean = 0.007, std = 0.778 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Tue Dec 1 18:38:17 EST 2015 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Dec 1 18:38:22 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Dec 1 18:38:24 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1056 labels changed using aseg relabeling using gibbs priors... 000: 3103 changed, 134383 examined... 001: 682 changed, 13015 examined... 002: 173 changed, 3852 examined... 003: 54 changed, 1023 examined... 004: 21 changed, 325 examined... 005: 7 changed, 127 examined... 006: 6 changed, 38 examined... 007: 6 changed, 37 examined... 008: 1 changed, 21 examined... 009: 0 changed, 7 examined... 262 labels changed using aseg 000: 103 total segments, 59 labels (174 vertices) changed 001: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1314 vertices marked for relabeling... 1314 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 52 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Dec 1 18:39:16 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.90 3528 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 58 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 4 with 589 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 20 points - only 0.00% unknown mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.55 2842 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4910133.5, rms=9.91 001: dt: 0.5000, sse=5581897.0, rms=7.091 (0.000%) 002: dt: 0.5000, sse=5969936.5, rms=5.414 (0.000%) 003: dt: 0.5000, sse=6294036.0, rms=4.408 (0.000%) 004: dt: 0.5000, sse=6537145.5, rms=3.792 (0.000%) 005: dt: 0.5000, sse=6679090.0, rms=3.482 (0.000%) 006: dt: 0.5000, sse=6778039.0, rms=3.292 (0.000%) 007: dt: 0.5000, sse=6831903.5, rms=3.217 (0.000%) 008: dt: 0.5000, sse=6847970.5, rms=3.144 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6847041.0, rms=3.127 (0.000%) 010: dt: 0.2500, sse=4111519.8, rms=2.116 (0.000%) 011: dt: 0.2500, sse=3782389.5, rms=1.872 (0.000%) 012: dt: 0.2500, sse=3636471.2, rms=1.817 (0.000%) rms = 1.79, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3588702.2, rms=1.787 (0.000%) rms = 1.76, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3530796.0, rms=1.757 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 141 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 5 with 503 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown deleting segment 10 with 13 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown deleting segment 14 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 6 points - only 0.00% unknown mean border=83.8, 43 (10) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.3 (%26.3))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.39) mean absolute distance = 0.26 +- 0.38 3194 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4126274.5, rms=4.65 015: dt: 0.5000, sse=4428417.5, rms=2.790 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4903927.0, rms=2.784 (0.000%) 017: dt: 0.2500, sse=4116609.8, rms=1.714 (0.000%) 018: dt: 0.2500, sse=3986968.5, rms=1.519 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3878579.5, rms=1.482 (0.000%) rms = 1.44, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3831825.8, rms=1.441 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 519 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 47 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown mean border=86.2, 34 (5) missing vertices, mean dist -0.1 [0.3 (%71.9)->0.2 (%28.1))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.50) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3358 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4036701.0, rms=3.28 021: dt: 0.5000, sse=4342123.5, rms=2.455 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4076523.0, rms=1.751 (0.000%) 023: dt: 0.2500, sse=4000223.8, rms=1.417 (0.000%) 024: dt: 0.2500, sse=3971807.5, rms=1.332 (0.000%) rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.32, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3949862.0, rms=1.318 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 542 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 15 points - only 0.00% unknown mean border=87.0, 45 (4) missing vertices, mean dist -0.0 [0.2 (%56.3)->0.2 (%43.7))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=3965833.5, rms=1.63 rms = 1.67, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4030579.2, rms=1.226 (0.000%) 027: dt: 0.2500, sse=4210250.0, rms=1.000 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4211942.0, rms=0.998 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.1, 63 (63) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.5 (%100.0))] %19 local maxima, %48 large gradients and %29 min vals, 2536 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21210330.0, rms=26.92 001: dt: 0.5000, sse=16190595.0, rms=22.998 (0.000%) 002: dt: 0.5000, sse=12521362.0, rms=19.671 (0.000%) 003: dt: 0.5000, sse=9938165.0, rms=16.901 (0.000%) 004: dt: 0.5000, sse=8274347.5, rms=14.603 (0.000%) 005: dt: 0.5000, sse=7200233.0, rms=12.720 (0.000%) 006: dt: 0.5000, sse=6567840.5, rms=11.201 (0.000%) 007: dt: 0.5000, sse=6195436.0, rms=9.893 (0.000%) 008: dt: 0.5000, sse=5953478.5, rms=8.748 (0.000%) 009: dt: 0.5000, sse=5823097.5, rms=7.723 (0.000%) 010: dt: 0.5000, sse=5755740.0, rms=6.818 (0.000%) 011: dt: 0.5000, sse=5771526.0, rms=6.010 (0.000%) 012: dt: 0.5000, sse=5770032.5, rms=5.284 (0.000%) 013: dt: 0.5000, sse=5831664.5, rms=4.697 (0.000%) 014: dt: 0.5000, sse=5903816.5, rms=4.271 (0.000%) 015: dt: 0.5000, sse=5991542.0, rms=3.985 (0.000%) 016: dt: 0.5000, sse=6059026.0, rms=3.792 (0.000%) 017: dt: 0.5000, sse=6113671.0, rms=3.670 (0.000%) 018: dt: 0.5000, sse=6117787.5, rms=3.576 (0.000%) 019: dt: 0.5000, sse=6162662.5, rms=3.519 (0.000%) rms = 3.47, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6164091.5, rms=3.470 (0.000%) 021: dt: 0.2500, sse=4430887.5, rms=2.863 (0.000%) 022: dt: 0.2500, sse=4274107.5, rms=2.709 (0.000%) rms = 2.69, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4183480.0, rms=2.687 (0.000%) 024: dt: 0.1250, sse=4032809.5, rms=2.613 (0.000%) rms = 2.61, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4015818.5, rms=2.607 (0.000%) positioning took 2.4 minutes mean border=57.7, 970 (29) missing vertices, mean dist 0.2 [0.2 (%45.0)->0.6 (%55.0))] %39 local maxima, %33 large gradients and %23 min vals, 968 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4649037.5, rms=4.74 026: dt: 0.5000, sse=4787437.5, rms=3.735 (0.000%) 027: dt: 0.5000, sse=6092889.0, rms=3.602 (0.000%) rms = 3.61, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5127987.5, rms=3.032 (0.000%) 029: dt: 0.2500, sse=4703083.0, rms=2.790 (0.000%) 030: dt: 0.2500, sse=4684753.0, rms=2.723 (0.000%) rms = 2.70, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4651405.5, rms=2.696 (0.000%) 032: dt: 0.1250, sse=4534031.5, rms=2.606 (0.000%) rms = 2.59, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4528865.5, rms=2.588 (0.000%) positioning took 0.9 minutes mean border=56.1, 1194 (26) missing vertices, mean dist 0.1 [0.2 (%38.2)->0.4 (%61.8))] %55 local maxima, %17 large gradients and %23 min vals, 1145 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4680251.5, rms=3.42 rms = 3.38, time step reduction 1 of 3 to 0.250... 034: dt: 0.5000, sse=4928660.0, rms=3.378 (0.000%) 035: dt: 0.2500, sse=4913630.5, rms=2.724 (0.000%) 036: dt: 0.2500, sse=4936017.0, rms=2.582 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4913444.0, rms=2.578 (0.000%) 038: dt: 0.1250, sse=4789696.0, rms=2.449 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4791635.5, rms=2.431 (0.000%) positioning took 0.6 minutes mean border=55.3, 2550 (26) missing vertices, mean dist 0.0 [0.2 (%44.6)->0.3 (%55.4))] %58 local maxima, %14 large gradients and %22 min vals, 909 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4815846.5, rms=2.61 rms = 3.00, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4723632.5, rms=2.451 (0.000%) rms = 2.40, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=4868891.5, rms=2.403 (0.000%) 042: dt: 0.1250, sse=4780392.0, rms=2.348 (0.000%) rms = 2.33, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4807761.0, rms=2.330 (0.000%) positioning took 0.5 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.06-->7.83) (max @ vno 48431 --> 47310) face area 0.41 +- 0.32 (0.00-->9.57) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 614:1142 truncations. 27931 vertices at 0 distance 88109 vertices at 1 distance 84334 vertices at 2 distance 38319 vertices at 3 distance 12427 vertices at 4 distance 3739 vertices at 5 distance 1252 vertices at 6 distance 382 vertices at 7 distance 138 vertices at 8 distance 63 vertices at 9 distance 59 vertices at 10 distance 39 vertices at 11 distance 26 vertices at 12 distance 23 vertices at 13 distance 16 vertices at 14 distance 21 vertices at 15 distance 12 vertices at 16 distance 10 vertices at 17 distance 8 vertices at 18 distance 14 vertices at 19 distance 12 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.thickness positioning took 10.3 minutes #-------------------------------------------- #@# Surf Volume lh Tue Dec 1 18:49:35 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Make White Surf rh Tue Dec 1 18:49:36 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.73 +- 0.91 3383 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=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.8, 20 (20) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.34) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2632 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5030457.5, rms=9.93 001: dt: 0.5000, sse=5796978.0, rms=7.147 (0.000%) 002: dt: 0.5000, sse=6204708.5, rms=5.513 (0.000%) 003: dt: 0.5000, sse=6478530.5, rms=4.508 (0.000%) 004: dt: 0.5000, sse=6741257.0, rms=3.876 (0.000%) 005: dt: 0.5000, sse=6849746.5, rms=3.534 (0.000%) 006: dt: 0.5000, sse=6977133.5, rms=3.321 (0.000%) 007: dt: 0.5000, sse=7007491.0, rms=3.232 (0.000%) 008: dt: 0.5000, sse=7045294.5, rms=3.150 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7019629.5, rms=3.130 (0.000%) 010: dt: 0.2500, sse=4337829.5, rms=2.129 (0.000%) 011: dt: 0.2500, sse=4012794.8, rms=1.885 (0.000%) 012: dt: 0.2500, sse=3854614.8, rms=1.833 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3814733.5, rms=1.803 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3753020.5, rms=1.766 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.7, 50 (5) missing vertices, mean dist -0.2 [0.4 (%72.0)->0.3 (%28.0))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.50) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.38 3705 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4290996.5, rms=4.34 015: dt: 0.5000, sse=4682878.0, rms=2.732 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4366005.0, rms=2.170 (0.000%) 017: dt: 0.2500, sse=4221162.5, rms=1.753 (0.000%) 018: dt: 0.2500, sse=4126458.0, rms=1.580 (0.000%) 019: dt: 0.2500, sse=4073992.0, rms=1.524 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4057223.8, rms=1.501 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4011195.2, rms=1.471 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.0, 37 (3) missing vertices, mean dist -0.1 [0.3 (%71.2)->0.2 (%28.8))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 (0.10-->4.55) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.89) mean absolute distance = 0.22 +- 0.31 2829 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4209697.5, rms=3.26 022: dt: 0.5000, sse=4551017.0, rms=2.427 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4264880.0, rms=1.765 (0.000%) 024: dt: 0.2500, sse=4191594.2, rms=1.437 (0.000%) 025: dt: 0.2500, sse=4152948.5, rms=1.352 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... rms = 1.34, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4130497.8, rms=1.336 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.8, 45 (2) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4145720.2, rms=1.68 rms = 1.69, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4214452.0, rms=1.265 (0.000%) 028: dt: 0.2500, sse=4405054.5, rms=1.016 (0.000%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4404326.0, rms=1.012 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 14 non-cortical segments detected only using segment with 2295 vertices erasing segment 1 (vno[0] = 45502) erasing segment 2 (vno[0] = 83943) erasing segment 3 (vno[0] = 94873) erasing segment 4 (vno[0] = 94892) erasing segment 5 (vno[0] = 94904) erasing segment 6 (vno[0] = 95880) erasing segment 7 (vno[0] = 96851) erasing segment 8 (vno[0] = 99617) erasing segment 9 (vno[0] = 101371) erasing segment 10 (vno[0] = 102196) erasing segment 11 (vno[0] = 102270) erasing segment 12 (vno[0] = 103084) erasing segment 13 (vno[0] = 103867) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv writing smoothed area to rh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.86) refinement took 5.0 minutes #-------------------------------------------- #@# Smooth2 rh Tue Dec 1 18:54:38 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Tue Dec 1 18:54:42 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 45.8 mm, total surface area = 81849 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.118 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 152 vertices thresholded to be in k1 ~ [-0.31 0.35], k2 ~ [-0.11 0.10] total integrated curvature = 0.566*4pi (7.107) --> 0 handles ICI = 1.4, FI = 8.6, variation=148.938 113 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 133 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats rh Tue Dec 1 18:56:33 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 245 ] Gb_filter = 0 WARN: S lookup min: -0.817811 WARN: S explicit min: 0.000000 vertex = 427 #-------------------------------------------- #@# Sphere rh Tue Dec 1 18:56:40 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %20.14 pass 1: epoch 2 of 3 starting distance error %20.07 unfolding complete - removing small folds... starting distance error %19.94 removing remaining folds... final distance error %19.96 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.81 hours #-------------------------------------------- #@# Surf Reg rh Tue Dec 1 19:45:32 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_register -curv ../surf/rh.sphere /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, 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 = 0.591 curvature mean = 0.043, std = 0.931 curvature mean = 0.021, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 16.00) sse = 361095.2, tmin=1.0552 d=32.00 min @ (0.00, 8.00, 0.00) sse = 327242.8, tmin=2.1162 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 305767.9, tmin=3.1835 d=4.00 min @ (1.00, 0.00, 1.00) sse = 304760.8, tmin=5.3916 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 304666.7, tmin=6.5096 d=1.00 min @ (0.25, 0.25, 0.00) sse = 304561.9, tmin=7.6094 d=0.50 min @ (-0.12, 0.00, -0.12) sse = 304536.6, tmin=8.7204 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.72 min curvature mean = 0.029, std = 0.960 curvature mean = 0.007, std = 0.938 curvature mean = 0.026, std = 0.969 curvature mean = 0.004, std = 0.971 curvature mean = 0.024, std = 0.969 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.026, std = 0.388 curvature mean = 0.006, std = 0.069 curvature mean = 0.048, std = 0.263 curvature mean = 0.006, std = 0.083 curvature mean = 0.024, std = 0.410 curvature mean = 0.007, std = 0.089 curvature mean = 0.014, std = 0.517 curvature mean = 0.007, std = 0.091 curvature mean = 0.005, std = 0.613 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Dec 1 20:11:49 EST 2015 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Dec 1 20:11:51 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Dec 1 20:11:53 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1202 labels changed using aseg relabeling using gibbs priors... 000: 3050 changed, 134806 examined... 001: 715 changed, 13277 examined... 002: 174 changed, 3906 examined... 003: 75 changed, 1057 examined... 004: 34 changed, 433 examined... 005: 17 changed, 206 examined... 006: 8 changed, 100 examined... 007: 4 changed, 41 examined... 008: 4 changed, 26 examined... 009: 1 changed, 22 examined... 010: 1 changed, 8 examined... 011: 2 changed, 8 examined... 012: 1 changed, 10 examined... 013: 0 changed, 7 examined... 159 labels changed using aseg 000: 95 total segments, 57 labels (335 vertices) changed 001: 41 total segments, 3 labels (4 vertices) changed 002: 38 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... 1082 vertices marked for relabeling... 1082 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 42 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Dec 1 20:12:35 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.73 +- 0.92 3430 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 384 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=80.8, 25 (24) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.34) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2670 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5040671.0, rms=9.92 001: dt: 0.5000, sse=5813598.0, rms=7.141 (0.000%) 002: dt: 0.5000, sse=6224298.5, rms=5.510 (0.000%) 003: dt: 0.5000, sse=6498853.5, rms=4.506 (0.000%) 004: dt: 0.5000, sse=6762585.5, rms=3.875 (0.000%) 005: dt: 0.5000, sse=6869478.0, rms=3.534 (0.000%) 006: dt: 0.5000, sse=6998033.0, rms=3.321 (0.000%) 007: dt: 0.5000, sse=7028486.0, rms=3.233 (0.000%) 008: dt: 0.5000, sse=7066930.0, rms=3.151 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7039925.0, rms=3.131 (0.000%) 010: dt: 0.2500, sse=4354474.0, rms=2.132 (0.000%) 011: dt: 0.2500, sse=4028360.5, rms=1.889 (0.000%) 012: dt: 0.2500, sse=3870135.0, rms=1.837 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3829512.0, rms=1.807 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3767567.2, rms=1.770 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 299 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 22 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown mean border=83.7, 54 (6) missing vertices, mean dist -0.2 [0.4 (%71.9)->0.3 (%28.1))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.50) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.39 3758 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4309256.5, rms=4.33 015: dt: 0.5000, sse=4700820.5, rms=2.732 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4385123.5, rms=2.172 (0.000%) 017: dt: 0.2500, sse=4242888.0, rms=1.755 (0.000%) 018: dt: 0.2500, sse=4147145.0, rms=1.583 (0.000%) 019: dt: 0.2500, sse=4094185.8, rms=1.528 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4076906.5, rms=1.504 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4030592.8, rms=1.474 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 303 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=86.0, 38 (3) missing vertices, mean dist -0.1 [0.3 (%71.1)->0.2 (%28.9))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 (0.10-->4.55) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.89) mean absolute distance = 0.22 +- 0.32 2871 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4229315.5, rms=3.25 022: dt: 0.5000, sse=4573934.5, rms=2.426 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4286142.5, rms=1.767 (0.000%) 024: dt: 0.2500, sse=4210874.5, rms=1.440 (0.000%) 025: dt: 0.2500, sse=4174444.5, rms=1.356 (0.000%) rms = 1.36, time step reduction 2 of 3 to 0.125... rms = 1.34, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4151896.8, rms=1.340 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 311 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=86.8, 47 (2) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4167169.2, rms=1.69 rms = 1.69, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4237478.0, rms=1.268 (0.000%) 028: dt: 0.2500, sse=4432497.0, rms=1.019 (0.000%) rms = 1.03, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4431764.5, rms=1.016 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=60.2, 52 (52) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.6 (%100.0))] %19 local maxima, %44 large gradients and %32 min vals, 2330 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21095174.0, rms=26.68 001: dt: 0.5000, sse=16219415.0, rms=22.858 (0.000%) 002: dt: 0.5000, sse=12634789.0, rms=19.614 (0.000%) 003: dt: 0.5000, sse=10127611.0, rms=16.925 (0.000%) 004: dt: 0.5000, sse=8511865.0, rms=14.699 (0.000%) 005: dt: 0.5000, sse=7457957.5, rms=12.869 (0.000%) 006: dt: 0.5000, sse=6784133.0, rms=11.402 (0.000%) 007: dt: 0.5000, sse=6385647.5, rms=10.144 (0.000%) 008: dt: 0.5000, sse=6107506.0, rms=9.027 (0.000%) 009: dt: 0.5000, sse=5971715.0, rms=7.991 (0.000%) 010: dt: 0.5000, sse=5883049.0, rms=7.059 (0.000%) 011: dt: 0.5000, sse=5875117.5, rms=6.211 (0.000%) 012: dt: 0.5000, sse=5878926.0, rms=5.469 (0.000%) 013: dt: 0.5000, sse=5950857.0, rms=4.853 (0.000%) 014: dt: 0.5000, sse=6024235.5, rms=4.415 (0.000%) 015: dt: 0.5000, sse=6134776.5, rms=4.094 (0.000%) 016: dt: 0.5000, sse=6184613.5, rms=3.893 (0.000%) 017: dt: 0.5000, sse=6226774.5, rms=3.746 (0.000%) 018: dt: 0.5000, sse=6247221.0, rms=3.669 (0.000%) 019: dt: 0.5000, sse=6298535.5, rms=3.597 (0.000%) rms = 3.56, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6292106.0, rms=3.561 (0.000%) 021: dt: 0.2500, sse=4602540.5, rms=2.967 (0.000%) 022: dt: 0.2500, sse=4443622.5, rms=2.815 (0.000%) rms = 2.79, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4347487.5, rms=2.789 (0.000%) 024: dt: 0.1250, sse=4178397.2, rms=2.706 (0.000%) rms = 2.70, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4153944.8, rms=2.698 (0.000%) positioning took 2.6 minutes mean border=58.0, 1075 (3) missing vertices, mean dist 0.2 [0.2 (%44.5)->0.6 (%55.5))] %38 local maxima, %31 large gradients and %25 min vals, 861 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4762497.5, rms=4.68 026: dt: 0.5000, sse=4969183.5, rms=3.783 (0.000%) 027: dt: 0.5000, sse=6246533.0, rms=3.640 (0.000%) rms = 3.64, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=6107095.5, rms=3.635 (0.000%) 029: dt: 0.2500, sse=5066130.5, rms=2.924 (0.000%) 030: dt: 0.2500, sse=4962338.0, rms=2.729 (0.000%) rms = 2.72, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4899494.0, rms=2.721 (0.000%) 032: dt: 0.1250, sse=4743177.5, rms=2.613 (0.000%) rms = 2.60, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4731522.5, rms=2.598 (0.000%) positioning took 0.8 minutes mean border=56.5, 1297 (2) missing vertices, mean dist 0.1 [0.2 (%39.1)->0.4 (%60.9))] %52 local maxima, %18 large gradients and %25 min vals, 965 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4869240.0, rms=3.34 rms = 3.42, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4704507.0, rms=2.982 (0.000%) 035: dt: 0.2500, sse=4726097.0, rms=2.761 (0.000%) 036: dt: 0.2500, sse=4896541.5, rms=2.690 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4960427.5, rms=2.668 (0.000%) 038: dt: 0.1250, sse=4843940.5, rms=2.586 (0.000%) rms = 2.57, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4865271.5, rms=2.570 (0.000%) positioning took 0.7 minutes mean border=55.8, 2773 (2) missing vertices, mean dist 0.1 [0.2 (%44.5)->0.3 (%55.5))] %55 local maxima, %14 large gradients and %25 min vals, 843 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4889507.0, rms=2.76 rms = 3.10, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4818572.5, rms=2.609 (0.000%) 041: dt: 0.2500, sse=5004985.5, rms=2.554 (0.000%) rms = 2.53, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5068982.0, rms=2.535 (0.000%) 043: dt: 0.1250, sse=4985673.0, rms=2.457 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5013903.0, rms=2.440 (0.000%) positioning took 0.6 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area.pial vertex spacing 1.01 +- 0.44 (0.04-->6.99) (max @ vno 101451 --> 134658) face area 0.40 +- 0.31 (0.00-->4.95) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 784:1305 truncations. 25877 vertices at 0 distance 84621 vertices at 1 distance 85363 vertices at 2 distance 41293 vertices at 3 distance 14079 vertices at 4 distance 4337 vertices at 5 distance 1349 vertices at 6 distance 484 vertices at 7 distance 202 vertices at 8 distance 107 vertices at 9 distance 64 vertices at 10 distance 54 vertices at 11 distance 47 vertices at 12 distance 40 vertices at 13 distance 26 vertices at 14 distance 22 vertices at 15 distance 11 vertices at 16 distance 10 vertices at 17 distance 20 vertices at 18 distance 9 vertices at 19 distance 3 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.thickness positioning took 11.0 minutes #-------------------------------------------- #@# Surf Volume rh Tue Dec 1 20:23:36 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Tue Dec 1 20:23:36 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.04-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 602 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=compu, 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 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=compu, 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=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [92.20 173.80], gm=133.00+-13.60, and vertices in regions > 126.2 14552 surface locations found to contain inconsistent values (14297 in, 255 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=472305.5, rms=0.21 001: dt: 0.5000, sse=444260.5, rms=0.205 (0.000%) 002: dt: 0.5000, sse=421809.5, rms=0.194 (0.000%) 003: dt: 0.5000, sse=407687.8, rms=0.185 (0.000%) 004: dt: 0.5000, sse=396863.3, rms=0.176 (0.000%) 005: dt: 0.5000, sse=388843.9, rms=0.168 (0.000%) 006: dt: 0.5000, sse=381906.5, rms=0.160 (0.000%) 007: dt: 0.5000, sse=376432.4, rms=0.154 (0.000%) 008: dt: 0.5000, sse=371905.8, rms=0.148 (0.000%) 009: dt: 0.5000, sse=367695.6, rms=0.142 (0.000%) 010: dt: 0.5000, sse=364125.8, rms=0.137 (0.000%) 011: dt: 0.5000, sse=361083.9, rms=0.133 (0.000%) 012: dt: 0.5000, sse=358422.6, rms=0.129 (0.000%) 013: dt: 0.5000, sse=356064.7, rms=0.125 (0.000%) 014: dt: 0.5000, sse=353791.0, rms=0.122 (0.000%) 015: dt: 0.5000, sse=351691.0, rms=0.119 (0.000%) 016: dt: 0.5000, sse=349777.4, rms=0.117 (0.000%) 017: dt: 0.5000, sse=348005.8, rms=0.115 (0.000%) 018: dt: 0.5000, sse=346400.8, rms=0.113 (0.000%) 019: dt: 0.5000, sse=344816.1, rms=0.112 (0.000%) 020: dt: 0.5000, sse=343302.3, rms=0.110 (0.000%) 021: dt: 0.5000, sse=341740.5, rms=0.109 (0.000%) 022: dt: 0.5000, sse=340381.9, rms=0.108 (0.000%) 023: dt: 0.5000, sse=339083.9, rms=0.108 (0.000%) 024: dt: 0.5000, sse=337783.5, rms=0.107 (0.000%) 025: dt: 0.5000, sse=336731.9, rms=0.107 (0.000%) 026: dt: 0.5000, sse=335736.1, rms=0.106 (0.000%) 027: dt: 0.5000, sse=334848.0, rms=0.106 (0.000%) 028: dt: 0.5000, sse=333960.9, rms=0.106 (0.000%) 029: dt: 0.5000, sse=332960.8, rms=0.106 (0.000%) 030: dt: 0.5000, sse=332064.1, rms=0.106 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 2866 surface locations found to contain inconsistent values (2659 in, 207 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=33232.4, rms=0.06 031: dt: 0.5000, sse=33124.9, rms=0.061 (0.000%) 032: dt: 0.5000, sse=33098.5, rms=0.057 (0.000%) 033: dt: 0.5000, sse=33131.1, rms=0.054 (0.000%) 034: dt: 0.5000, sse=33163.9, rms=0.052 (0.000%) 035: dt: 0.5000, sse=33191.3, rms=0.049 (0.000%) 036: dt: 0.5000, sse=33245.7, rms=0.047 (0.000%) 037: dt: 0.5000, sse=33280.5, rms=0.045 (0.000%) 038: dt: 0.5000, sse=33320.0, rms=0.044 (0.000%) 039: dt: 0.5000, sse=33365.9, rms=0.042 (0.000%) 040: dt: 0.5000, sse=33402.3, rms=0.040 (0.000%) 041: dt: 0.5000, sse=33440.8, rms=0.039 (0.000%) 042: dt: 0.5000, sse=33469.8, rms=0.037 (0.000%) 043: dt: 0.5000, sse=33489.4, rms=0.036 (0.000%) 044: dt: 0.5000, sse=33524.6, rms=0.035 (0.000%) 045: dt: 0.5000, sse=33544.5, rms=0.034 (0.000%) 046: dt: 0.5000, sse=33567.3, rms=0.032 (0.000%) 047: dt: 0.5000, sse=33609.8, rms=0.031 (0.000%) 048: dt: 0.5000, sse=33634.9, rms=0.030 (0.000%) 049: dt: 0.5000, sse=33649.1, rms=0.029 (0.000%) 050: dt: 0.5000, sse=33673.5, rms=0.029 (0.000%) 051: dt: 0.5000, sse=33697.0, rms=0.028 (0.000%) 052: dt: 0.5000, sse=33719.1, rms=0.027 (0.000%) 053: dt: 0.5000, sse=33735.4, rms=0.026 (0.000%) 054: dt: 0.5000, sse=33745.0, rms=0.026 (0.000%) 055: dt: 0.5000, sse=33772.2, rms=0.025 (0.000%) 056: dt: 0.5000, sse=33776.5, rms=0.024 (0.000%) 057: dt: 0.5000, sse=33785.8, rms=0.024 (0.000%) 058: dt: 0.5000, sse=33795.3, rms=0.023 (0.000%) 059: dt: 0.5000, sse=33814.4, rms=0.023 (0.000%) 060: dt: 0.5000, sse=33814.1, rms=0.022 (0.000%) positioning took 3.0 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 727 surface locations found to contain inconsistent values (529 in, 198 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3440.5, rms=0.02 061: dt: 0.5000, sse=3437.9, rms=0.022 (0.000%) 062: dt: 0.5000, sse=3437.1, rms=0.021 (0.000%) 063: dt: 0.5000, sse=3436.7, rms=0.020 (0.000%) 064: dt: 0.5000, sse=3436.0, rms=0.019 (0.000%) 065: dt: 0.5000, sse=3435.9, rms=0.019 (0.000%) 066: dt: 0.5000, sse=3436.4, rms=0.018 (0.000%) 067: dt: 0.5000, sse=3434.9, rms=0.018 (0.000%) 068: dt: 0.5000, sse=3434.3, rms=0.017 (0.000%) 069: dt: 0.5000, sse=3433.9, rms=0.017 (0.000%) 070: dt: 0.5000, sse=3434.3, rms=0.017 (0.000%) 071: dt: 0.5000, sse=3434.3, rms=0.016 (0.000%) 072: dt: 0.5000, sse=3434.1, rms=0.016 (0.000%) 073: dt: 0.5000, sse=3434.4, rms=0.016 (0.000%) 074: dt: 0.5000, sse=3434.1, rms=0.016 (0.000%) 075: dt: 0.5000, sse=3434.8, rms=0.016 (0.000%) 076: dt: 0.5000, sse=3434.8, rms=0.015 (0.000%) 077: dt: 0.5000, sse=3435.2, rms=0.015 (0.000%) 078: dt: 0.5000, sse=3435.1, rms=0.015 (0.000%) 079: dt: 0.5000, sse=3435.0, rms=0.015 (0.000%) 080: dt: 0.5000, sse=3435.4, rms=0.015 (0.000%) 081: dt: 0.5000, sse=3435.3, rms=0.015 (0.000%) 082: dt: 0.5000, sse=3435.1, rms=0.015 (0.000%) 083: dt: 0.5000, sse=3435.8, rms=0.015 (0.000%) 084: dt: 0.5000, sse=3435.8, rms=0.014 (0.000%) 085: dt: 0.5000, sse=3436.1, rms=0.014 (0.000%) 086: dt: 0.5000, sse=3436.3, rms=0.014 (0.000%) 087: dt: 0.5000, sse=3436.6, rms=0.014 (0.000%) 088: dt: 0.5000, sse=3436.4, rms=0.014 (0.000%) 089: dt: 0.5000, sse=3436.2, rms=0.014 (0.000%) 090: dt: 0.5000, sse=3436.9, rms=0.014 (0.000%) positioning took 2.9 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 262 surface locations found to contain inconsistent values (63 in, 199 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=366.2, rms=0.01 091: dt: 0.5000, sse=366.2, rms=0.014 (0.000%) 092: dt: 0.5000, sse=365.8, rms=0.014 (0.000%) 093: dt: 0.5000, sse=365.5, rms=0.014 (0.000%) 094: dt: 0.5000, sse=365.3, rms=0.014 (0.000%) 095: dt: 0.5000, sse=365.2, rms=0.014 (0.000%) 096: dt: 0.5000, sse=365.1, rms=0.014 (0.000%) 097: dt: 0.5000, sse=365.0, rms=0.014 (0.000%) 098: dt: 0.5000, sse=364.9, rms=0.014 (0.000%) 099: dt: 0.5000, sse=364.9, rms=0.014 (0.000%) 100: dt: 0.5000, sse=364.8, rms=0.014 (0.000%) 101: dt: 0.5000, sse=364.8, rms=0.013 (0.000%) 102: dt: 0.5000, sse=364.7, rms=0.013 (0.000%) 103: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 104: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 105: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 106: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 107: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 108: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 109: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 110: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 111: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 112: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 113: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 114: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 115: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 116: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 117: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 118: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 119: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 120: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) positioning took 2.9 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area.pial vertex spacing 1.00 +- 0.43 (0.04-->8.03) (max @ vno 92642 --> 92643) face area 0.39 +- 0.30 (0.00-->10.95) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 600:981 truncations. 28508 vertices at 0 distance 88163 vertices at 1 distance 83783 vertices at 2 distance 38396 vertices at 3 distance 12342 vertices at 4 distance 3767 vertices at 5 distance 1244 vertices at 6 distance 425 vertices at 7 distance 141 vertices at 8 distance 72 vertices at 9 distance 43 vertices at 10 distance 40 vertices at 11 distance 20 vertices at 12 distance 16 vertices at 13 distance 12 vertices at 14 distance 13 vertices at 15 distance 11 vertices at 16 distance 7 vertices at 17 distance 8 vertices at 18 distance 8 vertices at 19 distance 15 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.thickness positioning took 14.7 minutes /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 380 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.00, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.02, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=compu, 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 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.00, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=compu, 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=4390928.5, rms=0.00 rms = 1.02, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 13521 surface locations found to contain inconsistent values (13344 in, 177 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=489117.8, rms=0.21 001: dt: 0.5000, sse=457629.3, rms=0.199 (0.000%) 002: dt: 0.5000, sse=434001.4, rms=0.188 (0.000%) 003: dt: 0.5000, sse=419565.2, rms=0.180 (0.000%) 004: dt: 0.5000, sse=407977.9, rms=0.171 (0.000%) 005: dt: 0.5000, sse=399536.7, rms=0.164 (0.000%) 006: dt: 0.5000, sse=392343.6, rms=0.157 (0.000%) 007: dt: 0.5000, sse=386541.2, rms=0.151 (0.000%) 008: dt: 0.5000, sse=381371.6, rms=0.145 (0.000%) 009: dt: 0.5000, sse=377076.8, rms=0.140 (0.000%) 010: dt: 0.5000, sse=373152.3, rms=0.135 (0.000%) 011: dt: 0.5000, sse=369700.8, rms=0.131 (0.000%) 012: dt: 0.5000, sse=366605.1, rms=0.128 (0.000%) 013: dt: 0.5000, sse=363736.5, rms=0.124 (0.000%) 014: dt: 0.5000, sse=360975.4, rms=0.121 (0.000%) 015: dt: 0.5000, sse=358703.4, rms=0.118 (0.000%) 016: dt: 0.5000, sse=356400.9, rms=0.116 (0.000%) 017: dt: 0.5000, sse=354514.8, rms=0.114 (0.000%) 018: dt: 0.5000, sse=352853.1, rms=0.112 (0.000%) 019: dt: 0.5000, sse=350970.0, rms=0.110 (0.000%) 020: dt: 0.5000, sse=349133.9, rms=0.109 (0.000%) 021: dt: 0.5000, sse=347413.0, rms=0.107 (0.000%) 022: dt: 0.5000, sse=346105.8, rms=0.106 (0.000%) 023: dt: 0.5000, sse=344796.4, rms=0.105 (0.000%) 024: dt: 0.5000, sse=343241.6, rms=0.104 (0.000%) 025: dt: 0.5000, sse=342058.9, rms=0.104 (0.000%) 026: dt: 0.5000, sse=340694.0, rms=0.103 (0.000%) 027: dt: 0.5000, sse=339543.8, rms=0.102 (0.000%) 028: dt: 0.5000, sse=338511.8, rms=0.102 (0.000%) 029: dt: 0.5000, sse=337478.8, rms=0.102 (0.000%) 030: dt: 0.5000, sse=336519.2, rms=0.102 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 4103 surface locations found to contain inconsistent values (3938 in, 165 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=33749.7, rms=0.07 031: dt: 0.5000, sse=33605.8, rms=0.065 (0.000%) 032: dt: 0.5000, sse=33624.2, rms=0.061 (0.000%) 033: dt: 0.5000, sse=33699.0, rms=0.057 (0.000%) 034: dt: 0.5000, sse=33759.0, rms=0.054 (0.000%) 035: dt: 0.5000, sse=33808.3, rms=0.052 (0.000%) 036: dt: 0.5000, sse=33860.1, rms=0.049 (0.000%) 037: dt: 0.5000, sse=33900.6, rms=0.047 (0.000%) 038: dt: 0.5000, sse=33953.3, rms=0.045 (0.000%) 039: dt: 0.5000, sse=33991.1, rms=0.043 (0.000%) 040: dt: 0.5000, sse=34026.4, rms=0.041 (0.000%) 041: dt: 0.5000, sse=34062.4, rms=0.040 (0.000%) 042: dt: 0.5000, sse=34083.4, rms=0.038 (0.000%) 043: dt: 0.5000, sse=34114.1, rms=0.037 (0.000%) 044: dt: 0.5000, sse=34145.6, rms=0.035 (0.000%) 045: dt: 0.5000, sse=34177.8, rms=0.034 (0.000%) 046: dt: 0.5000, sse=34198.5, rms=0.033 (0.000%) 047: dt: 0.5000, sse=34226.3, rms=0.031 (0.000%) 048: dt: 0.5000, sse=34249.0, rms=0.030 (0.000%) 049: dt: 0.5000, sse=34279.6, rms=0.029 (0.000%) 050: dt: 0.5000, sse=34301.8, rms=0.029 (0.000%) 051: dt: 0.5000, sse=34317.2, rms=0.028 (0.000%) 052: dt: 0.5000, sse=34330.8, rms=0.027 (0.000%) 053: dt: 0.5000, sse=34351.1, rms=0.026 (0.000%) 054: dt: 0.5000, sse=34369.1, rms=0.026 (0.000%) 055: dt: 0.5000, sse=34373.8, rms=0.025 (0.000%) 056: dt: 0.5000, sse=34383.5, rms=0.024 (0.000%) 057: dt: 0.5000, sse=34392.1, rms=0.024 (0.000%) 058: dt: 0.5000, sse=34404.5, rms=0.023 (0.000%) 059: dt: 0.5000, sse=34414.8, rms=0.023 (0.000%) 060: dt: 0.5000, sse=34432.2, rms=0.023 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 755 surface locations found to contain inconsistent values (597 in, 158 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3496.5, rms=0.02 061: dt: 0.5000, sse=3495.3, rms=0.021 (0.000%) 062: dt: 0.5000, sse=3496.2, rms=0.020 (0.000%) 063: dt: 0.5000, sse=3497.6, rms=0.019 (0.000%) 064: dt: 0.5000, sse=3499.3, rms=0.019 (0.000%) 065: dt: 0.5000, sse=3500.1, rms=0.019 (0.000%) 066: dt: 0.5000, sse=3500.1, rms=0.018 (0.000%) 067: dt: 0.5000, sse=3499.9, rms=0.018 (0.000%) 068: dt: 0.5000, sse=3500.0, rms=0.018 (0.000%) 069: dt: 0.5000, sse=3499.6, rms=0.017 (0.000%) 070: dt: 0.5000, sse=3500.5, rms=0.017 (0.000%) 071: dt: 0.5000, sse=3499.0, rms=0.017 (0.000%) 072: dt: 0.5000, sse=3499.3, rms=0.017 (0.000%) 073: dt: 0.5000, sse=3499.9, rms=0.017 (0.000%) 074: dt: 0.5000, sse=3500.2, rms=0.016 (0.000%) 075: dt: 0.5000, sse=3499.7, rms=0.016 (0.000%) 076: dt: 0.5000, sse=3499.8, rms=0.016 (0.000%) 077: dt: 0.5000, sse=3500.0, rms=0.016 (0.000%) 078: dt: 0.5000, sse=3500.3, rms=0.016 (0.000%) 079: dt: 0.5000, sse=3500.5, rms=0.016 (0.000%) 080: dt: 0.5000, sse=3500.7, rms=0.016 (0.000%) 081: dt: 0.5000, sse=3501.3, rms=0.016 (0.000%) 082: dt: 0.5000, sse=3502.6, rms=0.016 (0.000%) 083: dt: 0.5000, sse=3502.9, rms=0.016 (0.000%) 084: dt: 0.5000, sse=3503.0, rms=0.016 (0.000%) 085: dt: 0.5000, sse=3503.2, rms=0.016 (0.000%) 086: dt: 0.5000, sse=3503.1, rms=0.016 (0.000%) 087: dt: 0.5000, sse=3504.2, rms=0.016 (0.000%) 088: dt: 0.5000, sse=3504.4, rms=0.016 (0.000%) 089: dt: 0.5000, sse=3504.1, rms=0.016 (0.000%) 090: dt: 0.5000, sse=3504.0, rms=0.016 (0.000%) positioning took 2.9 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 228 surface locations found to contain inconsistent values (75 in, 153 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=377.5, rms=0.02 091: dt: 0.5000, sse=378.6, rms=0.016 (0.000%) 092: dt: 0.5000, sse=378.0, rms=0.015 (0.000%) 093: dt: 0.5000, sse=378.4, rms=0.015 (0.000%) 094: dt: 0.5000, sse=377.9, rms=0.015 (0.000%) 095: dt: 0.5000, sse=377.5, rms=0.015 (0.000%) 096: dt: 0.5000, sse=377.1, rms=0.015 (0.000%) 097: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 098: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 099: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 100: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 101: dt: 0.5000, sse=377.6, rms=0.015 (0.000%) 102: dt: 0.5000, sse=377.9, rms=0.015 (0.000%) 103: dt: 0.5000, sse=377.5, rms=0.015 (0.000%) 104: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 105: dt: 0.5000, sse=377.4, rms=0.015 (0.000%) 106: dt: 0.5000, sse=377.3, rms=0.015 (0.000%) 107: dt: 0.5000, sse=377.1, rms=0.015 (0.000%) 108: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 109: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 110: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 111: dt: 0.5000, sse=377.7, rms=0.015 (0.000%) 112: dt: 0.5000, sse=377.6, rms=0.015 (0.000%) 113: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 114: dt: 0.5000, sse=376.9, rms=0.015 (0.000%) 115: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 116: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 117: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 118: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 119: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 120: dt: 0.5000, sse=376.7, rms=0.015 (0.000%) positioning took 2.9 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area.pial vertex spacing 0.99 +- 0.43 (0.05-->7.35) (max @ vno 101451 --> 134658) face area 0.39 +- 0.30 (0.00-->5.06) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 778:1103 truncations. 27462 vertices at 0 distance 86290 vertices at 1 distance 84109 vertices at 2 distance 40276 vertices at 3 distance 13389 vertices at 4 distance 4172 vertices at 5 distance 1366 vertices at 6 distance 465 vertices at 7 distance 229 vertices at 8 distance 115 vertices at 9 distance 58 vertices at 10 distance 37 vertices at 11 distance 51 vertices at 12 distance 49 vertices at 13 distance 21 vertices at 14 distance 8 vertices at 15 distance 13 vertices at 16 distance 9 vertices at 17 distance 7 vertices at 18 distance 7 vertices at 19 distance 3 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.thickness positioning took 15.0 minutes #-------------------------------------------- #@# Surf Volume lh Tue Dec 1 20:53:28 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Surf Volume rh Tue Dec 1 20:53:28 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Tue Dec 1 20:53:29 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1584 1096 2875 2.489 0.530 0.114 0.032 12 2.2 bankssts 789 507 1495 2.661 0.477 0.152 0.044 14 1.6 caudalanteriorcingulate 2765 1859 5182 2.593 0.570 0.140 0.067 167 8.6 caudalmiddlefrontal 1917 1225 2555 1.949 0.422 0.165 0.068 36 5.2 cuneus 622 410 1341 2.764 0.564 0.128 0.049 7 1.2 entorhinal 4867 3257 10270 2.835 0.561 0.162 0.071 103 14.5 fusiform 6836 4574 12418 2.499 0.486 0.145 0.055 113 15.5 inferiorparietal 4680 3132 10037 2.856 0.759 0.152 0.096 95 11.5 inferiortemporal 1431 927 2491 2.593 0.674 0.156 0.064 33 3.5 isthmuscingulate 8254 5273 11527 2.054 0.512 0.149 0.056 137 20.0 lateraloccipital 3790 2560 7678 2.731 0.683 0.153 0.067 70 10.7 lateralorbitofrontal 5400 3475 8106 2.183 0.558 0.159 0.064 91 14.0 lingual 2479 1635 4419 2.398 0.685 0.163 0.096 126 9.7 medialorbitofrontal 4545 3086 10932 2.876 0.668 0.142 0.052 77 9.5 middletemporal 1146 731 1953 2.407 0.561 0.121 0.039 10 2.0 parahippocampal 2004 1283 3370 2.399 0.476 0.130 0.112 89 10.2 paracentral 2911 2005 6138 2.715 0.416 0.134 0.046 39 5.4 parsopercularis 933 614 2243 2.827 0.529 0.169 0.153 61 8.6 parsorbitalis 1982 1338 4111 2.718 0.543 0.137 0.045 29 3.6 parstriangularis 2156 1370 2449 1.917 0.455 0.130 0.058 27 4.8 pericalcarine 6459 4112 10363 2.256 0.683 0.133 0.048 94 13.5 postcentral 1744 1188 3384 2.702 0.619 0.164 0.062 38 4.2 posteriorcingulate 7497 4785 13586 2.612 0.589 0.138 0.060 105 18.6 precentral 5881 4013 10123 2.358 0.548 0.145 0.068 99 11.7 precuneus 1067 686 2451 3.079 0.782 0.163 0.061 22 2.5 rostralanteriorcingulate 7995 5492 16389 2.553 0.628 0.162 0.070 162 22.1 rostralmiddlefrontal 9871 6735 23089 2.984 0.609 0.151 0.063 172 27.7 superiorfrontal 7763 5131 12315 2.194 0.506 0.144 0.064 396 16.2 superiorparietal 6185 4127 13956 2.914 0.607 0.129 0.051 79 12.3 superiortemporal 5512 3663 11335 2.782 0.548 0.144 0.058 100 12.6 supramarginal 280 192 765 2.981 0.448 0.260 0.176 16 2.1 frontalpole 620 433 2312 3.461 0.849 0.194 0.103 19 3.0 temporalpole 866 518 1557 2.562 0.544 0.134 0.105 16 4.9 transversetemporal 3115 2040 6764 3.227 0.793 0.118 0.048 38 6.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Tue Dec 1 20:53:42 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 180 labels changed using aseg relabeling using gibbs priors... 000: 9295 changed, 134383 examined... 001: 2265 changed, 35617 examined... 002: 701 changed, 11469 examined... 003: 273 changed, 3914 examined... 004: 121 changed, 1548 examined... 005: 53 changed, 686 examined... 006: 34 changed, 324 examined... 007: 17 changed, 185 examined... 008: 13 changed, 85 examined... 009: 11 changed, 66 examined... 010: 5 changed, 64 examined... 011: 3 changed, 30 examined... 012: 1 changed, 15 examined... 013: 0 changed, 7 examined... 94 labels changed using aseg 000: 304 total segments, 224 labels (3092 vertices) changed 001: 96 total segments, 17 labels (152 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 123 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 567 vertices marked for relabeling... 567 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 46 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Tue Dec 1 20:54:29 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1059 718 2124 2.409 0.714 0.185 0.091 27 3.9 G_and_S_frontomargin 1520 1033 2481 2.232 0.462 0.161 0.051 26 3.3 G_and_S_occipital_inf 1504 902 2436 2.243 0.480 0.131 0.100 80 9.4 G_and_S_paracentral 1564 1018 3374 2.905 0.584 0.161 0.067 32 4.1 G_and_S_subcentral 687 468 1759 2.610 0.694 0.225 0.132 29 3.5 G_and_S_transv_frontopol 2103 1400 4568 3.086 0.723 0.158 0.056 38 4.7 G_and_S_cingul-Ant 1068 723 2114 2.686 0.530 0.132 0.039 12 1.8 G_and_S_cingul-Mid-Ant 1302 914 2513 2.656 0.520 0.146 0.056 19 2.7 G_and_S_cingul-Mid-Post 516 342 1282 3.130 0.578 0.178 0.066 14 1.3 G_cingul-Post-dorsal 347 209 551 2.306 0.690 0.156 0.074 10 0.9 G_cingul-Post-ventral 1684 1029 2205 1.899 0.416 0.168 0.074 35 5.1 G_cuneus 1543 1077 4051 2.899 0.370 0.153 0.060 30 4.0 G_front_inf-Opercular 376 237 994 3.137 0.413 0.201 0.295 53 7.2 G_front_inf-Orbital 1332 892 3289 2.793 0.452 0.148 0.051 22 2.8 G_front_inf-Triangul 3939 2663 9777 2.889 0.548 0.179 0.091 224 15.2 G_front_middle 7353 4937 18691 3.066 0.576 0.162 0.083 160 24.7 G_front_sup 508 329 1250 3.470 0.768 0.120 0.049 6 0.9 G_Ins_lg_and_S_cent_ins 651 415 2213 3.936 0.742 0.137 0.077 16 2.4 G_insular_short 2876 1805 5803 2.518 0.460 0.163 0.059 58 6.6 G_occipital_middle 1469 933 2205 2.025 0.425 0.163 0.069 41 4.2 G_occipital_sup 1902 1258 4410 2.835 0.458 0.171 0.067 46 5.6 G_oc-temp_lat-fusifor 3696 2320 5802 2.156 0.576 0.168 0.074 71 10.7 G_oc-temp_med-Lingual 1341 837 2572 2.667 0.669 0.122 0.047 14 2.6 G_oc-temp_med-Parahip 2590 1753 6424 2.782 0.653 0.174 0.084 65 9.2 G_orbital 2191 1455 4520 2.584 0.514 0.163 0.078 52 7.1 G_pariet_inf-Angular 3224 2128 7698 2.941 0.516 0.151 0.067 72 8.5 G_pariet_inf-Supramar 2781 1841 5288 2.300 0.569 0.141 0.066 43 5.7 G_parietal_sup 2661 1594 4838 2.398 0.607 0.140 0.055 51 6.8 G_postcentral 3103 1793 6385 2.830 0.536 0.138 0.067 49 7.6 G_precentral 2675 1817 5617 2.472 0.537 0.162 0.062 60 6.6 G_precuneus 979 666 2196 2.510 0.659 0.184 0.097 34 4.0 G_rectus 485 284 630 2.195 0.769 0.169 0.192 78 3.8 G_subcallosal 674 392 1330 2.692 0.614 0.152 0.133 16 4.8 G_temp_sup-G_T_transv 2643 1720 7570 3.169 0.625 0.149 0.068 50 6.8 G_temp_sup-Lateral 467 296 1047 3.240 0.884 0.139 0.079 8 1.5 G_temp_sup-Plan_polar 1128 795 2309 2.630 0.509 0.108 0.026 7 1.3 G_temp_sup-Plan_tempo 2190 1467 5857 3.030 0.711 0.170 0.137 59 6.9 G_temporal_inf 2666 1800 7522 3.070 0.616 0.161 0.068 61 7.3 G_temporal_middle 308 203 447 2.720 0.582 0.115 0.031 2 0.4 Lat_Fis-ant-Horizont 318 218 466 2.537 0.401 0.099 0.026 1 0.3 Lat_Fis-ant-Vertical 1326 884 1819 2.636 0.514 0.121 0.039 12 2.1 Lat_Fis-post 2532 1503 2728 1.701 0.436 0.146 0.060 44 6.4 Pole_occipital 1857 1258 5737 3.377 0.791 0.188 0.106 52 8.0 Pole_temporal 3041 2002 3934 2.094 0.518 0.132 0.084 45 5.9 S_calcarine 3115 2130 3377 1.830 0.532 0.134 0.053 34 7.8 S_central 870 619 1301 2.260 0.484 0.126 0.036 8 1.4 S_cingul-Marginalis 469 316 832 2.983 0.508 0.108 0.031 3 0.7 S_circular_insula_ant 1463 972 2454 2.689 0.610 0.086 0.020 5 1.3 S_circular_insula_inf 1777 1193 2746 2.751 0.494 0.110 0.030 11 2.3 S_circular_insula_sup 1223 822 2414 2.933 0.670 0.152 0.103 27 3.4 S_collat_transv_ant 439 290 498 2.262 0.428 0.139 0.045 4 0.9 S_collat_transv_post 2518 1716 3879 2.324 0.463 0.124 0.038 24 3.9 S_front_inf 1512 1061 2544 2.429 0.504 0.136 0.050 18 2.8 S_front_middle 2386 1647 3970 2.464 0.463 0.122 0.040 25 4.0 S_front_sup 288 188 677 2.953 0.441 0.166 0.060 6 0.7 S_interm_prim-Jensen 3275 2201 4588 2.215 0.466 0.134 0.042 37 5.7 S_intrapariet_and_P_trans 1442 958 1635 1.931 0.378 0.140 0.043 16 2.7 S_oc_middle_and_Lunatus 1264 821 1581 2.038 0.369 0.133 0.088 285 2.0 S_oc_sup_and_transversal 1515 1017 2159 2.328 0.392 0.140 0.067 30 5.1 S_occipital_ant 755 519 1079 2.439 0.363 0.112 0.028 5 0.9 S_oc-temp_lat 2029 1418 3087 2.483 0.510 0.136 0.043 21 3.8 S_oc-temp_med_and_Lingual 291 198 390 2.175 0.395 0.121 0.037 2 0.5 S_orbital_lateral 741 503 992 2.291 0.675 0.112 0.026 5 0.8 S_orbital_med-olfact 1197 806 2188 2.765 0.721 0.147 0.063 22 2.9 S_orbital-H_Shaped 2562 1746 3463 2.186 0.571 0.130 0.037 25 4.1 S_parieto_occipital 846 540 968 2.421 0.604 0.175 0.062 25 2.1 S_pericallosal 2271 1530 3264 2.384 0.417 0.124 0.038 21 3.6 S_postcentral 1842 1285 2955 2.434 0.465 0.119 0.032 13 2.5 S_precentral-inf-part 723 523 1113 2.466 0.402 0.117 0.028 5 0.9 S_precentral-sup-part 603 412 956 2.544 0.646 0.148 0.052 8 1.3 S_suborbital 880 591 1466 2.487 0.553 0.137 0.048 10 1.7 S_subparietal 1458 983 2173 2.416 0.686 0.128 0.042 20 2.4 S_temporal_inf 5705 3919 9972 2.578 0.458 0.121 0.037 54 8.8 S_temporal_sup 308 218 429 2.446 0.386 0.130 0.036 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Tue Dec 1 20:54:43 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1245 labels changed using aseg relabeling using gibbs priors... 000: 2823 changed, 134383 examined... 001: 714 changed, 11751 examined... 002: 195 changed, 3818 examined... 003: 78 changed, 1129 examined... 004: 29 changed, 473 examined... 005: 19 changed, 171 examined... 006: 19 changed, 105 examined... 007: 11 changed, 94 examined... 008: 8 changed, 62 examined... 009: 3 changed, 40 examined... 010: 3 changed, 16 examined... 011: 2 changed, 20 examined... 012: 3 changed, 12 examined... 013: 1 changed, 13 examined... 014: 2 changed, 7 examined... 015: 0 changed, 11 examined... 268 labels changed using aseg 000: 68 total segments, 35 labels (229 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 578 vertices marked for relabeling... 578 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Tue Dec 1 20:55:23 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1491 967 2875 2.779 0.595 0.141 0.042 22 2.8 caudalanteriorcingulate 2798 1885 5279 2.596 0.568 0.140 0.067 167 8.7 caudalmiddlefrontal 3022 1927 4081 1.999 0.450 0.156 0.062 65 7.9 cuneus 583 385 1300 2.783 0.609 0.127 0.046 6 1.2 entorhinal 4214 2829 8391 2.747 0.491 0.157 0.066 85 11.5 fusiform 6577 4401 11978 2.496 0.487 0.147 0.056 112 15.4 inferiorparietal 4831 3206 11046 2.949 0.771 0.159 0.103 109 13.6 inferiortemporal 1435 926 2478 2.587 0.675 0.157 0.064 33 3.5 isthmuscingulate 8537 5447 11910 2.042 0.509 0.148 0.055 141 20.5 lateraloccipital 3855 2619 8316 2.762 0.735 0.163 0.076 83 12.1 lateralorbitofrontal 5382 3469 8094 2.182 0.556 0.158 0.064 90 13.9 lingual 2057 1363 3747 2.411 0.674 0.153 0.074 49 6.3 medialorbitofrontal 6086 4134 13353 2.772 0.676 0.137 0.049 90 11.9 middletemporal 1157 741 1985 2.414 0.565 0.122 0.039 11 2.0 parahippocampal 2336 1508 3980 2.445 0.501 0.130 0.103 92 10.8 paracentral 2491 1724 5212 2.704 0.400 0.132 0.044 33 4.4 parsopercularis 1015 682 2320 2.893 0.494 0.145 0.129 58 7.8 parsorbitalis 2474 1653 5097 2.658 0.564 0.139 0.048 32 4.9 parstriangularis 2141 1361 2434 1.920 0.457 0.131 0.060 27 5.0 pericalcarine 7052 4524 11432 2.277 0.671 0.134 0.047 102 14.6 postcentral 1841 1253 3491 2.701 0.605 0.161 0.061 38 4.3 posteriorcingulate 7527 4807 13485 2.610 0.590 0.138 0.060 105 18.8 precentral 5594 3834 9709 2.332 0.570 0.145 0.069 96 11.2 precuneus 1514 989 3193 2.902 0.840 0.177 0.098 98 6.0 rostralanteriorcingulate 5628 3835 11676 2.607 0.604 0.161 0.064 109 14.8 rostralmiddlefrontal 11130 7605 25636 2.882 0.635 0.158 0.072 223 34.2 superiorfrontal 6080 4033 9955 2.256 0.494 0.145 0.067 361 12.2 superiorparietal 8208 5522 19038 2.925 0.648 0.135 0.054 115 18.0 superiortemporal 5290 3507 10720 2.781 0.548 0.143 0.058 95 12.0 supramarginal 838 501 1497 2.529 0.510 0.133 0.107 16 4.8 transversetemporal 2762 1837 6269 3.243 0.792 0.112 0.042 31 5.0 insula #----------------------------------------- #@# WM/GM Contrast lh Tue Dec 1 20:55:38 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts pctsurfcon --s af1021_recon --lh-only Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts/pctsurfcon.log Tue Dec 1 20:55:38 EST 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-0.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10261/lh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 73420 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10261/lh.wm.mgh Dim: 134383 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10261/lh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 87295 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10261/lh.gm.mgh Dim: 134383 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10261/lh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10261/lh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-0.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh Vertex Area is 0.661663 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1584 1095.910 2 1002 caudalanteriorcingulate 789 506.564 3 1003 caudalmiddlefrontal 2765 1858.920 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 1917 1225.443 6 1006 entorhinal 622 409.929 7 1007 fusiform 4867 3257.278 8 1008 inferiorparietal 6836 4573.844 9 1009 inferiortemporal 4680 3131.517 10 1010 isthmuscingulate 1431 927.172 11 1011 lateraloccipital 8254 5273.195 12 1012 lateralorbitofrontal 3790 2559.588 13 1013 lingual 5400 3475.210 14 1014 medialorbitofrontal 2479 1635.068 15 1015 middletemporal 4545 3085.708 16 1016 parahippocampal 1146 731.078 17 1017 paracentral 2004 1283.079 18 1018 parsopercularis 2911 2005.479 19 1019 parsorbitalis 933 614.015 20 1020 parstriangularis 1982 1337.828 21 1021 pericalcarine 2156 1369.830 22 1022 postcentral 6459 4112.391 23 1023 posteriorcingulate 1744 1187.680 24 1024 precentral 7497 4785.458 25 1025 precuneus 5881 4012.888 26 1026 rostralanteriorcingulate 1067 686.341 27 1027 rostralmiddlefrontal 7995 5492.088 28 1028 superiorfrontal 9871 6735.381 29 1029 superiorparietal 7763 5130.734 30 1030 superiortemporal 6185 4126.916 31 1031 supramarginal 5512 3662.862 32 1032 frontalpole 280 191.547 33 1033 temporalpole 620 432.797 34 1034 transversetemporal 866 517.973 35 1035 insula 3115 2039.750 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Tue Dec 1 20:55:47 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1593 1109 3015 2.682 0.457 0.130 0.034 20 2.4 bankssts 1197 786 2345 2.626 0.751 0.153 0.052 22 2.2 caudalanteriorcingulate 3380 2338 6702 2.581 0.464 0.133 0.043 40 6.2 caudalmiddlefrontal 2179 1407 2986 1.922 0.475 0.168 0.077 51 7.5 cuneus 589 396 1566 2.976 0.716 0.168 0.091 12 1.8 entorhinal 5442 3646 11546 2.834 0.613 0.150 0.097 157 13.3 fusiform 8167 5545 14263 2.348 0.503 0.152 0.079 212 32.1 inferiorparietal 4320 2929 9483 2.858 0.725 0.152 0.080 89 11.4 inferiortemporal 1285 824 2162 2.568 0.679 0.147 0.062 22 2.9 isthmuscingulate 7233 4662 10989 2.190 0.516 0.154 0.067 142 18.6 lateraloccipital 3685 2495 7466 2.624 0.776 0.165 0.076 85 10.7 lateralorbitofrontal 5135 3408 7248 2.131 0.581 0.165 0.068 118 15.1 lingual 2768 1867 5430 2.512 0.830 0.157 0.083 77 9.3 medialorbitofrontal 4406 3036 10881 3.006 0.591 0.148 0.060 89 10.5 middletemporal 1247 797 2097 2.437 0.432 0.110 0.036 10 1.9 parahippocampal 2205 1371 3496 2.458 0.513 0.126 0.048 30 4.5 paracentral 2109 1406 4176 2.782 0.441 0.129 0.048 27 4.3 parsopercularis 1084 789 2817 2.747 0.665 0.188 0.331 287 3.4 parsorbitalis 2159 1445 4093 2.478 0.521 0.138 0.046 30 3.8 parstriangularis 2365 1581 2680 1.868 0.524 0.156 0.058 37 5.6 pericalcarine 5742 3591 8275 2.088 0.670 0.129 0.050 81 11.4 postcentral 1953 1314 3713 2.596 0.791 0.167 0.062 41 4.6 posteriorcingulate 7239 4713 12460 2.496 0.596 0.140 0.088 88 33.6 precentral 6267 4256 11047 2.501 0.561 0.147 0.052 99 12.7 precuneus 752 487 1602 2.699 0.958 0.143 0.063 12 1.6 rostralanteriorcingulate 8460 5766 15268 2.251 0.635 0.161 0.080 197 25.1 rostralmiddlefrontal 9201 6382 21012 2.862 0.663 0.146 0.055 139 19.8 superiorfrontal 7356 4758 11489 2.187 0.483 0.140 0.049 101 14.3 superiorparietal 5857 3902 13807 3.056 0.718 0.138 0.060 95 14.4 superiortemporal 6006 3985 11151 2.653 0.561 0.135 0.048 85 10.8 supramarginal 437 288 982 2.480 0.836 0.205 0.089 17 1.7 frontalpole 570 397 2015 3.578 1.067 0.204 0.325 36 3.5 temporalpole 720 426 1246 2.482 0.374 0.129 0.051 9 1.3 transversetemporal 3153 2056 6767 3.278 0.914 0.130 0.106 85 17.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Tue Dec 1 20:56:00 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 17 labels changed using aseg relabeling using gibbs priors... 000: 9780 changed, 134806 examined... 001: 2387 changed, 37288 examined... 002: 747 changed, 12158 examined... 003: 358 changed, 4168 examined... 004: 166 changed, 1995 examined... 005: 89 changed, 938 examined... 006: 44 changed, 485 examined... 007: 25 changed, 251 examined... 008: 7 changed, 160 examined... 009: 6 changed, 38 examined... 010: 6 changed, 40 examined... 011: 3 changed, 27 examined... 012: 2 changed, 19 examined... 013: 1 changed, 12 examined... 014: 0 changed, 8 examined... 10 labels changed using aseg 000: 319 total segments, 232 labels (2779 vertices) changed 001: 100 total segments, 15 labels (415 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 142 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 592 vertices marked for relabeling... 592 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Tue Dec 1 20:56:47 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1172 794 2040 2.075 0.737 0.179 0.074 29 4.0 G_and_S_frontomargin 1268 848 2580 2.712 0.432 0.153 0.050 20 2.7 G_and_S_occipital_inf 1375 764 2034 2.265 0.462 0.133 0.064 30 3.7 G_and_S_paracentral 1515 1018 3247 2.914 0.541 0.163 0.058 27 3.5 G_and_S_subcentral 738 508 1830 2.572 0.707 0.194 0.097 27 2.7 G_and_S_transv_frontopol 2530 1708 5175 2.828 0.751 0.150 0.067 46 6.1 G_and_S_cingul-Ant 1346 953 2891 2.867 0.551 0.142 0.048 19 2.4 G_and_S_cingul-Mid-Ant 1554 1040 2912 2.698 0.509 0.147 0.055 25 3.2 G_and_S_cingul-Mid-Post 469 322 1212 3.079 0.786 0.199 0.098 13 1.7 G_cingul-Post-dorsal 304 183 549 2.639 0.539 0.170 0.092 11 1.0 G_cingul-Post-ventral 1829 1192 2375 1.811 0.468 0.172 0.082 47 6.8 G_cuneus 1366 918 3160 2.843 0.424 0.152 0.062 26 3.4 G_front_inf-Opercular 313 211 774 2.762 0.548 0.171 0.071 8 0.8 G_front_inf-Orbital 1040 697 2383 2.651 0.489 0.149 0.048 17 2.0 G_front_inf-Triangul 3767 2631 8798 2.597 0.591 0.170 0.095 104 12.9 G_front_middle 6507 4428 16398 2.978 0.673 0.158 0.063 117 15.8 G_front_sup 389 262 1100 3.966 1.062 0.136 0.422 43 11.1 G_Ins_lg_and_S_cent_ins 589 373 1860 4.004 0.759 0.135 0.068 12 1.5 G_insular_short 2017 1282 4131 2.517 0.405 0.153 0.063 38 4.5 G_occipital_middle 1909 1196 3018 2.181 0.469 0.145 0.049 29 4.0 G_occipital_sup 2054 1333 4532 2.851 0.542 0.165 0.154 105 5.5 G_oc-temp_lat-fusifor 3335 2183 5036 2.163 0.583 0.175 0.077 67 10.5 G_oc-temp_med-Lingual 1701 1072 4086 2.939 0.766 0.146 0.076 32 4.6 G_oc-temp_med-Parahip 2739 1882 7222 2.882 0.755 0.198 0.207 356 11.4 G_orbital 2792 1905 5854 2.552 0.594 0.171 0.083 109 10.7 G_pariet_inf-Angular 2637 1683 5607 2.860 0.532 0.144 0.056 47 5.4 G_pariet_inf-Supramar 2263 1494 4210 2.313 0.453 0.148 0.057 34 5.2 G_parietal_sup 2223 1247 3241 2.073 0.576 0.123 0.060 41 5.3 G_postcentral 2737 1670 5254 2.599 0.544 0.141 0.144 31 22.9 G_precentral 2950 2026 6083 2.473 0.497 0.156 0.060 55 6.7 G_precuneus 813 525 2040 2.808 0.570 0.174 0.113 34 4.1 G_rectus 280 189 323 1.617 0.731 0.127 0.094 7 1.0 G_subcallosal 499 295 956 2.477 0.414 0.140 0.060 7 1.1 G_temp_sup-G_T_transv 2268 1512 7028 3.447 0.645 0.171 0.073 51 6.1 G_temp_sup-Lateral 596 389 1656 3.561 0.725 0.158 0.126 27 1.9 G_temp_sup-Plan_polar 959 657 1875 2.590 0.472 0.119 0.091 17 4.0 G_temp_sup-Plan_tempo 2295 1558 5995 3.056 0.815 0.163 0.077 57 7.1 G_temporal_inf 2554 1758 7329 3.131 0.523 0.163 0.075 68 7.4 G_temporal_middle 375 253 614 2.334 0.462 0.128 0.042 4 0.7 Lat_Fis-ant-Horizont 135 89 236 2.469 0.354 0.084 0.019 1 0.1 Lat_Fis-ant-Vertical 1988 1329 2931 2.591 0.447 0.125 0.038 19 3.0 Lat_Fis-post 3339 2116 4113 1.822 0.478 0.172 0.090 91 11.4 Pole_occipital 1805 1253 5748 3.226 0.894 0.187 0.188 57 8.0 Pole_temporal 2857 1909 3524 2.059 0.559 0.151 0.054 70 7.0 S_calcarine 2746 1906 2838 1.718 0.460 0.135 0.043 23 5.1 S_central 1337 912 2095 2.489 0.497 0.134 0.045 15 2.4 S_cingul-Marginalis 621 429 990 2.779 0.387 0.113 0.033 4 1.0 S_circular_insula_ant 1387 884 2188 2.669 0.628 0.093 0.033 9 1.4 S_circular_insula_inf 1530 1016 2554 2.846 0.656 0.119 0.043 14 2.9 S_circular_insula_sup 931 617 2000 3.080 0.718 0.145 0.080 15 2.0 S_collat_transv_ant 795 536 923 2.093 0.468 0.156 0.055 10 1.8 S_collat_transv_post 2634 1758 4386 2.430 0.510 0.130 0.040 27 4.6 S_front_inf 2106 1385 3029 2.022 0.551 0.149 0.063 37 4.7 S_front_middle 2417 1694 3868 2.302 0.475 0.116 0.033 19 3.4 S_front_sup 555 373 771 2.317 0.575 0.130 0.035 6 0.9 S_interm_prim-Jensen 3059 2042 4128 2.097 0.496 0.138 0.044 37 5.3 S_intrapariet_and_P_trans 1207 811 1634 2.085 0.403 0.133 0.044 13 2.0 S_oc_middle_and_Lunatus 1101 720 1302 2.006 0.344 0.130 0.053 16 2.7 S_oc_sup_and_transversal 1011 671 1489 2.480 0.311 0.128 0.042 11 1.6 S_occipital_ant 1243 875 1960 2.539 0.341 0.128 0.039 13 2.0 S_oc-temp_lat 2214 1517 3253 2.464 0.443 0.114 0.030 15 2.7 S_oc-temp_med_and_Lingual 509 353 673 2.102 0.460 0.127 0.038 4 0.8 S_orbital_lateral 760 551 1071 1.866 0.591 0.108 0.021 5 0.6 S_orbital_med-olfact 1359 921 2374 2.395 0.684 0.156 0.066 25 3.3 S_orbital-H_Shaped 2605 1713 3746 2.441 0.611 0.137 0.041 29 4.4 S_parieto_occipital 1569 985 1524 1.992 0.702 0.139 0.041 23 2.3 S_pericallosal 2138 1420 2628 2.022 0.425 0.111 0.030 15 2.7 S_postcentral 2059 1428 3664 2.586 0.489 0.123 0.052 22 5.1 S_precentral-inf-part 816 553 1169 2.472 0.501 0.122 0.033 6 1.2 S_precentral-sup-part 196 137 429 3.132 0.692 0.217 0.119 10 0.7 S_suborbital 946 638 1763 2.660 0.476 0.139 0.045 12 1.7 S_subparietal 843 568 1177 2.609 0.530 0.130 0.046 12 1.7 S_temporal_inf 7073 4882 12306 2.552 0.524 0.131 0.062 117 22.7 S_temporal_sup 303 205 382 2.370 0.228 0.128 0.029 2 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Tue Dec 1 20:57:02 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1169 labels changed using aseg relabeling using gibbs priors... 000: 2644 changed, 134806 examined... 001: 657 changed, 11528 examined... 002: 174 changed, 3541 examined... 003: 76 changed, 1035 examined... 004: 30 changed, 428 examined... 005: 17 changed, 157 examined... 006: 7 changed, 98 examined... 007: 5 changed, 45 examined... 008: 4 changed, 30 examined... 009: 4 changed, 22 examined... 010: 4 changed, 23 examined... 011: 6 changed, 28 examined... 012: 4 changed, 28 examined... 013: 6 changed, 24 examined... 014: 5 changed, 34 examined... 015: 6 changed, 34 examined... 016: 2 changed, 23 examined... 017: 1 changed, 12 examined... 018: 1 changed, 7 examined... 019: 0 changed, 7 examined... 154 labels changed using aseg 000: 57 total segments, 24 labels (104 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 669 vertices marked for relabeling... 669 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 41 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Tue Dec 1 20:57:43 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1185 777 2297 2.615 0.750 0.153 0.052 21 2.2 caudalanteriorcingulate 3339 2298 6590 2.597 0.459 0.134 0.044 41 6.2 caudalmiddlefrontal 2698 1754 3657 1.960 0.468 0.162 0.063 54 6.9 cuneus 632 430 1706 2.985 0.728 0.166 0.090 12 1.9 entorhinal 4727 3172 9720 2.829 0.618 0.147 0.099 137 10.6 fusiform 7720 5232 13354 2.345 0.510 0.154 0.081 204 31.4 inferiorparietal 5025 3394 11193 2.851 0.713 0.154 0.096 109 13.8 inferiortemporal 1288 829 2170 2.571 0.682 0.148 0.062 22 2.9 isthmuscingulate 7512 4841 11526 2.194 0.520 0.154 0.067 149 19.5 lateraloccipital 4220 2867 8781 2.530 0.825 0.174 0.081 110 13.6 lateralorbitofrontal 5152 3422 7267 2.135 0.578 0.165 0.068 117 15.0 lingual 2150 1446 4555 2.583 0.809 0.159 0.086 64 7.8 medialorbitofrontal 5317 3680 12593 2.946 0.576 0.144 0.055 99 11.7 middletemporal 1247 794 2072 2.437 0.430 0.109 0.035 10 1.8 parahippocampal 2254 1410 3589 2.465 0.524 0.125 0.048 30 4.5 paracentral 2268 1513 4389 2.753 0.444 0.128 0.047 28 4.4 parsopercularis 1200 826 2599 2.668 0.638 0.151 0.064 18 2.8 parsorbitalis 2243 1496 4260 2.458 0.529 0.138 0.045 32 4.2 parstriangularis 2438 1613 2739 1.852 0.519 0.157 0.069 45 7.6 pericalcarine 6136 3859 8925 2.095 0.662 0.130 0.050 87 12.1 postcentral 2075 1396 3972 2.616 0.768 0.167 0.063 43 5.1 posteriorcingulate 7111 4638 12173 2.491 0.601 0.141 0.089 87 33.4 precentral 6211 4206 11191 2.514 0.551 0.149 0.053 102 13.0 precuneus 882 572 1853 2.725 0.929 0.141 0.060 13 1.8 rostralanteriorcingulate 5759 3975 11015 2.331 0.620 0.162 0.131 401 17.2 rostralmiddlefrontal 11984 8253 25555 2.696 0.735 0.150 0.059 203 27.6 superiorfrontal 6337 4112 9949 2.196 0.486 0.136 0.047 83 11.9 superiorparietal 7802 5236 18462 3.044 0.757 0.144 0.068 155 20.7 superiortemporal 5722 3783 10504 2.642 0.552 0.133 0.048 80 10.3 supramarginal 718 425 1239 2.483 0.374 0.128 0.051 9 1.3 transversetemporal 2909 1910 6380 3.305 0.889 0.124 0.104 76 16.3 insula #----------------------------------------- #@# WM/GM Contrast rh Tue Dec 1 20:57:56 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts pctsurfcon --s af1021_recon --rh-only Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts/pctsurfcon.log Tue Dec 1 20:57:56 EST 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-0.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10645/rh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 73821 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10645/rh.wm.mgh Dim: 134806 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10645/rh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 87789 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10645/rh.gm.mgh Dim: 134806 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10645/rh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.10645/rh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-0.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh Vertex Area is 0.664253 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1593 1108.692 2 2002 caudalanteriorcingulate 1197 785.953 3 2003 caudalmiddlefrontal 3380 2338.266 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2179 1407.114 6 2006 entorhinal 589 396.363 7 2007 fusiform 5442 3645.660 8 2008 inferiorparietal 8167 5544.499 9 2009 inferiortemporal 4320 2929.486 10 2010 isthmuscingulate 1285 823.827 11 2011 lateraloccipital 7233 4662.327 12 2012 lateralorbitofrontal 3685 2494.787 13 2013 lingual 5135 3408.429 14 2014 medialorbitofrontal 2768 1866.921 15 2015 middletemporal 4406 3035.524 16 2016 parahippocampal 1247 797.235 17 2017 paracentral 2205 1371.040 18 2018 parsopercularis 2109 1406.215 19 2019 parsorbitalis 1084 789.439 20 2020 parstriangularis 2159 1444.928 21 2021 pericalcarine 2365 1580.832 22 2022 postcentral 5742 3590.525 23 2023 posteriorcingulate 1953 1313.774 24 2024 precentral 7239 4713.337 25 2025 precuneus 6267 4255.853 26 2026 rostralanteriorcingulate 752 486.565 27 2027 rostralmiddlefrontal 8460 5765.568 28 2028 superiorfrontal 9201 6381.974 29 2029 superiorparietal 7356 4757.753 30 2030 superiortemporal 5857 3902.342 31 2031 supramarginal 6006 3985.072 32 2032 frontalpole 437 288.075 33 2033 temporalpole 570 397.121 34 2034 transversetemporal 720 426.451 35 2035 insula 3153 2055.899 Reporting on 34 segmentations mri_segstats done Cleaning up #-------------------------------------------- #@# Cortical ribbon mask Tue Dec 1 20:58:05 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon af1021_recon SUBJECTS_DIR is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 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 = 141 writing volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Tue Dec 1 21:11:46 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon 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 /share/apps/freesurfer-5.3.0/ASegStatsLUT.txt --subject af1021_recon $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 /share/apps/freesurfer-5.3.0/ASegStatsLUT.txt --subject af1021_recon sysname Linux hostname compute-0-0.local machine x86_64 user twilliams UseRobust 0 atlas_icv (eTIV) = 1541622 mm^3 (det: 1.263673 ) Computing euler number orig.nofix lheno = -44, rheno = -32 orig.nofix lhholes = 23, rhholes = 17 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 239785.689 239722.000 diff= 63.7 pctdiff= 0.027 rhCtxGM: 236017.021 235804.000 diff= 213.0 pctdiff= 0.090 lhCtxWM: 218340.398 218144.000 diff= 196.4 pctdiff= 0.090 rhCtxWM: 221137.567 221480.000 diff= -342.4 pctdiff=-0.155 SubCortGMVol 62225.000 SupraTentVol 989576.675 (988404.000) diff=1172.675 pctdiff=0.119 SupraTentVolNotVent 978707.675 (977535.000) diff=1172.675 pctdiff=0.120 BrainSegVol 1120783.000 (1118799.000) diff=1984.000 pctdiff=0.177 BrainSegVolNotVent 1106900.000 (1106879.675) diff=20.325 pctdiff=0.002 BrainSegVolNotVent 1106900.000 CerebellumVol 129214.000 VentChorVol 10869.000 3rd4th5thCSF 3014.000 CSFVol 1046.000, OptChiasmVol 135.000 MaskVol 1600589.000 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 4657 4657.085 4 5 Left-Inf-Lat-Vent 147 147.216 5 7 Left-Cerebellum-White-Matter 15131 15130.936 6 8 Left-Cerebellum-Cortex 49465 49464.539 7 10 Left-Thalamus-Proper 8027 8026.642 8 11 Left-Caudate 3803 3803.185 9 12 Left-Putamen 6337 6336.562 10 13 Left-Pallidum 1648 1648.023 11 14 3rd-Ventricle 739 739.349 12 15 4th-Ventricle 1501 1501.291 13 16 Brain-Stem 21351 21351.275 14 17 Left-Hippocampus 4730 4730.166 15 18 Left-Amygdala 1888 1887.705 16 24 CSF 1110 1110.174 17 26 Left-Accumbens-area 749 748.657 18 28 Left-VentralDC 3769 3768.568 19 30 Left-vessel 85 85.161 20 31 Left-choroid-plexus 1057 1056.964 23 43 Right-Lateral-Ventricle 3857 3856.684 24 44 Right-Inf-Lat-Vent 108 107.650 25 46 Right-Cerebellum-White-Matter 14819 14818.603 26 47 Right-Cerebellum-Cortex 51367 51367.012 27 49 Right-Thalamus-Proper 7432 7432.446 28 50 Right-Caudate 4211 4210.721 29 51 Right-Putamen 5637 5636.977 30 52 Right-Pallidum 1575 1575.200 31 53 Right-Hippocampus 4560 4560.470 32 54 Right-Amygdala 1372 1371.704 33 58 Right-Accumbens-area 760 759.631 34 60 Right-VentralDC 3998 3997.655 35 62 Right-vessel 74 74.438 36 63 Right-choroid-plexus 1407 1406.849 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1237 1237.188 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 17 17.220 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 133 132.774 45 251 CC_Posterior 858 858.164 46 252 CC_Mid_Posterior 539 539.010 47 253 CC_Central 505 505.136 48 254 CC_Mid_Anterior 426 425.545 49 255 CC_Anterior 784 783.820 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Tue Dec 1 21:15:26 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --volmask SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 473290 Used brute-force search on 0 voxels Writing output aseg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --volmask --a2009s SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 473290 Used brute-force search on 0 voxels Writing output aseg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Tue Dec 1 21:18:45 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/ribbon.mgz Loading filled from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8437 vertices from left hemi Ripped 8545 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz Loading Ctx Seg File /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 911902 Used brute-force search on 43 voxels Fixing Parahip LH WM Found 9 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 3.000000 7 k 27.000000 8 k 1744.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1.000000 1 k 2065.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon 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 af1021_recon --surf-wm-vol --ctab /share/apps/freesurfer-5.3.0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject af1021_recon --surf-wm-vol --ctab /share/apps/freesurfer-5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-0.local machine x86_64 user twilliams UseRobust 0 atlas_icv (eTIV) = 1541622 mm^3 (det: 1.263673 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 239785.689 239722.000 diff= 63.7 pctdiff= 0.027 rhCtxGM: 236017.021 235804.000 diff= 213.0 pctdiff= 0.090 lhCtxWM: 218340.398 218144.000 diff= 196.4 pctdiff= 0.090 rhCtxWM: 221137.567 221480.000 diff= -342.4 pctdiff=-0.155 SubCortGMVol 62225.000 SupraTentVol 989576.675 (988404.000) diff=1172.675 pctdiff=0.119 SupraTentVolNotVent 978707.675 (977535.000) diff=1172.675 pctdiff=0.120 BrainSegVol 1120783.000 (1118799.000) diff=1984.000 pctdiff=0.177 BrainSegVolNotVent 1106900.000 (1106879.675) diff=20.325 pctdiff=0.002 BrainSegVolNotVent 1106900.000 CerebellumVol 129214.000 VentChorVol 10869.000 3rd4th5thCSF 3014.000 CSFVol 1046.000, OptChiasmVol 135.000 MaskVol 1600589.000 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 2344 2344.273 2 3002 wm-lh-caudalanteriorcingulate 2311 2311.051 3 3003 wm-lh-caudalmiddlefrontal 5321 5321.469 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 1997 1996.924 6 3006 wm-lh-entorhinal 1106 1105.882 7 3007 wm-lh-fusiform 5888 5888.177 8 3008 wm-lh-inferiorparietal 9937 9936.673 9 3009 wm-lh-inferiortemporal 6002 6002.427 10 3010 wm-lh-isthmuscingulate 3303 3302.840 11 3011 wm-lh-lateraloccipital 10050 10049.559 12 3012 wm-lh-lateralorbitofrontal 6212 6211.568 13 3013 wm-lh-lingual 6587 6586.856 14 3014 wm-lh-medialorbitofrontal 2839 2838.649 15 3015 wm-lh-middletemporal 5309 5309.288 16 3016 wm-lh-parahippocampal 1788 1787.837 17 3017 wm-lh-paracentral 3497 3497.255 18 3018 wm-lh-parsopercularis 4557 4557.250 19 3019 wm-lh-parsorbitalis 788 788.333 20 3020 wm-lh-parstriangularis 3174 3173.637 21 3021 wm-lh-pericalcarine 3449 3449.457 22 3022 wm-lh-postcentral 7535 7534.977 23 3023 wm-lh-posteriorcingulate 4296 4295.991 24 3024 wm-lh-precentral 12936 12936.485 25 3025 wm-lh-precuneus 9754 9754.364 26 3026 wm-lh-rostralanteriorcingulate 2415 2414.948 27 3027 wm-lh-rostralmiddlefrontal 11447 11447.485 28 3028 wm-lh-superiorfrontal 17092 17091.590 29 3029 wm-lh-superiorparietal 10885 10884.594 30 3030 wm-lh-superiortemporal 8594 8594.010 31 3031 wm-lh-supramarginal 8152 8152.295 32 3032 wm-lh-frontalpole 174 174.381 33 3033 wm-lh-temporalpole 558 557.755 34 3034 wm-lh-transversetemporal 771 771.418 35 3035 wm-lh-insula 8244 8244.409 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 2745 2745.338 120 4002 wm-rh-caudalanteriorcingulate 3277 3277.310 121 4003 wm-rh-caudalmiddlefrontal 5680 5680.276 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2076 2075.569 124 4006 wm-rh-entorhinal 756 755.761 125 4007 wm-rh-fusiform 6202 6202.351 126 4008 wm-rh-inferiorparietal 11103 11103.320 127 4009 wm-rh-inferiortemporal 5543 5543.002 128 4010 wm-rh-isthmuscingulate 2980 2980.250 129 4011 wm-rh-lateraloccipital 8910 8909.699 130 4012 wm-rh-lateralorbitofrontal 6387 6387.220 131 4013 wm-rh-lingual 6584 6583.537 132 4014 wm-rh-medialorbitofrontal 3336 3335.857 133 4015 wm-rh-middletemporal 5246 5246.438 134 4016 wm-rh-parahippocampal 2072 2071.721 135 4017 wm-rh-paracentral 4321 4321.378 136 4018 wm-rh-parsopercularis 3431 3431.199 137 4019 wm-rh-parsorbitalis 1059 1059.295 138 4020 wm-rh-parstriangularis 3135 3135.126 139 4021 wm-rh-pericalcarine 3741 3741.461 140 4022 wm-rh-postcentral 6895 6894.644 141 4023 wm-rh-posteriorcingulate 4600 4599.785 142 4024 wm-rh-precentral 12945 12945.029 143 4025 wm-rh-precuneus 10324 10324.216 144 4026 wm-rh-rostralanteriorcingulate 1900 1900.417 145 4027 wm-rh-rostralmiddlefrontal 11919 11919.202 146 4028 wm-rh-superiorfrontal 15647 15646.612 147 4029 wm-rh-superiorparietal 8818 8817.864 148 4030 wm-rh-superiortemporal 7913 7912.903 149 4031 wm-rh-supramarginal 8952 8952.393 150 4032 wm-rh-frontalpole 354 353.875 151 4033 wm-rh-temporalpole 544 544.304 152 4034 wm-rh-transversetemporal 643 642.564 153 4035 wm-rh-insula 8754 8754.361 154 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 28574 28574.098 237 5002 Right-UnsegmentedWhiteMatter 29781 29781.430 238 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label #-------------------------------------------- #@# BA Labels lh Tue Dec 1 21:29:20 EST 2015 mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.label --trgsubject af1021_recon --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 323 Checking for and removing duplicates Writing label file ./lh.BA1.label 4452 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.label --trgsubject af1021_recon --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./lh.BA2.label 8276 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.label --trgsubject af1021_recon --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.label --trgsubject af1021_recon --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 432 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6415 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.label --trgsubject af1021_recon --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 411 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6195 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.label --trgsubject af1021_recon --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.label --trgsubject af1021_recon --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1084 Checking for and removing duplicates Writing label file ./lh.BA6.label 14673 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.label --trgsubject af1021_recon --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 687 Checking for and removing duplicates Writing label file ./lh.BA44.label 4868 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.label --trgsubject af1021_recon --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 856 Checking for and removing duplicates Writing label file ./lh.BA45.label 4278 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.label --trgsubject af1021_recon --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1634 Checking for and removing duplicates Writing label file ./lh.V1.label 6275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.label --trgsubject af1021_recon --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 3389 Checking for and removing duplicates Writing label file ./lh.V2.label 11503 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.label --trgsubject af1021_recon --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 784 Checking for and removing duplicates Writing label file ./lh.MT.label 2802 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.perirhinal.label --trgsubject af1021_recon --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1081 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2230 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2211 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 467 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 352 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2264 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 421 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1572 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.thresh.label --trgsubject af1021_recon --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1147 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.thresh.label --trgsubject af1021_recon --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1520 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4854 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.thresh.label --trgsubject af1021_recon --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 736 mri_label2label: Done mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-0.local machine x86_64 user twilliams subject af1021_recon hemi lh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 92465 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.BA.annot mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-0.local machine x86_64 user twilliams subject af1021_recon hemi lh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 109651 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab af1021_recon lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1104 617 2022 2.446 0.498 0.144 0.054 18 2.4 BA1 3348 2200 5882 2.513 0.497 0.130 0.046 49 6.9 BA2 967 661 829 1.762 0.454 0.158 0.055 11 2.3 BA3a 2566 1647 3532 1.911 0.676 0.133 0.046 33 5.2 BA3b 1694 959 2837 2.602 0.473 0.124 0.096 27 3.6 BA4a 1322 871 1911 2.289 0.552 0.135 0.072 25 4.8 BA4p 8466 5596 19000 2.915 0.561 0.142 0.074 317 30.9 BA6 2744 1914 5943 2.698 0.472 0.138 0.049 40 5.5 BA44 3246 2203 6806 2.635 0.526 0.141 0.051 49 6.6 BA45 3830 2445 4376 1.802 0.470 0.142 0.061 57 9.0 V1 8960 5631 12455 2.072 0.519 0.158 0.076 174 23.4 V2 2557 1727 4523 2.392 0.503 0.150 0.063 52 7.5 MT 1114 712 2314 2.711 0.666 0.133 0.052 14 2.6 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab af1021_recon lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 723 394 1405 2.563 0.407 0.145 0.054 12 1.6 BA1 1489 975 2846 2.549 0.500 0.130 0.054 29 4.0 BA2 748 525 616 1.687 0.386 0.166 0.057 8 1.8 BA3a 1679 1087 1884 1.612 0.463 0.122 0.041 15 2.9 BA3b 1694 932 2803 2.638 0.437 0.122 0.085 30 3.7 BA4a 1062 727 1391 2.114 0.493 0.137 0.076 17 4.3 BA4p 4749 3079 10498 2.886 0.560 0.142 0.081 140 20.2 BA6 1881 1328 4132 2.698 0.366 0.144 0.050 30 4.1 BA44 1446 973 3419 2.735 0.465 0.156 0.058 24 3.4 BA45 4078 2601 4746 1.805 0.474 0.141 0.058 58 9.2 V1 4483 2745 5827 1.963 0.505 0.161 0.097 94 13.2 V2 700 475 1005 2.148 0.351 0.127 0.033 7 1.1 MT #-------------------------------------------- #@# BA Labels rh Tue Dec 1 21:32:57 EST 2015 mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.label --trgsubject af1021_recon --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./rh.BA1.label 4256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.label --trgsubject af1021_recon --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./rh.BA2.label 6999 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.label --trgsubject af1021_recon --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4093 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.label --trgsubject af1021_recon --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4850 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.label --trgsubject af1021_recon --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 326 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6073 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.label --trgsubject af1021_recon --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4638 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.label --trgsubject af1021_recon --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 732 Checking for and removing duplicates Writing label file ./rh.BA6.label 12988 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.label --trgsubject af1021_recon --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1343 Checking for and removing duplicates Writing label file ./rh.BA44.label 8255 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.label --trgsubject af1021_recon --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1143 Checking for and removing duplicates Writing label file ./rh.BA45.label 6498 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.label --trgsubject af1021_recon --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1819 Checking for and removing duplicates Writing label file ./rh.V1.label 6546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.label --trgsubject af1021_recon --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 3038 Checking for and removing duplicates Writing label file ./rh.V2.label 11054 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.label --trgsubject af1021_recon --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 500 Checking for and removing duplicates Writing label file ./rh.MT.label 2432 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.perirhinal.label --trgsubject af1021_recon --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 872 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 972 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2736 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1737 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2349 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1458 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1524 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 329 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7288 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1194 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1402 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.thresh.label --trgsubject af1021_recon --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1301 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4533 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.thresh.label --trgsubject af1021_recon --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1436 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4873 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.thresh.label --trgsubject af1021_recon --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 341 mri_label2label: Done mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-0.local machine x86_64 user twilliams subject af1021_recon hemi rh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 94394 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.BA.annot mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-0.local machine x86_64 user twilliams subject af1021_recon hemi rh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 113207 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab af1021_recon rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 913 458 1502 2.392 0.392 0.134 0.089 29 2.9 BA1 2655 1727 3775 2.124 0.518 0.109 0.029 18 3.1 BA2 979 642 801 1.639 0.365 0.146 0.049 11 1.9 BA3a 2049 1291 2488 1.687 0.500 0.128 0.044 24 3.9 BA3b 1524 870 2435 2.465 0.505 0.125 0.059 33 4.1 BA4a 1027 728 1301 1.953 0.506 0.143 0.048 9 2.2 BA4p 6912 4610 14506 2.787 0.563 0.140 0.083 67 30.2 BA6 4237 2873 8206 2.733 0.498 0.135 0.053 56 9.9 BA44 4395 2972 8863 2.505 0.564 0.147 0.061 73 11.0 BA45 4364 2894 5043 1.771 0.506 0.167 0.088 112 15.2 V1 8492 5513 11751 2.091 0.521 0.164 0.064 177 22.6 V2 2140 1448 3397 2.380 0.374 0.139 0.044 26 3.8 MT 725 484 1770 2.844 0.601 0.142 0.061 10 1.8 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab af1021_recon rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 616 284 976 2.407 0.388 0.135 0.105 26 2.1 BA1 1438 945 2080 2.116 0.547 0.105 0.029 9 1.7 BA2 835 539 628 1.640 0.341 0.152 0.051 10 1.8 BA3a 1612 1080 1719 1.502 0.359 0.119 0.035 13 2.5 BA3b 890 471 1474 2.574 0.451 0.126 0.065 28 2.7 BA4a 823 626 1041 1.883 0.525 0.147 0.049 7 1.8 BA4p 4347 2825 8733 2.736 0.532 0.138 0.094 31 24.9 BA6 918 633 1993 2.750 0.391 0.145 0.067 17 2.3 BA44 1101 730 2429 2.611 0.460 0.144 0.050 17 2.3 BA45 4207 2784 4782 1.764 0.499 0.166 0.088 108 14.8 V1 4497 2922 6025 1.995 0.572 0.173 0.073 115 13.9 V2 315 212 635 2.414 0.266 0.117 0.033 3 0.5 MT /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Tue Dec 1 21:36:35 EST 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o af1021_recon label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject af1021_recon. processing subject lh.EC_average... reading output surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1020 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label af1021_recon lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 385 218 877 2.767 0.674 0.147 0.104 11 1.8 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Tue Dec 1 21:36:48 EST 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o af1021_recon label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject af1021_recon. processing subject rh.EC_average... reading output surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 906 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label af1021_recon rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 325 203 882 2.977 0.494 0.174 0.084 7 1.2 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Tue Dec 1 17:22:02 EST 2015 Ended at Tue Dec 1 21:37:01 EST 2015 #@#%# recon-all-run-time-hours 4.250 recon-all -s af1021_recon finished without error at Tue Dec 1 21:37:01 EST 2015 New invocation of recon-all Wed Dec 2 15:10:32 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon /share/apps/freesurfer-5.3.0/bin/recon-all -subjid af1021_recon -FLAIRpial -autorecon-pial -no-isrunning subjid af1021_recon setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /share/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux compute-0-18.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 41943040 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 401408 total used free shared buffers cached Mem: 49449168 21774056 27675112 0 246612 20030344 -/+ buffers/cache: 1497100 47952068 Swap: 1020116 0 1020116 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 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: 2015/12/02-20:10:32-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/02-20:10:33-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/02-20:10:33-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:33-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:33-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:34-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:34-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:34-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:34-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:34-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:10:35-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:06-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/02-20:11:07-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/02-20:11:08-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:08-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:08-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:08-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:11:08-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: twilliams Machine: compute-0-18.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /share/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /share/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Mask BFS Wed Dec 2 15:11:08 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1558106 voxels in mask (pct= 9.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# Make White Surf lh Wed Dec 2 15:11:10 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.88 3435 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) New invocation of recon-all Wed Dec 2 15:16:17 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon /share/apps/freesurfer-5.3.0/bin/recon-all -subjid af1021_recon -FLAIRpial -autorecon2-wm -autorecon3 -no-isrunning subjid af1021_recon setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Actual FREESURFER_HOME /share/apps/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux compute-0-12.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse 41943040 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 368640 total used free shared buffers cached Mem: 45312604 44617228 695376 0 246272 42264920 -/+ buffers/cache: 2106036 43206568 Swap: 1020116 244 1019872 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 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: 2015/12/02-20:16:17-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/02-20:16:17-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/02-20:16:18-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:18-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:18-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:18-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:18-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:18-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:18-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:18-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:19-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:20-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 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: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/12/02-20:16:21-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: twilliams Machine: compute-0-12.local Platform: Linux PlatformVersion: 2.6.18-164.6.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /share/apps/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /share/apps/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Wed Dec 2 15:16:21 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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... 2842 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 68 (68), valley at 31 (31) csf peak at 10, setting threshold to 48 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 68 (68), valley at 31 (31) csf peak at 10, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 50 seconds. #-------------------------------------------- #@# Mask BFS Wed Dec 2 15:20:14 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1558106 voxels in mask (pct= 9.29) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Dec 2 15:20:16 EST 2015 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname compute-0-12.local machine x86_64 user twilliams input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname compute-0-12.local machine x86_64 user twilliams input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 104.6 +- 6.2 [80.0 --> 125.0] GM (73.0) : 71.5 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 81.1 setting top of gray matter range to 90.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 5040 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5172 filled 759 bright non-wm voxels segmented. 2815 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.63 minutes reading wm segmentation from wm.seg.mgz... 259 voxels added to wm to prevent paths from MTL structures to cortex 1780 additional wm voxels added 0 additional wm voxels added SEG EDIT: 35946 voxels turned on, 40715 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 18 found - 18 modified | TOTAL: 18 pass 2 (xy+): 0 found - 18 modified | TOTAL: 18 pass 1 (xy-): 8 found - 8 modified | TOTAL: 26 pass 2 (xy-): 0 found - 8 modified | TOTAL: 26 pass 1 (yz+): 24 found - 24 modified | TOTAL: 50 pass 2 (yz+): 0 found - 24 modified | TOTAL: 50 pass 1 (yz-): 31 found - 31 modified | TOTAL: 81 pass 2 (yz-): 0 found - 31 modified | TOTAL: 81 pass 1 (xz+): 11 found - 11 modified | TOTAL: 92 pass 2 (xz+): 0 found - 11 modified | TOTAL: 92 pass 1 (xz-): 15 found - 15 modified | TOTAL: 107 pass 2 (xz-): 0 found - 15 modified | TOTAL: 107 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 6 found - 6 modified | TOTAL: 10 pass 2 (+++): 0 found - 6 modified | TOTAL: 10 pass 1 (+++): 9 found - 9 modified | TOTAL: 19 pass 2 (+++): 0 found - 9 modified | TOTAL: 19 pass 1 (+++): 13 found - 13 modified | TOTAL: 32 pass 2 (+++): 0 found - 13 modified | TOTAL: 32 Iteration Number : 1 pass 1 (++): 63 found - 63 modified | TOTAL: 63 pass 2 (++): 0 found - 63 modified | TOTAL: 63 pass 1 (+-): 123 found - 123 modified | TOTAL: 186 pass 2 (+-): 0 found - 123 modified | TOTAL: 186 pass 1 (--): 108 found - 108 modified | TOTAL: 294 pass 2 (--): 0 found - 108 modified | TOTAL: 294 pass 1 (-+): 135 found - 135 modified | TOTAL: 429 pass 2 (-+): 0 found - 135 modified | TOTAL: 429 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 7 found - 7 modified | TOTAL: 9 pass 2 (yz+): 0 found - 7 modified | TOTAL: 9 pass 1 (yz-): 6 found - 6 modified | TOTAL: 15 pass 2 (yz-): 0 found - 6 modified | TOTAL: 15 pass 1 (xz+): 5 found - 5 modified | TOTAL: 20 pass 2 (xz+): 0 found - 5 modified | TOTAL: 20 pass 1 (xz-): 1 found - 1 modified | TOTAL: 21 pass 2 (xz-): 0 found - 1 modified | TOTAL: 21 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 2 found - 2 modified | TOTAL: 5 pass 2 (--): 0 found - 2 modified | TOTAL: 5 pass 1 (-+): 2 found - 2 modified | TOTAL: 7 pass 2 (-+): 0 found - 2 modified | TOTAL: 7 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 597 (out of 529595: 0.112728) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Wed Dec 2 15:22:46 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.125 0.026 -0.048 -15.419; -0.026 1.169 -0.033 8.848; 0.062 0.039 1.001 -35.560; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1362 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (126, 112, 88), TAL = (2.0, -40.0, 16.0) talairach voxel to voxel transform 0.886 -0.021 0.042 15.340; 0.018 0.854 0.029 -6.252; -0.055 -0.032 0.995 34.827; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 112, 88) --> (2.0, -40.0, 16.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (2.00, -40.00, 16.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -40.00, 16.00) SRC: (112.34, 93.87, 112.94) search lh wm seed point around talairach space (-16.00, -40.00, 16.00), SRC: (144.23, 94.52, 110.95) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Wed Dec 2 15:23:39 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 2 found - 2 modified | TOTAL: 6 pass 2 (yz+): 0 found - 2 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 3 found - 3 modified | TOTAL: 11 pass 2 (xz+): 0 found - 3 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 254789: 0.005887) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 797 vertices, 889 faces slice 60: 5526 vertices, 5728 faces slice 70: 12871 vertices, 13135 faces slice 80: 21291 vertices, 21628 faces slice 90: 31254 vertices, 31595 faces slice 100: 41085 vertices, 41421 faces slice 110: 51073 vertices, 51413 faces slice 120: 62569 vertices, 62982 faces slice 130: 74831 vertices, 75282 faces slice 140: 86318 vertices, 86660 faces slice 150: 96554 vertices, 96931 faces slice 160: 106040 vertices, 106351 faces slice 170: 114009 vertices, 114302 faces slice 180: 121009 vertices, 121278 faces slice 190: 127640 vertices, 127884 faces slice 200: 132807 vertices, 133000 faces slice 210: 135887 vertices, 135989 faces slice 220: 136234 vertices, 136278 faces slice 230: 136234 vertices, 136278 faces slice 240: 136234 vertices, 136278 faces slice 250: 136234 vertices, 136278 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 136234 voxel in cpt #1: X=-44 [v=136234,e=408834,f=272556] located at (-26.273779, -3.643892, 33.029758) For the whole surface: X=-44 [v=136234,e=408834,f=272556] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Dec 2 15:23:47 EST 2015 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Dec 2 15:23:51 EST 2015 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts avg radius = 46.9 mm, total surface area = 71799 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.033 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Dec 2 15:24:23 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.58 (0.00-->6.87) (max @ vno 55345 --> 56522) face area 0.02 +- 0.03 (-0.21-->0.62) scaling brain by 0.302... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.289, avgs=0 005/300: dt: 0.9000, rms radial error=177.030, avgs=0 010/300: dt: 0.9000, rms radial error=176.476, avgs=0 015/300: dt: 0.9000, rms radial error=175.748, avgs=0 020/300: dt: 0.9000, rms radial error=174.917, avgs=0 025/300: dt: 0.9000, rms radial error=174.028, avgs=0 030/300: dt: 0.9000, rms radial error=173.106, avgs=0 035/300: dt: 0.9000, rms radial error=172.167, avgs=0 040/300: dt: 0.9000, rms radial error=171.221, avgs=0 045/300: dt: 0.9000, rms radial error=170.271, avgs=0 050/300: dt: 0.9000, rms radial error=169.322, avgs=0 055/300: dt: 0.9000, rms radial error=168.376, avgs=0 060/300: dt: 0.9000, rms radial error=167.433, avgs=0 065/300: dt: 0.9000, rms radial error=166.497, avgs=0 070/300: dt: 0.9000, rms radial error=165.565, avgs=0 075/300: dt: 0.9000, rms radial error=164.639, avgs=0 080/300: dt: 0.9000, rms radial error=163.717, avgs=0 085/300: dt: 0.9000, rms radial error=162.800, avgs=0 090/300: dt: 0.9000, rms radial error=161.888, avgs=0 095/300: dt: 0.9000, rms radial error=160.980, avgs=0 100/300: dt: 0.9000, rms radial error=160.078, avgs=0 105/300: dt: 0.9000, rms radial error=159.180, avgs=0 110/300: dt: 0.9000, rms radial error=158.288, avgs=0 115/300: dt: 0.9000, rms radial error=157.400, avgs=0 120/300: dt: 0.9000, rms radial error=156.517, avgs=0 125/300: dt: 0.9000, rms radial error=155.639, avgs=0 130/300: dt: 0.9000, rms radial error=154.766, avgs=0 135/300: dt: 0.9000, rms radial error=153.897, avgs=0 140/300: dt: 0.9000, rms radial error=153.033, avgs=0 145/300: dt: 0.9000, rms radial error=152.174, avgs=0 150/300: dt: 0.9000, rms radial error=151.319, avgs=0 155/300: dt: 0.9000, rms radial error=150.469, avgs=0 160/300: dt: 0.9000, rms radial error=149.624, avgs=0 165/300: dt: 0.9000, rms radial error=148.783, avgs=0 170/300: dt: 0.9000, rms radial error=147.947, avgs=0 175/300: dt: 0.9000, rms radial error=147.115, avgs=0 180/300: dt: 0.9000, rms radial error=146.288, avgs=0 185/300: dt: 0.9000, rms radial error=145.466, avgs=0 190/300: dt: 0.9000, rms radial error=144.647, avgs=0 195/300: dt: 0.9000, rms radial error=143.834, avgs=0 200/300: dt: 0.9000, rms radial error=143.025, avgs=0 205/300: dt: 0.9000, rms radial error=142.220, avgs=0 210/300: dt: 0.9000, rms radial error=141.419, avgs=0 215/300: dt: 0.9000, rms radial error=140.623, avgs=0 220/300: dt: 0.9000, rms radial error=139.832, avgs=0 225/300: dt: 0.9000, rms radial error=139.044, avgs=0 230/300: dt: 0.9000, rms radial error=138.262, avgs=0 235/300: dt: 0.9000, rms radial error=137.483, avgs=0 240/300: dt: 0.9000, rms radial error=136.709, avgs=0 245/300: dt: 0.9000, rms radial error=135.939, avgs=0 250/300: dt: 0.9000, rms radial error=135.173, avgs=0 255/300: dt: 0.9000, rms radial error=134.412, avgs=0 260/300: dt: 0.9000, rms radial error=133.654, avgs=0 265/300: dt: 0.9000, rms radial error=132.901, avgs=0 270/300: dt: 0.9000, rms radial error=132.153, avgs=0 275/300: dt: 0.9000, rms radial error=131.408, avgs=0 280/300: dt: 0.9000, rms radial error=130.668, avgs=0 285/300: dt: 0.9000, rms radial error=129.932, avgs=0 290/300: dt: 0.9000, rms radial error=129.199, avgs=0 295/300: dt: 0.9000, rms radial error=128.471, avgs=0 300/300: dt: 0.9000, rms radial error=127.747, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16087.29 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 = 2736.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 292.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00482 epoch 4 (K=640.0), pass 1, starting sse = 20.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00731 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Wed Dec 2 15:28:36 EST 2015 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 af1021_recon lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-44 (nv=136234, nf=272556, ne=408834, g=23) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 3927 ambiguous faces found in tessellation segmenting defects... 28 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 28 defects to be corrected 0 vertices coincident reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2548 (-4.6274) -vertex loglikelihood: -6.1560 (-3.0780) -normal dot loglikelihood: -3.6201 (-3.6201) -quad curv loglikelihood: -6.3204 (-3.1602) Total Loglikelihood : -25.3512 CORRECTING DEFECT 0 (vertices=50, convex hull=98) After retessellation of defect 0, euler #=-22 (133881,400806,266903) : difference with theory (-25) = -3 CORRECTING DEFECT 1 (vertices=29, convex hull=86) After retessellation of defect 1, euler #=-21 (133890,400866,266955) : difference with theory (-24) = -3 CORRECTING DEFECT 2 (vertices=9, convex hull=27) After retessellation of defect 2, euler #=-20 (133891,400877,266966) : difference with theory (-23) = -3 CORRECTING DEFECT 3 (vertices=259, convex hull=205) After retessellation of defect 3, euler #=-19 (133940,401120,267161) : difference with theory (-22) = -3 CORRECTING DEFECT 4 (vertices=6, convex hull=16) After retessellation of defect 4, euler #=-18 (133941,401125,267166) : difference with theory (-21) = -3 CORRECTING DEFECT 5 (vertices=136, convex hull=145) After retessellation of defect 5, euler #=-17 (133985,401326,267324) : difference with theory (-20) = -3 CORRECTING DEFECT 6 (vertices=46, convex hull=67) After retessellation of defect 6, euler #=-16 (134012,401437,267409) : difference with theory (-19) = -3 CORRECTING DEFECT 7 (vertices=87, convex hull=95) After retessellation of defect 7, euler #=-17 (134064,401642,267561) : difference with theory (-18) = -1 CORRECTING DEFECT 8 (vertices=5, convex hull=20) After retessellation of defect 8, euler #=-16 (134064,401647,267567) : difference with theory (-17) = -1 CORRECTING DEFECT 9 (vertices=11, convex hull=10) After retessellation of defect 9, euler #=-15 (134064,401650,267571) : difference with theory (-16) = -1 CORRECTING DEFECT 10 (vertices=42, convex hull=70) After retessellation of defect 10, euler #=-14 (134090,401754,267650) : difference with theory (-15) = -1 CORRECTING DEFECT 11 (vertices=36, convex hull=27) After retessellation of defect 11, euler #=-13 (134096,401780,267671) : difference with theory (-14) = -1 CORRECTING DEFECT 12 (vertices=23, convex hull=20) After retessellation of defect 12, euler #=-12 (134099,401796,267685) : difference with theory (-13) = -1 CORRECTING DEFECT 13 (vertices=28, convex hull=44) After retessellation of defect 13, euler #=-11 (134108,401839,267720) : difference with theory (-12) = -1 CORRECTING DEFECT 14 (vertices=134, convex hull=112) After retessellation of defect 14, euler #=-10 (134163,402056,267883) : difference with theory (-11) = -1 CORRECTING DEFECT 15 (vertices=887, convex hull=214) After retessellation of defect 15, euler #=-9 (134225,402346,268112) : difference with theory (-10) = -1 CORRECTING DEFECT 16 (vertices=29, convex hull=51) After retessellation of defect 16, euler #=-9 (134239,402410,268162) : difference with theory (-9) = 0 CORRECTING DEFECT 17 (vertices=27, convex hull=74) After retessellation of defect 17, euler #=-8 (134255,402487,268224) : difference with theory (-8) = 0 CORRECTING DEFECT 18 (vertices=19, convex hull=50) After retessellation of defect 18, euler #=-7 (134264,402532,268261) : difference with theory (-7) = 0 CORRECTING DEFECT 19 (vertices=39, convex hull=45) After retessellation of defect 19, euler #=-6 (134269,402567,268292) : difference with theory (-6) = 0 CORRECTING DEFECT 20 (vertices=67, convex hull=66) After retessellation of defect 20, euler #=-5 (134287,402654,268362) : difference with theory (-5) = 0 CORRECTING DEFECT 21 (vertices=17, convex hull=30) After retessellation of defect 21, euler #=-4 (134291,402677,268382) : difference with theory (-4) = 0 CORRECTING DEFECT 22 (vertices=61, convex hull=95) After retessellation of defect 22, euler #=-3 (134321,402814,268490) : difference with theory (-3) = 0 CORRECTING DEFECT 23 (vertices=57, convex hull=58) After retessellation of defect 23, euler #=-2 (134337,402886,268547) : difference with theory (-2) = 0 CORRECTING DEFECT 24 (vertices=78, convex hull=95) After retessellation of defect 24, euler #=-1 (134358,402990,268631) : difference with theory (-1) = 0 CORRECTING DEFECT 25 (vertices=23, convex hull=49) After retessellation of defect 25, euler #=0 (134365,403028,268663) : difference with theory (0) = 0 CORRECTING DEFECT 26 (vertices=116, convex hull=100) normal vector of length zero at vertex 136109 with 4 faces After retessellation of defect 26, euler #=1 (134381,403122,268742) : difference with theory (1) = 0 CORRECTING DEFECT 27 (vertices=41, convex hull=36) After retessellation of defect 27, euler #=2 (134383,403143,268762) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.11-->7.44) (max @ vno 125519 --> 129730) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.11-->7.44) (max @ vno 125519 --> 129730) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 97 mutations (34.2%), 187 crossovers (65.8%), 249 vertices were eliminated building final representation... 1851 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134383, nf=268762, ne=403143, g=0) writing corrected surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 22.4 minutes 0 defective edges removing intersecting faces 000: 221 intersecting 001: 3 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 134383 - 403143 + 268762 = 2 --> 0 holes F =2V-4: 268762 = 268766-4 (0) 2E=3F: 806286 = 806286 (0) total defect index = 0 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 17 intersecting 001: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Dec 2 15:51:04 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.88 3435 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.54 2744 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4895479.5, rms=9.93 001: dt: 0.5000, sse=5563255.0, rms=7.101 (0.000%) 002: dt: 0.5000, sse=5950070.0, rms=5.421 (0.000%) 003: dt: 0.5000, sse=6270018.0, rms=4.412 (0.000%) 004: dt: 0.5000, sse=6508964.0, rms=3.792 (0.000%) 005: dt: 0.5000, sse=6643423.0, rms=3.481 (0.000%) 006: dt: 0.5000, sse=6742135.0, rms=3.291 (0.000%) 007: dt: 0.5000, sse=6790056.0, rms=3.216 (0.000%) 008: dt: 0.5000, sse=6807864.0, rms=3.143 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6803028.0, rms=3.125 (0.000%) 010: dt: 0.2500, sse=4088114.0, rms=2.112 (0.000%) 011: dt: 0.2500, sse=3760371.5, rms=1.869 (0.000%) 012: dt: 0.2500, sse=3613746.8, rms=1.813 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3566466.2, rms=1.783 (0.000%) rms = 1.75, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3509115.8, rms=1.752 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.8, 40 (7) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.3 (%26.2))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.40) mean absolute distance = 0.25 +- 0.37 3098 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4100148.5, rms=4.66 015: dt: 0.5000, sse=4398513.5, rms=2.790 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4864968.5, rms=2.784 (0.000%) 017: dt: 0.2500, sse=4087508.5, rms=1.707 (0.000%) 018: dt: 0.2500, sse=3955543.5, rms=1.511 (0.000%) rms = 1.47, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3846167.8, rms=1.474 (0.000%) rms = 1.43, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3800323.0, rms=1.432 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.2, 21 (3) missing vertices, mean dist -0.1 [0.3 (%72.0)->0.2 (%28.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.53) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3167 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4003219.2, rms=3.28 021: dt: 0.5000, sse=4305613.5, rms=2.452 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4040969.5, rms=1.742 (0.000%) 023: dt: 0.2500, sse=3963460.0, rms=1.401 (0.000%) 024: dt: 0.2500, sse=3935674.0, rms=1.316 (0.000%) rms = 1.32, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3906902.0, rms=1.316 (0.000%) rms = 1.29, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3874962.5, rms=1.290 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.0, 26 (2) missing vertices, mean dist -0.0 [0.2 (%56.8)->0.2 (%43.2))] %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3889749.0, rms=1.61 rms = 1.61, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=4959261.5, rms=1.605 (0.000%) 028: dt: 0.2500, sse=4232694.5, rms=1.227 (0.000%) 029: dt: 0.2500, sse=4419370.0, rms=1.057 (0.000%) rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.03, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4386916.0, rms=1.031 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 23 non-cortical segments detected only using segment with 2186 vertices erasing segment 1 (vno[0] = 57470) erasing segment 2 (vno[0] = 77359) erasing segment 3 (vno[0] = 78446) erasing segment 4 (vno[0] = 82313) erasing segment 5 (vno[0] = 83246) erasing segment 6 (vno[0] = 89295) erasing segment 7 (vno[0] = 93408) erasing segment 8 (vno[0] = 95389) erasing segment 9 (vno[0] = 97402) erasing segment 10 (vno[0] = 97413) erasing segment 11 (vno[0] = 97437) erasing segment 12 (vno[0] = 97489) erasing segment 13 (vno[0] = 98353) erasing segment 14 (vno[0] = 98456) erasing segment 15 (vno[0] = 99252) erasing segment 16 (vno[0] = 99310) erasing segment 17 (vno[0] = 100095) erasing segment 18 (vno[0] = 101770) erasing segment 19 (vno[0] = 101844) erasing segment 20 (vno[0] = 105977) erasing segment 21 (vno[0] = 106623) erasing segment 22 (vno[0] = 134247) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv writing smoothed area to lh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.22) refinement took 5.0 minutes #-------------------------------------------- #@# Smooth2 lh Wed Dec 2 15:56:03 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Dec 2 15:56:07 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.0 mm, total surface area = 81449 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 141 vertices thresholded to be in k1 ~ [-0.21 0.36], k2 ~ [-0.11 0.22] total integrated curvature = 0.528*4pi (6.640) --> 0 handles ICI = 1.6, FI = 9.9, variation=172.230 95 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 144 vertices thresholded to be in [-0.13 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Wed Dec 2 15:57:58 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 264 ] Gb_filter = 0 WARN: S lookup min: -0.500392 WARN: S explicit min: 0.000000 vertex = 245 #-------------------------------------------- #@# Sphere lh Wed Dec 2 15:58:04 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.283... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %19.75 pass 1: epoch 2 of 3 starting distance error %19.72 unfolding complete - removing small folds... starting distance error %19.69 removing remaining folds... final distance error %19.71 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.72 hours #-------------------------------------------- #@# Surf Reg lh Wed Dec 2 16:41:10 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_register -curv ../surf/lh.sphere /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 0.577 curvature mean = 0.040, std = 0.936 curvature mean = 0.023, std = 0.857 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 343481.7, tmin=0.9484 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 279147.0, tmin=1.9046 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 252608.6, tmin=2.8693 d=8.00 min @ (0.00, 2.00, 0.00) sse = 251924.4, tmin=3.8419 d=4.00 min @ (1.00, -1.00, -1.00) sse = 250820.9, tmin=4.8197 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 250138.2, tmin=5.8063 d=1.00 min @ (0.00, 0.25, 0.00) sse = 250049.8, tmin=6.7990 d=0.50 min @ (0.00, 0.00, -0.12) sse = 250048.6, tmin=7.8035 tol=1.0e+00, sigma=0.5, host=compu, 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 7.80 min curvature mean = 0.014, std = 0.962 curvature mean = 0.010, std = 0.940 curvature mean = 0.011, std = 0.974 curvature mean = 0.005, std = 0.973 curvature mean = 0.009, std = 0.976 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.029, std = 0.296 curvature mean = 0.003, std = 0.067 curvature mean = 0.066, std = 0.343 curvature mean = 0.003, std = 0.080 curvature mean = 0.032, std = 0.529 curvature mean = 0.003, std = 0.086 curvature mean = 0.017, std = 0.670 curvature mean = 0.003, std = 0.089 curvature mean = 0.007, std = 0.778 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Wed Dec 2 17:03:40 EST 2015 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Wed Dec 2 17:03:42 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Dec 2 17:03:44 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1056 labels changed using aseg relabeling using gibbs priors... 000: 3103 changed, 134383 examined... 001: 682 changed, 13015 examined... 002: 173 changed, 3852 examined... 003: 54 changed, 1023 examined... 004: 21 changed, 325 examined... 005: 7 changed, 127 examined... 006: 6 changed, 38 examined... 007: 6 changed, 37 examined... 008: 1 changed, 21 examined... 009: 0 changed, 7 examined... 262 labels changed using aseg 000: 103 total segments, 59 labels (174 vertices) changed 001: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1314 vertices marked for relabeling... 1314 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 40 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Dec 2 17:04:24 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.96) (max @ vno 56177 --> 133931) face area 0.28 +- 0.12 (0.00-->3.86) mean absolute distance = 0.71 +- 0.90 3528 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 58 points - only 0.00% unknown deleting segment 1 with 18 points - only 0.00% unknown deleting segment 4 with 589 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown deleting segment 13 with 20 points - only 0.00% unknown mean border=80.6, 53 (53) missing vertices, mean dist 0.3 [0.6 (%33.4)->0.8 (%66.6))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.07-->5.14) (max @ vno 48431 --> 48432) face area 0.28 +- 0.13 (0.00-->4.28) mean absolute distance = 0.35 +- 0.55 2842 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4910133.5, rms=9.91 001: dt: 0.5000, sse=5581897.0, rms=7.091 (0.000%) 002: dt: 0.5000, sse=5969936.5, rms=5.414 (0.000%) 003: dt: 0.5000, sse=6294036.0, rms=4.408 (0.000%) 004: dt: 0.5000, sse=6537145.5, rms=3.792 (0.000%) 005: dt: 0.5000, sse=6679090.0, rms=3.482 (0.000%) 006: dt: 0.5000, sse=6778039.0, rms=3.292 (0.000%) 007: dt: 0.5000, sse=6831903.5, rms=3.217 (0.000%) 008: dt: 0.5000, sse=6847970.5, rms=3.144 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6847041.0, rms=3.127 (0.000%) 010: dt: 0.2500, sse=4111519.8, rms=2.116 (0.000%) 011: dt: 0.2500, sse=3782389.5, rms=1.872 (0.000%) 012: dt: 0.2500, sse=3636471.2, rms=1.817 (0.000%) rms = 1.79, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3588702.2, rms=1.787 (0.000%) rms = 1.76, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3530796.0, rms=1.757 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 141 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 5 with 503 points - only 0.00% unknown deleting segment 8 with 7 points - only 0.00% unknown deleting segment 10 with 13 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown deleting segment 14 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 6 points - only 0.00% unknown mean border=83.8, 43 (10) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.3 (%26.3))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->6.05) (max @ vno 48431 --> 48432) face area 0.35 +- 0.16 (0.00-->5.39) mean absolute distance = 0.26 +- 0.38 3194 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4126274.5, rms=4.65 015: dt: 0.5000, sse=4428417.5, rms=2.790 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=4903927.0, rms=2.784 (0.000%) 017: dt: 0.2500, sse=4116609.8, rms=1.714 (0.000%) 018: dt: 0.2500, sse=3986968.5, rms=1.519 (0.000%) rms = 1.48, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3878579.5, rms=1.482 (0.000%) rms = 1.44, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3831825.8, rms=1.441 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 519 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 47 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 12 points - only 0.00% unknown deleting segment 8 with 15 points - only 0.00% unknown mean border=86.2, 34 (5) missing vertices, mean dist -0.1 [0.3 (%71.9)->0.2 (%28.1))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->6.50) (max @ vno 48431 --> 48432) face area 0.34 +- 0.16 (0.00-->5.30) mean absolute distance = 0.21 +- 0.30 3358 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4036701.0, rms=3.28 021: dt: 0.5000, sse=4342123.5, rms=2.455 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4076523.0, rms=1.751 (0.000%) 023: dt: 0.2500, sse=4000223.8, rms=1.417 (0.000%) 024: dt: 0.2500, sse=3971807.5, rms=1.332 (0.000%) rms = 1.33, time step reduction 2 of 3 to 0.125... rms = 1.32, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3949862.0, rms=1.318 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 140 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 542 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 13 points - only 0.00% unknown deleting segment 5 with 8 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 15 points - only 0.00% unknown mean border=87.0, 45 (4) missing vertices, mean dist -0.0 [0.2 (%56.3)->0.2 (%43.7))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=3965833.5, rms=1.63 rms = 1.67, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4030579.2, rms=1.226 (0.000%) 027: dt: 0.2500, sse=4210250.0, rms=1.000 (0.000%) rms = 1.01, time step reduction 2 of 3 to 0.125... rms = 1.00, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4211942.0, rms=0.998 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=60.1, 63 (63) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.5 (%100.0))] %19 local maxima, %48 large gradients and %29 min vals, 2536 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21210330.0, rms=26.92 001: dt: 0.5000, sse=16190595.0, rms=22.998 (0.000%) 002: dt: 0.5000, sse=12521362.0, rms=19.671 (0.000%) 003: dt: 0.5000, sse=9938165.0, rms=16.901 (0.000%) 004: dt: 0.5000, sse=8274347.5, rms=14.603 (0.000%) 005: dt: 0.5000, sse=7200233.0, rms=12.720 (0.000%) 006: dt: 0.5000, sse=6567840.5, rms=11.201 (0.000%) 007: dt: 0.5000, sse=6195436.0, rms=9.893 (0.000%) 008: dt: 0.5000, sse=5953478.5, rms=8.748 (0.000%) 009: dt: 0.5000, sse=5823097.5, rms=7.723 (0.000%) 010: dt: 0.5000, sse=5755740.0, rms=6.818 (0.000%) 011: dt: 0.5000, sse=5771526.0, rms=6.010 (0.000%) 012: dt: 0.5000, sse=5770032.5, rms=5.284 (0.000%) 013: dt: 0.5000, sse=5831664.5, rms=4.697 (0.000%) 014: dt: 0.5000, sse=5903816.5, rms=4.271 (0.000%) 015: dt: 0.5000, sse=5991542.0, rms=3.985 (0.000%) 016: dt: 0.5000, sse=6059026.0, rms=3.792 (0.000%) 017: dt: 0.5000, sse=6113671.0, rms=3.670 (0.000%) 018: dt: 0.5000, sse=6117787.5, rms=3.576 (0.000%) 019: dt: 0.5000, sse=6162662.5, rms=3.519 (0.000%) rms = 3.47, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6164091.5, rms=3.470 (0.000%) 021: dt: 0.2500, sse=4430887.5, rms=2.863 (0.000%) 022: dt: 0.2500, sse=4274107.5, rms=2.709 (0.000%) rms = 2.69, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4183480.0, rms=2.687 (0.000%) 024: dt: 0.1250, sse=4032809.5, rms=2.613 (0.000%) rms = 2.61, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4015818.5, rms=2.607 (0.000%) positioning took 2.5 minutes mean border=57.7, 970 (29) missing vertices, mean dist 0.2 [0.2 (%45.0)->0.6 (%55.0))] %39 local maxima, %33 large gradients and %23 min vals, 968 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4649037.5, rms=4.74 026: dt: 0.5000, sse=4787437.5, rms=3.735 (0.000%) 027: dt: 0.5000, sse=6092889.0, rms=3.602 (0.000%) rms = 3.61, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5127987.5, rms=3.032 (0.000%) 029: dt: 0.2500, sse=4703083.0, rms=2.790 (0.000%) 030: dt: 0.2500, sse=4684753.0, rms=2.723 (0.000%) rms = 2.70, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4651405.5, rms=2.696 (0.000%) 032: dt: 0.1250, sse=4534031.5, rms=2.606 (0.000%) rms = 2.59, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4528865.5, rms=2.588 (0.000%) positioning took 0.9 minutes mean border=56.1, 1194 (26) missing vertices, mean dist 0.1 [0.2 (%38.2)->0.4 (%61.8))] %55 local maxima, %17 large gradients and %23 min vals, 1145 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4680251.5, rms=3.42 rms = 3.38, time step reduction 1 of 3 to 0.250... 034: dt: 0.5000, sse=4928660.0, rms=3.378 (0.000%) 035: dt: 0.2500, sse=4913630.5, rms=2.724 (0.000%) 036: dt: 0.2500, sse=4936017.0, rms=2.582 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4913444.0, rms=2.578 (0.000%) 038: dt: 0.1250, sse=4789696.0, rms=2.449 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4791635.5, rms=2.431 (0.000%) positioning took 0.6 minutes mean border=55.3, 2550 (26) missing vertices, mean dist 0.0 [0.2 (%44.6)->0.3 (%55.4))] %58 local maxima, %14 large gradients and %22 min vals, 909 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4815846.5, rms=2.61 rms = 3.00, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4723632.5, rms=2.451 (0.000%) rms = 2.40, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=4868891.5, rms=2.403 (0.000%) 042: dt: 0.1250, sse=4780392.0, rms=2.348 (0.000%) rms = 2.33, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4807761.0, rms=2.330 (0.000%) positioning took 0.5 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area.pial vertex spacing 1.01 +- 0.43 (0.06-->7.83) (max @ vno 48431 --> 47310) face area 0.41 +- 0.32 (0.00-->9.57) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 614:1142 truncations. 27931 vertices at 0 distance 88109 vertices at 1 distance 84334 vertices at 2 distance 38319 vertices at 3 distance 12427 vertices at 4 distance 3739 vertices at 5 distance 1252 vertices at 6 distance 382 vertices at 7 distance 138 vertices at 8 distance 63 vertices at 9 distance 59 vertices at 10 distance 39 vertices at 11 distance 26 vertices at 12 distance 23 vertices at 13 distance 16 vertices at 14 distance 21 vertices at 15 distance 12 vertices at 16 distance 10 vertices at 17 distance 8 vertices at 18 distance 14 vertices at 19 distance 12 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.thickness positioning took 10.5 minutes #-------------------------------------------- #@# Surf Volume lh Wed Dec 2 17:14:54 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Tessellate rh Wed Dec 2 17:14:54 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 254379: 0.001572) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 60: 1433 vertices, 1540 faces slice 70: 6181 vertices, 6407 faces slice 80: 13052 vertices, 13308 faces slice 90: 21514 vertices, 21856 faces slice 100: 31864 vertices, 32228 faces slice 110: 42481 vertices, 42864 faces slice 120: 54336 vertices, 54740 faces slice 130: 67248 vertices, 67687 faces slice 140: 79843 vertices, 80285 faces slice 150: 91429 vertices, 91817 faces slice 160: 101695 vertices, 102034 faces slice 170: 109545 vertices, 109817 faces slice 180: 117416 vertices, 117726 faces slice 190: 124512 vertices, 124785 faces slice 200: 130623 vertices, 130864 faces slice 210: 135029 vertices, 135167 faces slice 220: 135960 vertices, 135992 faces slice 230: 135960 vertices, 135992 faces slice 240: 135960 vertices, 135992 faces slice 250: 135960 vertices, 135992 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 135960 voxel in cpt #1: X=-32 [v=135960,e=407976,f=271984] located at (25.719248, 2.998522, 35.666489) For the whole surface: X=-32 [v=135960,e=407976,f=271984] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Dec 2 17:15:01 EST 2015 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Dec 2 17:15:04 EST 2015 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts avg radius = 45.7 mm, total surface area = 70897 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.075 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.029 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Wed Dec 2 17:15:31 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.56 (0.00-->6.85) (max @ vno 45690 --> 46760) face area 0.03 +- 0.03 (-0.09-->0.76) scaling brain by 0.311... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.055, avgs=0 005/300: dt: 0.9000, rms radial error=176.795, avgs=0 010/300: dt: 0.9000, rms radial error=176.236, avgs=0 015/300: dt: 0.9000, rms radial error=175.501, avgs=0 020/300: dt: 0.9000, rms radial error=174.671, avgs=0 025/300: dt: 0.9000, rms radial error=173.782, avgs=0 030/300: dt: 0.9000, rms radial error=172.860, avgs=0 035/300: dt: 0.9000, rms radial error=171.922, avgs=0 040/300: dt: 0.9000, rms radial error=170.976, avgs=0 045/300: dt: 0.9000, rms radial error=170.028, avgs=0 050/300: dt: 0.9000, rms radial error=169.081, avgs=0 055/300: dt: 0.9000, rms radial error=168.137, avgs=0 060/300: dt: 0.9000, rms radial error=167.196, avgs=0 065/300: dt: 0.9000, rms radial error=166.260, avgs=0 070/300: dt: 0.9000, rms radial error=165.328, avgs=0 075/300: dt: 0.9000, rms radial error=164.400, avgs=0 080/300: dt: 0.9000, rms radial error=163.478, avgs=0 085/300: dt: 0.9000, rms radial error=162.561, avgs=0 090/300: dt: 0.9000, rms radial error=161.649, avgs=0 095/300: dt: 0.9000, rms radial error=160.741, avgs=0 100/300: dt: 0.9000, rms radial error=159.838, avgs=0 105/300: dt: 0.9000, rms radial error=158.940, avgs=0 110/300: dt: 0.9000, rms radial error=158.047, avgs=0 115/300: dt: 0.9000, rms radial error=157.159, avgs=0 120/300: dt: 0.9000, rms radial error=156.276, avgs=0 125/300: dt: 0.9000, rms radial error=155.398, avgs=0 130/300: dt: 0.9000, rms radial error=154.524, avgs=0 135/300: dt: 0.9000, rms radial error=153.656, avgs=0 140/300: dt: 0.9000, rms radial error=152.792, avgs=0 145/300: dt: 0.9000, rms radial error=151.932, avgs=0 150/300: dt: 0.9000, rms radial error=151.078, avgs=0 155/300: dt: 0.9000, rms radial error=150.228, avgs=0 160/300: dt: 0.9000, rms radial error=149.383, avgs=0 165/300: dt: 0.9000, rms radial error=148.543, avgs=0 170/300: dt: 0.9000, rms radial error=147.707, avgs=0 175/300: dt: 0.9000, rms radial error=146.875, avgs=0 180/300: dt: 0.9000, rms radial error=146.049, avgs=0 185/300: dt: 0.9000, rms radial error=145.227, avgs=0 190/300: dt: 0.9000, rms radial error=144.410, avgs=0 195/300: dt: 0.9000, rms radial error=143.598, avgs=0 200/300: dt: 0.9000, rms radial error=142.790, avgs=0 205/300: dt: 0.9000, rms radial error=141.986, avgs=0 210/300: dt: 0.9000, rms radial error=141.187, avgs=0 215/300: dt: 0.9000, rms radial error=140.392, avgs=0 220/300: dt: 0.9000, rms radial error=139.602, avgs=0 225/300: dt: 0.9000, rms radial error=138.816, avgs=0 230/300: dt: 0.9000, rms radial error=138.035, avgs=0 235/300: dt: 0.9000, rms radial error=137.257, avgs=0 240/300: dt: 0.9000, rms radial error=136.484, avgs=0 245/300: dt: 0.9000, rms radial error=135.716, avgs=0 250/300: dt: 0.9000, rms radial error=134.951, avgs=0 255/300: dt: 0.9000, rms radial error=134.191, avgs=0 260/300: dt: 0.9000, rms radial error=133.436, avgs=0 265/300: dt: 0.9000, rms radial error=132.684, avgs=0 270/300: dt: 0.9000, rms radial error=131.937, avgs=0 275/300: dt: 0.9000, rms radial error=131.193, avgs=0 280/300: dt: 0.9000, rms radial error=130.454, avgs=0 285/300: dt: 0.9000, rms radial error=129.719, avgs=0 290/300: dt: 0.9000, rms radial error=128.988, avgs=0 295/300: dt: 0.9000, rms radial error=128.262, avgs=0 300/300: dt: 0.9000, rms radial error=127.539, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15904.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 2638.92 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 = 268.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00631 epoch 4 (K=640.0), pass 1, starting sse = 15.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/13 = 0.00492 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Wed Dec 2 17:19:21 EST 2015 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 af1021_recon rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-32 (nv=135960, nf=271984, ne=407976, g=17) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 2506 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 11 24 defects to be corrected 0 vertices coincident reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2556 (-4.6278) -vertex loglikelihood: -6.1765 (-3.0883) -normal dot loglikelihood: -3.6583 (-3.6583) -quad curv loglikelihood: -6.5684 (-3.2842) Total Loglikelihood : -25.6589 CORRECTING DEFECT 0 (vertices=31, convex hull=61) After retessellation of defect 0, euler #=-22 (134430,402642,268190) : difference with theory (-21) = 1 CORRECTING DEFECT 1 (vertices=29, convex hull=82) After retessellation of defect 1, euler #=-21 (134444,402716,268251) : difference with theory (-20) = 1 CORRECTING DEFECT 2 (vertices=23, convex hull=70) After retessellation of defect 2, euler #=-20 (134461,402794,268313) : difference with theory (-19) = 1 CORRECTING DEFECT 3 (vertices=6, convex hull=14) After retessellation of defect 3, euler #=-19 (134462,402801,268320) : difference with theory (-18) = 1 CORRECTING DEFECT 4 (vertices=42, convex hull=70) After retessellation of defect 4, euler #=-18 (134489,402912,268405) : difference with theory (-17) = 1 CORRECTING DEFECT 5 (vertices=30, convex hull=83) After retessellation of defect 5, euler #=-17 (134506,402998,268475) : difference with theory (-16) = 1 CORRECTING DEFECT 6 (vertices=54, convex hull=37) After retessellation of defect 6, euler #=-16 (134512,403026,268498) : difference with theory (-15) = 1 CORRECTING DEFECT 7 (vertices=121, convex hull=132) After retessellation of defect 7, euler #=-15 (134549,403197,268633) : difference with theory (-14) = 1 CORRECTING DEFECT 8 (vertices=159, convex hull=78) After retessellation of defect 8, euler #=-14 (134579,403327,268734) : difference with theory (-13) = 1 CORRECTING DEFECT 9 (vertices=47, convex hull=87) After retessellation of defect 9, euler #=-13 (134601,403433,268819) : difference with theory (-12) = 1 CORRECTING DEFECT 10 (vertices=6, convex hull=22) After retessellation of defect 10, euler #=-12 (134602,403442,268828) : difference with theory (-11) = 1 CORRECTING DEFECT 11 (vertices=113, convex hull=118) After retessellation of defect 11, euler #=-10 (134645,403628,268973) : difference with theory (-10) = 0 CORRECTING DEFECT 12 (vertices=28, convex hull=62) After retessellation of defect 12, euler #=-9 (134656,403684,269019) : difference with theory (-9) = 0 CORRECTING DEFECT 13 (vertices=219, convex hull=70) After retessellation of defect 13, euler #=-8 (134669,403754,269077) : difference with theory (-8) = 0 CORRECTING DEFECT 14 (vertices=198, convex hull=101) After retessellation of defect 14, euler #=-7 (134705,403905,269193) : difference with theory (-7) = 0 CORRECTING DEFECT 15 (vertices=25, convex hull=31) After retessellation of defect 15, euler #=-6 (134708,403923,269209) : difference with theory (-6) = 0 CORRECTING DEFECT 16 (vertices=87, convex hull=122) After retessellation of defect 16, euler #=-5 (134741,404073,269327) : difference with theory (-5) = 0 CORRECTING DEFECT 17 (vertices=23, convex hull=54) After retessellation of defect 17, euler #=-4 (134751,404126,269371) : difference with theory (-4) = 0 CORRECTING DEFECT 18 (vertices=15, convex hull=23) After retessellation of defect 18, euler #=-3 (134754,404142,269385) : difference with theory (-3) = 0 CORRECTING DEFECT 19 (vertices=16, convex hull=15) After retessellation of defect 19, euler #=-2 (134754,404146,269390) : difference with theory (-2) = 0 CORRECTING DEFECT 20 (vertices=19, convex hull=51) After retessellation of defect 20, euler #=-1 (134766,404200,269433) : difference with theory (-1) = 0 CORRECTING DEFECT 21 (vertices=118, convex hull=65) After retessellation of defect 21, euler #=0 (134777,404262,269485) : difference with theory (0) = 0 CORRECTING DEFECT 22 (vertices=105, convex hull=95) After retessellation of defect 22, euler #=1 (134796,404361,269566) : difference with theory (1) = 0 CORRECTING DEFECT 23 (vertices=33, convex hull=60) After retessellation of defect 23, euler #=2 (134806,404412,269608) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.10-->8.46) (max @ vno 51160 --> 56118) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.10-->8.46) (max @ vno 51160 --> 56118) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (37.2%), 137 crossovers (62.8%), 85 vertices were eliminated building final representation... 1154 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134806, nf=269608, ne=404412, g=0) writing corrected surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 11.8 minutes 0 defective edges removing intersecting faces 000: 171 intersecting 001: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 134806 - 404412 + 269608 = 2 --> 0 holes F =2V-4: 269608 = 269612-4 (0) 2E=3F: 808824 = 808824 (0) total defect index = 0 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 43 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Wed Dec 2 17:31:15 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs af1021_recon rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.73 +- 0.91 3383 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=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.8, 20 (20) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.34) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2632 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5030457.5, rms=9.93 001: dt: 0.5000, sse=5796978.0, rms=7.147 (0.000%) 002: dt: 0.5000, sse=6204708.5, rms=5.513 (0.000%) 003: dt: 0.5000, sse=6478530.5, rms=4.508 (0.000%) 004: dt: 0.5000, sse=6741257.0, rms=3.876 (0.000%) 005: dt: 0.5000, sse=6849746.5, rms=3.534 (0.000%) 006: dt: 0.5000, sse=6977133.5, rms=3.321 (0.000%) 007: dt: 0.5000, sse=7007491.0, rms=3.232 (0.000%) 008: dt: 0.5000, sse=7045294.5, rms=3.150 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7019629.5, rms=3.130 (0.000%) 010: dt: 0.2500, sse=4337829.5, rms=2.129 (0.000%) 011: dt: 0.2500, sse=4012794.8, rms=1.885 (0.000%) 012: dt: 0.2500, sse=3854614.8, rms=1.833 (0.000%) rms = 1.80, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3814733.5, rms=1.803 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3753020.5, rms=1.766 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.7, 50 (5) missing vertices, mean dist -0.2 [0.4 (%72.0)->0.3 (%28.0))] %79 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.50) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.38 3705 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4290996.5, rms=4.34 015: dt: 0.5000, sse=4682878.0, rms=2.732 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4366005.0, rms=2.170 (0.000%) 017: dt: 0.2500, sse=4221162.5, rms=1.753 (0.000%) 018: dt: 0.2500, sse=4126458.0, rms=1.580 (0.000%) 019: dt: 0.2500, sse=4073992.0, rms=1.524 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4057223.8, rms=1.501 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4011195.2, rms=1.471 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.0, 37 (3) missing vertices, mean dist -0.1 [0.3 (%71.2)->0.2 (%28.8))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 (0.10-->4.55) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.89) mean absolute distance = 0.22 +- 0.31 2829 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4209697.5, rms=3.26 022: dt: 0.5000, sse=4551017.0, rms=2.427 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4264880.0, rms=1.765 (0.000%) 024: dt: 0.2500, sse=4191594.2, rms=1.437 (0.000%) 025: dt: 0.2500, sse=4152948.5, rms=1.352 (0.000%) rms = 1.35, time step reduction 2 of 3 to 0.125... rms = 1.34, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4130497.8, rms=1.336 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.8, 45 (2) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4145720.2, rms=1.68 rms = 1.69, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4214452.0, rms=1.265 (0.000%) 028: dt: 0.2500, sse=4405054.5, rms=1.016 (0.000%) rms = 1.02, time step reduction 2 of 3 to 0.125... rms = 1.01, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4404326.0, rms=1.012 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 14 non-cortical segments detected only using segment with 2295 vertices erasing segment 1 (vno[0] = 45502) erasing segment 2 (vno[0] = 83943) erasing segment 3 (vno[0] = 94873) erasing segment 4 (vno[0] = 94892) erasing segment 5 (vno[0] = 94904) erasing segment 6 (vno[0] = 95880) erasing segment 7 (vno[0] = 96851) erasing segment 8 (vno[0] = 99617) erasing segment 9 (vno[0] = 101371) erasing segment 10 (vno[0] = 102196) erasing segment 11 (vno[0] = 102270) erasing segment 12 (vno[0] = 103084) erasing segment 13 (vno[0] = 103867) writing cortex label to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label... writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv writing smoothed area to rh.area writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.86) refinement took 5.1 minutes #-------------------------------------------- #@# Smooth2 rh Wed Dec 2 17:36:22 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Wed Dec 2 17:36:26 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 45.8 mm, total surface area = 81849 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.118 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 148 vertices thresholded to be in k1 ~ [-0.30 0.35], k2 ~ [-0.11 0.09] total integrated curvature = 0.564*4pi (7.088) --> 0 handles ICI = 1.4, FI = 8.6, variation=148.940 113 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 135 vertices thresholded to be in [-0.14 0.16] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.022 done. #----------------------------------------- #@# Curvature Stats rh Wed Dec 2 17:38:19 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm af1021_recon 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 [ af1021_recon/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 [ 245 ] Gb_filter = 0 WARN: S lookup min: -0.817811 WARN: S explicit min: 0.000000 vertex = 427 #-------------------------------------------- #@# Sphere rh Wed Dec 2 17:38:26 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.288... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %20.14 pass 1: epoch 2 of 3 starting distance error %20.07 unfolding complete - removing small folds... starting distance error %19.94 removing remaining folds... final distance error %19.96 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.78 hours #-------------------------------------------- #@# Surf Reg rh Wed Dec 2 18:25:23 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_register -curv ../surf/rh.sphere /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, 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=compu, 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 = 0.591 curvature mean = 0.043, std = 0.931 curvature mean = 0.021, std = 0.861 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, 16.00) sse = 361095.2, tmin=1.0541 d=32.00 min @ (0.00, 8.00, 0.00) sse = 327242.8, tmin=2.1149 d=16.00 min @ (-4.00, -4.00, 0.00) sse = 305767.9, tmin=3.1817 d=4.00 min @ (1.00, 0.00, 1.00) sse = 304760.8, tmin=5.3901 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 304666.7, tmin=6.5158 d=1.00 min @ (0.25, 0.25, 0.00) sse = 304561.9, tmin=7.6125 d=0.50 min @ (-0.12, 0.00, -0.12) sse = 304536.6, tmin=8.7087 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 8.71 min curvature mean = 0.029, std = 0.960 curvature mean = 0.007, std = 0.938 curvature mean = 0.026, std = 0.969 curvature mean = 0.004, std = 0.971 curvature mean = 0.024, std = 0.969 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.026, std = 0.388 curvature mean = 0.006, std = 0.069 curvature mean = 0.048, std = 0.263 curvature mean = 0.006, std = 0.083 curvature mean = 0.024, std = 0.410 curvature mean = 0.007, std = 0.089 curvature mean = 0.014, std = 0.517 curvature mean = 0.007, std = 0.091 curvature mean = 0.005, std = 0.613 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Wed Dec 2 18:51:46 EST 2015 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Wed Dec 2 18:51:48 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mrisp_paint -a 5 /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /share/apps/freesurfer-5.3.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Wed Dec 2 18:51:50 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1202 labels changed using aseg relabeling using gibbs priors... 000: 3050 changed, 134806 examined... 001: 715 changed, 13277 examined... 002: 174 changed, 3906 examined... 003: 75 changed, 1057 examined... 004: 34 changed, 433 examined... 005: 17 changed, 206 examined... 006: 8 changed, 100 examined... 007: 4 changed, 41 examined... 008: 4 changed, 26 examined... 009: 1 changed, 22 examined... 010: 1 changed, 8 examined... 011: 2 changed, 8 examined... 012: 1 changed, 10 examined... 013: 0 changed, 7 examined... 159 labels changed using aseg 000: 95 total segments, 57 labels (335 vertices) changed 001: 41 total segments, 3 labels (4 vertices) changed 002: 38 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... 1082 vertices marked for relabeling... 1082 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 41 seconds. #-------------------------------------------- #@# Make Pial Surf rh Wed Dec 2 18:52:31 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.02-->3.74) (max @ vno 102277 --> 104722) face area 0.28 +- 0.12 (0.00-->2.85) mean absolute distance = 0.73 +- 0.92 3430 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown deleting segment 3 with 384 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=80.8, 25 (24) missing vertices, mean dist 0.3 [0.6 (%35.0)->0.8 (%65.0))] %70 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.91 +- 0.26 (0.05-->4.34) (max @ vno 101451 --> 134658) face area 0.28 +- 0.13 (0.00-->2.26) mean absolute distance = 0.35 +- 0.56 2670 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5040671.0, rms=9.92 001: dt: 0.5000, sse=5813598.0, rms=7.141 (0.000%) 002: dt: 0.5000, sse=6224298.5, rms=5.510 (0.000%) 003: dt: 0.5000, sse=6498853.5, rms=4.506 (0.000%) 004: dt: 0.5000, sse=6762585.5, rms=3.875 (0.000%) 005: dt: 0.5000, sse=6869478.0, rms=3.534 (0.000%) 006: dt: 0.5000, sse=6998033.0, rms=3.321 (0.000%) 007: dt: 0.5000, sse=7028486.0, rms=3.233 (0.000%) 008: dt: 0.5000, sse=7066930.0, rms=3.151 (0.000%) rms = 3.13, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7039925.0, rms=3.131 (0.000%) 010: dt: 0.2500, sse=4354474.0, rms=2.132 (0.000%) 011: dt: 0.2500, sse=4028360.5, rms=1.889 (0.000%) 012: dt: 0.2500, sse=3870135.0, rms=1.837 (0.000%) rms = 1.81, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3829512.0, rms=1.807 (0.000%) rms = 1.77, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=3767567.2, rms=1.770 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 3 with 299 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 6 with 9 points - only 0.00% unknown deleting segment 7 with 22 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown mean border=83.7, 54 (6) missing vertices, mean dist -0.2 [0.4 (%71.9)->0.3 (%28.1))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.50) (max @ vno 101451 --> 134658) face area 0.35 +- 0.16 (0.00-->2.92) mean absolute distance = 0.27 +- 0.39 3758 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4309256.5, rms=4.33 015: dt: 0.5000, sse=4700820.5, rms=2.732 (0.000%) rms = 2.81, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=4385123.5, rms=2.172 (0.000%) 017: dt: 0.2500, sse=4242888.0, rms=1.755 (0.000%) 018: dt: 0.2500, sse=4147145.0, rms=1.583 (0.000%) 019: dt: 0.2500, sse=4094185.8, rms=1.528 (0.000%) rms = 1.50, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4076906.5, rms=1.504 (0.000%) rms = 1.47, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4030592.8, rms=1.474 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 303 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=86.0, 38 (3) missing vertices, mean dist -0.1 [0.3 (%71.1)->0.2 (%28.9))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 (0.10-->4.55) (max @ vno 101451 --> 134658) face area 0.34 +- 0.16 (0.00-->2.89) mean absolute distance = 0.22 +- 0.32 2871 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4229315.5, rms=3.25 022: dt: 0.5000, sse=4573934.5, rms=2.426 (0.000%) rms = 2.69, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4286142.5, rms=1.767 (0.000%) 024: dt: 0.2500, sse=4210874.5, rms=1.440 (0.000%) 025: dt: 0.2500, sse=4174444.5, rms=1.356 (0.000%) rms = 1.36, time step reduction 2 of 3 to 0.125... rms = 1.34, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4151896.8, rms=1.340 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 311 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 9 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=86.8, 47 (2) missing vertices, mean dist -0.0 [0.2 (%57.0)->0.2 (%43.0))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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=4167169.2, rms=1.69 rms = 1.69, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4237478.0, rms=1.268 (0.000%) 028: dt: 0.2500, sse=4432497.0, rms=1.019 (0.000%) rms = 1.03, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4431764.5, rms=1.016 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=60.2, 52 (52) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.6 (%100.0))] %19 local maxima, %44 large gradients and %32 min vals, 2330 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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=21095174.0, rms=26.68 001: dt: 0.5000, sse=16219415.0, rms=22.858 (0.000%) 002: dt: 0.5000, sse=12634789.0, rms=19.614 (0.000%) 003: dt: 0.5000, sse=10127611.0, rms=16.925 (0.000%) 004: dt: 0.5000, sse=8511865.0, rms=14.699 (0.000%) 005: dt: 0.5000, sse=7457957.5, rms=12.869 (0.000%) 006: dt: 0.5000, sse=6784133.0, rms=11.402 (0.000%) 007: dt: 0.5000, sse=6385647.5, rms=10.144 (0.000%) 008: dt: 0.5000, sse=6107506.0, rms=9.027 (0.000%) 009: dt: 0.5000, sse=5971715.0, rms=7.991 (0.000%) 010: dt: 0.5000, sse=5883049.0, rms=7.059 (0.000%) 011: dt: 0.5000, sse=5875117.5, rms=6.211 (0.000%) 012: dt: 0.5000, sse=5878926.0, rms=5.469 (0.000%) 013: dt: 0.5000, sse=5950857.0, rms=4.853 (0.000%) 014: dt: 0.5000, sse=6024235.5, rms=4.415 (0.000%) 015: dt: 0.5000, sse=6134776.5, rms=4.094 (0.000%) 016: dt: 0.5000, sse=6184613.5, rms=3.893 (0.000%) 017: dt: 0.5000, sse=6226774.5, rms=3.746 (0.000%) 018: dt: 0.5000, sse=6247221.0, rms=3.669 (0.000%) 019: dt: 0.5000, sse=6298535.5, rms=3.597 (0.000%) rms = 3.56, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=6292106.0, rms=3.561 (0.000%) 021: dt: 0.2500, sse=4602540.5, rms=2.967 (0.000%) 022: dt: 0.2500, sse=4443622.5, rms=2.815 (0.000%) rms = 2.79, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4347487.5, rms=2.789 (0.000%) 024: dt: 0.1250, sse=4178397.2, rms=2.706 (0.000%) rms = 2.70, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4153944.8, rms=2.698 (0.000%) positioning took 2.5 minutes mean border=58.0, 1075 (3) missing vertices, mean dist 0.2 [0.2 (%44.5)->0.6 (%55.5))] %38 local maxima, %31 large gradients and %25 min vals, 861 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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=4762497.5, rms=4.68 026: dt: 0.5000, sse=4969183.5, rms=3.783 (0.000%) 027: dt: 0.5000, sse=6246533.0, rms=3.640 (0.000%) rms = 3.64, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=6107095.5, rms=3.635 (0.000%) 029: dt: 0.2500, sse=5066130.5, rms=2.924 (0.000%) 030: dt: 0.2500, sse=4962338.0, rms=2.729 (0.000%) rms = 2.72, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4899494.0, rms=2.721 (0.000%) 032: dt: 0.1250, sse=4743177.5, rms=2.613 (0.000%) rms = 2.60, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4731522.5, rms=2.598 (0.000%) positioning took 0.8 minutes mean border=56.5, 1297 (2) missing vertices, mean dist 0.1 [0.2 (%39.1)->0.4 (%60.9))] %52 local maxima, %18 large gradients and %25 min vals, 965 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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=4869240.0, rms=3.34 rms = 3.42, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4704507.0, rms=2.982 (0.000%) 035: dt: 0.2500, sse=4726097.0, rms=2.761 (0.000%) 036: dt: 0.2500, sse=4896541.5, rms=2.690 (0.000%) rms = 2.67, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=4960427.5, rms=2.668 (0.000%) 038: dt: 0.1250, sse=4843940.5, rms=2.586 (0.000%) rms = 2.57, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4865271.5, rms=2.570 (0.000%) positioning took 0.7 minutes mean border=55.8, 2773 (2) missing vertices, mean dist 0.1 [0.2 (%44.5)->0.3 (%55.5))] %55 local maxima, %14 large gradients and %25 min vals, 843 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4889507.0, rms=2.76 rms = 3.10, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4818572.5, rms=2.609 (0.000%) 041: dt: 0.2500, sse=5004985.5, rms=2.554 (0.000%) rms = 2.53, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5068982.0, rms=2.535 (0.000%) 043: dt: 0.1250, sse=4985673.0, rms=2.457 (0.000%) rms = 2.44, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5013903.0, rms=2.440 (0.000%) positioning took 0.6 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area.pial vertex spacing 1.01 +- 0.44 (0.04-->6.99) (max @ vno 101451 --> 134658) face area 0.40 +- 0.31 (0.00-->4.95) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 784:1305 truncations. 25877 vertices at 0 distance 84621 vertices at 1 distance 85363 vertices at 2 distance 41293 vertices at 3 distance 14079 vertices at 4 distance 4337 vertices at 5 distance 1349 vertices at 6 distance 484 vertices at 7 distance 202 vertices at 8 distance 107 vertices at 9 distance 64 vertices at 10 distance 54 vertices at 11 distance 47 vertices at 12 distance 40 vertices at 13 distance 26 vertices at 14 distance 22 vertices at 15 distance 11 vertices at 16 distance 10 vertices at 17 distance 20 vertices at 18 distance 9 vertices at 19 distance 3 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.thickness positioning took 10.8 minutes #-------------------------------------------- #@# Surf Volume rh Wed Dec 2 19:03:21 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Wed Dec 2 19:03:21 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 af1021_recon lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12567 bright wm thresholded. 1000 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.3 +- 8.1 [70.0 --> 110.0] GM (82.0) : 80.2 +- 10.9 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.1 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 48.1 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=70 mean inside = 94.6, mean outside = 77.1 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.04-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 602 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown deleting segment 14 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=compu, 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 (0.06-->6.67) (max @ vno 48431 --> 48432) face area 0.33 +- 0.16 (0.00-->5.19) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 123 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 602 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=compu, 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=4373064.0, rms=0.00 rms = 0.93, time step reduction 1 of 3 to 0.250... rms = 0.24, time step reduction 2 of 3 to 0.125... rms = 0.03, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4373064.0, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [92.20 173.80], gm=133.00+-13.60, and vertices in regions > 126.2 14552 surface locations found to contain inconsistent values (14297 in, 255 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=472305.5, rms=0.21 001: dt: 0.5000, sse=444260.5, rms=0.205 (0.000%) 002: dt: 0.5000, sse=421809.5, rms=0.194 (0.000%) 003: dt: 0.5000, sse=407687.8, rms=0.185 (0.000%) 004: dt: 0.5000, sse=396863.3, rms=0.176 (0.000%) 005: dt: 0.5000, sse=388843.9, rms=0.168 (0.000%) 006: dt: 0.5000, sse=381906.5, rms=0.160 (0.000%) 007: dt: 0.5000, sse=376432.4, rms=0.154 (0.000%) 008: dt: 0.5000, sse=371905.8, rms=0.148 (0.000%) 009: dt: 0.5000, sse=367695.6, rms=0.142 (0.000%) 010: dt: 0.5000, sse=364125.8, rms=0.137 (0.000%) 011: dt: 0.5000, sse=361083.9, rms=0.133 (0.000%) 012: dt: 0.5000, sse=358422.6, rms=0.129 (0.000%) 013: dt: 0.5000, sse=356064.7, rms=0.125 (0.000%) 014: dt: 0.5000, sse=353791.0, rms=0.122 (0.000%) 015: dt: 0.5000, sse=351691.0, rms=0.119 (0.000%) 016: dt: 0.5000, sse=349777.4, rms=0.117 (0.000%) 017: dt: 0.5000, sse=348005.8, rms=0.115 (0.000%) 018: dt: 0.5000, sse=346400.8, rms=0.113 (0.000%) 019: dt: 0.5000, sse=344816.1, rms=0.112 (0.000%) 020: dt: 0.5000, sse=343302.3, rms=0.110 (0.000%) 021: dt: 0.5000, sse=341740.5, rms=0.109 (0.000%) 022: dt: 0.5000, sse=340381.9, rms=0.108 (0.000%) 023: dt: 0.5000, sse=339083.9, rms=0.108 (0.000%) 024: dt: 0.5000, sse=337783.5, rms=0.107 (0.000%) 025: dt: 0.5000, sse=336731.9, rms=0.107 (0.000%) 026: dt: 0.5000, sse=335736.1, rms=0.106 (0.000%) 027: dt: 0.5000, sse=334848.0, rms=0.106 (0.000%) 028: dt: 0.5000, sse=333960.9, rms=0.106 (0.000%) 029: dt: 0.5000, sse=332960.8, rms=0.106 (0.000%) 030: dt: 0.5000, sse=332064.1, rms=0.106 (0.000%) positioning took 3.4 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 2866 surface locations found to contain inconsistent values (2659 in, 207 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=33232.4, rms=0.06 031: dt: 0.5000, sse=33124.9, rms=0.061 (0.000%) 032: dt: 0.5000, sse=33098.5, rms=0.057 (0.000%) 033: dt: 0.5000, sse=33131.1, rms=0.054 (0.000%) 034: dt: 0.5000, sse=33163.9, rms=0.052 (0.000%) 035: dt: 0.5000, sse=33191.3, rms=0.049 (0.000%) 036: dt: 0.5000, sse=33245.7, rms=0.047 (0.000%) 037: dt: 0.5000, sse=33280.5, rms=0.045 (0.000%) 038: dt: 0.5000, sse=33320.0, rms=0.044 (0.000%) 039: dt: 0.5000, sse=33365.9, rms=0.042 (0.000%) 040: dt: 0.5000, sse=33402.3, rms=0.040 (0.000%) 041: dt: 0.5000, sse=33440.8, rms=0.039 (0.000%) 042: dt: 0.5000, sse=33469.8, rms=0.037 (0.000%) 043: dt: 0.5000, sse=33489.4, rms=0.036 (0.000%) 044: dt: 0.5000, sse=33524.6, rms=0.035 (0.000%) 045: dt: 0.5000, sse=33544.5, rms=0.034 (0.000%) 046: dt: 0.5000, sse=33567.3, rms=0.032 (0.000%) 047: dt: 0.5000, sse=33609.8, rms=0.031 (0.000%) 048: dt: 0.5000, sse=33634.9, rms=0.030 (0.000%) 049: dt: 0.5000, sse=33649.1, rms=0.029 (0.000%) 050: dt: 0.5000, sse=33673.5, rms=0.029 (0.000%) 051: dt: 0.5000, sse=33697.0, rms=0.028 (0.000%) 052: dt: 0.5000, sse=33719.1, rms=0.027 (0.000%) 053: dt: 0.5000, sse=33735.4, rms=0.026 (0.000%) 054: dt: 0.5000, sse=33745.0, rms=0.026 (0.000%) 055: dt: 0.5000, sse=33772.2, rms=0.025 (0.000%) 056: dt: 0.5000, sse=33776.5, rms=0.024 (0.000%) 057: dt: 0.5000, sse=33785.8, rms=0.024 (0.000%) 058: dt: 0.5000, sse=33795.3, rms=0.023 (0.000%) 059: dt: 0.5000, sse=33814.4, rms=0.023 (0.000%) 060: dt: 0.5000, sse=33814.1, rms=0.022 (0.000%) positioning took 3.3 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 727 surface locations found to contain inconsistent values (529 in, 198 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3440.5, rms=0.02 061: dt: 0.5000, sse=3437.9, rms=0.022 (0.000%) 062: dt: 0.5000, sse=3437.1, rms=0.021 (0.000%) 063: dt: 0.5000, sse=3436.7, rms=0.020 (0.000%) 064: dt: 0.5000, sse=3436.0, rms=0.019 (0.000%) 065: dt: 0.5000, sse=3435.9, rms=0.019 (0.000%) 066: dt: 0.5000, sse=3436.4, rms=0.018 (0.000%) 067: dt: 0.5000, sse=3434.9, rms=0.018 (0.000%) 068: dt: 0.5000, sse=3434.3, rms=0.017 (0.000%) 069: dt: 0.5000, sse=3433.9, rms=0.017 (0.000%) 070: dt: 0.5000, sse=3434.3, rms=0.017 (0.000%) 071: dt: 0.5000, sse=3434.3, rms=0.016 (0.000%) 072: dt: 0.5000, sse=3434.1, rms=0.016 (0.000%) 073: dt: 0.5000, sse=3434.4, rms=0.016 (0.000%) 074: dt: 0.5000, sse=3434.1, rms=0.016 (0.000%) 075: dt: 0.5000, sse=3434.8, rms=0.016 (0.000%) 076: dt: 0.5000, sse=3434.8, rms=0.015 (0.000%) 077: dt: 0.5000, sse=3435.2, rms=0.015 (0.000%) 078: dt: 0.5000, sse=3435.1, rms=0.015 (0.000%) 079: dt: 0.5000, sse=3435.0, rms=0.015 (0.000%) 080: dt: 0.5000, sse=3435.4, rms=0.015 (0.000%) 081: dt: 0.5000, sse=3435.3, rms=0.015 (0.000%) 082: dt: 0.5000, sse=3435.1, rms=0.015 (0.000%) 083: dt: 0.5000, sse=3435.8, rms=0.015 (0.000%) 084: dt: 0.5000, sse=3435.8, rms=0.014 (0.000%) 085: dt: 0.5000, sse=3436.1, rms=0.014 (0.000%) 086: dt: 0.5000, sse=3436.3, rms=0.014 (0.000%) 087: dt: 0.5000, sse=3436.6, rms=0.014 (0.000%) 088: dt: 0.5000, sse=3436.4, rms=0.014 (0.000%) 089: dt: 0.5000, sse=3436.2, rms=0.014 (0.000%) 090: dt: 0.5000, sse=3436.9, rms=0.014 (0.000%) positioning took 3.0 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.10 175.90], gm=133.00+-14.30, and vertices in regions > 125.8 262 surface locations found to contain inconsistent values (63 in, 199 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=366.2, rms=0.01 091: dt: 0.5000, sse=366.2, rms=0.014 (0.000%) 092: dt: 0.5000, sse=365.8, rms=0.014 (0.000%) 093: dt: 0.5000, sse=365.5, rms=0.014 (0.000%) 094: dt: 0.5000, sse=365.3, rms=0.014 (0.000%) 095: dt: 0.5000, sse=365.2, rms=0.014 (0.000%) 096: dt: 0.5000, sse=365.1, rms=0.014 (0.000%) 097: dt: 0.5000, sse=365.0, rms=0.014 (0.000%) 098: dt: 0.5000, sse=364.9, rms=0.014 (0.000%) 099: dt: 0.5000, sse=364.9, rms=0.014 (0.000%) 100: dt: 0.5000, sse=364.8, rms=0.014 (0.000%) 101: dt: 0.5000, sse=364.8, rms=0.013 (0.000%) 102: dt: 0.5000, sse=364.7, rms=0.013 (0.000%) 103: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 104: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 105: dt: 0.5000, sse=364.6, rms=0.013 (0.000%) 106: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 107: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 108: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 109: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 110: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 111: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 112: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 113: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 114: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 115: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 116: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 117: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 118: dt: 0.5000, sse=364.4, rms=0.013 (0.000%) 119: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) 120: dt: 0.5000, sse=364.5, rms=0.013 (0.000%) positioning took 2.9 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.area.pial vertex spacing 1.00 +- 0.43 (0.04-->8.03) (max @ vno 92642 --> 92643) face area 0.39 +- 0.30 (0.00-->10.95) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed 0 of 134383 vertices processed 25000 of 134383 vertices processed 50000 of 134383 vertices processed 75000 of 134383 vertices processed 100000 of 134383 vertices processed 125000 of 134383 vertices processed thickness calculation complete, 600:981 truncations. 28508 vertices at 0 distance 88163 vertices at 1 distance 83783 vertices at 2 distance 38396 vertices at 3 distance 12342 vertices at 4 distance 3767 vertices at 5 distance 1244 vertices at 6 distance 425 vertices at 7 distance 141 vertices at 8 distance 72 vertices at 9 distance 43 vertices at 10 distance 40 vertices at 11 distance 20 vertices at 12 distance 16 vertices at 13 distance 12 vertices at 14 distance 13 vertices at 15 distance 11 vertices at 16 distance 7 vertices at 17 distance 8 vertices at 18 distance 8 vertices at 19 distance 15 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.thickness positioning took 15.4 minutes /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 af1021_recon rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/brain.finalsurfs.mgz... reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... 12104 bright wm thresholded. 921 bright non-wm voxels segmented. reading original surface position from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.orig... computing class statistics... border white: 249239 voxels (1.49%) border gray 279159 voxels (1.66%) WM (94.0): 95.2 +- 8.0 [70.0 --> 110.0] GM (82.0) : 80.3 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.0 (was 70) setting MAX_BORDER_WHITE to 111.0 (was 105) setting MIN_BORDER_WHITE to 70.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 95.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=70 mean inside = 94.3, mean outside = 77.0 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 380 points - only 0.00% unknown deleting segment 7 with 8 points - only 0.00% unknown deleting segment 8 with 12 points - only 0.00% unknown deleting segment 9 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=compu, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.00, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=compu, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.02, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=compu, 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 (0.02-->4.57) (max @ vno 101451 --> 134658) face area 0.33 +- 0.16 (0.00-->2.85) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4390928.5, rms=0.00 rms = 1.00, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 380 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown deleting segment 5 with 12 points - only 0.00% unknown deleting segment 6 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=compu, 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=4390928.5, rms=0.00 rms = 1.02, time step reduction 1 of 3 to 0.250... rms = 0.33, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4390928.5, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 13521 surface locations found to contain inconsistent values (13344 in, 177 out) tol=1.0e-04, sigma=2.0, host=compu, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=489117.8, rms=0.21 001: dt: 0.5000, sse=457629.3, rms=0.199 (0.000%) 002: dt: 0.5000, sse=434001.4, rms=0.188 (0.000%) 003: dt: 0.5000, sse=419565.2, rms=0.180 (0.000%) 004: dt: 0.5000, sse=407977.9, rms=0.171 (0.000%) 005: dt: 0.5000, sse=399536.7, rms=0.164 (0.000%) 006: dt: 0.5000, sse=392343.6, rms=0.157 (0.000%) 007: dt: 0.5000, sse=386541.2, rms=0.151 (0.000%) 008: dt: 0.5000, sse=381371.6, rms=0.145 (0.000%) 009: dt: 0.5000, sse=377076.8, rms=0.140 (0.000%) 010: dt: 0.5000, sse=373152.3, rms=0.135 (0.000%) 011: dt: 0.5000, sse=369700.8, rms=0.131 (0.000%) 012: dt: 0.5000, sse=366605.1, rms=0.128 (0.000%) 013: dt: 0.5000, sse=363736.5, rms=0.124 (0.000%) 014: dt: 0.5000, sse=360975.4, rms=0.121 (0.000%) 015: dt: 0.5000, sse=358703.4, rms=0.118 (0.000%) 016: dt: 0.5000, sse=356400.9, rms=0.116 (0.000%) 017: dt: 0.5000, sse=354514.8, rms=0.114 (0.000%) 018: dt: 0.5000, sse=352853.1, rms=0.112 (0.000%) 019: dt: 0.5000, sse=350970.0, rms=0.110 (0.000%) 020: dt: 0.5000, sse=349133.9, rms=0.109 (0.000%) 021: dt: 0.5000, sse=347413.0, rms=0.107 (0.000%) 022: dt: 0.5000, sse=346105.8, rms=0.106 (0.000%) 023: dt: 0.5000, sse=344796.4, rms=0.105 (0.000%) 024: dt: 0.5000, sse=343241.6, rms=0.104 (0.000%) 025: dt: 0.5000, sse=342058.9, rms=0.104 (0.000%) 026: dt: 0.5000, sse=340694.0, rms=0.103 (0.000%) 027: dt: 0.5000, sse=339543.8, rms=0.102 (0.000%) 028: dt: 0.5000, sse=338511.8, rms=0.102 (0.000%) 029: dt: 0.5000, sse=337478.8, rms=0.102 (0.000%) 030: dt: 0.5000, sse=336519.2, rms=0.102 (0.000%) positioning took 3.1 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 4103 surface locations found to contain inconsistent values (3938 in, 165 out) tol=1.0e-04, sigma=1.0, host=compu, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=33749.7, rms=0.07 031: dt: 0.5000, sse=33605.8, rms=0.065 (0.000%) 032: dt: 0.5000, sse=33624.2, rms=0.061 (0.000%) 033: dt: 0.5000, sse=33699.0, rms=0.057 (0.000%) 034: dt: 0.5000, sse=33759.0, rms=0.054 (0.000%) 035: dt: 0.5000, sse=33808.3, rms=0.052 (0.000%) 036: dt: 0.5000, sse=33860.1, rms=0.049 (0.000%) 037: dt: 0.5000, sse=33900.6, rms=0.047 (0.000%) 038: dt: 0.5000, sse=33953.3, rms=0.045 (0.000%) 039: dt: 0.5000, sse=33991.1, rms=0.043 (0.000%) 040: dt: 0.5000, sse=34026.4, rms=0.041 (0.000%) 041: dt: 0.5000, sse=34062.4, rms=0.040 (0.000%) 042: dt: 0.5000, sse=34083.4, rms=0.038 (0.000%) 043: dt: 0.5000, sse=34114.1, rms=0.037 (0.000%) 044: dt: 0.5000, sse=34145.6, rms=0.035 (0.000%) 045: dt: 0.5000, sse=34177.8, rms=0.034 (0.000%) 046: dt: 0.5000, sse=34198.5, rms=0.033 (0.000%) 047: dt: 0.5000, sse=34226.3, rms=0.031 (0.000%) 048: dt: 0.5000, sse=34249.0, rms=0.030 (0.000%) 049: dt: 0.5000, sse=34279.6, rms=0.029 (0.000%) 050: dt: 0.5000, sse=34301.8, rms=0.029 (0.000%) 051: dt: 0.5000, sse=34317.2, rms=0.028 (0.000%) 052: dt: 0.5000, sse=34330.8, rms=0.027 (0.000%) 053: dt: 0.5000, sse=34351.1, rms=0.026 (0.000%) 054: dt: 0.5000, sse=34369.1, rms=0.026 (0.000%) 055: dt: 0.5000, sse=34373.8, rms=0.025 (0.000%) 056: dt: 0.5000, sse=34383.5, rms=0.024 (0.000%) 057: dt: 0.5000, sse=34392.1, rms=0.024 (0.000%) 058: dt: 0.5000, sse=34404.5, rms=0.023 (0.000%) 059: dt: 0.5000, sse=34414.8, rms=0.023 (0.000%) 060: dt: 0.5000, sse=34432.2, rms=0.023 (0.000%) positioning took 3.0 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 755 surface locations found to contain inconsistent values (597 in, 158 out) tol=1.0e-04, sigma=0.5, host=compu, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3496.5, rms=0.02 061: dt: 0.5000, sse=3495.3, rms=0.021 (0.000%) 062: dt: 0.5000, sse=3496.2, rms=0.020 (0.000%) 063: dt: 0.5000, sse=3497.6, rms=0.019 (0.000%) 064: dt: 0.5000, sse=3499.3, rms=0.019 (0.000%) 065: dt: 0.5000, sse=3500.1, rms=0.019 (0.000%) 066: dt: 0.5000, sse=3500.1, rms=0.018 (0.000%) 067: dt: 0.5000, sse=3499.9, rms=0.018 (0.000%) 068: dt: 0.5000, sse=3500.0, rms=0.018 (0.000%) 069: dt: 0.5000, sse=3499.6, rms=0.017 (0.000%) 070: dt: 0.5000, sse=3500.5, rms=0.017 (0.000%) 071: dt: 0.5000, sse=3499.0, rms=0.017 (0.000%) 072: dt: 0.5000, sse=3499.3, rms=0.017 (0.000%) 073: dt: 0.5000, sse=3499.9, rms=0.017 (0.000%) 074: dt: 0.5000, sse=3500.2, rms=0.016 (0.000%) 075: dt: 0.5000, sse=3499.7, rms=0.016 (0.000%) 076: dt: 0.5000, sse=3499.8, rms=0.016 (0.000%) 077: dt: 0.5000, sse=3500.0, rms=0.016 (0.000%) 078: dt: 0.5000, sse=3500.3, rms=0.016 (0.000%) 079: dt: 0.5000, sse=3500.5, rms=0.016 (0.000%) 080: dt: 0.5000, sse=3500.7, rms=0.016 (0.000%) 081: dt: 0.5000, sse=3501.3, rms=0.016 (0.000%) 082: dt: 0.5000, sse=3502.6, rms=0.016 (0.000%) 083: dt: 0.5000, sse=3502.9, rms=0.016 (0.000%) 084: dt: 0.5000, sse=3503.0, rms=0.016 (0.000%) 085: dt: 0.5000, sse=3503.2, rms=0.016 (0.000%) 086: dt: 0.5000, sse=3503.1, rms=0.016 (0.000%) 087: dt: 0.5000, sse=3504.2, rms=0.016 (0.000%) 088: dt: 0.5000, sse=3504.4, rms=0.016 (0.000%) 089: dt: 0.5000, sse=3504.1, rms=0.016 (0.000%) 090: dt: 0.5000, sse=3504.0, rms=0.016 (0.000%) positioning took 2.9 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [90.80 171.20], gm=131.00+-13.40, and vertices in regions > 124.3 228 surface locations found to contain inconsistent values (75 in, 153 out) tol=1.0e-04, sigma=0.2, host=compu, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=377.5, rms=0.02 091: dt: 0.5000, sse=378.6, rms=0.016 (0.000%) 092: dt: 0.5000, sse=378.0, rms=0.015 (0.000%) 093: dt: 0.5000, sse=378.4, rms=0.015 (0.000%) 094: dt: 0.5000, sse=377.9, rms=0.015 (0.000%) 095: dt: 0.5000, sse=377.5, rms=0.015 (0.000%) 096: dt: 0.5000, sse=377.1, rms=0.015 (0.000%) 097: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 098: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 099: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 100: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 101: dt: 0.5000, sse=377.6, rms=0.015 (0.000%) 102: dt: 0.5000, sse=377.9, rms=0.015 (0.000%) 103: dt: 0.5000, sse=377.5, rms=0.015 (0.000%) 104: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 105: dt: 0.5000, sse=377.4, rms=0.015 (0.000%) 106: dt: 0.5000, sse=377.3, rms=0.015 (0.000%) 107: dt: 0.5000, sse=377.1, rms=0.015 (0.000%) 108: dt: 0.5000, sse=377.0, rms=0.015 (0.000%) 109: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 110: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 111: dt: 0.5000, sse=377.7, rms=0.015 (0.000%) 112: dt: 0.5000, sse=377.6, rms=0.015 (0.000%) 113: dt: 0.5000, sse=377.2, rms=0.015 (0.000%) 114: dt: 0.5000, sse=376.9, rms=0.015 (0.000%) 115: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 116: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 117: dt: 0.5000, sse=376.8, rms=0.015 (0.000%) 118: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 119: dt: 0.5000, sse=376.6, rms=0.015 (0.000%) 120: dt: 0.5000, sse=376.7, rms=0.015 (0.000%) positioning took 2.9 minutes writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.area.pial vertex spacing 0.99 +- 0.43 (0.05-->7.35) (max @ vno 101451 --> 134658) face area 0.39 +- 0.30 (0.00-->5.06) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed 0 of 134806 vertices processed 25000 of 134806 vertices processed 50000 of 134806 vertices processed 75000 of 134806 vertices processed 100000 of 134806 vertices processed 125000 of 134806 vertices processed thickness calculation complete, 778:1103 truncations. 27462 vertices at 0 distance 86290 vertices at 1 distance 84109 vertices at 2 distance 40276 vertices at 3 distance 13389 vertices at 4 distance 4172 vertices at 5 distance 1366 vertices at 6 distance 465 vertices at 7 distance 229 vertices at 8 distance 115 vertices at 9 distance 58 vertices at 10 distance 37 vertices at 11 distance 51 vertices at 12 distance 49 vertices at 13 distance 21 vertices at 14 distance 8 vertices at 15 distance 13 vertices at 16 distance 9 vertices at 17 distance 7 vertices at 18 distance 7 vertices at 19 distance 3 vertices at 20 distance writing curvature file /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.thickness positioning took 14.6 minutes #-------------------------------------------- #@# Surf Volume lh Wed Dec 2 19:33:33 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Surf Volume rh Wed Dec 2 19:33:33 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Wed Dec 2 19:33:34 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1584 1096 2875 2.489 0.530 0.114 0.032 12 2.2 bankssts 789 507 1495 2.661 0.477 0.152 0.044 14 1.6 caudalanteriorcingulate 2765 1859 5182 2.593 0.570 0.140 0.067 167 8.6 caudalmiddlefrontal 1917 1225 2555 1.949 0.422 0.165 0.068 36 5.2 cuneus 622 410 1341 2.764 0.564 0.128 0.049 7 1.2 entorhinal 4867 3257 10270 2.835 0.561 0.162 0.071 103 14.5 fusiform 6836 4574 12418 2.499 0.486 0.145 0.055 113 15.5 inferiorparietal 4680 3132 10037 2.856 0.759 0.152 0.096 95 11.5 inferiortemporal 1431 927 2491 2.593 0.674 0.156 0.064 33 3.5 isthmuscingulate 8254 5273 11527 2.054 0.512 0.149 0.056 137 20.0 lateraloccipital 3790 2560 7678 2.731 0.683 0.153 0.067 70 10.7 lateralorbitofrontal 5400 3475 8106 2.183 0.558 0.159 0.064 91 14.0 lingual 2479 1635 4419 2.398 0.685 0.163 0.096 126 9.7 medialorbitofrontal 4545 3086 10932 2.876 0.668 0.142 0.052 77 9.5 middletemporal 1146 731 1953 2.407 0.561 0.121 0.039 10 2.0 parahippocampal 2004 1283 3370 2.399 0.476 0.130 0.112 89 10.2 paracentral 2911 2005 6138 2.715 0.416 0.134 0.046 39 5.4 parsopercularis 933 614 2243 2.827 0.529 0.169 0.153 61 8.6 parsorbitalis 1982 1338 4111 2.718 0.543 0.137 0.045 29 3.6 parstriangularis 2156 1370 2449 1.917 0.455 0.130 0.058 27 4.8 pericalcarine 6459 4112 10363 2.256 0.683 0.133 0.048 94 13.5 postcentral 1744 1188 3384 2.702 0.619 0.164 0.062 38 4.2 posteriorcingulate 7497 4785 13586 2.612 0.589 0.138 0.060 105 18.6 precentral 5881 4013 10123 2.358 0.548 0.145 0.068 99 11.7 precuneus 1067 686 2451 3.079 0.782 0.163 0.061 22 2.5 rostralanteriorcingulate 7995 5492 16389 2.553 0.628 0.162 0.070 162 22.1 rostralmiddlefrontal 9871 6735 23089 2.984 0.609 0.151 0.063 172 27.7 superiorfrontal 7763 5131 12315 2.194 0.506 0.144 0.064 396 16.2 superiorparietal 6185 4127 13956 2.914 0.607 0.129 0.051 79 12.3 superiortemporal 5512 3663 11335 2.782 0.548 0.144 0.058 100 12.6 supramarginal 280 192 765 2.981 0.448 0.260 0.176 16 2.1 frontalpole 620 433 2312 3.461 0.849 0.194 0.103 19 3.0 temporalpole 866 518 1557 2.562 0.544 0.134 0.105 16 4.9 transversetemporal 3115 2040 6764 3.227 0.793 0.118 0.048 38 6.3 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Dec 2 19:33:47 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 180 labels changed using aseg relabeling using gibbs priors... 000: 9295 changed, 134383 examined... 001: 2265 changed, 35617 examined... 002: 701 changed, 11469 examined... 003: 273 changed, 3914 examined... 004: 121 changed, 1548 examined... 005: 53 changed, 686 examined... 006: 34 changed, 324 examined... 007: 17 changed, 185 examined... 008: 13 changed, 85 examined... 009: 11 changed, 66 examined... 010: 5 changed, 64 examined... 011: 3 changed, 30 examined... 012: 1 changed, 15 examined... 013: 0 changed, 7 examined... 94 labels changed using aseg 000: 304 total segments, 224 labels (3092 vertices) changed 001: 96 total segments, 17 labels (152 vertices) changed 002: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 123 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 567 vertices marked for relabeling... 567 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Dec 2 19:34:34 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1059 718 2124 2.409 0.714 0.185 0.091 27 3.9 G_and_S_frontomargin 1520 1033 2481 2.232 0.462 0.161 0.051 26 3.3 G_and_S_occipital_inf 1504 902 2436 2.243 0.480 0.131 0.100 80 9.4 G_and_S_paracentral 1564 1018 3374 2.905 0.584 0.161 0.067 32 4.1 G_and_S_subcentral 687 468 1759 2.610 0.694 0.225 0.132 29 3.5 G_and_S_transv_frontopol 2103 1400 4568 3.086 0.723 0.158 0.056 38 4.7 G_and_S_cingul-Ant 1068 723 2114 2.686 0.530 0.132 0.039 12 1.8 G_and_S_cingul-Mid-Ant 1302 914 2513 2.656 0.520 0.146 0.056 19 2.7 G_and_S_cingul-Mid-Post 516 342 1282 3.130 0.578 0.178 0.066 14 1.3 G_cingul-Post-dorsal 347 209 551 2.306 0.690 0.156 0.074 10 0.9 G_cingul-Post-ventral 1684 1029 2205 1.899 0.416 0.168 0.074 35 5.1 G_cuneus 1543 1077 4051 2.899 0.370 0.153 0.060 30 4.0 G_front_inf-Opercular 376 237 994 3.137 0.413 0.201 0.295 53 7.2 G_front_inf-Orbital 1332 892 3289 2.793 0.452 0.148 0.051 22 2.8 G_front_inf-Triangul 3939 2663 9777 2.889 0.548 0.179 0.091 224 15.2 G_front_middle 7353 4937 18691 3.066 0.576 0.162 0.083 160 24.7 G_front_sup 508 329 1250 3.470 0.768 0.120 0.049 6 0.9 G_Ins_lg_and_S_cent_ins 651 415 2213 3.936 0.742 0.137 0.077 16 2.4 G_insular_short 2876 1805 5803 2.518 0.460 0.163 0.059 58 6.6 G_occipital_middle 1469 933 2205 2.025 0.425 0.163 0.069 41 4.2 G_occipital_sup 1902 1258 4410 2.835 0.458 0.171 0.067 46 5.6 G_oc-temp_lat-fusifor 3696 2320 5802 2.156 0.576 0.168 0.074 71 10.7 G_oc-temp_med-Lingual 1341 837 2572 2.667 0.669 0.122 0.047 14 2.6 G_oc-temp_med-Parahip 2590 1753 6424 2.782 0.653 0.174 0.084 65 9.2 G_orbital 2191 1455 4520 2.584 0.514 0.163 0.078 52 7.1 G_pariet_inf-Angular 3224 2128 7698 2.941 0.516 0.151 0.067 72 8.5 G_pariet_inf-Supramar 2781 1841 5288 2.300 0.569 0.141 0.066 43 5.7 G_parietal_sup 2661 1594 4838 2.398 0.607 0.140 0.055 51 6.8 G_postcentral 3103 1793 6385 2.830 0.536 0.138 0.067 49 7.6 G_precentral 2675 1817 5617 2.472 0.537 0.162 0.062 60 6.6 G_precuneus 979 666 2196 2.510 0.659 0.184 0.097 34 4.0 G_rectus 485 284 630 2.195 0.769 0.169 0.192 78 3.8 G_subcallosal 674 392 1330 2.692 0.614 0.152 0.133 16 4.8 G_temp_sup-G_T_transv 2643 1720 7570 3.169 0.625 0.149 0.068 50 6.8 G_temp_sup-Lateral 467 296 1047 3.240 0.884 0.139 0.079 8 1.5 G_temp_sup-Plan_polar 1128 795 2309 2.630 0.509 0.108 0.026 7 1.3 G_temp_sup-Plan_tempo 2190 1467 5857 3.030 0.711 0.170 0.137 59 6.9 G_temporal_inf 2666 1800 7522 3.070 0.616 0.161 0.068 61 7.3 G_temporal_middle 308 203 447 2.720 0.582 0.115 0.031 2 0.4 Lat_Fis-ant-Horizont 318 218 466 2.537 0.401 0.099 0.026 1 0.3 Lat_Fis-ant-Vertical 1326 884 1819 2.636 0.514 0.121 0.039 12 2.1 Lat_Fis-post 2532 1503 2728 1.701 0.436 0.146 0.060 44 6.4 Pole_occipital 1857 1258 5737 3.377 0.791 0.188 0.106 52 8.0 Pole_temporal 3041 2002 3934 2.094 0.518 0.132 0.084 45 5.9 S_calcarine 3115 2130 3377 1.830 0.532 0.134 0.053 34 7.8 S_central 870 619 1301 2.260 0.484 0.126 0.036 8 1.4 S_cingul-Marginalis 469 316 832 2.983 0.508 0.108 0.031 3 0.7 S_circular_insula_ant 1463 972 2454 2.689 0.610 0.086 0.020 5 1.3 S_circular_insula_inf 1777 1193 2746 2.751 0.494 0.110 0.030 11 2.3 S_circular_insula_sup 1223 822 2414 2.933 0.670 0.152 0.103 27 3.4 S_collat_transv_ant 439 290 498 2.262 0.428 0.139 0.045 4 0.9 S_collat_transv_post 2518 1716 3879 2.324 0.463 0.124 0.038 24 3.9 S_front_inf 1512 1061 2544 2.429 0.504 0.136 0.050 18 2.8 S_front_middle 2386 1647 3970 2.464 0.463 0.122 0.040 25 4.0 S_front_sup 288 188 677 2.953 0.441 0.166 0.060 6 0.7 S_interm_prim-Jensen 3275 2201 4588 2.215 0.466 0.134 0.042 37 5.7 S_intrapariet_and_P_trans 1442 958 1635 1.931 0.378 0.140 0.043 16 2.7 S_oc_middle_and_Lunatus 1264 821 1581 2.038 0.369 0.133 0.088 285 2.0 S_oc_sup_and_transversal 1515 1017 2159 2.328 0.392 0.140 0.067 30 5.1 S_occipital_ant 755 519 1079 2.439 0.363 0.112 0.028 5 0.9 S_oc-temp_lat 2029 1418 3087 2.483 0.510 0.136 0.043 21 3.8 S_oc-temp_med_and_Lingual 291 198 390 2.175 0.395 0.121 0.037 2 0.5 S_orbital_lateral 741 503 992 2.291 0.675 0.112 0.026 5 0.8 S_orbital_med-olfact 1197 806 2188 2.765 0.721 0.147 0.063 22 2.9 S_orbital-H_Shaped 2562 1746 3463 2.186 0.571 0.130 0.037 25 4.1 S_parieto_occipital 846 540 968 2.421 0.604 0.175 0.062 25 2.1 S_pericallosal 2271 1530 3264 2.384 0.417 0.124 0.038 21 3.6 S_postcentral 1842 1285 2955 2.434 0.465 0.119 0.032 13 2.5 S_precentral-inf-part 723 523 1113 2.466 0.402 0.117 0.028 5 0.9 S_precentral-sup-part 603 412 956 2.544 0.646 0.148 0.052 8 1.3 S_suborbital 880 591 1466 2.487 0.553 0.137 0.048 10 1.7 S_subparietal 1458 983 2173 2.416 0.686 0.128 0.042 20 2.4 S_temporal_inf 5705 3919 9972 2.578 0.458 0.121 0.037 54 8.8 S_temporal_sup 308 218 429 2.446 0.386 0.130 0.036 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Dec 2 19:34:48 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon lh ../surf/lh.sphere.reg /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1245 labels changed using aseg relabeling using gibbs priors... 000: 2823 changed, 134383 examined... 001: 714 changed, 11751 examined... 002: 195 changed, 3818 examined... 003: 78 changed, 1129 examined... 004: 29 changed, 473 examined... 005: 19 changed, 171 examined... 006: 19 changed, 105 examined... 007: 11 changed, 94 examined... 008: 8 changed, 62 examined... 009: 3 changed, 40 examined... 010: 3 changed, 16 examined... 011: 2 changed, 20 examined... 012: 3 changed, 12 examined... 013: 1 changed, 13 examined... 014: 2 changed, 7 examined... 015: 0 changed, 11 examined... 268 labels changed using aseg 000: 68 total segments, 35 labels (229 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 28 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 578 vertices marked for relabeling... 578 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Dec 2 19:35:29 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1491 967 2875 2.779 0.595 0.141 0.042 22 2.8 caudalanteriorcingulate 2798 1885 5279 2.596 0.568 0.140 0.067 167 8.7 caudalmiddlefrontal 3022 1927 4081 1.999 0.450 0.156 0.062 65 7.9 cuneus 583 385 1300 2.783 0.609 0.127 0.046 6 1.2 entorhinal 4214 2829 8391 2.747 0.491 0.157 0.066 85 11.5 fusiform 6577 4401 11978 2.496 0.487 0.147 0.056 112 15.4 inferiorparietal 4831 3206 11046 2.949 0.771 0.159 0.103 109 13.6 inferiortemporal 1435 926 2478 2.587 0.675 0.157 0.064 33 3.5 isthmuscingulate 8537 5447 11910 2.042 0.509 0.148 0.055 141 20.5 lateraloccipital 3855 2619 8316 2.762 0.735 0.163 0.076 83 12.1 lateralorbitofrontal 5382 3469 8094 2.182 0.556 0.158 0.064 90 13.9 lingual 2057 1363 3747 2.411 0.674 0.153 0.074 49 6.3 medialorbitofrontal 6086 4134 13353 2.772 0.676 0.137 0.049 90 11.9 middletemporal 1157 741 1985 2.414 0.565 0.122 0.039 11 2.0 parahippocampal 2336 1508 3980 2.445 0.501 0.130 0.103 92 10.8 paracentral 2491 1724 5212 2.704 0.400 0.132 0.044 33 4.4 parsopercularis 1015 682 2320 2.893 0.494 0.145 0.129 58 7.8 parsorbitalis 2474 1653 5097 2.658 0.564 0.139 0.048 32 4.9 parstriangularis 2141 1361 2434 1.920 0.457 0.131 0.060 27 5.0 pericalcarine 7052 4524 11432 2.277 0.671 0.134 0.047 102 14.6 postcentral 1841 1253 3491 2.701 0.605 0.161 0.061 38 4.3 posteriorcingulate 7527 4807 13485 2.610 0.590 0.138 0.060 105 18.8 precentral 5594 3834 9709 2.332 0.570 0.145 0.069 96 11.2 precuneus 1514 989 3193 2.902 0.840 0.177 0.098 98 6.0 rostralanteriorcingulate 5628 3835 11676 2.607 0.604 0.161 0.064 109 14.8 rostralmiddlefrontal 11130 7605 25636 2.882 0.635 0.158 0.072 223 34.2 superiorfrontal 6080 4033 9955 2.256 0.494 0.145 0.067 361 12.2 superiorparietal 8208 5522 19038 2.925 0.648 0.135 0.054 115 18.0 superiortemporal 5290 3507 10720 2.781 0.548 0.143 0.058 95 12.0 supramarginal 838 501 1497 2.529 0.510 0.133 0.107 16 4.8 transversetemporal 2762 1837 6269 3.243 0.792 0.112 0.042 31 5.0 insula #----------------------------------------- #@# WM/GM Contrast lh Wed Dec 2 19:35:42 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts pctsurfcon --s af1021_recon --lh-only Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts/pctsurfcon.log Wed Dec 2 19:35:43 EST 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-12.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.6868/lh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 73420 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.6868/lh.wm.mgh Dim: 134383 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.6868/lh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 87295 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.6868/lh.gm.mgh Dim: 134383 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.6868/lh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.6868/lh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh --annot af1021_recon lh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-12.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.w-g.pct.mgh Vertex Area is 0.661663 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1584 1095.910 2 1002 caudalanteriorcingulate 789 506.564 3 1003 caudalmiddlefrontal 2765 1858.920 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 1917 1225.443 6 1006 entorhinal 622 409.929 7 1007 fusiform 4867 3257.278 8 1008 inferiorparietal 6836 4573.844 9 1009 inferiortemporal 4680 3131.517 10 1010 isthmuscingulate 1431 927.172 11 1011 lateraloccipital 8254 5273.195 12 1012 lateralorbitofrontal 3790 2559.588 13 1013 lingual 5400 3475.210 14 1014 medialorbitofrontal 2479 1635.068 15 1015 middletemporal 4545 3085.708 16 1016 parahippocampal 1146 731.078 17 1017 paracentral 2004 1283.079 18 1018 parsopercularis 2911 2005.479 19 1019 parsorbitalis 933 614.015 20 1020 parstriangularis 1982 1337.828 21 1021 pericalcarine 2156 1369.830 22 1022 postcentral 6459 4112.391 23 1023 posteriorcingulate 1744 1187.680 24 1024 precentral 7497 4785.458 25 1025 precuneus 5881 4012.888 26 1026 rostralanteriorcingulate 1067 686.341 27 1027 rostralmiddlefrontal 7995 5492.088 28 1028 superiorfrontal 9871 6735.381 29 1029 superiorparietal 7763 5130.734 30 1030 superiortemporal 6185 4126.916 31 1031 supramarginal 5512 3662.862 32 1032 frontalpole 280 191.547 33 1033 temporalpole 620 432.797 34 1034 transversetemporal 866 517.973 35 1035 insula 3115 2039.750 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Wed Dec 2 19:35:51 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1593 1109 3015 2.682 0.457 0.130 0.034 20 2.4 bankssts 1197 786 2345 2.626 0.751 0.153 0.052 22 2.2 caudalanteriorcingulate 3380 2338 6702 2.581 0.464 0.133 0.043 40 6.2 caudalmiddlefrontal 2179 1407 2986 1.922 0.475 0.168 0.077 51 7.5 cuneus 589 396 1566 2.976 0.716 0.168 0.091 12 1.8 entorhinal 5442 3646 11546 2.834 0.613 0.150 0.097 157 13.3 fusiform 8167 5545 14263 2.348 0.503 0.152 0.079 212 32.1 inferiorparietal 4320 2929 9483 2.858 0.725 0.152 0.080 89 11.4 inferiortemporal 1285 824 2162 2.568 0.679 0.147 0.062 22 2.9 isthmuscingulate 7233 4662 10989 2.190 0.516 0.154 0.067 142 18.6 lateraloccipital 3685 2495 7466 2.624 0.776 0.165 0.076 85 10.7 lateralorbitofrontal 5135 3408 7248 2.131 0.581 0.165 0.068 118 15.1 lingual 2768 1867 5430 2.512 0.830 0.157 0.083 77 9.3 medialorbitofrontal 4406 3036 10881 3.006 0.591 0.148 0.060 89 10.5 middletemporal 1247 797 2097 2.437 0.432 0.110 0.036 10 1.9 parahippocampal 2205 1371 3496 2.458 0.513 0.126 0.048 30 4.5 paracentral 2109 1406 4176 2.782 0.441 0.129 0.048 27 4.3 parsopercularis 1084 789 2817 2.747 0.665 0.188 0.331 287 3.4 parsorbitalis 2159 1445 4093 2.478 0.521 0.138 0.046 30 3.8 parstriangularis 2365 1581 2680 1.868 0.524 0.156 0.058 37 5.6 pericalcarine 5742 3591 8275 2.088 0.670 0.129 0.050 81 11.4 postcentral 1953 1314 3713 2.596 0.791 0.167 0.062 41 4.6 posteriorcingulate 7239 4713 12460 2.496 0.596 0.140 0.088 88 33.6 precentral 6267 4256 11047 2.501 0.561 0.147 0.052 99 12.7 precuneus 752 487 1602 2.699 0.958 0.143 0.063 12 1.6 rostralanteriorcingulate 8460 5766 15268 2.251 0.635 0.161 0.080 197 25.1 rostralmiddlefrontal 9201 6382 21012 2.862 0.663 0.146 0.055 139 19.8 superiorfrontal 7356 4758 11489 2.187 0.483 0.140 0.049 101 14.3 superiorparietal 5857 3902 13807 3.056 0.718 0.138 0.060 95 14.4 superiortemporal 6006 3985 11151 2.653 0.561 0.135 0.048 85 10.8 supramarginal 437 288 982 2.480 0.836 0.205 0.089 17 1.7 frontalpole 570 397 2015 3.578 1.067 0.204 0.325 36 3.5 temporalpole 720 426 1246 2.482 0.374 0.129 0.051 9 1.3 transversetemporal 3153 2056 6767 3.278 0.914 0.130 0.106 85 17.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Wed Dec 2 19:36:05 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 17 labels changed using aseg relabeling using gibbs priors... 000: 9780 changed, 134806 examined... 001: 2387 changed, 37288 examined... 002: 747 changed, 12158 examined... 003: 358 changed, 4168 examined... 004: 166 changed, 1995 examined... 005: 89 changed, 938 examined... 006: 44 changed, 485 examined... 007: 25 changed, 251 examined... 008: 7 changed, 160 examined... 009: 6 changed, 38 examined... 010: 6 changed, 40 examined... 011: 3 changed, 27 examined... 012: 2 changed, 19 examined... 013: 1 changed, 12 examined... 014: 0 changed, 8 examined... 10 labels changed using aseg 000: 319 total segments, 232 labels (2779 vertices) changed 001: 100 total segments, 15 labels (415 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 142 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 592 vertices marked for relabeling... 592 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 48 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Wed Dec 2 19:36:53 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1172 794 2040 2.075 0.737 0.179 0.074 29 4.0 G_and_S_frontomargin 1268 848 2580 2.712 0.432 0.153 0.050 20 2.7 G_and_S_occipital_inf 1375 764 2034 2.265 0.462 0.133 0.064 30 3.7 G_and_S_paracentral 1515 1018 3247 2.914 0.541 0.163 0.058 27 3.5 G_and_S_subcentral 738 508 1830 2.572 0.707 0.194 0.097 27 2.7 G_and_S_transv_frontopol 2530 1708 5175 2.828 0.751 0.150 0.067 46 6.1 G_and_S_cingul-Ant 1346 953 2891 2.867 0.551 0.142 0.048 19 2.4 G_and_S_cingul-Mid-Ant 1554 1040 2912 2.698 0.509 0.147 0.055 25 3.2 G_and_S_cingul-Mid-Post 469 322 1212 3.079 0.786 0.199 0.098 13 1.7 G_cingul-Post-dorsal 304 183 549 2.639 0.539 0.170 0.092 11 1.0 G_cingul-Post-ventral 1829 1192 2375 1.811 0.468 0.172 0.082 47 6.8 G_cuneus 1366 918 3160 2.843 0.424 0.152 0.062 26 3.4 G_front_inf-Opercular 313 211 774 2.762 0.548 0.171 0.071 8 0.8 G_front_inf-Orbital 1040 697 2383 2.651 0.489 0.149 0.048 17 2.0 G_front_inf-Triangul 3767 2631 8798 2.597 0.591 0.170 0.095 104 12.9 G_front_middle 6507 4428 16398 2.978 0.673 0.158 0.063 117 15.8 G_front_sup 389 262 1100 3.966 1.062 0.136 0.422 43 11.1 G_Ins_lg_and_S_cent_ins 589 373 1860 4.004 0.759 0.135 0.068 12 1.5 G_insular_short 2017 1282 4131 2.517 0.405 0.153 0.063 38 4.5 G_occipital_middle 1909 1196 3018 2.181 0.469 0.145 0.049 29 4.0 G_occipital_sup 2054 1333 4532 2.851 0.542 0.165 0.154 105 5.5 G_oc-temp_lat-fusifor 3335 2183 5036 2.163 0.583 0.175 0.077 67 10.5 G_oc-temp_med-Lingual 1701 1072 4086 2.939 0.766 0.146 0.076 32 4.6 G_oc-temp_med-Parahip 2739 1882 7222 2.882 0.755 0.198 0.207 356 11.4 G_orbital 2792 1905 5854 2.552 0.594 0.171 0.083 109 10.7 G_pariet_inf-Angular 2637 1683 5607 2.860 0.532 0.144 0.056 47 5.4 G_pariet_inf-Supramar 2263 1494 4210 2.313 0.453 0.148 0.057 34 5.2 G_parietal_sup 2223 1247 3241 2.073 0.576 0.123 0.060 41 5.3 G_postcentral 2737 1670 5254 2.599 0.544 0.141 0.144 31 22.9 G_precentral 2950 2026 6083 2.473 0.497 0.156 0.060 55 6.7 G_precuneus 813 525 2040 2.808 0.570 0.174 0.113 34 4.1 G_rectus 280 189 323 1.617 0.731 0.127 0.094 7 1.0 G_subcallosal 499 295 956 2.477 0.414 0.140 0.060 7 1.1 G_temp_sup-G_T_transv 2268 1512 7028 3.447 0.645 0.171 0.073 51 6.1 G_temp_sup-Lateral 596 389 1656 3.561 0.725 0.158 0.126 27 1.9 G_temp_sup-Plan_polar 959 657 1875 2.590 0.472 0.119 0.091 17 4.0 G_temp_sup-Plan_tempo 2295 1558 5995 3.056 0.815 0.163 0.077 57 7.1 G_temporal_inf 2554 1758 7329 3.131 0.523 0.163 0.075 68 7.4 G_temporal_middle 375 253 614 2.334 0.462 0.128 0.042 4 0.7 Lat_Fis-ant-Horizont 135 89 236 2.469 0.354 0.084 0.019 1 0.1 Lat_Fis-ant-Vertical 1988 1329 2931 2.591 0.447 0.125 0.038 19 3.0 Lat_Fis-post 3339 2116 4113 1.822 0.478 0.172 0.090 91 11.4 Pole_occipital 1805 1253 5748 3.226 0.894 0.187 0.188 57 8.0 Pole_temporal 2857 1909 3524 2.059 0.559 0.151 0.054 70 7.0 S_calcarine 2746 1906 2838 1.718 0.460 0.135 0.043 23 5.1 S_central 1337 912 2095 2.489 0.497 0.134 0.045 15 2.4 S_cingul-Marginalis 621 429 990 2.779 0.387 0.113 0.033 4 1.0 S_circular_insula_ant 1387 884 2188 2.669 0.628 0.093 0.033 9 1.4 S_circular_insula_inf 1530 1016 2554 2.846 0.656 0.119 0.043 14 2.9 S_circular_insula_sup 931 617 2000 3.080 0.718 0.145 0.080 15 2.0 S_collat_transv_ant 795 536 923 2.093 0.468 0.156 0.055 10 1.8 S_collat_transv_post 2634 1758 4386 2.430 0.510 0.130 0.040 27 4.6 S_front_inf 2106 1385 3029 2.022 0.551 0.149 0.063 37 4.7 S_front_middle 2417 1694 3868 2.302 0.475 0.116 0.033 19 3.4 S_front_sup 555 373 771 2.317 0.575 0.130 0.035 6 0.9 S_interm_prim-Jensen 3059 2042 4128 2.097 0.496 0.138 0.044 37 5.3 S_intrapariet_and_P_trans 1207 811 1634 2.085 0.403 0.133 0.044 13 2.0 S_oc_middle_and_Lunatus 1101 720 1302 2.006 0.344 0.130 0.053 16 2.7 S_oc_sup_and_transversal 1011 671 1489 2.480 0.311 0.128 0.042 11 1.6 S_occipital_ant 1243 875 1960 2.539 0.341 0.128 0.039 13 2.0 S_oc-temp_lat 2214 1517 3253 2.464 0.443 0.114 0.030 15 2.7 S_oc-temp_med_and_Lingual 509 353 673 2.102 0.460 0.127 0.038 4 0.8 S_orbital_lateral 760 551 1071 1.866 0.591 0.108 0.021 5 0.6 S_orbital_med-olfact 1359 921 2374 2.395 0.684 0.156 0.066 25 3.3 S_orbital-H_Shaped 2605 1713 3746 2.441 0.611 0.137 0.041 29 4.4 S_parieto_occipital 1569 985 1524 1.992 0.702 0.139 0.041 23 2.3 S_pericallosal 2138 1420 2628 2.022 0.425 0.111 0.030 15 2.7 S_postcentral 2059 1428 3664 2.586 0.489 0.123 0.052 22 5.1 S_precentral-inf-part 816 553 1169 2.472 0.501 0.122 0.033 6 1.2 S_precentral-sup-part 196 137 429 3.132 0.692 0.217 0.119 10 0.7 S_suborbital 946 638 1763 2.660 0.476 0.139 0.045 12 1.7 S_subparietal 843 568 1177 2.609 0.530 0.130 0.046 12 1.7 S_temporal_inf 7073 4882 12306 2.552 0.524 0.131 0.062 117 22.7 S_temporal_sup 303 205 382 2.370 0.228 0.128 0.029 2 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Wed Dec 2 19:37:37 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 af1021_recon rh ../surf/rh.sphere.reg /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /share/apps/freesurfer-5.3.0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1169 labels changed using aseg relabeling using gibbs priors... 000: 2644 changed, 134806 examined... 001: 657 changed, 11528 examined... 002: 174 changed, 3541 examined... 003: 76 changed, 1035 examined... 004: 30 changed, 428 examined... 005: 17 changed, 157 examined... 006: 7 changed, 98 examined... 007: 5 changed, 45 examined... 008: 4 changed, 30 examined... 009: 4 changed, 22 examined... 010: 4 changed, 23 examined... 011: 6 changed, 28 examined... 012: 4 changed, 28 examined... 013: 6 changed, 24 examined... 014: 5 changed, 34 examined... 015: 6 changed, 34 examined... 016: 2 changed, 23 examined... 017: 1 changed, 12 examined... 018: 1 changed, 7 examined... 019: 0 changed, 7 examined... 154 labels changed using aseg 000: 57 total segments, 24 labels (104 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 669 vertices marked for relabeling... 669 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 41 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Wed Dec 2 19:38:18 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 af1021_recon rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1185 777 2297 2.615 0.750 0.153 0.052 21 2.2 caudalanteriorcingulate 3339 2298 6590 2.597 0.459 0.134 0.044 41 6.2 caudalmiddlefrontal 2698 1754 3657 1.960 0.468 0.162 0.063 54 6.9 cuneus 632 430 1706 2.985 0.728 0.166 0.090 12 1.9 entorhinal 4727 3172 9720 2.829 0.618 0.147 0.099 137 10.6 fusiform 7720 5232 13354 2.345 0.510 0.154 0.081 204 31.4 inferiorparietal 5025 3394 11193 2.851 0.713 0.154 0.096 109 13.8 inferiortemporal 1288 829 2170 2.571 0.682 0.148 0.062 22 2.9 isthmuscingulate 7512 4841 11526 2.194 0.520 0.154 0.067 149 19.5 lateraloccipital 4220 2867 8781 2.530 0.825 0.174 0.081 110 13.6 lateralorbitofrontal 5152 3422 7267 2.135 0.578 0.165 0.068 117 15.0 lingual 2150 1446 4555 2.583 0.809 0.159 0.086 64 7.8 medialorbitofrontal 5317 3680 12593 2.946 0.576 0.144 0.055 99 11.7 middletemporal 1247 794 2072 2.437 0.430 0.109 0.035 10 1.8 parahippocampal 2254 1410 3589 2.465 0.524 0.125 0.048 30 4.5 paracentral 2268 1513 4389 2.753 0.444 0.128 0.047 28 4.4 parsopercularis 1200 826 2599 2.668 0.638 0.151 0.064 18 2.8 parsorbitalis 2243 1496 4260 2.458 0.529 0.138 0.045 32 4.2 parstriangularis 2438 1613 2739 1.852 0.519 0.157 0.069 45 7.6 pericalcarine 6136 3859 8925 2.095 0.662 0.130 0.050 87 12.1 postcentral 2075 1396 3972 2.616 0.768 0.167 0.063 43 5.1 posteriorcingulate 7111 4638 12173 2.491 0.601 0.141 0.089 87 33.4 precentral 6211 4206 11191 2.514 0.551 0.149 0.053 102 13.0 precuneus 882 572 1853 2.725 0.929 0.141 0.060 13 1.8 rostralanteriorcingulate 5759 3975 11015 2.331 0.620 0.162 0.131 401 17.2 rostralmiddlefrontal 11984 8253 25555 2.696 0.735 0.150 0.059 203 27.6 superiorfrontal 6337 4112 9949 2.196 0.486 0.136 0.047 83 11.9 superiorparietal 7802 5236 18462 3.044 0.757 0.144 0.068 155 20.7 superiortemporal 5722 3783 10504 2.642 0.552 0.133 0.048 80 10.3 supramarginal 718 425 1239 2.483 0.374 0.128 0.051 9 1.3 transversetemporal 2909 1910 6380 3.305 0.889 0.124 0.104 76 16.3 insula #----------------------------------------- #@# WM/GM Contrast rh Wed Dec 2 19:38:31 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts pctsurfcon --s af1021_recon --rh-only Log file is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts/pctsurfcon.log Wed Dec 2 19:38:31 EST 2015 setenv SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 cd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/scripts /share/apps/freesurfer-5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux compute-0-12.local 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /share/apps/freesurfer-5.3.0 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.7153/rh.wm.mgh --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 73821 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.7153/rh.wm.mgh Dim: 134806 1 1 mri_vol2surf --mov /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.7153/rh.gm.mgh --projfrac 0.3 --regheader af1021_recon --cortex srcvol = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 INFO: changing type to float Done loading volume Computing registration from header. Using /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/orig.mgz as target reference. Loading label /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Reading surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Done reading source surface Reading thickness /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 87789 Masking with /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.cortex.label Writing to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.7153/rh.gm.mgh Dim: 134806 1 1 mri_concat /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.7153/rh.wm.mgh /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/tmp.pctsurfcon.7153/rh.gm.mgh --paired-diff-norm --mul 100 --o /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh mri_segstats --in /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh --annot af1021_recon rh aparc --sum /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-12.local machine x86_64 user twilliams 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.w-g.pct.mgh Vertex Area is 0.664253 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1593 1108.692 2 2002 caudalanteriorcingulate 1197 785.953 3 2003 caudalmiddlefrontal 3380 2338.266 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2179 1407.114 6 2006 entorhinal 589 396.363 7 2007 fusiform 5442 3645.660 8 2008 inferiorparietal 8167 5544.499 9 2009 inferiortemporal 4320 2929.486 10 2010 isthmuscingulate 1285 823.827 11 2011 lateraloccipital 7233 4662.327 12 2012 lateralorbitofrontal 3685 2494.787 13 2013 lingual 5135 3408.429 14 2014 medialorbitofrontal 2768 1866.921 15 2015 middletemporal 4406 3035.524 16 2016 parahippocampal 1247 797.235 17 2017 paracentral 2205 1371.040 18 2018 parsopercularis 2109 1406.215 19 2019 parsorbitalis 1084 789.439 20 2020 parstriangularis 2159 1444.928 21 2021 pericalcarine 2365 1580.832 22 2022 postcentral 5742 3590.525 23 2023 posteriorcingulate 1953 1313.774 24 2024 precentral 7239 4713.337 25 2025 precuneus 6267 4255.853 26 2026 rostralanteriorcingulate 752 486.565 27 2027 rostralmiddlefrontal 8460 5765.568 28 2028 superiorfrontal 9201 6381.974 29 2029 superiorparietal 7356 4757.753 30 2030 superiortemporal 5857 3902.342 31 2031 supramarginal 6006 3985.072 32 2032 frontalpole 437 288.075 33 2033 temporalpole 570 397.121 34 2034 transversetemporal 720 426.451 35 2035 insula 3153 2055.899 Reporting on 34 segmentations mri_segstats done Cleaning up #-------------------------------------------- #@# Cortical ribbon mask Wed Dec 2 19:38:40 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon af1021_recon SUBJECTS_DIR is /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 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 = 141 writing volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Wed Dec 2 19:52:14 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon 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 /share/apps/freesurfer-5.3.0/ASegStatsLUT.txt --subject af1021_recon $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 /share/apps/freesurfer-5.3.0/ASegStatsLUT.txt --subject af1021_recon sysname Linux hostname compute-0-12.local machine x86_64 user twilliams UseRobust 0 atlas_icv (eTIV) = 1541622 mm^3 (det: 1.263673 ) Computing euler number orig.nofix lheno = -44, rheno = -32 orig.nofix lhholes = 23, rhholes = 17 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 239785.689 239722.000 diff= 63.7 pctdiff= 0.027 rhCtxGM: 236017.021 235804.000 diff= 213.0 pctdiff= 0.090 lhCtxWM: 218340.398 218144.000 diff= 196.4 pctdiff= 0.090 rhCtxWM: 221137.567 221480.000 diff= -342.4 pctdiff=-0.155 SubCortGMVol 62225.000 SupraTentVol 989576.675 (988404.000) diff=1172.675 pctdiff=0.119 SupraTentVolNotVent 978707.675 (977535.000) diff=1172.675 pctdiff=0.120 BrainSegVol 1120783.000 (1118799.000) diff=1984.000 pctdiff=0.177 BrainSegVolNotVent 1106900.000 (1106879.675) diff=20.325 pctdiff=0.002 BrainSegVolNotVent 1106900.000 CerebellumVol 129214.000 VentChorVol 10869.000 3rd4th5thCSF 3014.000 CSFVol 1046.000, OptChiasmVol 135.000 MaskVol 1600589.000 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 4657 4657.085 4 5 Left-Inf-Lat-Vent 147 147.216 5 7 Left-Cerebellum-White-Matter 15131 15130.936 6 8 Left-Cerebellum-Cortex 49465 49464.539 7 10 Left-Thalamus-Proper 8027 8026.642 8 11 Left-Caudate 3803 3803.185 9 12 Left-Putamen 6337 6336.562 10 13 Left-Pallidum 1648 1648.023 11 14 3rd-Ventricle 739 739.349 12 15 4th-Ventricle 1501 1501.291 13 16 Brain-Stem 21351 21351.275 14 17 Left-Hippocampus 4730 4730.166 15 18 Left-Amygdala 1888 1887.705 16 24 CSF 1110 1110.174 17 26 Left-Accumbens-area 749 748.657 18 28 Left-VentralDC 3769 3768.568 19 30 Left-vessel 85 85.161 20 31 Left-choroid-plexus 1057 1056.964 23 43 Right-Lateral-Ventricle 3857 3856.684 24 44 Right-Inf-Lat-Vent 108 107.650 25 46 Right-Cerebellum-White-Matter 14819 14818.603 26 47 Right-Cerebellum-Cortex 51367 51367.012 27 49 Right-Thalamus-Proper 7432 7432.446 28 50 Right-Caudate 4211 4210.721 29 51 Right-Putamen 5637 5636.977 30 52 Right-Pallidum 1575 1575.200 31 53 Right-Hippocampus 4560 4560.470 32 54 Right-Amygdala 1372 1371.704 33 58 Right-Accumbens-area 760 759.631 34 60 Right-VentralDC 3998 3997.655 35 62 Right-vessel 74 74.438 36 63 Right-choroid-plexus 1407 1406.849 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 1237 1237.188 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 17 17.220 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 133 132.774 45 251 CC_Posterior 858 858.164 46 252 CC_Mid_Posterior 539 539.010 47 253 CC_Central 505 505.136 48 254 CC_Mid_Anterior 426 425.545 49 255 CC_Anterior 784 783.820 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Wed Dec 2 19:55:40 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --volmask SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 473290 Used brute-force search on 0 voxels Writing output aseg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --volmask --a2009s SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 473290 Used brute-force search on 0 voxels Writing output aseg to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Wed Dec 2 19:58:58 EST 2015 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon mri_aparc2aseg --s af1021_recon --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 subject af1021_recon outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aparc+aseg.mgz Reading lh white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading lh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial Loading lh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading rh pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial Loading rh annotations from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/ribbon.mgz Loading filled from /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/filled.mgz Ripping vertices labeled as unkown Ripped 8437 vertices from left hemi Ripped 8545 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/aseg.mgz Loading Ctx Seg File /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 = 911902 Used brute-force search on 43 voxels Fixing Parahip LH WM Found 9 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 3.000000 7 k 27.000000 8 k 1744.000000 Fixing Parahip RH WM Found 9 clusters 0 k 1.000000 1 k 2065.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon 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 af1021_recon --surf-wm-vol --ctab /share/apps/freesurfer-5.3.0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject af1021_recon --surf-wm-vol --ctab /share/apps/freesurfer-5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-12.local machine x86_64 user twilliams UseRobust 0 atlas_icv (eTIV) = 1541622 mm^3 (det: 1.263673 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 239785.689 239722.000 diff= 63.7 pctdiff= 0.027 rhCtxGM: 236017.021 235804.000 diff= 213.0 pctdiff= 0.090 lhCtxWM: 218340.398 218144.000 diff= 196.4 pctdiff= 0.090 rhCtxWM: 221137.567 221480.000 diff= -342.4 pctdiff=-0.155 SubCortGMVol 62225.000 SupraTentVol 989576.675 (988404.000) diff=1172.675 pctdiff=0.119 SupraTentVolNotVent 978707.675 (977535.000) diff=1172.675 pctdiff=0.120 BrainSegVol 1120783.000 (1118799.000) diff=1984.000 pctdiff=0.177 BrainSegVolNotVent 1106900.000 (1106879.675) diff=20.325 pctdiff=0.002 BrainSegVolNotVent 1106900.000 CerebellumVol 129214.000 VentChorVol 10869.000 3rd4th5thCSF 3014.000 CSFVol 1046.000, OptChiasmVol 135.000 MaskVol 1600589.000 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 2344 2344.273 2 3002 wm-lh-caudalanteriorcingulate 2311 2311.051 3 3003 wm-lh-caudalmiddlefrontal 5321 5321.469 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 1997 1996.924 6 3006 wm-lh-entorhinal 1106 1105.882 7 3007 wm-lh-fusiform 5888 5888.177 8 3008 wm-lh-inferiorparietal 9937 9936.673 9 3009 wm-lh-inferiortemporal 6002 6002.427 10 3010 wm-lh-isthmuscingulate 3303 3302.840 11 3011 wm-lh-lateraloccipital 10050 10049.559 12 3012 wm-lh-lateralorbitofrontal 6212 6211.568 13 3013 wm-lh-lingual 6587 6586.856 14 3014 wm-lh-medialorbitofrontal 2839 2838.649 15 3015 wm-lh-middletemporal 5309 5309.288 16 3016 wm-lh-parahippocampal 1788 1787.837 17 3017 wm-lh-paracentral 3497 3497.255 18 3018 wm-lh-parsopercularis 4557 4557.250 19 3019 wm-lh-parsorbitalis 788 788.333 20 3020 wm-lh-parstriangularis 3174 3173.637 21 3021 wm-lh-pericalcarine 3449 3449.457 22 3022 wm-lh-postcentral 7535 7534.977 23 3023 wm-lh-posteriorcingulate 4296 4295.991 24 3024 wm-lh-precentral 12936 12936.485 25 3025 wm-lh-precuneus 9754 9754.364 26 3026 wm-lh-rostralanteriorcingulate 2415 2414.948 27 3027 wm-lh-rostralmiddlefrontal 11447 11447.485 28 3028 wm-lh-superiorfrontal 17092 17091.590 29 3029 wm-lh-superiorparietal 10885 10884.594 30 3030 wm-lh-superiortemporal 8594 8594.010 31 3031 wm-lh-supramarginal 8152 8152.295 32 3032 wm-lh-frontalpole 174 174.381 33 3033 wm-lh-temporalpole 558 557.755 34 3034 wm-lh-transversetemporal 771 771.418 35 3035 wm-lh-insula 8244 8244.409 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 2745 2745.338 120 4002 wm-rh-caudalanteriorcingulate 3277 3277.310 121 4003 wm-rh-caudalmiddlefrontal 5680 5680.276 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2076 2075.569 124 4006 wm-rh-entorhinal 756 755.761 125 4007 wm-rh-fusiform 6202 6202.351 126 4008 wm-rh-inferiorparietal 11103 11103.320 127 4009 wm-rh-inferiortemporal 5543 5543.002 128 4010 wm-rh-isthmuscingulate 2980 2980.250 129 4011 wm-rh-lateraloccipital 8910 8909.699 130 4012 wm-rh-lateralorbitofrontal 6387 6387.220 131 4013 wm-rh-lingual 6584 6583.537 132 4014 wm-rh-medialorbitofrontal 3336 3335.857 133 4015 wm-rh-middletemporal 5246 5246.438 134 4016 wm-rh-parahippocampal 2072 2071.721 135 4017 wm-rh-paracentral 4321 4321.378 136 4018 wm-rh-parsopercularis 3431 3431.199 137 4019 wm-rh-parsorbitalis 1059 1059.295 138 4020 wm-rh-parstriangularis 3135 3135.126 139 4021 wm-rh-pericalcarine 3741 3741.461 140 4022 wm-rh-postcentral 6895 6894.644 141 4023 wm-rh-posteriorcingulate 4600 4599.785 142 4024 wm-rh-precentral 12945 12945.029 143 4025 wm-rh-precuneus 10324 10324.216 144 4026 wm-rh-rostralanteriorcingulate 1900 1900.417 145 4027 wm-rh-rostralmiddlefrontal 11919 11919.202 146 4028 wm-rh-superiorfrontal 15647 15646.612 147 4029 wm-rh-superiorparietal 8818 8817.864 148 4030 wm-rh-superiortemporal 7913 7912.903 149 4031 wm-rh-supramarginal 8952 8952.393 150 4032 wm-rh-frontalpole 354 353.875 151 4033 wm-rh-temporalpole 544 544.304 152 4034 wm-rh-transversetemporal 643 642.564 153 4035 wm-rh-insula 8754 8754.361 154 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 28574 28574.098 237 5002 Right-UnsegmentedWhiteMatter 29781 29781.430 238 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label #-------------------------------------------- #@# BA Labels lh Wed Dec 2 20:09:15 EST 2015 mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.label --trgsubject af1021_recon --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 323 Checking for and removing duplicates Writing label file ./lh.BA1.label 4452 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.label --trgsubject af1021_recon --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./lh.BA2.label 8276 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.label --trgsubject af1021_recon --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4260 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.label --trgsubject af1021_recon --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 432 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6415 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.label --trgsubject af1021_recon --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 411 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6195 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.label --trgsubject af1021_recon --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4283 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.label --trgsubject af1021_recon --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1084 Checking for and removing duplicates Writing label file ./lh.BA6.label 14673 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.label --trgsubject af1021_recon --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 687 Checking for and removing duplicates Writing label file ./lh.BA44.label 4868 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.label --trgsubject af1021_recon --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 856 Checking for and removing duplicates Writing label file ./lh.BA45.label 4278 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.label --trgsubject af1021_recon --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1634 Checking for and removing duplicates Writing label file ./lh.V1.label 6275 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.label --trgsubject af1021_recon --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 3389 Checking for and removing duplicates Writing label file ./lh.V2.label 11503 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.label --trgsubject af1021_recon --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 784 Checking for and removing duplicates Writing label file ./lh.MT.label 2802 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.perirhinal.label --trgsubject af1021_recon --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 185 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1384 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1081 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2230 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2211 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 216 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2535 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1627 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 467 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7502 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 352 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2264 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.thresh.label --trgsubject af1021_recon --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 421 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1572 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.thresh.label --trgsubject af1021_recon --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1147 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.thresh.label --trgsubject af1021_recon --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 1520 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4854 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.thresh.label --trgsubject af1021_recon --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134383 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 736 mri_label2label: Done mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-12.local machine x86_64 user twilliams subject af1021_recon hemi lh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 92465 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.BA.annot mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi lh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-12.local machine x86_64 user twilliams subject af1021_recon hemi lh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 109651 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab af1021_recon lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1104 617 2022 2.446 0.498 0.144 0.054 18 2.4 BA1 3348 2200 5882 2.513 0.497 0.130 0.046 49 6.9 BA2 967 661 829 1.762 0.454 0.158 0.055 11 2.3 BA3a 2566 1647 3532 1.911 0.676 0.133 0.046 33 5.2 BA3b 1694 959 2837 2.602 0.473 0.124 0.096 27 3.6 BA4a 1322 871 1911 2.289 0.552 0.135 0.072 25 4.8 BA4p 8466 5596 19000 2.915 0.561 0.142 0.074 317 30.9 BA6 2744 1914 5943 2.698 0.472 0.138 0.049 40 5.5 BA44 3246 2203 6806 2.635 0.526 0.141 0.051 49 6.6 BA45 3830 2445 4376 1.802 0.470 0.142 0.061 57 9.0 V1 8960 5631 12455 2.072 0.519 0.158 0.076 174 23.4 V2 2557 1727 4523 2.392 0.503 0.150 0.063 52 7.5 MT 1114 712 2314 2.711 0.666 0.133 0.052 14 2.6 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab af1021_recon lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 723 394 1405 2.563 0.407 0.145 0.054 12 1.6 BA1 1489 975 2846 2.549 0.500 0.130 0.054 29 4.0 BA2 748 525 616 1.687 0.386 0.166 0.057 8 1.8 BA3a 1679 1087 1884 1.612 0.463 0.122 0.041 15 2.9 BA3b 1694 932 2803 2.638 0.437 0.122 0.085 30 3.7 BA4a 1062 727 1391 2.114 0.493 0.137 0.076 17 4.3 BA4p 4749 3079 10498 2.886 0.560 0.142 0.081 140 20.2 BA6 1881 1328 4132 2.698 0.366 0.144 0.050 30 4.1 BA44 1446 973 3419 2.735 0.465 0.156 0.058 24 3.4 BA45 4078 2601 4746 1.805 0.474 0.141 0.058 58 9.2 V1 4483 2745 5827 1.963 0.505 0.161 0.097 94 13.2 V2 700 475 1005 2.148 0.351 0.127 0.033 7 1.1 MT #-------------------------------------------- #@# BA Labels rh Wed Dec 2 20:13:00 EST 2015 mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.label --trgsubject af1021_recon --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./rh.BA1.label 4256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.label --trgsubject af1021_recon --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./rh.BA2.label 6999 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.label --trgsubject af1021_recon --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 113 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4093 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.label --trgsubject af1021_recon --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 328 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4850 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.label --trgsubject af1021_recon --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 326 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6073 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.label --trgsubject af1021_recon --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 165 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4638 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.label --trgsubject af1021_recon --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 732 Checking for and removing duplicates Writing label file ./rh.BA6.label 12988 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.label --trgsubject af1021_recon --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1343 Checking for and removing duplicates Writing label file ./rh.BA44.label 8255 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.label --trgsubject af1021_recon --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1143 Checking for and removing duplicates Writing label file ./rh.BA45.label 6498 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.label --trgsubject af1021_recon --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1819 Checking for and removing duplicates Writing label file ./rh.V1.label 6546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.label --trgsubject af1021_recon --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 3038 Checking for and removing duplicates Writing label file ./rh.V2.label 11054 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.label --trgsubject af1021_recon --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 500 Checking for and removing duplicates Writing label file ./rh.MT.label 2432 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.perirhinal.label --trgsubject af1021_recon --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 872 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 972 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 48 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2736 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 39 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1737 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 166 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2349 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1458 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 35 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1524 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 329 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7288 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 182 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1194 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.thresh.label --trgsubject af1021_recon --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 224 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1402 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.thresh.label --trgsubject af1021_recon --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1301 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 4533 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.thresh.label --trgsubject af1021_recon --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 1436 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4873 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.thresh.label --trgsubject af1021_recon --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = af1021_recon 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 /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 FREESURFER_HOME /share/apps/freesurfer-5.3.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white Reading target registration /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 134806 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 341 mri_label2label: Done mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-12.local machine x86_64 user twilliams subject af1021_recon hemi rh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 94394 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.BA.annot mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label cmdline mris_label2annot --s af1021_recon --hemi rh --ctab /share/apps/freesurfer-5.3.0/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname compute-0-12.local machine x86_64 user twilliams subject af1021_recon hemi rh SUBJECTS_DIR /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3 ColorTable /share/apps/freesurfer-5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 113207 unhit vertices Writing annot to /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab af1021_recon rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 913 458 1502 2.392 0.392 0.134 0.089 29 2.9 BA1 2655 1727 3775 2.124 0.518 0.109 0.029 18 3.1 BA2 979 642 801 1.639 0.365 0.146 0.049 11 1.9 BA3a 2049 1291 2488 1.687 0.500 0.128 0.044 24 3.9 BA3b 1524 870 2435 2.465 0.505 0.125 0.059 33 4.1 BA4a 1027 728 1301 1.953 0.506 0.143 0.048 9 2.2 BA4p 6912 4610 14506 2.787 0.563 0.140 0.083 67 30.2 BA6 4237 2873 8206 2.733 0.498 0.135 0.053 56 9.9 BA44 4395 2972 8863 2.505 0.564 0.147 0.061 73 11.0 BA45 4364 2894 5043 1.771 0.506 0.167 0.088 112 15.2 V1 8492 5513 11751 2.091 0.521 0.164 0.064 177 22.6 V2 2140 1448 3397 2.380 0.374 0.139 0.044 26 3.8 MT 725 484 1770 2.844 0.601 0.142 0.061 10 1.8 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab af1021_recon rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /share/apps/freesurfer-5.3.0/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 616 284 976 2.407 0.388 0.135 0.105 26 2.1 BA1 1438 945 2080 2.116 0.547 0.105 0.029 9 1.7 BA2 835 539 628 1.640 0.341 0.152 0.051 10 1.8 BA3a 1612 1080 1719 1.502 0.359 0.119 0.035 13 2.5 BA3b 890 471 1474 2.574 0.451 0.126 0.065 28 2.7 BA4a 823 626 1041 1.883 0.525 0.147 0.049 7 1.8 BA4p 4347 2825 8733 2.736 0.532 0.138 0.094 31 24.9 BA6 918 633 1993 2.750 0.391 0.145 0.067 17 2.3 BA44 1101 730 2429 2.611 0.460 0.144 0.050 17 2.3 BA45 4207 2784 4782 1.764 0.499 0.166 0.088 108 14.8 V1 4497 2922 6025 1.995 0.572 0.173 0.073 115 13.9 V2 315 212 635 2.414 0.266 0.117 0.033 3 0.5 MT /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Wed Dec 2 20:16:43 EST 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o af1021_recon label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject af1021_recon. processing subject lh.EC_average... reading output surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 1020 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label af1021_recon lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/lh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 385 218 877 2.767 0.674 0.147 0.104 11 1.8 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Wed Dec 2 20:16:56 EST 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o af1021_recon label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject af1021_recon. processing subject rh.EC_average... reading output surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 906 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label af1021_recon rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/mri/wm.mgz... reading input surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.white... reading input pial surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/surf/rh.pial... reading input white surface /share/VA_Imaging/Projects/shayes/tori/Aerofit_v5.3/af1021_recon/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 325 203 882 2.977 0.494 0.174 0.084 7 1.2 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Wed Dec 2 15:16:17 EST 2015 Ended at Wed Dec 2 20:17:09 EST 2015 #@#%# recon-all-run-time-hours 5.014 recon-all -s af1021_recon finished without error at Wed Dec 2 20:17:09 EST 2015