Thu Dec 5 19:09:02 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1 /soft/freesurfer/5.3.0/bin/recon-all -all -subjid MPS3007-1 subjid MPS3007-1 setenv SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Actual FREESURFER_HOME /panfs/roc/itascasoft/freesurfer/5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux node1109 2.6.32-358.14.1.el6.x86_64 #1 SMP Tue Jul 16 23:51:20 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize 3840000 kbytes stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse 3840000 kbytes vmemoryuse unlimited descriptors 32768 memorylocked unlimited maxproc 514935 total used free shared buffers cached Mem: 65932244 7469888 58462356 0 4216 4229952 -/+ buffers/cache: 3235720 62696524 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:03-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/12/06-01:09:18-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: kovacv Machine: node1109 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /soft/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 /soft/freesurfer/5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Thu Dec 5 19:09:19 CST 2013 Found 1 runs /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig/001.mgz /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/rawavg.mgz /lustre/kovacv/FS/MPSIII-post/MPS3007-1 mri_convert /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/rawavg.mgz /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz --conform mri_convert /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/rawavg.mgz /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/rawavg.mgz... TR=2530.00, TE=3.65, TI=1100.00, flip angle=7.00 i_ras = (-0.0244322, -0.999701, 0) j_ras = (-0, -0, -1) k_ras = (-0.999701, 0.0244322, 0) 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz... mri_add_xform_to_header -c /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/transforms/talairach.xfm /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Dec 5 19:10:17 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Dec 5 19:17:05 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4675, pval=0.1049 >= threshold=0.0050) awk -f /soft/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/transforms/talairach_avi.log tal_QC_AZS /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/transforms/talairach_avi.log TalAviQA: 0.97207 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Thu Dec 5 19:17:06 CST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri /soft/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 node1109 2.6.32-358.14.1.el6.x86_64 #1 SMP Tue Jul 16 23:51:20 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Dec 5 19:17:07 CST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.15646 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15646/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15646/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=3.65, TI=1100.00, flip angle=7.00 i_ras = (-1, -3.72529e-09, 0) j_ras = (0, 0, -1) k_ras = (2.42144e-08, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.15646/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Dec 5 19:17:15 CST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.15646/nu0.mnc ./tmp.mri_nu_correct.mni.15646/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.15646/0/ [kovacv@node1109:/lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/] [2013-12-05 19:17:15] running: /soft/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.15646/0/ ./tmp.mri_nu_correct.mni.15646/nu0.mnc ./tmp.mri_nu_correct.mni.15646/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 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[kovacv@node1109:/lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/] [2013-12-05 19:20:23] running: /soft/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.15646/nu0.mnc ./tmp.mri_nu_correct.mni.15646/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Dec 5 19:21:00 CST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.15646/nu1.mnc ./tmp.mri_nu_correct.mni.15646/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.15646/1/ [kovacv@node1109:/lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/] [2013-12-05 19:21:01] running: /soft/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.15646/1/ ./tmp.mri_nu_correct.mni.15646/nu1.mnc ./tmp.mri_nu_correct.mni.15646/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 21 CV of field change: 0.000949595 [kovacv@node1109:/lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/] [2013-12-05 19:22:26] running: /soft/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.15646/nu1.mnc ./tmp.mri_nu_correct.mni.15646/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.15646/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.15646/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.15646/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.15646/ones.mgz sysname Linux hostname node1109 machine x86_64 user kovacv input ./tmp.mri_nu_correct.mni.15646/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.15646/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.15646/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15646/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15646/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.15646/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15646/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15646/input.mean.dat sysname Linux hostname node1109 machine x86_64 user kovacv UseRobust 0 Loading ./tmp.mri_nu_correct.mni.15646/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.15646/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.15646/ones.mgz --i ./tmp.mri_nu_correct.mni.15646/nu2.mnc --sum ./tmp.mri_nu_correct.mni.15646/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15646/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.15646/ones.mgz --i ./tmp.mri_nu_correct.mni.15646/nu2.mnc --sum ./tmp.mri_nu_correct.mni.15646/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15646/output.mean.dat sysname Linux hostname node1109 machine x86_64 user kovacv UseRobust 0 Loading ./tmp.mri_nu_correct.mni.15646/ones.mgz Loading ./tmp.mri_nu_correct.mni.15646/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.15646/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.15646/nu2.mnc ./tmp.mri_nu_correct.mni.15646/nu2.mnc mul .94372054325264915648 Saving result to './tmp.mri_nu_correct.mni.15646/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.15646/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.15646/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.15646/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -3.72529e-09, 0) j_ras = (0, 0, -1) k_ras = (2.42144e-08, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 25 seconds. mapping (21, 127) to ( 3, 110) Thu Dec 5 19:25:56 CST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Dec 5 19:26:00 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.020 -0.056 0.012 -2.485; -0.043 1.084 -0.145 -33.733; -0.006 0.181 1.189 -23.145; 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 = 8 Starting OpenSpline(): npoints = 8 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 91 gm peak at 72 (72), valley at 52 (52) csf peak at 38, setting threshold to 60 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 91 gm peak at 72 (72), valley at 46 (46) csf peak at 37, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 9 minutes and 12 seconds. #-------------------------------------------- #@# Skull Stripping Thu Dec 5 19:35:15 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_em_register -skull nu.mgz /soft/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/soft/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=18.0 skull bounding box = (54, 43, 35) --> (201, 255, 207) using (103, 114, 121) as brain centroid... mean wm in atlas = 126, using box (85,88,100) --> (121, 140,142) to find MRI wm before smoothing, mri peak at 104 after smoothing, mri peak at 104, scaling input intensities by 1.212 scaling channel 0 by 1.21154 initial log_p = -4.6 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.531380 @ (0.000, 0.000, 0.000) max log p = -4.531380 @ (0.000, 0.000, 0.000) max log p = -4.518702 @ (-2.273, -6.818, -11.364) max log p = -4.493745 @ (1.136, 5.682, 3.409) max log p = -4.486980 @ (-0.568, -0.568, 5.114) max log p = -4.486980 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -1.7, -2.8): log p = -4.487 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.5 (thresh=-4.5) 1.064 0.000 0.000 -9.830; 0.000 1.226 -0.161 -2.247; 0.000 0.150 1.140 -43.908; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.064 0.000 0.000 -9.830; 0.000 1.318 -0.173 -11.499; 0.000 0.150 1.140 -43.908; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.064 0.000 0.000 -9.830; 0.000 1.383 -0.345 0.814; 0.000 0.297 1.025 -47.487; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.064 0.000 0.000 -9.830; 0.000 1.383 -0.345 0.814; 0.000 0.297 1.025 -47.487; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.023 0.012 0.030 -9.601; -0.005 1.426 -0.282 -10.795; -0.037 0.209 1.064 -37.255; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.023 0.012 0.030 -9.601; -0.005 1.426 -0.282 -10.795; -0.037 0.209 1.064 -37.255; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.025 0.000 0.033 -9.182; 0.004 1.427 -0.301 -10.001; -0.037 0.232 1.056 -38.436; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.025 0.000 0.033 -9.651; 0.004 1.429 -0.292 -11.179; -0.037 0.220 1.058 -37.827; 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 1.02459 0.00031 0.03289 -9.65095; 0.00403 1.42917 -0.29197 -11.17887; -0.03657 0.22016 1.05793 -37.82708; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02459 0.00031 0.03289 -9.65095; 0.00403 1.42917 -0.29197 -11.17887; -0.03657 0.22016 1.05793 -37.82708; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.025 0.000 0.033 -9.651; 0.004 1.429 -0.292 -11.179; -0.037 0.220 1.058 -37.827; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.6) transform before final EM align: 1.025 0.000 0.033 -9.651; 0.004 1.429 -0.292 -11.179; -0.037 0.220 1.058 -37.827; 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 1.02459 0.00031 0.03289 -9.65095; 0.00403 1.42917 -0.29197 -11.17887; -0.03657 0.22016 1.05793 -37.82708; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02459 0.00031 0.03289 -9.65095; 0.00403 1.42917 -0.29197 -11.17887; -0.03657 0.22016 1.05793 -37.82708; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.5 tol 0.000000 final transform: 1.025 0.000 0.033 -9.651; 0.004 1.429 -0.292 -11.179; -0.037 0.220 1.058 -37.827; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 188 minutes and 47 seconds. mri_watershed -T1 -brain_atlas /soft/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=126 y=127 z=119 r=80 first estimation of the main basin volume: 2177686 voxels Looking for seedpoints 2 found in the cerebellum 11 found in the rest of the brain global maximum in x=153, y=120, z=112, Imax=255 CSF=18, 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=15802707434 voxels, voxel volume =1.000 = 15802707434 mmm3 = 15802706.944 cm3 done. PostAnalyze...Basin Prior 50 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=115, z=113, r=9361 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45800 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1045934085 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1092612943 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1078744978 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1070850320 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1075225466 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 8, 49, 68 after analyzing : 4, 35, 49, 43 RIGHT_CER before analyzing : 4, 8, 49, 67 after analyzing : 4, 35, 49, 43 LEFT_CER before analyzing : 4, 8, 47, 66 after analyzing : 4, 34, 47, 42 RIGHT_BRAIN before analyzing : 4, 8, 49, 68 after analyzing : 4, 35, 49, 43 LEFT_BRAIN before analyzing : 5, 10, 49, 70 after analyzing : 5, 36, 49, 44 OTHER before analyzing : 4, 6, 51, 88 after analyzing : 4, 36, 51, 49 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.679, std = 7.867 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 9.72, sigma = 15.23 after rotation: sse = 9.72, sigma = 15.23 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 11.05, its var is 15.73 before Erosion-Dilatation 11.87% of inacurate vertices after Erosion-Dilatation 17.14% 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...38 iterations mri_strip_skull: done peeling brain Brain Size = 1532046 voxels, voxel volume = 1.000 mm3 = 1532046 mmm3 = 1532.046 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Dec 5 22:45:59 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /soft/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/soft/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=27.9 skull bounding box = (57, 57, 39) --> (198, 162, 194) using (104, 92, 117) as brain centroid... mean wm in atlas = 107, using box (87,79,98) --> (121, 104,136) to find MRI wm before smoothing, mri peak at 102 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.218714 @ (-9.091, 9.091, -9.091) max log p = -4.137237 @ (4.545, -4.545, -4.545) max log p = -4.117743 @ (2.273, 2.273, 6.818) max log p = -4.117743 @ (0.000, 0.000, 0.000) max log p = -4.106371 @ (1.705, -2.841, -0.568) max log p = -4.106371 @ (0.000, 0.000, 0.000) Found translation: (-0.6, 4.0, -7.4): log p = -4.106 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.1 (thresh=-4.1) 1.000 0.000 0.000 -0.568; 0.000 1.220 -0.182 -0.845; 0.000 0.120 1.071 -29.202; 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) 1.000 0.000 0.000 -0.568; 0.000 1.220 -0.182 -0.845; 0.000 0.111 0.991 -19.112; 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 =-3.9 (thresh=-3.9) 1.018 0.009 0.031 -9.194; -0.005 1.197 -0.173 -0.705; -0.034 0.119 1.007 -21.228; 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) 1.018 0.009 0.031 -9.194; -0.005 1.197 -0.173 -0.705; -0.034 0.119 1.007 -21.228; 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=-3.7, old_max_log_p =-3.8 (thresh=-3.8) 1.019 0.028 0.028 -11.728; -0.021 1.193 -0.182 2.853; -0.034 0.129 1.006 -20.817; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.7, old_max_log_p =-3.7 (thresh=-3.7) 1.019 0.028 0.028 -11.728; -0.021 1.193 -0.182 2.853; -0.034 0.128 1.002 -20.374; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.7, old_max_log_p =-3.7 (thresh=-3.7) 1.019 0.028 0.028 -11.728; -0.021 1.193 -0.182 2.853; -0.034 0.128 1.002 -20.374; 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 1.01927 0.02826 0.02782 -11.72832; -0.02085 1.19330 -0.18169 2.85299; -0.03415 0.12810 1.00201 -20.37359; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.01927 0.02826 0.02782 -11.72832; -0.02085 1.19330 -0.18169 2.85299; -0.03415 0.12810 1.00201 -20.37359; 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: 1.019 0.028 0.028 -11.728; -0.021 1.193 -0.182 2.853; -0.034 0.128 1.002 -20.374; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.7 (old=-4.3) transform before final EM align: 1.019 0.028 0.028 -11.728; -0.021 1.193 -0.182 2.853; -0.034 0.128 1.002 -20.374; 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 1.01927 0.02826 0.02782 -11.72832; -0.02085 1.19330 -0.18169 2.85299; -0.03415 0.12810 1.00201 -20.37359; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.01927 0.02826 0.02782 -11.72832; -0.02085 1.19330 -0.18169 2.85299; -0.03415 0.12810 1.00201 -20.37359; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.19, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) dfp_em_step_func: 011: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.19, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) dfp_em_step_func: 012: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.19, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) dfp_em_step_func: 013: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.19, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) dfp_em_step_func: 014: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.19, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) 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... dfp_em_step_func: 015: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.19, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) dfp_em_step_func: 016: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.20, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) dfp_em_step_func: 017: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.20, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) dfp_em_step_func: 018: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.20, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) dfp_em_step_func: 019: -log(p) = 4.1 after pass:transform: ( 1.02, 0.03, 0.03, -11.73) ( -0.02, 1.20, -0.18, 2.85) ( -0.03, 0.13, 1.00, -20.37) 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 3 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) = 4.1 tol 0.000000 final transform: 1.021 0.030 0.030 -11.728; -0.019 1.195 -0.179 2.853; -0.034 0.128 1.002 -20.374; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 132 minutes and 49 seconds. #-------------------------------------- #@# CA Normalize Fri Dec 6 00:58:49 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /soft/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 '/soft/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=27.9 skull bounding box = (57, 57, 39) --> (198, 162, 195) using (104, 92, 117) as brain centroid... mean wm in atlas = 107, using box (87,79,98) --> (121, 104,136) to find MRI wm before smoothing, mri peak at 102 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 using 244171 sample points... INFO: compute sample coordinates transform 1.021 0.030 0.030 -11.728; -0.019 1.195 -0.179 2.853; -0.034 0.128 1.002 -20.374; 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 (128, 59, 35) --> (193, 162, 202) Left_Cerebral_White_Matter: limiting intensities to 128.0 --> 186.0 5 of 6 (83.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 59, 36) --> (129, 161, 201) Right_Cerebral_White_Matter: limiting intensities to 105.0 --> 186.0 2 of 6 (33.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 54) --> (177, 162, 108) Left_Cerebellum_White_Matter: limiting intensities to 106.0 --> 186.0 0 of 17 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 124, 51) --> (129, 162, 107) Right_Cerebellum_White_Matter: limiting intensities to 111.0 --> 186.0 0 of 5 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 124, 84) --> (143, 179, 120) Brain_Stem: limiting intensities to 110.0 --> 186.0 3 of 5 (60.0%) samples deleted using 39 total control points for intensity normalization... bias field = 0.802 +- 0.059 0 of 29 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 59, 35) --> (193, 162, 202) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 152.0 22 of 71 (31.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 59, 36) --> (129, 161, 201) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 152.0 30 of 67 (44.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 54) --> (177, 162, 108) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 152.0 23 of 47 (48.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 124, 51) --> (129, 162, 107) Right_Cerebellum_White_Matter: limiting intensities to 70.0 --> 152.0 0 of 39 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 124, 84) --> (143, 179, 120) Brain_Stem: limiting intensities to 71.0 --> 152.0 0 of 62 (0.0%) samples deleted using 286 total control points for intensity normalization... bias field = 1.050 +- 0.079 0 of 211 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 59, 35) --> (193, 162, 202) Left_Cerebral_White_Matter: limiting intensities to 84.0 --> 116.0 33 of 132 (25.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 59, 36) --> (129, 161, 201) Right_Cerebral_White_Matter: limiting intensities to 100.0 --> 158.0 61 of 128 (47.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 124, 54) --> (177, 162, 108) Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 158.0 0 of 77 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 124, 51) --> (129, 162, 107) Right_Cerebellum_White_Matter: limiting intensities to 85.0 --> 158.0 0 of 41 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 124, 84) --> (143, 179, 120) Brain_Stem: limiting intensities to 89.0 --> 158.0 34 of 118 (28.8%) samples deleted using 496 total control points for intensity normalization... bias field = 0.980 +- 0.081 0 of 368 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 6 minutes and 36 seconds. #-------------------------------------- #@# CA Reg Fri Dec 6 01:05:28 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /soft/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/soft/freesurfer/5.3.0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.25 (predicted orig area = 6.4) 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=0.934, neg=0, invalid=96777 0001: dt=129.472000, rms=0.818 (12.416%), neg=0, invalid=96777 0002: dt=221.952000, rms=0.786 (3.926%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.772 (1.766%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.769 (0.364%), neg=0, invalid=96777 0005: dt=369.920000, rms=0.758 (1.406%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.756 (0.358%), neg=0, invalid=96777 0007: dt=32.368000, rms=0.755 (0.120%), neg=0, invalid=96777 0008: dt=32.368000, rms=0.754 (0.038%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.754 (0.006%), neg=0, invalid=96777 0010: dt=32.368000, rms=0.754 (0.020%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.753 (0.113%), neg=0, invalid=96777 0012: dt=32.368000, rms=0.751 (0.292%), neg=0, invalid=96777 0013: dt=32.368000, rms=0.748 (0.370%), neg=0, invalid=96777 0014: dt=32.368000, rms=0.746 (0.347%), neg=0, invalid=96777 0015: dt=32.368000, rms=0.744 (0.284%), neg=0, invalid=96777 0016: dt=32.368000, rms=0.742 (0.228%), neg=0, invalid=96777 0017: dt=32.368000, rms=0.741 (0.171%), neg=0, invalid=96777 0018: dt=32.368000, rms=0.740 (0.124%), neg=0, invalid=96777 0019: dt=32.368000, rms=0.739 (0.136%), neg=0, invalid=96777 0020: dt=32.368000, rms=0.737 (0.200%), neg=0, invalid=96777 0021: dt=32.368000, rms=0.735 (0.257%), neg=0, invalid=96777 0022: dt=32.368000, rms=0.733 (0.251%), neg=0, invalid=96777 0023: dt=32.368000, rms=0.732 (0.204%), neg=0, invalid=96777 0024: dt=32.368000, rms=0.731 (0.178%), neg=0, invalid=96777 0025: dt=32.368000, rms=0.730 (0.155%), neg=0, invalid=96777 0026: dt=32.368000, rms=0.729 (0.124%), neg=0, invalid=96777 0027: dt=32.368000, rms=0.728 (0.119%), neg=0, invalid=96777 0028: dt=295.936000, rms=0.725 (0.321%), neg=0, invalid=96777 0029: dt=27.744000, rms=0.725 (0.018%), neg=0, invalid=96777 0030: dt=27.744000, rms=0.725 (0.010%), neg=0, invalid=96777 0031: dt=27.744000, rms=0.725 (-0.024%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.725, neg=0, invalid=96777 0032: dt=18.496000, rms=0.725 (0.005%), neg=0, invalid=96777 0033: dt=0.000000, rms=0.725 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.729, neg=0, invalid=96777 0034: dt=145.152000, rms=0.705 (3.349%), neg=0, invalid=96777 0035: dt=36.288000, rms=0.696 (1.243%), neg=0, invalid=96777 0036: dt=36.288000, rms=0.695 (0.222%), neg=0, invalid=96777 0037: dt=36.288000, rms=0.689 (0.778%), neg=0, invalid=96777 0038: dt=36.288000, rms=0.684 (0.837%), neg=0, invalid=96777 0039: dt=36.288000, rms=0.678 (0.866%), neg=0, invalid=96777 0040: dt=36.288000, rms=0.671 (0.966%), neg=0, invalid=96777 0041: dt=36.288000, rms=0.662 (1.288%), neg=0, invalid=96777 0042: dt=36.288000, rms=0.656 (0.992%), neg=0, invalid=96777 0043: dt=36.288000, rms=0.652 (0.657%), neg=0, invalid=96777 0044: dt=36.288000, rms=0.648 (0.473%), neg=0, invalid=96777 0045: dt=36.288000, rms=0.645 (0.537%), neg=0, invalid=96777 0046: dt=36.288000, rms=0.643 (0.378%), neg=0, invalid=96777 0047: dt=36.288000, rms=0.641 (0.279%), neg=0, invalid=96777 0048: dt=36.288000, rms=0.640 (0.186%), neg=0, invalid=96777 0049: dt=36.288000, rms=0.638 (0.273%), neg=0, invalid=96777 0050: dt=36.288000, rms=0.635 (0.439%), neg=0, invalid=96777 0051: dt=36.288000, rms=0.633 (0.264%), neg=0, invalid=96777 0052: dt=36.288000, rms=0.632 (0.209%), neg=0, invalid=96777 0053: dt=36.288000, rms=0.631 (0.164%), neg=0, invalid=96777 0054: dt=36.288000, rms=0.629 (0.240%), neg=0, invalid=96777 0055: dt=36.288000, rms=0.628 (0.166%), neg=0, invalid=96777 0056: dt=36.288000, rms=0.628 (0.133%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.627 (0.118%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.626 (0.157%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.625 (0.178%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.624 (0.108%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.624 (0.059%), neg=0, invalid=96777 0062: dt=145.152000, rms=0.622 (0.201%), neg=0, invalid=96777 0063: dt=2.268000, rms=0.622 (0.001%), neg=0, invalid=96777 0064: dt=2.268000, rms=0.622 (0.000%), neg=0, invalid=96777 0065: dt=2.268000, rms=0.622 (0.001%), neg=0, invalid=96777 0066: dt=2.268000, rms=0.622 (0.001%), neg=0, invalid=96777 0067: dt=2.268000, rms=0.622 (0.002%), neg=0, invalid=96777 0068: dt=2.268000, rms=0.622 (0.000%), neg=0, invalid=96777 0069: dt=2.268000, rms=0.622 (0.001%), neg=0, invalid=96777 0070: dt=2.268000, rms=0.622 (0.003%), neg=0, invalid=96777 0071: dt=2.268000, rms=0.622 (0.007%), neg=0, invalid=96777 0072: dt=2.268000, rms=0.622 (0.008%), neg=0, invalid=96777 0073: dt=2.268000, rms=0.622 (0.009%), neg=0, invalid=96777 0074: dt=2.268000, rms=0.622 (0.012%), neg=0, invalid=96777 0075: dt=2.268000, rms=0.622 (0.013%), neg=0, invalid=96777 0076: dt=2.268000, rms=0.622 (0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0077: dt=82.944000, rms=0.621 (0.187%), neg=0, invalid=96777 0078: dt=9.072000, rms=0.621 (0.002%), neg=0, invalid=96777 0079: dt=9.072000, rms=0.621 (0.003%), neg=0, invalid=96777 0080: dt=9.072000, rms=0.621 (0.006%), neg=0, invalid=96777 0081: dt=9.072000, rms=0.621 (0.004%), neg=0, invalid=96777 0082: dt=9.072000, rms=0.621 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.654, neg=0, invalid=96777 0083: dt=3.500000, rms=0.654 (0.041%), neg=0, invalid=96777 0084: dt=2.000000, rms=0.654 (0.007%), neg=0, invalid=96777 0085: dt=2.000000, rms=0.654 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.654, neg=0, invalid=96777 0086: dt=0.300000, rms=0.654 (0.000%), neg=0, invalid=96777 0087: dt=0.009375, rms=0.654 (0.001%), neg=0, invalid=96777 0088: dt=0.000000, rms=0.654 (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=0.746, neg=0, invalid=96777 0089: dt=4.945892, rms=0.722 (3.176%), neg=0, invalid=96777 0090: dt=4.219512, rms=0.719 (0.384%), neg=0, invalid=96777 0091: dt=1.008000, rms=0.719 (0.015%), neg=0, invalid=96777 0092: dt=1.008000, rms=0.719 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.719, neg=0, invalid=96777 0093: dt=0.000000, rms=0.719 (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=0.796, neg=0, invalid=96777 0094: dt=0.547619, rms=0.794 (0.186%), neg=0, invalid=96777 0095: dt=1.160000, rms=0.792 (0.269%), neg=0, invalid=96777 0096: dt=2.391753, rms=0.788 (0.559%), neg=0, invalid=96777 0097: dt=0.448000, rms=0.788 (0.024%), neg=0, invalid=96777 0098: dt=0.448000, rms=0.787 (0.033%), neg=0, invalid=96777 0099: dt=0.448000, rms=0.787 (0.052%), neg=0, invalid=96777 0100: dt=0.448000, rms=0.786 (0.047%), neg=0, invalid=96777 0101: dt=0.448000, rms=0.786 (0.010%), neg=0, invalid=96777 0102: dt=1.792000, rms=0.786 (0.071%), neg=0, invalid=96777 0103: dt=0.080000, rms=0.786 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.786, neg=0, invalid=96777 0104: dt=0.822430, rms=0.785 (0.062%), neg=0, invalid=96777 0105: dt=0.000000, rms=0.785 (-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=0.739, neg=0, invalid=96777 0106: dt=0.160511, rms=0.730 (1.193%), neg=0, invalid=96777 0107: dt=0.000000, rms=0.730 (0.003%), neg=0, invalid=96777 0108: dt=0.050000, rms=0.730 (-0.018%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.730, neg=0, invalid=96777 0109: dt=0.276756, rms=0.728 (0.363%), neg=0, invalid=96777 0110: dt=0.096000, rms=0.726 (0.177%), neg=0, invalid=96777 0111: dt=0.096000, rms=0.726 (0.046%), neg=0, invalid=96777 0112: dt=0.096000, rms=0.725 (0.086%), neg=0, invalid=96777 0113: dt=0.096000, rms=0.724 (0.136%), neg=0, invalid=96777 0114: dt=0.096000, rms=0.723 (0.160%), neg=0, invalid=96777 0115: dt=0.096000, rms=0.722 (0.158%), neg=0, invalid=96777 0116: dt=0.096000, rms=0.721 (0.138%), neg=0, invalid=96777 0117: dt=0.096000, rms=0.721 (0.000%), neg=0, invalid=96777 0118: dt=0.096000, rms=0.721 (0.000%), neg=0, invalid=96777 0119: dt=0.096000, rms=0.721 (0.010%), neg=0, invalid=96777 0120: dt=0.096000, rms=0.721 (0.017%), neg=0, invalid=96777 0121: dt=0.096000, rms=0.721 (0.027%), neg=0, invalid=96777 0122: dt=0.096000, rms=0.720 (0.037%), neg=0, invalid=96777 0123: dt=0.096000, rms=0.720 (0.046%), neg=0, invalid=96777 0124: dt=0.096000, rms=0.720 (0.054%), neg=0, invalid=96777 0125: dt=0.096000, rms=0.719 (0.061%), neg=0, invalid=96777 0126: dt=0.096000, rms=0.719 (0.063%), neg=0, invalid=96777 0127: dt=0.096000, rms=0.718 (0.062%), neg=0, invalid=96777 0128: dt=0.112000, rms=0.718 (0.001%), neg=0, invalid=96777 0129: dt=0.112000, rms=0.718 (0.004%), neg=0, invalid=96777 0130: dt=0.112000, rms=0.718 (0.005%), neg=0, invalid=96777 0131: dt=0.112000, rms=0.718 (0.008%), neg=0, invalid=96777 0132: dt=0.112000, rms=0.718 (0.010%), neg=0, invalid=96777 0133: dt=0.112000, rms=0.718 (0.013%), neg=0, invalid=96777 0134: dt=0.112000, rms=0.718 (0.015%), neg=0, invalid=96777 0135: dt=0.112000, rms=0.718 (0.016%), neg=0, invalid=96777 0136: dt=0.112000, rms=0.718 (0.016%), neg=0, invalid=96777 0137: dt=0.112000, rms=0.718 (0.016%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.16430 (11) Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (1614 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1614 voxels, peak = 8), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.12152 (12) Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (738 voxels, overlap=0.092) Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (738 voxels, peak = 9), gca=8.9 gca peak = 0.24234 (100) mri peak = 0.08933 (87) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (426 voxels, overlap=0.104) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (426 voxels, peak = 88), gca=87.5 gca peak = 0.19192 (97) mri peak = 0.06939 (86) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (395 voxels, overlap=0.303) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (395 voxels, peak = 85), gca=84.9 gca peak = 0.24007 (63) mri peak = 0.08023 (69) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (888 voxels, overlap=0.872) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (888 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.12317 (67) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (688 voxels, overlap=0.993) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (688 voxels, peak = 66), gca=65.6 gca peak = 0.12541 (104) mri peak = 0.05157 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56719 voxels, overlap=0.972) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56719 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.04803 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (52057 voxels, overlap=0.904) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (52057 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03991 (76) Left_Cerebral_Cortex (3): linear fit = 1.22 x + 0.0 (22053 voxels, overlap=0.110) Left_Cerebral_Cortex (3): linear fit = 1.22 x + 0.0 (22053 voxels, peak = 77), gca=76.5 gca peak = 0.13270 (63) mri peak = 0.04508 (74) Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (26201 voxels, overlap=0.361) Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (26201 voxels, peak = 72), gca=71.5 gca peak = 0.15182 (70) mri peak = 0.10286 (81) Right_Caudate (50): linear fit = 1.08 x + 0.0 (255 voxels, overlap=0.597) Right_Caudate (50): linear fit = 1.08 x + 0.0 (255 voxels, peak = 75), gca=75.2 gca peak = 0.14251 (76) mri peak = 0.08532 (80) Left_Caudate (11): linear fit = 1.00 x + 0.0 (804 voxels, overlap=0.967) Left_Caudate (11): linear fit = 1.00 x + 0.0 (804 voxels, peak = 76), gca=76.0 gca peak = 0.12116 (60) mri peak = 0.05203 (69) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (20447 voxels, overlap=0.606) Left_Cerebellum_Cortex (8): linear fit = 1.15 x + 0.0 (20447 voxels, peak = 69), gca=69.3 gca peak = 0.12723 (61) mri peak = 0.05435 (65) Right_Cerebellum_Cortex (47): linear fit = 1.10 x + 0.0 (24647 voxels, overlap=0.810) Right_Cerebellum_Cortex (47): linear fit = 1.10 x + 0.0 (24647 voxels, peak = 67), gca=66.8 gca peak = 0.22684 (88) mri peak = 0.05041 (99) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (6993 voxels, overlap=0.112) Left_Cerebellum_White_Matter (7): linear fit = 1.12 x + 0.0 (6993 voxels, peak = 99), gca=99.0 gca peak = 0.21067 (87) mri peak = 0.03513 (72) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6502 voxels, overlap=0.022) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6502 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.12195 (70) Left_Amygdala (18): linear fit = 1.07 x + 0.0 (410 voxels, overlap=0.873) Left_Amygdala (18): linear fit = 1.07 x + 0.0 (410 voxels, peak = 66), gca=66.0 gca peak = 0.39668 (62) mri peak = 0.13610 (68) Right_Amygdala (54): linear fit = 1.07 x + 0.0 (359 voxels, overlap=0.879) Right_Amygdala (54): linear fit = 1.07 x + 0.0 (359 voxels, peak = 66), gca=66.0 gca peak = 0.10129 (93) mri peak = 0.04447 (104) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (4761 voxels, overlap=0.484) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (4761 voxels, peak = 106), gca=105.6 gca peak = 0.12071 (89) mri peak = 0.04787 (100) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (3239 voxels, overlap=0.596) Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (3239 voxels, peak = 98), gca=98.3 gca peak = 0.13716 (82) mri peak = 0.04807 (86) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2542 voxels, overlap=0.906) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2542 voxels, peak = 87), gca=86.5 gca peak = 0.15214 (84) mri peak = 0.05060 (78) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2461 voxels, overlap=0.990) Right_Putamen (51): linear fit = 0.96 x + 0.0 (2461 voxels, peak = 81), gca=81.1 gca peak = 0.08983 (85) mri peak = 0.05019 (99) Brain_Stem (16): linear fit = 1.15 x + 0.0 (9089 voxels, overlap=0.607) Brain_Stem (16): linear fit = 1.15 x + 0.0 (9089 voxels, peak = 98), gca=98.2 gca peak = 0.11809 (92) mri peak = 0.06318 (95) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (721 voxels, overlap=0.548) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (721 voxels, peak = 103), gca=102.6 gca peak = 0.12914 (94) mri peak = 0.06241 (91) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (658 voxels, overlap=0.733) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (658 voxels, peak = 104), gca=103.9 gca peak = 0.21100 (36) mri peak = 1.00000 (15) gca peak = 0.13542 (27) mri peak = 0.11188 ( 7) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (330 voxels, overlap=0.027) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (330 voxels, peak = 6), gca=6.1 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 1.09 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.757, neg=0, invalid=96777 0138: dt=92.480000, rms=0.745 (1.533%), neg=0, invalid=96777 0139: dt=73.984000, rms=0.744 (0.127%), neg=0, invalid=96777 0140: dt=295.936000, rms=0.738 (0.839%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.738 (0.032%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.737 (0.064%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.736 (0.121%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.735 (0.193%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.733 (0.261%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.731 (0.293%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.729 (0.277%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.727 (0.212%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.726 (0.154%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.726 (0.103%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.725 (0.076%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.724 (0.093%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.723 (0.116%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.723 (0.130%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.722 (0.138%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.720 (0.151%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.719 (0.157%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.718 (0.162%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.717 (0.162%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.716 (0.167%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.715 (0.169%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.713 (0.153%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.712 (0.142%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.712 (0.128%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.711 (0.114%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.710 (0.114%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.709 (0.108%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.708 (0.110%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.708 (0.113%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.707 (0.112%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.706 (0.112%), neg=0, invalid=96777 0172: dt=32.368000, rms=0.705 (0.108%), neg=0, invalid=96777 0173: dt=32.368000, rms=0.705 (0.106%), neg=0, invalid=96777 0174: dt=32.368000, rms=0.704 (0.101%), neg=0, invalid=96777 0175: dt=32.368000, rms=0.703 (0.104%), neg=0, invalid=96777 0176: dt=32.368000, rms=0.702 (0.099%), neg=0, invalid=96777 0177: dt=32.368000, rms=0.702 (0.100%), neg=0, invalid=96777 0178: dt=32.368000, rms=0.701 (0.106%), neg=0, invalid=96777 0179: dt=32.368000, rms=0.700 (0.106%), neg=0, invalid=96777 0180: dt=32.368000, rms=0.700 (0.086%), neg=0, invalid=96777 0181: dt=32.368000, rms=0.699 (0.079%), neg=0, invalid=96777 0182: dt=32.368000, rms=0.699 (0.070%), neg=0, invalid=96777 0183: dt=32.368000, rms=0.698 (0.071%), neg=0, invalid=96777 0184: dt=32.368000, rms=0.698 (0.075%), neg=0, invalid=96777 0185: dt=32.368000, rms=0.697 (0.089%), neg=0, invalid=96777 0186: dt=32.368000, rms=0.696 (0.097%), neg=0, invalid=96777 0187: dt=32.368000, rms=0.696 (0.088%), neg=0, invalid=96777 0188: dt=32.368000, rms=0.695 (0.073%), neg=0, invalid=96777 0189: dt=32.368000, rms=0.695 (0.061%), neg=0, invalid=96777 0190: dt=32.368000, rms=0.694 (0.062%), neg=0, invalid=96777 0191: dt=32.368000, rms=0.694 (0.058%), neg=0, invalid=96777 0192: dt=32.368000, rms=0.693 (0.061%), neg=0, invalid=96777 0193: dt=32.368000, rms=0.693 (0.064%), neg=0, invalid=96777 0194: dt=32.368000, rms=0.692 (0.071%), neg=0, invalid=96777 0195: dt=32.368000, rms=0.692 (0.067%), neg=0, invalid=96777 0196: dt=32.368000, rms=0.692 (0.066%), neg=0, invalid=96777 0197: dt=32.368000, rms=0.691 (0.068%), neg=0, invalid=96777 0198: dt=32.368000, rms=0.691 (0.065%), neg=0, invalid=96777 0199: dt=32.368000, rms=0.690 (0.065%), neg=0, invalid=96777 0200: dt=32.368000, rms=0.690 (0.051%), neg=0, invalid=96777 0201: dt=32.368000, rms=0.690 (0.047%), neg=0, invalid=96777 0202: dt=32.368000, rms=0.689 (0.052%), neg=0, invalid=96777 0203: dt=32.368000, rms=0.689 (0.058%), neg=0, invalid=96777 0204: dt=32.368000, rms=0.688 (0.062%), neg=0, invalid=96777 0205: dt=32.368000, rms=0.688 (0.060%), neg=0, invalid=96777 0206: dt=32.368000, rms=0.688 (0.053%), neg=0, invalid=96777 0207: dt=32.368000, rms=0.687 (0.047%), neg=0, invalid=96777 0208: dt=32.368000, rms=0.687 (0.044%), neg=0, invalid=96777 0209: dt=32.368000, rms=0.687 (0.046%), neg=0, invalid=96777 0210: dt=32.368000, rms=0.686 (0.048%), neg=0, invalid=96777 0211: dt=32.368000, rms=0.686 (0.047%), neg=0, invalid=96777 0212: dt=32.368000, rms=0.686 (0.044%), neg=0, invalid=96777 0213: dt=32.368000, rms=0.685 (0.037%), neg=0, invalid=96777 0214: dt=32.368000, rms=0.685 (0.032%), neg=0, invalid=96777 0215: dt=32.368000, rms=0.685 (0.027%), neg=0, invalid=96777 0216: dt=32.368000, rms=0.685 (0.030%), neg=0, invalid=96777 0217: dt=32.368000, rms=0.685 (0.040%), neg=0, invalid=96777 0218: dt=32.368000, rms=0.684 (0.048%), neg=0, invalid=96777 0219: dt=32.368000, rms=0.684 (0.049%), neg=0, invalid=96777 0220: dt=32.368000, rms=0.684 (0.045%), neg=0, invalid=96777 0221: dt=32.368000, rms=0.683 (0.038%), neg=0, invalid=96777 0222: dt=32.368000, rms=0.683 (0.032%), neg=0, invalid=96777 0223: dt=32.368000, rms=0.683 (0.030%), neg=0, invalid=96777 0224: dt=32.368000, rms=0.683 (0.033%), neg=0, invalid=96777 0225: dt=32.368000, rms=0.682 (0.038%), neg=0, invalid=96777 0226: dt=32.368000, rms=0.682 (0.037%), neg=0, invalid=96777 0227: dt=32.368000, rms=0.682 (0.036%), neg=0, invalid=96777 0228: dt=32.368000, rms=0.682 (0.034%), neg=0, invalid=96777 0229: dt=32.368000, rms=0.681 (0.031%), neg=0, invalid=96777 0230: dt=32.368000, rms=0.681 (0.026%), neg=0, invalid=96777 0231: dt=32.368000, rms=0.681 (0.027%), neg=0, invalid=96777 0232: dt=32.368000, rms=0.681 (0.029%), neg=0, invalid=96777 0233: dt=32.368000, rms=0.681 (0.032%), neg=0, invalid=96777 0234: dt=32.368000, rms=0.680 (0.037%), neg=0, invalid=96777 0235: dt=32.368000, rms=0.680 (0.037%), neg=0, invalid=96777 0236: dt=32.368000, rms=0.680 (0.036%), neg=0, invalid=96777 0237: dt=32.368000, rms=0.680 (0.033%), neg=0, invalid=96777 0238: dt=32.368000, rms=0.679 (0.029%), neg=0, invalid=96777 0239: dt=32.368000, rms=0.679 (0.026%), neg=0, invalid=96777 0240: dt=32.368000, rms=0.679 (0.016%), neg=0, invalid=96777 0241: dt=32.368000, rms=0.679 (0.017%), neg=0, invalid=96777 0242: dt=32.368000, rms=0.679 (0.020%), neg=0, invalid=96777 0243: dt=32.368000, rms=0.679 (0.029%), neg=0, invalid=96777 0244: dt=32.368000, rms=0.679 (0.032%), neg=0, invalid=96777 0245: dt=32.368000, rms=0.678 (0.032%), neg=0, invalid=96777 0246: dt=32.368000, rms=0.678 (0.029%), neg=0, invalid=96777 0247: dt=32.368000, rms=0.678 (0.025%), neg=0, invalid=96777 0248: dt=32.368000, rms=0.678 (0.021%), neg=0, invalid=96777 0249: dt=0.006773, rms=0.678 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.678, neg=0, invalid=96777 0250: dt=110.976000, rms=0.677 (0.061%), neg=0, invalid=96777 0251: dt=295.936000, rms=0.675 (0.384%), neg=0, invalid=96777 0252: dt=27.744000, rms=0.675 (0.020%), neg=0, invalid=96777 0253: dt=27.744000, rms=0.675 (-0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.677, neg=0, invalid=96777 0254: dt=36.288000, rms=0.674 (0.437%), neg=0, invalid=96777 0255: dt=331.776000, rms=0.653 (3.088%), neg=0, invalid=96777 0256: dt=36.288000, rms=0.649 (0.665%), neg=0, invalid=96777 0257: dt=124.416000, rms=0.641 (1.210%), neg=0, invalid=96777 0258: dt=31.104000, rms=0.638 (0.414%), neg=0, invalid=96777 0259: dt=36.288000, rms=0.637 (0.178%), neg=0, invalid=96777 0260: dt=82.944000, rms=0.635 (0.369%), neg=0, invalid=96777 0261: dt=31.104000, rms=0.633 (0.222%), neg=0, invalid=96777 0262: dt=82.944000, rms=0.631 (0.351%), neg=0, invalid=96777 0263: dt=25.920000, rms=0.629 (0.236%), neg=0, invalid=96777 0264: dt=103.680000, rms=0.627 (0.406%), neg=0, invalid=96777 0265: dt=25.920000, rms=0.626 (0.173%), neg=0, invalid=96777 0266: dt=145.152000, rms=0.623 (0.529%), neg=0, invalid=96777 0267: dt=20.736000, rms=0.622 (0.159%), neg=0, invalid=96777 0268: dt=145.152000, rms=0.619 (0.375%), neg=0, invalid=96777 0269: dt=36.288000, rms=0.618 (0.212%), neg=0, invalid=96777 0270: dt=82.944000, rms=0.617 (0.104%), neg=0, invalid=96777 0271: dt=31.104000, rms=0.616 (0.218%), neg=0, invalid=96777 0272: dt=31.104000, rms=0.615 (0.071%), neg=0, invalid=96777 0273: dt=36.288000, rms=0.615 (0.140%), neg=0, invalid=96777 0274: dt=580.608000, rms=0.610 (0.817%), neg=0, invalid=96777 0275: dt=31.104000, rms=0.606 (0.563%), neg=0, invalid=96777 0276: dt=20.736000, rms=0.606 (0.058%), neg=0, invalid=96777 0277: dt=145.152000, rms=0.605 (0.212%), neg=0, invalid=96777 0278: dt=145.152000, rms=0.603 (0.286%), neg=0, invalid=96777 0279: dt=20.736000, rms=0.603 (0.028%), neg=0, invalid=96777 0280: dt=20.736000, rms=0.603 (0.014%), neg=0, invalid=96777 0281: dt=20.736000, rms=0.602 (0.027%), neg=0, invalid=96777 0282: dt=20.736000, rms=0.602 (0.061%), neg=0, invalid=96777 0283: dt=20.736000, rms=0.601 (0.105%), neg=0, invalid=96777 0284: dt=20.736000, rms=0.601 (0.144%), neg=0, invalid=96777 0285: dt=20.736000, rms=0.599 (0.174%), neg=0, invalid=96777 0286: dt=20.736000, rms=0.599 (0.158%), neg=0, invalid=96777 0287: dt=20.736000, rms=0.598 (0.146%), neg=0, invalid=96777 0288: dt=20.736000, rms=0.597 (0.138%), neg=0, invalid=96777 0289: dt=20.736000, rms=0.596 (0.130%), neg=0, invalid=96777 0290: dt=20.736000, rms=0.595 (0.138%), neg=0, invalid=96777 0291: dt=20.736000, rms=0.594 (0.160%), neg=0, invalid=96777 0292: dt=20.736000, rms=0.593 (0.169%), neg=0, invalid=96777 0293: dt=20.736000, rms=0.592 (0.164%), neg=0, invalid=96777 0294: dt=20.736000, rms=0.591 (0.160%), neg=0, invalid=96777 0295: dt=20.736000, rms=0.590 (0.148%), neg=0, invalid=96777 0296: dt=20.736000, rms=0.590 (0.152%), neg=0, invalid=96777 0297: dt=20.736000, rms=0.589 (0.136%), neg=0, invalid=96777 0298: dt=20.736000, rms=0.588 (0.125%), neg=0, invalid=96777 0299: dt=20.736000, rms=0.587 (0.111%), neg=0, invalid=96777 0300: dt=20.736000, rms=0.587 (0.106%), neg=0, invalid=96777 0301: dt=20.736000, rms=0.586 (0.100%), neg=0, invalid=96777 0302: dt=20.736000, rms=0.586 (0.106%), neg=0, invalid=96777 0303: dt=20.736000, rms=0.585 (0.111%), neg=0, invalid=96777 0304: dt=20.736000, rms=0.584 (0.109%), neg=0, invalid=96777 0305: dt=20.736000, rms=0.584 (0.099%), neg=0, invalid=96777 0306: dt=20.736000, rms=0.583 (0.100%), neg=0, invalid=96777 0307: dt=20.736000, rms=0.583 (0.095%), neg=0, invalid=96777 0308: dt=20.736000, rms=0.582 (0.080%), neg=0, invalid=96777 0309: dt=20.736000, rms=0.582 (0.059%), neg=0, invalid=96777 0310: dt=20.736000, rms=0.581 (0.065%), neg=0, invalid=96777 0311: dt=20.736000, rms=0.581 (0.069%), neg=0, invalid=96777 0312: dt=20.736000, rms=0.581 (0.068%), neg=0, invalid=96777 0313: dt=20.736000, rms=0.580 (0.070%), neg=0, invalid=96777 0314: dt=20.736000, rms=0.580 (0.067%), neg=0, invalid=96777 0315: dt=20.736000, rms=0.579 (0.058%), neg=0, invalid=96777 0316: dt=20.736000, rms=0.579 (0.066%), neg=0, invalid=96777 0317: dt=20.736000, rms=0.579 (0.068%), neg=0, invalid=96777 0318: dt=20.736000, rms=0.579 (0.016%), neg=0, invalid=96777 0319: dt=20.736000, rms=0.578 (0.022%), neg=0, invalid=96777 0320: dt=20.736000, rms=0.578 (0.025%), neg=0, invalid=96777 0321: dt=20.736000, rms=0.578 (0.024%), neg=0, invalid=96777 0322: dt=20.736000, rms=0.578 (0.026%), neg=0, invalid=96777 0323: dt=20.736000, rms=0.578 (0.032%), neg=0, invalid=96777 0324: dt=20.736000, rms=0.578 (0.038%), neg=0, invalid=96777 0325: dt=20.736000, rms=0.577 (0.037%), neg=0, invalid=96777 0326: dt=20.736000, rms=0.577 (0.036%), neg=0, invalid=96777 0327: dt=20.736000, rms=0.577 (0.036%), neg=0, invalid=96777 0328: dt=20.736000, rms=0.577 (0.030%), neg=0, invalid=96777 0329: dt=20.736000, rms=0.577 (0.025%), neg=0, invalid=96777 0330: dt=20.736000, rms=0.576 (0.032%), neg=0, invalid=96777 0331: dt=20.736000, rms=0.576 (0.035%), neg=0, invalid=96777 0332: dt=20.736000, rms=0.576 (0.043%), neg=0, invalid=96777 0333: dt=20.736000, rms=0.576 (0.043%), neg=0, invalid=96777 0334: dt=20.736000, rms=0.576 (0.043%), neg=0, invalid=96777 0335: dt=20.736000, rms=0.575 (0.041%), neg=0, invalid=96777 0336: dt=20.736000, rms=0.575 (0.044%), neg=0, invalid=96777 0337: dt=20.736000, rms=0.575 (0.043%), neg=0, invalid=96777 0338: dt=20.736000, rms=0.575 (0.035%), neg=0, invalid=96777 0339: dt=20.736000, rms=0.574 (0.035%), neg=0, invalid=96777 0340: dt=20.736000, rms=0.574 (0.037%), neg=0, invalid=96777 0341: dt=20.736000, rms=0.574 (0.042%), neg=0, invalid=96777 0342: dt=20.736000, rms=0.574 (0.051%), neg=0, invalid=96777 0343: dt=20.736000, rms=0.573 (0.053%), neg=0, invalid=96777 0344: dt=20.736000, rms=0.573 (0.052%), neg=0, invalid=96777 0345: dt=20.736000, rms=0.573 (0.047%), neg=0, invalid=96777 0346: dt=20.736000, rms=0.573 (0.043%), neg=0, invalid=96777 0347: dt=20.736000, rms=0.572 (0.040%), neg=0, invalid=96777 0348: dt=20.736000, rms=0.572 (0.043%), neg=0, invalid=96777 0349: dt=20.736000, rms=0.572 (0.036%), neg=0, invalid=96777 0350: dt=20.736000, rms=0.572 (0.031%), neg=0, invalid=96777 0351: dt=20.736000, rms=0.571 (0.035%), neg=0, invalid=96777 0352: dt=20.736000, rms=0.571 (0.030%), neg=0, invalid=96777 0353: dt=20.736000, rms=0.571 (0.038%), neg=0, invalid=96777 0354: dt=20.736000, rms=0.571 (0.040%), neg=0, invalid=96777 0355: dt=20.736000, rms=0.571 (0.038%), neg=0, invalid=96777 0356: dt=20.736000, rms=0.570 (0.038%), neg=0, invalid=96777 0357: dt=20.736000, rms=0.570 (0.033%), neg=0, invalid=96777 0358: dt=20.736000, rms=0.570 (0.033%), neg=0, invalid=96777 0359: dt=20.736000, rms=0.570 (0.032%), neg=0, invalid=96777 0360: dt=20.736000, rms=0.570 (0.040%), neg=0, invalid=96777 0361: dt=20.736000, rms=0.569 (0.031%), neg=0, invalid=96777 0362: dt=20.736000, rms=0.569 (0.024%), neg=0, invalid=96777 0363: dt=20.736000, rms=0.569 (0.016%), neg=0, invalid=96777 0364: dt=145.152000, rms=0.569 (0.043%), neg=0, invalid=96777 0365: dt=0.001012, rms=0.569 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=96777 0366: dt=36.288000, rms=0.567 (0.352%), neg=0, invalid=96777 0367: dt=82.944000, rms=0.566 (0.196%), neg=0, invalid=96777 0368: dt=20.736000, rms=0.565 (0.072%), neg=0, invalid=96777 0369: dt=145.152000, rms=0.565 (0.127%), neg=0, invalid=96777 0370: dt=9.072000, rms=0.565 (0.009%), neg=0, invalid=96777 0371: dt=9.072000, rms=0.565 (0.008%), neg=0, invalid=96777 0372: dt=9.072000, rms=0.565 (0.008%), neg=0, invalid=96777 0373: dt=9.072000, rms=0.565 (0.012%), neg=0, invalid=96777 0374: dt=9.072000, rms=0.565 (0.011%), neg=0, invalid=96777 0375: dt=36.288000, rms=0.564 (0.029%), neg=0, invalid=96777 0376: dt=124.416000, rms=0.564 (0.040%), neg=0, invalid=96777 0377: dt=36.288000, rms=0.564 (0.035%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.581, neg=0, invalid=96777 0378: dt=19.200000, rms=0.579 (0.319%), neg=0, invalid=96777 0379: dt=11.200000, rms=0.577 (0.354%), neg=0, invalid=96777 0380: dt=32.000000, rms=0.575 (0.363%), neg=0, invalid=96777 0381: dt=11.322404, rms=0.572 (0.447%), neg=0, invalid=96777 0382: dt=11.200000, rms=0.571 (0.261%), neg=0, invalid=96777 0383: dt=11.200000, rms=0.570 (0.176%), neg=0, invalid=96777 0384: dt=11.200000, rms=0.568 (0.254%), neg=0, invalid=96777 0385: dt=32.000000, rms=0.567 (0.298%), neg=0, invalid=96777 0386: dt=8.000000, rms=0.566 (0.150%), neg=0, invalid=96777 0387: dt=15.560440, rms=0.563 (0.458%), neg=0, invalid=96777 0388: dt=5.080292, rms=0.563 (0.058%), neg=0, invalid=96777 0389: dt=11.200000, rms=0.562 (0.082%), neg=0, invalid=96777 0390: dt=32.000000, rms=0.560 (0.393%), neg=0, invalid=96777 0391: dt=0.700000, rms=0.560 (-0.013%), neg=0, invalid=96777 0392: dt=0.700000, rms=0.560 (0.005%), neg=0, invalid=96777 0393: dt=0.000171, rms=0.560 (0.001%), neg=0, invalid=96777 0394: dt=0.000085, rms=0.560 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.560, neg=0, invalid=96777 0395: dt=0.000000, rms=0.560 (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=0.602, neg=0, invalid=96777 0396: dt=0.720000, rms=0.601 (0.134%), neg=0, invalid=96777 0397: dt=0.252000, rms=0.601 (0.053%), neg=0, invalid=96777 0398: dt=0.063000, rms=0.601 (0.013%), neg=0, invalid=96777 0399: dt=0.031500, rms=0.601 (0.006%), neg=0, invalid=96777 0400: dt=0.003938, rms=0.601 (0.001%), neg=0, invalid=96777 0401: dt=0.000492, rms=0.601 (0.000%), neg=0, invalid=96777 0402: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=96777 0403: dt=0.000000, rms=0.601 (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=0.679, neg=0, invalid=96777 0404: dt=0.384000, rms=0.676 (0.545%), neg=0, invalid=96777 0405: dt=0.448000, rms=0.672 (0.569%), neg=0, invalid=96777 0406: dt=0.384000, rms=0.669 (0.421%), neg=0, invalid=96777 0407: dt=0.112000, rms=0.668 (0.115%), neg=0, invalid=96777 0408: dt=0.384000, rms=0.666 (0.366%), neg=0, invalid=96777 0409: dt=0.448000, rms=0.663 (0.386%), neg=0, invalid=96777 0410: dt=0.448000, rms=0.661 (0.341%), neg=0, invalid=96777 0411: dt=0.448000, rms=0.659 (0.297%), neg=0, invalid=96777 0412: dt=0.384000, rms=0.657 (0.229%), neg=0, invalid=96777 0413: dt=0.448000, rms=0.656 (0.240%), neg=0, invalid=96777 0414: dt=0.448000, rms=0.654 (0.221%), neg=0, invalid=96777 0415: dt=0.448000, rms=0.653 (0.202%), neg=0, invalid=96777 0416: dt=0.448000, rms=0.652 (0.177%), neg=0, invalid=96777 0417: dt=0.448000, rms=0.651 (0.163%), neg=0, invalid=96777 0418: dt=0.448000, rms=0.650 (0.148%), neg=0, invalid=96777 0419: dt=0.448000, rms=0.649 (0.137%), neg=0, invalid=96777 0420: dt=0.448000, rms=0.648 (0.125%), neg=0, invalid=96777 0421: dt=0.448000, rms=0.647 (0.117%), neg=0, invalid=96777 0422: dt=0.448000, rms=0.647 (0.108%), neg=0, invalid=96777 0423: dt=1.208333, rms=0.645 (0.258%), neg=0, invalid=96777 0424: dt=0.448000, rms=0.644 (0.090%), neg=0, invalid=96777 0425: dt=0.320000, rms=0.644 (0.055%), neg=0, invalid=96777 0426: dt=0.448000, rms=0.644 (0.075%), neg=0, invalid=96777 0427: dt=0.448000, rms=0.643 (0.069%), neg=0, invalid=96777 0428: dt=0.750000, rms=0.642 (0.111%), neg=0, invalid=96777 0429: dt=0.448000, rms=0.642 (0.059%), neg=0, invalid=96777 0430: dt=0.448000, rms=0.642 (0.060%), neg=0, invalid=96777 0431: dt=0.448000, rms=0.641 (0.058%), neg=0, invalid=96777 0432: dt=0.320000, rms=0.641 (0.040%), neg=0, invalid=96777 0433: dt=0.320000, rms=0.641 (0.037%), neg=0, invalid=96777 0434: dt=0.320000, rms=0.640 (0.070%), neg=0, invalid=96777 0435: dt=0.320000, rms=0.640 (0.093%), neg=0, invalid=96777 0436: dt=0.320000, rms=0.640 (0.031%), neg=0, invalid=96777 0437: dt=0.320000, rms=0.639 (0.060%), neg=0, invalid=96777 0438: dt=0.320000, rms=0.639 (0.081%), neg=0, invalid=96777 0439: dt=0.320000, rms=0.638 (0.100%), neg=0, invalid=96777 0440: dt=0.320000, rms=0.637 (0.112%), neg=0, invalid=96777 0441: dt=0.320000, rms=0.637 (0.022%), neg=0, invalid=96777 0442: dt=0.320000, rms=0.637 (0.049%), neg=0, invalid=96777 0443: dt=0.320000, rms=0.636 (0.064%), neg=0, invalid=96777 0444: dt=0.320000, rms=0.636 (0.079%), neg=0, invalid=96777 0445: dt=0.320000, rms=0.635 (0.083%), neg=0, invalid=96777 0446: dt=0.320000, rms=0.635 (0.089%), neg=0, invalid=96777 0447: dt=0.320000, rms=0.634 (0.090%), neg=0, invalid=96777 0448: dt=0.320000, rms=0.634 (0.083%), neg=0, invalid=96777 0449: dt=0.320000, rms=0.633 (0.079%), neg=0, invalid=96777 0450: dt=0.320000, rms=0.633 (0.076%), neg=0, invalid=96777 0451: dt=0.320000, rms=0.632 (0.065%), neg=0, invalid=96777 0452: dt=0.320000, rms=0.632 (0.053%), neg=0, invalid=96777 0453: dt=0.320000, rms=0.632 (0.047%), neg=0, invalid=96777 0454: dt=0.320000, rms=0.631 (0.039%), neg=0, invalid=96777 0455: dt=0.320000, rms=0.631 (0.032%), neg=0, invalid=96777 0456: dt=0.320000, rms=0.631 (0.039%), neg=0, invalid=96777 0457: dt=0.320000, rms=0.631 (0.042%), neg=0, invalid=96777 0458: dt=0.320000, rms=0.630 (0.045%), neg=0, invalid=96777 0459: dt=0.320000, rms=0.630 (0.043%), neg=0, invalid=96777 0460: dt=0.320000, rms=0.630 (0.047%), neg=0, invalid=96777 0461: dt=0.320000, rms=0.630 (0.048%), neg=0, invalid=96777 0462: dt=0.320000, rms=0.629 (0.054%), neg=0, invalid=96777 0463: dt=0.320000, rms=0.629 (0.050%), neg=0, invalid=96777 0464: dt=0.320000, rms=0.629 (0.046%), neg=0, invalid=96777 0465: dt=0.320000, rms=0.628 (0.051%), neg=0, invalid=96777 0466: dt=0.320000, rms=0.628 (0.051%), neg=0, invalid=96777 0467: dt=0.320000, rms=0.628 (0.053%), neg=0, invalid=96777 0468: dt=0.320000, rms=0.627 (0.051%), neg=0, invalid=96777 0469: dt=0.320000, rms=0.627 (0.053%), neg=0, invalid=96777 0470: dt=0.320000, rms=0.627 (0.057%), neg=0, invalid=96777 0471: dt=0.320000, rms=0.626 (0.054%), neg=0, invalid=96777 0472: dt=0.320000, rms=0.626 (0.059%), neg=0, invalid=96777 0473: dt=0.320000, rms=0.626 (0.059%), neg=0, invalid=96777 0474: dt=0.320000, rms=0.625 (0.059%), neg=0, invalid=96777 0475: dt=0.320000, rms=0.625 (0.055%), neg=0, invalid=96777 0476: dt=0.320000, rms=0.625 (0.054%), neg=0, invalid=96777 0477: dt=0.320000, rms=0.624 (0.050%), neg=0, invalid=96777 0478: dt=0.320000, rms=0.624 (0.050%), neg=0, invalid=96777 0479: dt=0.320000, rms=0.624 (0.044%), neg=0, invalid=96777 0480: dt=0.320000, rms=0.623 (0.041%), neg=0, invalid=96777 0481: dt=0.320000, rms=0.623 (0.038%), neg=0, invalid=96777 0482: dt=0.320000, rms=0.623 (0.033%), neg=0, invalid=96777 0483: dt=0.320000, rms=0.623 (0.028%), neg=0, invalid=96777 0484: dt=0.320000, rms=0.623 (0.029%), neg=0, invalid=96777 0485: dt=0.320000, rms=0.622 (0.028%), neg=0, invalid=96777 0486: dt=0.320000, rms=0.622 (0.025%), neg=0, invalid=96777 0487: dt=0.320000, rms=0.622 (0.024%), neg=0, invalid=96777 0488: dt=1.536000, rms=0.622 (0.005%), neg=0, invalid=96777 0489: dt=0.768000, rms=0.622 (0.002%), neg=0, invalid=96777 0490: dt=0.768000, rms=0.622 (0.003%), neg=0, invalid=96777 0491: dt=0.768000, rms=0.622 (0.003%), neg=0, invalid=96777 0492: dt=0.384000, rms=0.622 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0493: dt=0.448000, rms=0.622 (0.071%), neg=0, invalid=96777 0494: dt=0.448000, rms=0.621 (0.063%), neg=0, invalid=96777 0495: dt=0.448000, rms=0.621 (0.054%), neg=0, invalid=96777 0496: dt=0.607143, rms=0.620 (0.059%), neg=0, invalid=96777 0497: dt=0.500000, rms=0.620 (0.042%), neg=0, invalid=96777 0498: dt=0.500000, rms=0.620 (0.035%), neg=0, invalid=96777 0499: dt=0.500000, rms=0.620 (0.058%), neg=0, invalid=96777 0500: dt=0.500000, rms=0.619 (0.068%), neg=0, invalid=96777 0501: dt=0.500000, rms=0.619 (0.065%), neg=0, invalid=96777 0502: dt=0.500000, rms=0.618 (0.050%), neg=0, invalid=96777 0503: dt=0.500000, rms=0.618 (0.031%), neg=0, invalid=96777 0504: dt=0.500000, rms=0.618 (0.014%), neg=0, invalid=96777 0505: dt=0.500000, rms=0.618 (0.008%), neg=0, invalid=96777 0506: dt=0.448000, rms=0.618 (0.002%), neg=0, invalid=96777 0507: dt=0.448000, rms=0.618 (0.002%), neg=0, invalid=96777 0508: dt=0.448000, rms=0.618 (0.001%), neg=0, invalid=96777 0509: dt=0.448000, rms=0.618 (0.002%), neg=0, invalid=96777 0510: dt=0.224000, rms=0.618 (0.002%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.602, neg=0, invalid=96777 0511: dt=0.028000, rms=0.601 (0.265%), neg=0, invalid=96777 0512: dt=0.028000, rms=0.599 (0.254%), neg=0, invalid=96777 0513: dt=0.007000, rms=0.599 (0.060%), neg=0, invalid=96777 0514: dt=0.028000, rms=0.597 (0.239%), neg=0, invalid=96777 0515: dt=0.028000, rms=0.596 (0.228%), neg=0, invalid=96777 0516: dt=0.028000, rms=0.595 (0.218%), neg=0, invalid=96777 0517: dt=0.028000, rms=0.593 (0.207%), neg=0, invalid=96777 0518: dt=0.028000, rms=0.592 (0.197%), neg=0, invalid=96777 0519: dt=0.028000, rms=0.591 (0.190%), neg=0, invalid=96777 0520: dt=0.024000, rms=0.590 (0.154%), neg=0, invalid=96777 0521: dt=0.001750, rms=0.590 (0.011%), neg=0, invalid=96777 0522: dt=0.001750, rms=0.590 (0.011%), neg=0, invalid=96777 0523: dt=0.001750, rms=0.590 (0.021%), neg=0, invalid=96777 0524: dt=0.001750, rms=0.590 (0.029%), neg=0, invalid=96777 0525: dt=0.001750, rms=0.590 (0.037%), neg=0, invalid=96777 0526: dt=0.001750, rms=0.589 (0.044%), neg=0, invalid=96777 0527: dt=0.001750, rms=0.589 (0.050%), neg=0, invalid=96777 0528: dt=0.001750, rms=0.589 (0.055%), neg=0, invalid=96777 0529: dt=0.001750, rms=0.588 (0.060%), neg=0, invalid=96777 0530: dt=0.001750, rms=0.588 (0.064%), neg=0, invalid=96777 0531: dt=0.001750, rms=0.588 (0.067%), neg=0, invalid=96777 0532: dt=0.001750, rms=0.587 (0.070%), neg=0, invalid=96777 0533: dt=0.001750, rms=0.587 (0.072%), neg=0, invalid=96777 0534: dt=0.001750, rms=0.586 (0.074%), neg=0, invalid=96777 0535: dt=0.001750, rms=0.586 (0.076%), neg=0, invalid=96777 0536: dt=0.001750, rms=0.585 (0.078%), neg=0, invalid=96777 0537: dt=0.001750, rms=0.585 (0.077%), neg=0, invalid=96777 0538: dt=0.001750, rms=0.585 (0.078%), neg=0, invalid=96777 0539: dt=0.001750, rms=0.584 (0.079%), neg=0, invalid=96777 0540: dt=0.001750, rms=0.584 (0.079%), neg=0, invalid=96777 0541: dt=0.001750, rms=0.583 (0.079%), neg=0, invalid=96777 0542: dt=0.001750, rms=0.583 (0.077%), neg=0, invalid=96777 0543: dt=0.001750, rms=0.582 (0.078%), neg=0, invalid=96777 0544: dt=0.001750, rms=0.582 (0.079%), neg=0, invalid=96777 0545: dt=0.001750, rms=0.581 (0.076%), neg=0, invalid=96777 0546: dt=0.001750, rms=0.581 (0.076%), neg=0, invalid=96777 0547: dt=0.001750, rms=0.580 (0.075%), neg=0, invalid=96777 0548: dt=0.001750, rms=0.580 (0.074%), neg=0, invalid=96777 0549: dt=0.001750, rms=0.580 (0.072%), neg=0, invalid=96777 0550: dt=0.001750, rms=0.579 (0.070%), neg=0, invalid=96777 0551: dt=0.001750, rms=0.579 (0.070%), neg=0, invalid=96777 0552: dt=0.001750, rms=0.578 (0.068%), neg=0, invalid=96777 0553: dt=0.001750, rms=0.578 (0.067%), neg=0, invalid=96777 0554: dt=0.001750, rms=0.578 (0.066%), neg=0, invalid=96777 0555: dt=0.001750, rms=0.577 (0.064%), neg=0, invalid=96777 0556: dt=0.001750, rms=0.577 (0.063%), neg=0, invalid=96777 0557: dt=0.001750, rms=0.577 (0.061%), neg=0, invalid=96777 0558: dt=0.001750, rms=0.576 (0.060%), neg=0, invalid=96777 0559: dt=0.001750, rms=0.576 (0.058%), neg=0, invalid=96777 0560: dt=0.001750, rms=0.576 (0.057%), neg=0, invalid=96777 0561: dt=0.001750, rms=0.575 (0.056%), neg=0, invalid=96777 0562: dt=0.001750, rms=0.575 (0.054%), neg=0, invalid=96777 0563: dt=0.001750, rms=0.575 (0.052%), neg=0, invalid=96777 0564: dt=0.001750, rms=0.574 (0.051%), neg=0, invalid=96777 0565: dt=0.001750, rms=0.574 (0.050%), neg=0, invalid=96777 0566: dt=0.001750, rms=0.574 (0.049%), neg=0, invalid=96777 0567: dt=0.001750, rms=0.573 (0.047%), neg=0, invalid=96777 0568: dt=0.001750, rms=0.573 (0.046%), neg=0, invalid=96777 0569: dt=0.001750, rms=0.573 (0.045%), neg=0, invalid=96777 0570: dt=0.001750, rms=0.573 (0.044%), neg=0, invalid=96777 0571: dt=0.001750, rms=0.572 (0.043%), neg=0, invalid=96777 0572: dt=0.001750, rms=0.572 (0.042%), neg=0, invalid=96777 0573: dt=0.001750, rms=0.572 (0.041%), neg=0, invalid=96777 0574: dt=0.001750, rms=0.572 (0.040%), neg=0, invalid=96777 0575: dt=0.001750, rms=0.572 (0.039%), neg=0, invalid=96777 0576: dt=0.001750, rms=0.571 (0.036%), neg=0, invalid=96777 0577: dt=0.001750, rms=0.571 (0.036%), neg=0, invalid=96777 0578: dt=0.001750, rms=0.571 (0.036%), neg=0, invalid=96777 0579: dt=0.001750, rms=0.571 (0.034%), neg=0, invalid=96777 0580: dt=0.001750, rms=0.571 (0.034%), neg=0, invalid=96777 0581: dt=0.001750, rms=0.570 (0.033%), neg=0, invalid=96777 0582: dt=0.001750, rms=0.570 (0.032%), neg=0, invalid=96777 0583: dt=0.001750, rms=0.570 (0.032%), neg=0, invalid=96777 0584: dt=0.001750, rms=0.570 (0.031%), neg=0, invalid=96777 0585: dt=0.001750, rms=0.570 (0.030%), neg=0, invalid=96777 0586: dt=0.001750, rms=0.569 (0.030%), neg=0, invalid=96777 0587: dt=0.001750, rms=0.569 (0.029%), neg=0, invalid=96777 0588: dt=0.001750, rms=0.569 (0.030%), neg=0, invalid=96777 0589: dt=0.001750, rms=0.569 (0.028%), neg=0, invalid=96777 0590: dt=0.001750, rms=0.569 (0.027%), neg=0, invalid=96777 0591: dt=0.001750, rms=0.569 (0.026%), neg=0, invalid=96777 0592: dt=0.001750, rms=0.569 (0.026%), neg=0, invalid=96777 0593: dt=0.001750, rms=0.568 (0.025%), neg=0, invalid=96777 0594: dt=0.001750, rms=0.568 (0.025%), neg=0, invalid=96777 0595: dt=0.001750, rms=0.568 (0.024%), neg=0, invalid=96777 0596: dt=0.112000, rms=0.567 (0.126%), neg=0, invalid=96777 0597: dt=0.001750, rms=0.567 (-0.000%), neg=0, invalid=96777 0598: dt=0.001750, rms=0.567 (0.002%), neg=0, invalid=96777 0599: dt=0.001750, rms=0.567 (0.004%), neg=0, invalid=96777 0600: dt=0.001750, rms=0.567 (0.005%), neg=0, invalid=96777 0601: dt=0.001750, rms=0.567 (0.006%), neg=0, invalid=96777 0602: dt=0.001750, rms=0.567 (0.008%), neg=0, invalid=96777 0603: dt=0.001750, rms=0.567 (0.009%), neg=0, invalid=96777 0604: dt=0.001750, rms=0.567 (0.009%), neg=0, invalid=96777 0605: dt=0.001750, rms=0.567 (0.011%), neg=0, invalid=96777 0606: dt=0.001750, rms=0.567 (0.011%), neg=0, invalid=96777 0607: dt=0.001750, rms=0.567 (0.012%), neg=0, invalid=96777 0608: dt=0.001750, rms=0.567 (0.012%), neg=0, invalid=96777 0609: dt=0.001750, rms=0.567 (0.013%), neg=0, invalid=96777 0610: dt=0.001750, rms=0.567 (0.013%), neg=0, invalid=96777 0611: dt=0.001750, rms=0.567 (0.015%), neg=0, invalid=96777 0612: dt=0.001750, rms=0.567 (0.014%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.567, neg=0, invalid=96777 0613: dt=0.007000, rms=0.566 (0.027%), neg=0, invalid=96777 0614: dt=0.007000, rms=0.566 (0.026%), neg=0, invalid=96777 0615: dt=0.007000, rms=0.566 (0.026%), neg=0, invalid=96777 0616: dt=0.007000, rms=0.566 (0.026%), neg=0, invalid=96777 0617: dt=0.001750, rms=0.566 (0.005%), neg=0, invalid=96777 0618: dt=0.001750, rms=0.566 (0.012%), neg=0, invalid=96777 0619: dt=0.001750, rms=0.566 (0.016%), neg=0, invalid=96777 0620: dt=0.000875, rms=0.566 (0.005%), neg=0, invalid=96777 0621: dt=0.007000, rms=0.566 (0.025%), neg=0, invalid=96777 0622: dt=0.005000, rms=0.566 (0.015%), neg=0, invalid=96777 0623: dt=0.005000, rms=0.565 (0.020%), neg=0, invalid=96777 0624: dt=0.005000, rms=0.565 (0.030%), neg=0, invalid=96777 0625: dt=0.005000, rms=0.565 (0.046%), neg=0, invalid=96777 0626: dt=0.002500, rms=0.565 (0.010%), neg=0, invalid=96777 0627: dt=0.002500, rms=0.565 (0.013%), neg=0, invalid=96777 0628: dt=0.002500, rms=0.565 (0.023%), neg=0, invalid=96777 0629: dt=0.002500, rms=0.565 (0.009%), neg=0, invalid=96777 0630: dt=0.024000, rms=0.564 (0.074%), neg=0, invalid=96777 0631: dt=0.001750, rms=0.564 (0.004%), neg=0, invalid=96777 0632: dt=0.001750, rms=0.564 (0.006%), neg=0, invalid=96777 0633: dt=0.001750, rms=0.564 (0.010%), neg=0, invalid=96777 0634: dt=0.001750, rms=0.564 (0.015%), neg=0, invalid=96777 0635: dt=0.001750, rms=0.564 (0.018%), neg=0, invalid=96777 0636: dt=0.001750, rms=0.564 (0.021%), neg=0, invalid=96777 0637: dt=0.001750, rms=0.564 (0.022%), neg=0, invalid=96777 0638: dt=0.001750, rms=0.564 (0.026%), neg=0, invalid=96777 0639: dt=0.001750, rms=0.563 (0.029%), neg=0, invalid=96777 0640: dt=0.001750, rms=0.563 (0.030%), neg=0, invalid=96777 0641: dt=0.001750, rms=0.563 (0.032%), neg=0, invalid=96777 0642: dt=0.001750, rms=0.563 (0.032%), neg=0, invalid=96777 0643: dt=0.001750, rms=0.563 (0.035%), neg=0, invalid=96777 0644: dt=0.001750, rms=0.562 (0.037%), neg=0, invalid=96777 0645: dt=0.001750, rms=0.562 (0.036%), neg=0, invalid=96777 0646: dt=0.001750, rms=0.562 (0.035%), neg=0, invalid=96777 0647: dt=0.001750, rms=0.562 (0.036%), neg=0, invalid=96777 0648: dt=0.001750, rms=0.562 (0.037%), neg=0, invalid=96777 0649: dt=0.001750, rms=0.561 (0.034%), neg=0, invalid=96777 0650: dt=0.001750, rms=0.561 (0.036%), neg=0, invalid=96777 0651: dt=0.001750, rms=0.561 (0.036%), neg=0, invalid=96777 0652: dt=0.001750, rms=0.561 (0.036%), neg=0, invalid=96777 0653: dt=0.001750, rms=0.561 (0.035%), neg=0, invalid=96777 0654: dt=0.001750, rms=0.560 (0.036%), neg=0, invalid=96777 0655: dt=0.001750, rms=0.560 (0.034%), neg=0, invalid=96777 0656: dt=0.001750, rms=0.560 (0.033%), neg=0, invalid=96777 0657: dt=0.001750, rms=0.560 (0.034%), neg=0, invalid=96777 0658: dt=0.001750, rms=0.560 (0.032%), neg=0, invalid=96777 0659: dt=0.001750, rms=0.560 (0.031%), neg=0, invalid=96777 0660: dt=0.001750, rms=0.559 (0.031%), neg=0, invalid=96777 0661: dt=0.001750, rms=0.559 (0.031%), neg=0, invalid=96777 0662: dt=0.001750, rms=0.559 (0.029%), neg=0, invalid=96777 0663: dt=0.001750, rms=0.559 (0.028%), neg=0, invalid=96777 0664: dt=0.001750, rms=0.559 (0.027%), neg=0, invalid=96777 0665: dt=0.001750, rms=0.559 (0.027%), neg=0, invalid=96777 0666: dt=0.001750, rms=0.558 (0.025%), neg=0, invalid=96777 0667: dt=0.001750, rms=0.558 (0.026%), neg=0, invalid=96777 0668: dt=0.001750, rms=0.558 (0.024%), neg=0, invalid=96777 0669: dt=0.001750, rms=0.558 (0.025%), neg=0, invalid=96777 0670: dt=0.001750, rms=0.558 (0.024%), neg=0, invalid=96777 0671: dt=0.001750, rms=0.558 (0.022%), neg=0, invalid=96777 0672: dt=0.112000, rms=0.557 (0.098%), neg=0, invalid=96777 0673: dt=0.001750, rms=0.557 (-0.002%), neg=0, invalid=96777 0674: dt=0.001750, rms=0.557 (0.001%), neg=0, invalid=96777 0675: dt=0.001750, rms=0.557 (0.003%), neg=0, invalid=96777 0676: dt=0.001750, rms=0.557 (0.004%), neg=0, invalid=96777 0677: dt=0.001750, rms=0.557 (0.005%), neg=0, invalid=96777 0678: dt=0.001750, rms=0.557 (0.005%), neg=0, invalid=96777 0679: dt=0.001750, rms=0.557 (0.006%), neg=0, invalid=96777 0680: dt=0.001750, rms=0.557 (0.007%), neg=0, invalid=96777 0681: dt=0.001750, rms=0.557 (0.007%), neg=0, invalid=96777 0682: dt=0.001750, rms=0.557 (0.007%), neg=0, invalid=96777 0683: dt=0.001750, rms=0.557 (0.008%), neg=0, invalid=96777 0684: dt=0.001750, rms=0.557 (0.009%), neg=0, invalid=96777 0685: dt=0.001750, rms=0.557 (0.009%), neg=0, invalid=96777 0686: dt=0.001750, rms=0.557 (0.009%), neg=0, invalid=96777 0687: dt=0.001750, rms=0.557 (0.009%), neg=0, invalid=96777 0688: dt=0.001750, rms=0.557 (0.009%), 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=0.554, neg=0, invalid=96777 0689: dt=0.000723, rms=0.554 (0.001%), neg=0, invalid=96777 0690: dt=0.000000, rms=0.554 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.554, neg=0, invalid=96777 0691: dt=23.120000, rms=0.554 (0.016%), neg=0, invalid=96777 0692: dt=32.368000, rms=0.554 (0.013%), neg=0, invalid=96777 0693: dt=32.368000, rms=0.554 (0.023%), neg=0, invalid=96777 0694: dt=32.368000, rms=0.554 (0.037%), neg=0, invalid=96777 0695: dt=32.368000, rms=0.554 (0.041%), neg=0, invalid=96777 0696: dt=32.368000, rms=0.553 (0.046%), neg=0, invalid=96777 0697: dt=32.368000, rms=0.553 (0.049%), neg=0, invalid=96777 0698: dt=32.368000, rms=0.553 (0.049%), neg=0, invalid=96777 0699: dt=32.368000, rms=0.553 (0.046%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.553, neg=0, invalid=96777 0700: dt=20.736000, rms=0.552 (0.121%), neg=0, invalid=96777 0701: dt=36.288000, rms=0.551 (0.164%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0702: dt=36.288000, rms=0.550 (0.172%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=1, neg = 0 0703: dt=82.944000, rms=0.549 (0.183%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 15 iterations, nbhd size=2, neg = 0 0704: dt=36.288000, rms=0.548 (0.116%), neg=0, invalid=96777 0705: dt=36.288000, rms=0.548 (0.133%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 32 iterations, nbhd size=4, neg = 0 0706: dt=36.288000, rms=0.547 (0.143%), neg=0, invalid=96777 iter 0, gcam->neg = 20 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.002000: new neg 0, old_neg 2, delta 2, rms=0.003 (29.258%) 0707: dt=36.288000, rms=0.546 (0.091%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 0 iterations, nbhd size=0, neg = 0 0708: dt=36.288000, rms=0.546 (0.041%), neg=0, invalid=96777 0709: dt=31.104000, rms=0.546 (0.060%), neg=0, invalid=96777 0710: dt=31.104000, rms=0.546 (0.035%), neg=0, invalid=96777 0711: dt=31.104000, rms=0.545 (0.066%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.005, neg=3, removing folds in lattice.... iter 1, dt=0.000875: new neg 0, old_neg 3, delta 3, rms=0.004 (28.753%) 0712: dt=31.104000, rms=0.545 (0.072%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0713: dt=31.104000, rms=0.545 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0714: dt=31.104000, rms=0.545 (0.050%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=4, neg = 6 starting rms=0.007, neg=6, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 6, delta 5, rms=0.005 (29.200%) iter 2, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.005 (7.415%) 0715: dt=31.104000, rms=0.544 (0.079%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.005 (31.888%) iter 2, dt=0.001966: new neg 0, old_neg 1, delta 1, rms=0.005 (5.538%) 0716: dt=31.104000, rms=0.544 (0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.544, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 3, old_neg 7, delta 4, rms=0.003 (51.567%) iter 2, dt=0.001311: new neg 0, old_neg 3, delta 3, rms=0.003 (14.467%) 0717: dt=103.680000, rms=0.536 (1.411%), neg=0, invalid=96777 0718: dt=20.736000, rms=0.535 (0.251%), neg=0, invalid=96777 0719: dt=36.288000, rms=0.534 (0.112%), neg=0, invalid=96777 0720: dt=36.288000, rms=0.534 (0.127%), neg=0, invalid=96777 0721: dt=36.288000, rms=0.533 (0.191%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=4, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 7, delta 3, rms=0.003 (50.372%) iter 2, dt=0.000573: new neg 0, old_neg 4, delta 4, rms=0.003 (21.327%) 0722: dt=36.288000, rms=0.532 (0.232%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0723: dt=36.288000, rms=0.531 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 8 starting rms=0.007, neg=8, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 8, delta 4, rms=0.004 (50.142%) iter 2, dt=0.000573: new neg 0, old_neg 4, delta 4, rms=0.003 (22.446%) 0724: dt=36.288000, rms=0.530 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0725: dt=36.288000, rms=0.530 (0.033%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=1, neg = 9 starting rms=0.007, neg=9, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 9, delta 5, rms=0.004 (49.197%) iter 2, dt=0.000573: new neg 1, old_neg 4, delta 3, rms=0.003 (22.859%) iter 3, dt=0.001311: new neg 0, old_neg 1, delta 1, rms=0.003 (5.550%) 0726: dt=36.288000, rms=0.530 (0.078%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 10 starting rms=0.008, neg=10, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 10, delta 6, rms=0.004 (49.267%) iter 2, dt=0.000573: new neg 2, old_neg 4, delta 2, rms=0.003 (23.454%) iter 3, dt=0.001311: new neg 0, old_neg 2, delta 2, rms=0.003 (5.468%) 0727: dt=36.288000, rms=0.529 (0.058%), neg=0, invalid=96777 iter 0, gcam->neg = 25 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.008, neg=10, removing folds in lattice.... iter 1, dt=0.000875: new neg 7, old_neg 10, delta 3, rms=0.005 (42.871%) iter 2, dt=0.000573: new neg 2, old_neg 7, delta 5, rms=0.003 (26.308%) iter 3, dt=0.000573: new neg 0, old_neg 2, delta 2, rms=0.003 (5.670%) 0728: dt=331.776000, rms=0.529 (0.139%), neg=0, invalid=96777 0729: dt=31.104000, rms=0.528 (0.203%), neg=0, invalid=96777 0730: dt=6.480000, rms=0.528 (0.006%), neg=0, invalid=96777 0731: dt=6.480000, rms=0.528 (0.000%), neg=0, invalid=96777 0732: dt=6.480000, rms=0.528 (-0.014%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.529, neg=0, invalid=96777 iter 0, gcam->neg = 77 after 200 iterations, nbhd size=1, neg = 8 starting rms=0.010, neg=8, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 8, delta 4, rms=0.007 (28.896%) iter 2, dt=0.000983: new neg 1, old_neg 4, delta 3, rms=0.006 (10.622%) iter 3, dt=0.001966: new neg 1, old_neg 1, delta 0, rms=0.006 (4.602%) iter 4, dt=0.001638: new neg 0, old_neg 1, delta 1, rms=0.006 (5.543%) 0733: dt=25.600000, rms=0.526 (0.638%), neg=0, invalid=96777 iter 0, gcam->neg = 90 after 200 iterations, nbhd size=2, neg = 9 starting rms=0.009, neg=9, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 9, delta 5, rms=0.006 (32.947%) iter 2, dt=0.000573: new neg 1, old_neg 4, delta 3, rms=0.005 (10.319%) iter 3, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.005 (5.939%) 0734: dt=32.000000, rms=0.521 (0.960%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 31 iterations, nbhd size=3, neg = 0 0735: dt=7.023622, rms=0.520 (0.267%), neg=0, invalid=96777 iter 0, gcam->neg = 24 after 200 iterations, nbhd size=3, neg = 7 starting rms=0.010, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 7, delta 3, rms=0.007 (23.811%) iter 2, dt=0.000983: new neg 1, old_neg 4, delta 3, rms=0.007 (5.899%) iter 3, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.007 (3.927%) iter 4, dt=0.001638: new neg 0, old_neg 1, delta 1, rms=0.007 (2.649%) 0736: dt=32.000000, rms=0.518 (0.312%), neg=0, invalid=96777 iter 0, gcam->neg = 31 after 200 iterations, nbhd size=4, neg = 7 starting rms=0.009, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 7, delta 3, rms=0.006 (28.346%) iter 2, dt=0.000573: new neg 0, old_neg 4, delta 4, rms=0.006 (7.254%) 0737: dt=19.200000, rms=0.515 (0.519%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 7 starting rms=0.009, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 7, delta 3, rms=0.007 (26.619%) iter 2, dt=0.000573: new neg 0, old_neg 4, delta 4, rms=0.006 (5.978%) 0738: dt=9.600000, rms=0.515 (0.150%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=1, neg = 8 starting rms=0.009, neg=8, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 8, delta 4, rms=0.007 (25.645%) iter 2, dt=0.000573: new neg 0, old_neg 4, delta 4, rms=0.006 (5.454%) 0739: dt=9.600000, rms=0.514 (0.165%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.009, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 4, old_neg 7, delta 3, rms=0.007 (24.878%) iter 2, dt=0.000573: new neg 0, old_neg 4, delta 4, rms=0.007 (4.953%) 0740: dt=9.600000, rms=0.513 (0.128%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.009, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 3, old_neg 7, delta 4, rms=0.007 (24.395%) iter 2, dt=0.000573: new neg 0, old_neg 3, delta 3, rms=0.007 (4.691%) 0741: dt=9.600000, rms=0.512 (0.122%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.009, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 3, old_neg 7, delta 4, rms=0.007 (24.068%) iter 2, dt=0.000573: new neg 0, old_neg 3, delta 3, rms=0.007 (4.476%) 0742: dt=9.600000, rms=0.512 (0.119%), neg=0, invalid=96777 iter 0, gcam->neg = 374 after 200 iterations, nbhd size=2, neg = 5 starting rms=0.013, neg=5, removing folds in lattice.... iter 1, dt=0.001500: new neg 2, old_neg 5, delta 3, rms=0.012 (13.682%) iter 2, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.011 (4.907%) iter 3, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.010 (4.798%) 0743: dt=179.200000, rms=0.506 (1.209%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=4, neg = 5 starting rms=0.010, neg=5, removing folds in lattice.... iter 1, dt=0.000875: new neg 2, old_neg 5, delta 3, rms=0.009 (13.570%) iter 2, dt=0.000573: new neg 0, old_neg 2, delta 2, rms=0.009 (1.598%) 0744: dt=8.000000, rms=0.505 (0.092%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.010, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.008 (16.114%) iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.008 (1.245%) 0745: dt=8.000000, rms=0.505 (0.099%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.010, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 2, old_neg 7, delta 5, rms=0.008 (16.732%) iter 2, dt=0.000573: new neg 0, old_neg 2, delta 2, rms=0.008 (1.300%) 0746: dt=8.000000, rms=0.504 (0.050%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.010, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 2, old_neg 7, delta 5, rms=0.008 (16.883%) iter 2, dt=0.000573: new neg 0, old_neg 2, delta 2, rms=0.008 (1.578%) 0747: dt=8.000000, rms=0.504 (0.056%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.010, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 2, old_neg 7, delta 5, rms=0.008 (17.027%) iter 2, dt=0.000573: new neg 0, old_neg 2, delta 2, rms=0.008 (1.829%) 0748: dt=8.000000, rms=0.504 (0.032%), neg=0, invalid=96777 iter 0, gcam->neg = 38 after 200 iterations, nbhd size=3, neg = 7 starting rms=0.010, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 2, old_neg 7, delta 5, rms=0.008 (17.592%) iter 2, dt=0.000983: new neg 0, old_neg 2, delta 2, rms=0.008 (2.979%) 0749: dt=44.800000, rms=0.503 (0.144%), neg=0, invalid=96777 0750: dt=4.800000, rms=0.503 (0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.503, neg=0, invalid=96777 iter 0, gcam->neg = 8 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 2, old_neg 7, delta 5, rms=0.005 (35.141%) iter 2, dt=0.000573: new neg 0, old_neg 2, delta 2, rms=0.004 (5.520%) 0751: dt=32.000000, rms=0.498 (0.966%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 2, old_neg 7, delta 5, rms=0.004 (36.287%) iter 2, dt=0.000573: new neg 0, old_neg 2, delta 2, rms=0.004 (5.584%) 0752: dt=9.010989, rms=0.497 (0.325%), neg=0, invalid=96777 iter 0, gcam->neg = 39 after 200 iterations, nbhd size=3, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.004 (37.749%) iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.004 (4.465%) 0753: dt=44.800000, rms=0.494 (0.459%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.004 (39.350%) iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.004 (5.640%) 0754: dt=11.200000, rms=0.494 (0.155%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.004 (39.895%) iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.004 (5.703%) 0755: dt=11.200000, rms=0.493 (0.057%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.004 (40.131%) iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.004 (6.301%) 0756: dt=11.200000, rms=0.493 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.004 (40.260%) iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.004 (6.285%) 0757: dt=11.200000, rms=0.493 (0.066%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.004 (40.754%) iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.004 (6.578%) 0758: dt=11.200000, rms=0.492 (0.073%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 7 starting rms=0.007, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.004 (41.041%) iter 2, dt=0.000983: new neg 0, old_neg 1, delta 1, rms=0.004 (6.713%) 0759: dt=11.200000, rms=0.492 (0.051%), neg=0, invalid=96777 iter 0, gcam->neg = 98 after 200 iterations, nbhd size=2, neg = 7 starting rms=0.008, neg=7, removing folds in lattice.... iter 1, dt=0.000875: new neg 1, old_neg 7, delta 6, rms=0.005 (39.283%) iter 2, dt=0.001311: new neg 0, old_neg 1, delta 1, rms=0.004 (7.228%) 0760: dt=128.000000, rms=0.490 (0.491%), neg=0, invalid=96777 0761: dt=2.800000, rms=0.490 (0.008%), neg=0, invalid=96777 0762: dt=2.800000, rms=0.489 (0.018%), neg=0, invalid=96777 0763: dt=2.800000, rms=0.489 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0764: dt=2.800000, rms=0.489 (0.005%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0765: dt=44.800000, rms=0.489 (0.125%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0766: dt=2.800000, rms=0.489 (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=0.501, neg=0, invalid=96777 0767: dt=1.008000, rms=0.501 (0.035%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 19 iterations, nbhd size=2, neg = 0 0768: dt=2.500000, rms=0.501 (0.021%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=4, neg = 6 starting rms=0.006, neg=6, removing folds in lattice.... iter 1, dt=0.000750: new neg 1, old_neg 6, delta 5, rms=0.003 (48.938%) iter 2, dt=0.001966: new neg 0, old_neg 1, delta 1, rms=0.003 (4.728%) 0769: dt=2.500000, rms=0.501 (-0.020%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.501, neg=0, invalid=96777 iter 0, gcam->neg = 14 after 200 iterations, nbhd size=1, neg = 6 starting rms=0.006, neg=6, removing folds in lattice.... iter 1, dt=0.000750: new neg 1, old_neg 6, delta 5, rms=0.003 (54.269%) iter 2, dt=0.001966: new neg 0, old_neg 1, delta 1, rms=0.003 (5.792%) 0770: dt=2.880000, rms=0.500 (0.047%), neg=0, invalid=96777 iter 0, gcam->neg = 24 after 200 iterations, nbhd size=3, neg = 6 starting rms=0.006, neg=6, removing folds in lattice.... iter 1, dt=0.000750: new neg 1, old_neg 6, delta 5, rms=0.003 (56.579%) iter 2, dt=0.002294: new neg 0, old_neg 1, delta 1, rms=0.002 (5.365%) 0771: dt=2.880000, rms=0.500 (0.050%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 200 iterations, nbhd size=3, neg = 6 starting rms=0.006, neg=6, removing folds in lattice.... iter 1, dt=0.000750: new neg 0, old_neg 6, delta 6, rms=0.002 (58.832%) 0772: dt=3.456000, rms=0.500 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 32 after 200 iterations, nbhd size=2, neg = 4 starting rms=0.005, neg=4, removing folds in lattice.... iter 1, dt=0.000875: new neg 0, old_neg 4, delta 4, rms=0.002 (58.029%) 0773: dt=3.456000, rms=0.500 (0.048%), neg=0, invalid=96777 iter 0, gcam->neg = 34 after 200 iterations, nbhd size=2, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000750: new neg 0, old_neg 5, delta 5, rms=0.002 (61.057%) 0774: dt=3.456000, rms=0.500 (0.029%), neg=0, invalid=96777 iter 0, gcam->neg = 34 after 200 iterations, nbhd size=1, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000875: new neg 0, old_neg 5, delta 5, rms=0.002 (60.660%) 0775: dt=3.456000, rms=0.499 (0.064%), neg=0, invalid=96777 iter 0, gcam->neg = 43 after 200 iterations, nbhd size=2, neg = 5 starting rms=0.005, neg=5, removing folds in lattice.... iter 1, dt=0.000875: new neg 0, old_neg 5, delta 5, rms=0.002 (61.187%) 0776: dt=3.456000, rms=0.499 (0.048%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=96777 0777: dt=0.000000, rms=0.514 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=96777 0778: dt=0.000000, rms=0.514 (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=0.489, neg=0, invalid=96777 iter 0, gcam->neg = 1043 after 21 iterations, nbhd size=1, neg = 0 0779: dt=1.725658, rms=0.446 (8.688%), neg=0, invalid=96777 0780: dt=0.000250, rms=0.446 (0.003%), neg=0, invalid=96777 0781: dt=0.000250, rms=0.446 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.446, neg=0, invalid=96777 0782: dt=0.000438, rms=0.446 (0.000%), neg=0, invalid=96777 0783: dt=0.000000, rms=0.446 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 66 after 7 iterations, nbhd size=1, neg = 0 0784: dt=0.050000, rms=0.446 (-0.258%), 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=0.433, neg=0, invalid=96777 0785: dt=0.000000, rms=0.434 (-0.313%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=96777 0786: dt=0.000000, rms=0.434 (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=0.434, neg=0, invalid=96777 0787: dt=0.000000, rms=0.434 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=96777 0788: dt=20.736000, rms=0.434 (0.019%), neg=0, invalid=96777 0789: dt=31.104000, rms=0.434 (0.014%), neg=0, invalid=96777 0790: dt=31.104000, rms=0.434 (0.016%), neg=0, invalid=96777 0791: dt=31.104000, rms=0.434 (0.013%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0792: dt=31.104000, rms=0.434 (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=0.434, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0793: dt=9.600000, rms=0.434 (0.100%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0794: dt=6.400000, rms=0.434 (0.030%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 22 iterations, nbhd size=3, neg = 0 0795: dt=6.400000, rms=0.434 (0.039%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0796: dt=6.400000, 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 iter 0, gcam->neg = 54 after 37 iterations, nbhd size=3, neg = 0 0797: dt=32.000000, rms=0.431 (0.671%), neg=0, invalid=96777 0798: dt=2.800000, rms=0.431 (0.050%), neg=0, invalid=96777 0799: dt=2.800000, rms=0.430 (0.064%), neg=0, invalid=96777 0800: dt=2.800000, rms=0.430 (0.104%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0801: dt=2.800000, rms=0.429 (0.119%), neg=0, invalid=96777 0802: dt=2.800000, rms=0.429 (0.114%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 17 iterations, nbhd size=2, neg = 0 0803: dt=2.800000, rms=0.428 (0.114%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 14 iterations, nbhd size=2, neg = 0 0804: dt=11.200000, rms=0.428 (0.067%), 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 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0805: dt=1.008000, rms=0.431 (0.031%), neg=0, invalid=96777 iter 0, gcam->neg = 44 after 17 iterations, nbhd size=2, neg = 0 0806: dt=4.032000, rms=0.430 (0.248%), neg=0, invalid=96777 0807: dt=0.011250, rms=0.430 (0.000%), neg=0, invalid=96777 0808: dt=0.011250, rms=0.430 (0.000%), neg=0, invalid=96777 0809: dt=0.011250, rms=0.430 (0.000%), neg=0, invalid=96777 0810: dt=0.011250, rms=0.430 (0.001%), neg=0, invalid=96777 0811: dt=0.011250, rms=0.430 (0.001%), neg=0, invalid=96777 0812: dt=0.011250, rms=0.430 (0.001%), neg=0, invalid=96777 0813: dt=0.011250, rms=0.430 (0.002%), neg=0, invalid=96777 0814: dt=0.011250, rms=0.430 (0.002%), neg=0, invalid=96777 0815: dt=0.011250, rms=0.430 (0.002%), neg=0, invalid=96777 0816: dt=0.011250, rms=0.430 (0.003%), neg=0, invalid=96777 0817: dt=0.011250, rms=0.430 (0.003%), neg=0, invalid=96777 0818: dt=0.011250, rms=0.430 (0.003%), neg=0, invalid=96777 0819: dt=0.011250, rms=0.430 (0.003%), neg=0, invalid=96777 0820: dt=0.011250, rms=0.429 (0.004%), neg=0, invalid=96777 0821: dt=0.011250, rms=0.429 (0.004%), neg=0, invalid=96777 0822: dt=0.011250, rms=0.429 (0.004%), neg=0, invalid=96777 0823: dt=0.011250, rms=0.429 (0.004%), neg=0, invalid=96777 0824: dt=0.011250, rms=0.429 (0.004%), neg=0, invalid=96777 0825: dt=0.011250, rms=0.429 (0.004%), neg=0, invalid=96777 0826: dt=0.011250, rms=0.429 (0.004%), neg=0, invalid=96777 0827: dt=0.011250, rms=0.429 (0.004%), neg=0, invalid=96777 0828: dt=0.011250, rms=0.429 (0.005%), neg=0, invalid=96777 0829: dt=0.011250, rms=0.429 (0.005%), neg=0, invalid=96777 0830: dt=0.011250, rms=0.429 (0.005%), neg=0, invalid=96777 0831: dt=0.011250, rms=0.429 (0.005%), neg=0, invalid=96777 0832: dt=0.011250, rms=0.429 (0.005%), neg=0, invalid=96777 0833: dt=0.011250, rms=0.429 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.429, neg=0, invalid=96777 iter 0, gcam->neg = 217 after 41 iterations, nbhd size=3, neg = 0 0834: dt=13.134328, rms=0.425 (0.898%), neg=0, invalid=96777 0835: dt=0.015750, rms=0.425 (0.001%), neg=0, invalid=96777 0836: dt=0.015750, rms=0.425 (0.001%), neg=0, invalid=96777 0837: dt=0.015750, rms=0.425 (0.001%), neg=0, invalid=96777 0838: dt=0.015750, rms=0.425 (0.001%), neg=0, invalid=96777 0839: dt=0.015750, rms=0.425 (0.001%), neg=0, invalid=96777 0840: dt=0.015750, rms=0.425 (0.001%), neg=0, invalid=96777 0841: dt=0.015750, rms=0.425 (0.002%), neg=0, invalid=96777 0842: dt=0.015750, rms=0.425 (0.002%), neg=0, invalid=96777 0843: dt=0.015750, rms=0.425 (0.003%), neg=0, invalid=96777 0844: dt=0.015750, rms=0.425 (0.003%), neg=0, invalid=96777 0845: dt=0.015750, rms=0.425 (0.003%), neg=0, invalid=96777 0846: dt=0.015750, rms=0.425 (0.004%), neg=0, invalid=96777 0847: dt=0.015750, rms=0.425 (0.004%), neg=0, invalid=96777 0848: dt=0.015750, rms=0.425 (0.004%), neg=0, invalid=96777 0849: dt=0.015750, rms=0.425 (0.004%), neg=0, invalid=96777 0850: dt=0.015750, rms=0.425 (0.005%), neg=0, invalid=96777 0851: dt=0.015750, rms=0.425 (0.005%), neg=0, invalid=96777 0852: dt=0.015750, rms=0.425 (0.005%), neg=0, invalid=96777 0853: dt=0.015750, rms=0.425 (0.005%), neg=0, invalid=96777 0854: dt=0.015750, rms=0.425 (0.005%), neg=0, invalid=96777 0855: dt=0.015750, rms=0.425 (0.005%), neg=0, invalid=96777 0856: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 0857: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 0858: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 0859: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 0860: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 0861: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 0862: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 0863: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 0864: dt=0.015750, rms=0.425 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 163 after 46 iterations, nbhd size=3, neg = 0 0865: dt=12.208333, rms=0.424 (0.276%), neg=0, invalid=96777 0866: dt=0.003938, rms=0.424 (0.000%), neg=0, invalid=96777 0867: dt=0.003938, rms=0.424 (0.000%), neg=0, invalid=96777 0868: dt=0.003938, rms=0.424 (0.000%), neg=0, invalid=96777 0869: dt=0.003938, rms=0.424 (-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=0.430, neg=0, invalid=96777 0870: dt=0.000000, rms=0.430 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=96777 0871: dt=0.000000, rms=0.430 (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=0.419, neg=0, invalid=96777 iter 0, gcam->neg = 362 after 34 iterations, nbhd size=3, neg = 0 0872: dt=0.533217, rms=0.410 (2.264%), neg=0, invalid=96777 0873: dt=0.000020, rms=0.410 (0.002%), neg=0, invalid=96777 0874: dt=0.000020, rms=0.410 (0.000%), neg=0, invalid=96777 0875: dt=0.000020, rms=0.410 (0.000%), neg=0, invalid=96777 0876: dt=0.000020, rms=0.410 (0.000%), neg=0, invalid=96777 0877: dt=0.000020, rms=0.410 (0.000%), neg=0, invalid=96777 0878: dt=0.000250, rms=0.410 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0879: dt=0.020017, rms=0.410 (0.033%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0880: dt=0.000250, rms=0.410 (0.001%), neg=0, invalid=96777 0881: dt=0.000250, rms=0.410 (0.001%), neg=0, invalid=96777 0882: dt=0.000250, rms=0.410 (0.001%), neg=0, invalid=96777 0883: dt=0.000250, rms=0.410 (0.002%), neg=0, invalid=96777 0884: dt=0.000250, rms=0.410 (0.002%), neg=0, invalid=96777 0885: dt=0.000250, rms=0.410 (0.002%), neg=0, invalid=96777 0886: dt=0.000250, rms=0.410 (0.003%), neg=0, invalid=96777 0887: dt=0.000250, rms=0.410 (0.003%), neg=0, invalid=96777 0888: dt=0.000250, rms=0.410 (0.003%), neg=0, invalid=96777 0889: dt=0.000250, rms=0.410 (0.004%), neg=0, invalid=96777 0890: dt=0.000250, rms=0.410 (0.004%), neg=0, invalid=96777 0891: dt=0.000250, rms=0.410 (0.004%), neg=0, invalid=96777 0892: dt=0.000250, rms=0.409 (0.004%), neg=0, invalid=96777 0893: dt=0.000250, rms=0.409 (0.004%), neg=0, invalid=96777 0894: dt=0.000250, rms=0.409 (0.004%), neg=0, invalid=96777 0895: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0896: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0897: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0898: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0899: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0900: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0901: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0902: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0903: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0904: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0905: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0906: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0907: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0908: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0909: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0910: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0911: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 0912: dt=0.000250, rms=0.409 (0.005%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 18 hours, 51 minutes and 3 seconds. #-------------------------------------- #@# CA Reg Inv Fri Dec 6 19:56:32 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 Dec 6 19:58:53 CST 2013 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /soft/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 '/soft/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... 11393969 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 2 minutes and 27 seconds. #-------------------------------------- #@# SkullLTA Fri Dec 6 20:01:20 CST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /soft/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/soft/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 = (49, 44, 27) --> (206, 200, 215) using (101, 96, 121) as brain centroid... mean wm in atlas = 126, using box (82,77,98) --> (120, 115,144) to find MRI wm before smoothing, mri peak at 103 after smoothing, mri peak at 103, scaling input intensities by 1.223 scaling channel 0 by 1.2233 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.021 0.030 0.030 -11.728; -0.025 1.295 -0.030 -25.327; -0.039 -0.011 1.254 -32.307; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.021 0.030 0.030 -11.728; -0.025 1.295 -0.030 -25.327; -0.039 -0.011 1.254 -32.307; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.059 0.025 0.032 -16.169; -0.027 1.244 -0.107 -10.196; -0.038 0.070 1.180 -35.193; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.059 0.025 0.032 -16.169; -0.027 1.244 -0.107 -10.196; -0.038 0.070 1.180 -35.193; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.057 -0.017 0.014 -9.491; 0.006 1.249 -0.059 -21.208; -0.020 0.019 1.187 -33.844; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.055 -0.017 0.014 -9.174; 0.006 1.249 -0.059 -21.208; -0.020 0.019 1.192 -33.867; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.055 -0.017 0.014 -9.174; 0.006 1.249 -0.059 -21.208; -0.020 0.019 1.192 -33.867; 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 1.05497 -0.01650 0.01436 -9.17367; 0.00603 1.24931 -0.05854 -21.20787; -0.01999 0.01932 1.19166 -33.86700; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.05497 -0.01650 0.01436 -9.17367; 0.00603 1.24931 -0.05854 -21.20787; -0.01999 0.01932 1.19166 -33.86700; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.055 -0.017 0.014 -9.174; 0.006 1.249 -0.059 -21.208; -0.020 0.019 1.192 -33.867; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.2) transform before final EM align: 1.055 -0.017 0.014 -9.174; 0.006 1.249 -0.059 -21.208; -0.020 0.019 1.192 -33.867; 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 1.05497 -0.01650 0.01436 -9.17367; 0.00603 1.24931 -0.05854 -21.20787; -0.01999 0.01932 1.19166 -33.86700; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.05497 -0.01650 0.01436 -9.17367; 0.00603 1.24931 -0.05854 -21.20787; -0.01999 0.01932 1.19166 -33.86700; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 4.5 after pass:transform: ( 1.05, -0.02, 0.01, -9.17) ( 0.01, 1.25, -0.06, -21.21) ( -0.02, 0.02, 1.19, -33.87) 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 TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.5 tol 0.000000 final transform: 1.055 -0.017 0.014 -9.174; 0.006 1.249 -0.059 -21.208; -0.020 0.019 1.192 -33.867; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 94 minutes and 46 seconds. #-------------------------------------- #@# SubCort Seg Fri Dec 6 21:36:06 CST 2013 mri_ca_label -align norm.mgz transforms/talairach.m3z /soft/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname node1109 machine x86_64 setenv SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post cd /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /soft/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 /soft/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 /soft/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 = 0.12982 (11) Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (2803 voxels, overlap=0.007) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2803 voxels, peak = 9), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.14600 (12) Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (694 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.41 x + 0.0 (694 voxels, peak = 8), gca=8.1 gca peak = 0.28003 (97) mri peak = 0.08411 (95) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (320 voxels, overlap=0.998) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (320 voxels, peak = 91), gca=90.7 gca peak = 0.18160 (96) mri peak = 0.08019 (92) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (211 voxels, overlap=0.944) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (211 voxels, peak = 91), gca=90.7 gca peak = 0.27536 (62) mri peak = 0.11150 (68) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (298 voxels, overlap=0.998) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (298 voxels, peak = 64), gca=63.5 gca peak = 0.32745 (63) mri peak = 0.11043 (67) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (735 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (735 voxels, peak = 66), gca=66.5 gca peak = 0.08597 (105) mri peak = 0.05842 (109) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (16766 voxels, overlap=0.855) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (16766 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.05137 (109) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (16733 voxels, overlap=0.820) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (16733 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04378 (71) Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (26352 voxels, overlap=0.477) Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (26352 voxels, peak = 73), gca=73.4 gca peak = 0.08598 (64) mri peak = 0.04656 (73) Right_Cerebral_Cortex (42): linear fit = 1.11 x + 0.0 (30150 voxels, overlap=0.734) Right_Cerebral_Cortex (42): linear fit = 1.11 x + 0.0 (30150 voxels, peak = 71), gca=70.7 gca peak = 0.24164 (71) mri peak = 0.10327 (81) Right_Caudate (50): linear fit = 1.14 x + 0.0 (394 voxels, overlap=0.450) Right_Caudate (50): linear fit = 1.14 x + 0.0 (394 voxels, peak = 81), gca=81.3 gca peak = 0.18227 (75) mri peak = 0.12730 (82) Left_Caudate (11): linear fit = 1.02 x + 0.0 (512 voxels, overlap=0.990) Left_Caudate (11): linear fit = 1.02 x + 0.0 (512 voxels, peak = 77), gca=76.9 gca peak = 0.10629 (62) mri peak = 0.05688 (69) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (25050 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (25050 voxels, peak = 70), gca=70.4 gca peak = 0.11668 (59) mri peak = 0.06285 (66) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (28282 voxels, overlap=0.658) Right_Cerebellum_Cortex (47): linear fit = 1.12 x + 0.0 (28282 voxels, peak = 66), gca=65.8 gca peak = 0.17849 (88) mri peak = 0.09644 (99) Left_Cerebellum_White_Matter (7): linear fit = 1.13 x + 0.0 (3708 voxels, overlap=0.003) Left_Cerebellum_White_Matter (7): linear fit = 1.13 x + 0.0 (3708 voxels, peak = 100), gca=99.9 gca peak = 0.16819 (86) mri peak = 0.08086 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (4412 voxels, overlap=0.425) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (4412 voxels, peak = 94), gca=94.2 gca peak = 0.41688 (64) mri peak = 0.11743 (69) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (262 voxels, overlap=0.651) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (262 voxels, peak = 71), gca=70.7 gca peak = 0.42394 (62) mri peak = 0.13876 (69) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (209 voxels, overlap=0.602) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (209 voxels, peak = 69), gca=68.5 gca peak = 0.10041 (96) mri peak = 0.05405 (103) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (3099 voxels, overlap=0.541) Left_Thalamus_Proper (10): linear fit = 1.13 x + 0.0 (3099 voxels, peak = 109), gca=109.0 gca peak = 0.13978 (88) mri peak = 0.06148 (101) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (2590 voxels, overlap=0.587) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (2590 voxels, peak = 95), gca=95.5 gca peak = 0.08514 (81) mri peak = 0.07063 (93) Left_Putamen (12): linear fit = 1.09 x + 0.0 (885 voxels, overlap=0.669) Left_Putamen (12): linear fit = 1.09 x + 0.0 (885 voxels, peak = 88), gca=87.9 gca peak = 0.09624 (82) mri peak = 0.05834 (80) Right_Putamen (51): linear fit = 1.04 x + 0.0 (977 voxels, overlap=0.856) Right_Putamen (51): linear fit = 1.04 x + 0.0 (977 voxels, peak = 86), gca=85.7 gca peak = 0.07543 (88) mri peak = 0.05254 (99) Brain_Stem (16): linear fit = 1.12 x + 0.0 (8099 voxels, overlap=0.539) Brain_Stem (16): linear fit = 1.12 x + 0.0 (8099 voxels, peak = 99), gca=99.0 gca peak = 0.12757 (95) mri peak = 0.05585 (108) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (745 voxels, overlap=0.605) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (745 voxels, peak = 107), gca=106.9 gca peak = 0.17004 (92) mri peak = 0.05394 (106) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (673 voxels, overlap=0.834) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (673 voxels, peak = 104), gca=103.5 gca peak = 0.21361 (36) mri peak = 0.20792 (15) Third_Ventricle (14): linear fit = 0.37 x + 0.0 (100 voxels, overlap=0.056) Third_Ventricle (14): linear fit = 0.37 x + 0.0 (100 voxels, peak = 13), gca=13.1 gca peak = 0.26069 (23) mri peak = 0.14885 (11) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (260 voxels, overlap=0.027) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (260 voxels, peak = 10), gca=10.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.09 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31602 (11) mri peak = 0.12982 (11) Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (2803 voxels, overlap=0.942) Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (2803 voxels, peak = 10), gca=10.2 gca peak = 0.28786 ( 9) mri peak = 0.14600 (12) Right_Lateral_Ventricle (43): linear fit = 1.07 x + 0.0 (694 voxels, overlap=0.963) Right_Lateral_Ventricle (43): linear fit = 1.07 x + 0.0 (694 voxels, peak = 10), gca=9.6 gca peak = 0.29539 (91) mri peak = 0.08411 (95) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (320 voxels, overlap=1.012) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (320 voxels, peak = 94), gca=94.2 gca peak = 0.18335 (91) mri peak = 0.08019 (92) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (211 voxels, overlap=0.996) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (211 voxels, peak = 90), gca=89.6 gca peak = 0.25087 (64) mri peak = 0.11150 (68) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (298 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (298 voxels, peak = 65), gca=65.0 gca peak = 0.24992 (70) mri peak = 0.11043 (67) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (735 voxels, overlap=1.006) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (735 voxels, peak = 70), gca=70.0 gca peak = 0.08544 (107) mri peak = 0.05842 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (16766 voxels, overlap=0.874) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (16766 voxels, peak = 108), gca=107.5 gca peak = 0.08517 (108) mri peak = 0.05137 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (16733 voxels, overlap=0.892) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (16733 voxels, peak = 109), gca=108.5 gca peak = 0.06857 (73) mri peak = 0.04378 (71) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (26352 voxels, overlap=0.887) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (26352 voxels, peak = 72), gca=71.9 gca peak = 0.07934 (70) mri peak = 0.04656 (73) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (30150 voxels, overlap=0.934) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (30150 voxels, peak = 70), gca=70.0 gca peak = 0.21989 (84) mri peak = 0.10327 (81) Right_Caudate (50): linear fit = 1.00 x + 0.0 (394 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.00 x + 0.0 (394 voxels, peak = 84), gca=84.0 gca peak = 0.18158 (77) mri peak = 0.12730 (82) Left_Caudate (11): linear fit = 1.00 x + 0.0 (512 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (512 voxels, peak = 77), gca=77.0 gca peak = 0.09277 (69) mri peak = 0.05688 (69) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (25050 voxels, overlap=0.988) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (25050 voxels, peak = 69), gca=69.0 gca peak = 0.10775 (66) mri peak = 0.06285 (66) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (28282 voxels, overlap=0.989) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (28282 voxels, peak = 65), gca=65.0 gca peak = 0.16280 (99) mri peak = 0.09644 (99) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3708 voxels, overlap=0.959) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3708 voxels, peak = 99), gca=99.5 gca peak = 0.13939 (94) mri peak = 0.08086 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4412 voxels, overlap=0.993) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (4412 voxels, peak = 95), gca=95.4 gca peak = 0.32647 (70) mri peak = 0.11743 (69) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (262 voxels, overlap=1.018) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (262 voxels, peak = 72), gca=72.4 gca peak = 0.35000 (69) mri peak = 0.13876 (69) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (209 voxels, overlap=1.009) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (209 voxels, peak = 69), gca=69.0 gca peak = 0.10193 (107) mri peak = 0.05405 (103) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3099 voxels, overlap=1.000) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3099 voxels, peak = 106), gca=106.5 gca peak = 0.10892 (95) mri peak = 0.06148 (101) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2590 voxels, overlap=0.981) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (2590 voxels, peak = 96), gca=96.4 gca peak = 0.07892 (88) mri peak = 0.07063 (93) Left_Putamen (12): linear fit = 0.99 x + 0.0 (885 voxels, overlap=0.920) Left_Putamen (12): linear fit = 0.99 x + 0.0 (885 voxels, peak = 87), gca=86.7 gca peak = 0.09981 (79) mri peak = 0.05834 (80) Right_Putamen (51): linear fit = 1.00 x + 0.0 (977 voxels, overlap=0.953) Right_Putamen (51): linear fit = 1.00 x + 0.0 (977 voxels, peak = 79), gca=78.6 gca peak = 0.07064 (99) mri peak = 0.05254 (99) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8099 voxels, overlap=0.878) Brain_Stem (16): linear fit = 1.00 x + 0.0 (8099 voxels, peak = 99), gca=99.5 gca peak = 0.10581 (102) mri peak = 0.05585 (108) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (745 voxels, overlap=0.789) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (745 voxels, peak = 102), gca=102.0 gca peak = 0.14922 (104) mri peak = 0.05394 (106) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (673 voxels, overlap=0.840) Left_VentralDC (28): linear fit = 0.99 x + 0.0 (673 voxels, peak = 102), gca=102.4 gca peak = 0.34527 (15) mri peak = 0.20792 (15) Third_Ventricle (14): linear fit = 0.96 x + 0.0 (100 voxels, overlap=0.968) Third_Ventricle (14): linear fit = 0.96 x + 0.0 (100 voxels, peak = 14), gca=14.5 gca peak = 0.31292 ( 9) mri peak = 0.14885 (11) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (260 voxels, overlap=0.936) Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (260 voxels, peak = 10), gca=10.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.30831 (37) gca peak CSF = 0.29903 (16) gca peak Left_Accumbens_area = 0.46929 (72) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.21323 (33) gca peak Right_Accumbens_area = 0.36950 (82) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.17515 (83) gca peak non_WM_hypointensities = 0.12111 (54) gca peak Optic_Chiasm = 0.34836 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 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 23354 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 360 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 79655 changed. image ll: -2.184, PF=1.000 pass 2: 13109 changed. image ll: -2.181, PF=1.000 pass 3: 4360 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 48 minutes and 3 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/transforms/cc_up.lta MPS3007-1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/transforms/cc_up.lta reading aseg from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aseg.auto_noCCseg.mgz reading norm from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/norm.mgz 34406 voxels in left wm, 31261 in right wm, xrange [123, 134] searching rotation angles z=[-7 7], y=[-3 11] searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 global minimum found at slice 127.6, rotations (3.52, -0.39) final transformation (x=127.6, yr=3.516, zr=-0.390): 0.998 0.007 0.061 -7.992; -0.007 1.000 -0.000 14.923; -0.061 0.000 0.998 8.068; 0.000 0.000 0.000 1.000; updating x range to be [124, 132] in xformed coordinates best xformed slice 127 cc center is found at 127 141 149 eigenvectors: -0.003 0.006 1.000; 0.368 -0.930 0.007; 0.930 0.368 0.001; writing aseg with callosum to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 2.2 minutes #-------------------------------------- #@# Merge ASeg Fri Dec 6 22:29:04 CST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Dec 6 22:29:04 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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... 4087 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 91 gm peak at 72 (72), valley at 39 (39) csf peak at 37, setting threshold to 60 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 91 gm peak at 72 (72), valley at 38 (38) csf peak at 37, setting threshold to 60 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 10 minutes and 35 seconds. #-------------------------------------------- #@# Mask BFS Fri Dec 6 22:40:10 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1430412 voxels in mask (pct= 8.53) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Dec 6 22:41:20 CST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (101.0): 100.6 +- 8.2 [80.0 --> 125.0] GM (74.0) : 72.3 +- 9.5 [30.0 --> 96.0] setting bottom of white matter range to 81.8 setting top of gray matter range to 91.3 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... 17774 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5576 filled 58 bright non-wm voxels segmented. 8335 diagonally connected voxels added... white matter segmentation took 4.9 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 2.60 minutes reading wm segmentation from wm.seg.mgz... 2577 voxels added to wm to prevent paths from MTL structures to cortex 4477 additional wm voxels added 0 additional wm voxels added SEG EDIT: 62258 voxels turned on, 33723 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 103 new 103 115,126,128 old 103 new 103 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 62 found - 62 modified | TOTAL: 62 pass 2 (xy+): 0 found - 62 modified | TOTAL: 62 pass 1 (xy-): 89 found - 89 modified | TOTAL: 151 pass 2 (xy-): 0 found - 89 modified | TOTAL: 151 pass 1 (yz+): 95 found - 95 modified | TOTAL: 246 pass 2 (yz+): 0 found - 95 modified | TOTAL: 246 pass 1 (yz-): 119 found - 119 modified | TOTAL: 365 pass 2 (yz-): 0 found - 119 modified | TOTAL: 365 pass 1 (xz+): 81 found - 81 modified | TOTAL: 446 pass 2 (xz+): 0 found - 81 modified | TOTAL: 446 pass 1 (xz-): 64 found - 64 modified | TOTAL: 510 pass 2 (xz-): 0 found - 64 modified | TOTAL: 510 Iteration Number : 1 pass 1 (+++): 72 found - 72 modified | TOTAL: 72 pass 2 (+++): 0 found - 72 modified | TOTAL: 72 pass 1 (+++): 97 found - 97 modified | TOTAL: 169 pass 2 (+++): 0 found - 97 modified | TOTAL: 169 pass 1 (+++): 59 found - 59 modified | TOTAL: 228 pass 2 (+++): 0 found - 59 modified | TOTAL: 228 pass 1 (+++): 74 found - 74 modified | TOTAL: 302 pass 2 (+++): 0 found - 74 modified | TOTAL: 302 Iteration Number : 1 pass 1 (++): 290 found - 290 modified | TOTAL: 290 pass 2 (++): 0 found - 290 modified | TOTAL: 290 pass 1 (+-): 357 found - 357 modified | TOTAL: 647 pass 2 (+-): 1 found - 358 modified | TOTAL: 648 pass 3 (+-): 0 found - 358 modified | TOTAL: 648 pass 1 (--): 278 found - 278 modified | TOTAL: 926 pass 2 (--): 0 found - 278 modified | TOTAL: 926 pass 1 (-+): 357 found - 357 modified | TOTAL: 1283 pass 2 (-+): 0 found - 357 modified | TOTAL: 1283 Iteration Number : 2 pass 1 (xy+): 36 found - 36 modified | TOTAL: 36 pass 2 (xy+): 0 found - 36 modified | TOTAL: 36 pass 1 (xy-): 46 found - 46 modified | TOTAL: 82 pass 2 (xy-): 0 found - 46 modified | TOTAL: 82 pass 1 (yz+): 34 found - 34 modified | TOTAL: 116 pass 2 (yz+): 0 found - 34 modified | TOTAL: 116 pass 1 (yz-): 33 found - 33 modified | TOTAL: 149 pass 2 (yz-): 0 found - 33 modified | TOTAL: 149 pass 1 (xz+): 30 found - 30 modified | TOTAL: 179 pass 2 (xz+): 0 found - 30 modified | TOTAL: 179 pass 1 (xz-): 34 found - 34 modified | TOTAL: 213 pass 2 (xz-): 0 found - 34 modified | TOTAL: 213 Iteration Number : 2 pass 1 (+++): 11 found - 11 modified | TOTAL: 11 pass 2 (+++): 0 found - 11 modified | TOTAL: 11 pass 1 (+++): 14 found - 14 modified | TOTAL: 25 pass 2 (+++): 0 found - 14 modified | TOTAL: 25 pass 1 (+++): 10 found - 10 modified | TOTAL: 35 pass 2 (+++): 0 found - 10 modified | TOTAL: 35 pass 1 (+++): 11 found - 11 modified | TOTAL: 46 pass 2 (+++): 0 found - 11 modified | TOTAL: 46 Iteration Number : 2 pass 1 (++): 15 found - 15 modified | TOTAL: 15 pass 2 (++): 0 found - 15 modified | TOTAL: 15 pass 1 (+-): 15 found - 15 modified | TOTAL: 30 pass 2 (+-): 0 found - 15 modified | TOTAL: 30 pass 1 (--): 13 found - 13 modified | TOTAL: 43 pass 2 (--): 0 found - 13 modified | TOTAL: 43 pass 1 (-+): 20 found - 20 modified | TOTAL: 63 pass 2 (-+): 0 found - 20 modified | TOTAL: 63 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 7 found - 7 modified | TOTAL: 11 pass 2 (xy-): 0 found - 7 modified | TOTAL: 11 pass 1 (yz+): 2 found - 2 modified | TOTAL: 13 pass 2 (yz+): 0 found - 2 modified | TOTAL: 13 pass 1 (yz-): 3 found - 3 modified | TOTAL: 16 pass 2 (yz-): 0 found - 3 modified | TOTAL: 16 pass 1 (xz+): 5 found - 5 modified | TOTAL: 21 pass 2 (xz+): 0 found - 5 modified | TOTAL: 21 pass 1 (xz-): 4 found - 4 modified | TOTAL: 25 pass 2 (xz-): 0 found - 4 modified | TOTAL: 25 Iteration Number : 3 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 Iteration Number : 3 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 2 found - 2 modified | TOTAL: 7 pass 2 (+-): 0 found - 2 modified | TOTAL: 7 pass 1 (--): 6 found - 6 modified | TOTAL: 13 pass 2 (--): 0 found - 6 modified | TOTAL: 13 pass 1 (-+): 1 found - 1 modified | TOTAL: 14 pass 2 (-+): 0 found - 1 modified | TOTAL: 14 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 6 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 : 6 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 : 6 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 = 2463 (out of 389960: 0.631603) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Dec 6 22:51:18 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 1.021 0.030 0.030 -11.728; -0.019 1.195 -0.179 2.853; -0.034 0.128 1.002 -20.374; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.021 0.030 0.030 -11.728; -0.019 1.195 -0.179 2.853; -0.034 0.128 1.002 -20.374; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 112 (min = 350, max = 1400), aspect = 0.65 (min = 0.10, max = 0.75) need search nearby using seed (124, 106, 97), TAL = (4.0, -31.0, 22.0) talairach voxel to voxel transform 0.978 -0.021 -0.033 10.854; 0.020 0.820 0.146 0.874; 0.030 -0.106 0.978 20.583; 0.000 0.000 0.000 1.000; segmentation indicates cc at (124, 106, 97) --> (4.0, -31.0, 22.0) done. writing output to filled.mgz... filling took 2.0 minutes talairach cc position changed to (4.00, -31.00, 22.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -31.00, 22.00) SRC: (109.09, 104.14, 107.47) search lh wm seed point around talairach space (-14.00, -31.00, 22.00), SRC: (144.30, 104.86, 108.56) 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 Dec 6 22:55:15 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 3 found - 3 modified | TOTAL: 6 pass 2 (yz+): 0 found - 3 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 3 found - 3 modified | TOTAL: 12 pass 2 (xz-): 0 found - 3 modified | TOTAL: 12 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 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 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 22 (out of 188616: 0.011664) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 594 vertices, 675 faces slice 50: 5834 vertices, 6082 faces slice 60: 14264 vertices, 14658 faces slice 70: 24777 vertices, 25264 faces slice 80: 35915 vertices, 36563 faces slice 90: 48614 vertices, 49279 faces slice 100: 60392 vertices, 61122 faces slice 110: 72329 vertices, 73068 faces slice 120: 83955 vertices, 84785 faces slice 130: 93988 vertices, 94779 faces slice 140: 101159 vertices, 101861 faces slice 150: 106559 vertices, 107237 faces slice 160: 112275 vertices, 112990 faces slice 170: 118313 vertices, 119020 faces slice 180: 123701 vertices, 124385 faces slice 190: 127368 vertices, 127959 faces slice 200: 128200 vertices, 128714 faces slice 210: 128200 vertices, 128714 faces slice 220: 128200 vertices, 128714 faces slice 230: 128200 vertices, 128714 faces slice 240: 128200 vertices, 128714 faces slice 250: 128200 vertices, 128714 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... 128200 voxel in cpt #1: X=-514 [v=128200,e=386142,f=257428] located at (-29.315905, -22.171553, 21.028027) For the whole surface: X=-514 [v=128200,e=386142,f=257428] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Dec 6 23:12:19 CST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 Dec 6 23:12:30 CST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts avg radius = 45.6 mm, total surface area = 63542 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 28.2 minutes Not saving sulc step 000: RMS=0.136 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.094 (target=0.015) step 015: RMS=0.087 (target=0.015) step 020: RMS=0.084 (target=0.015) step 025: RMS=0.080 (target=0.015) step 030: RMS=0.078 (target=0.015) step 035: RMS=0.076 (target=0.015) step 040: RMS=0.075 (target=0.015) step 045: RMS=0.075 (target=0.015) step 050: RMS=0.073 (target=0.015) step 055: RMS=0.073 (target=0.015) step 060: RMS=0.073 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Dec 6 23:41:40 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.71 (0.00-->8.58) (max @ vno 58732 --> 59919) face area 0.02 +- 0.04 (-0.21-->0.90) scaling brain by 0.314... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.280, avgs=0 005/300: dt: 0.9000, rms radial error=177.025, avgs=0 010/300: dt: 0.9000, rms radial error=176.477, avgs=0 015/300: dt: 0.9000, rms radial error=175.758, avgs=0 020/300: dt: 0.9000, rms radial error=174.938, avgs=0 025/300: dt: 0.9000, rms radial error=174.061, avgs=0 030/300: dt: 0.9000, rms radial error=173.150, avgs=0 035/300: dt: 0.9000, rms radial error=172.223, avgs=0 040/300: dt: 0.9000, rms radial error=171.289, avgs=0 045/300: dt: 0.9000, rms radial error=170.350, avgs=0 050/300: dt: 0.9000, rms radial error=169.412, avgs=0 055/300: dt: 0.9000, rms radial error=168.475, avgs=0 060/300: dt: 0.9000, rms radial error=167.540, avgs=0 065/300: dt: 0.9000, rms radial error=166.609, avgs=0 070/300: dt: 0.9000, rms radial error=165.682, avgs=0 075/300: dt: 0.9000, rms radial error=164.758, avgs=0 080/300: dt: 0.9000, rms radial error=163.839, avgs=0 085/300: dt: 0.9000, rms radial error=162.925, avgs=0 090/300: dt: 0.9000, rms radial error=162.015, avgs=0 095/300: dt: 0.9000, rms radial error=161.109, avgs=0 100/300: dt: 0.9000, rms radial error=160.208, avgs=0 105/300: dt: 0.9000, rms radial error=159.311, avgs=0 110/300: dt: 0.9000, rms radial error=158.422, avgs=0 115/300: dt: 0.9000, rms radial error=157.539, avgs=0 120/300: dt: 0.9000, rms radial error=156.660, avgs=0 125/300: dt: 0.9000, rms radial error=155.780, avgs=0 130/300: dt: 0.9000, rms radial error=154.904, avgs=0 135/300: dt: 0.9000, rms radial error=154.033, avgs=0 140/300: dt: 0.9000, rms radial error=153.167, avgs=0 145/300: dt: 0.9000, rms radial error=152.305, avgs=0 150/300: dt: 0.9000, rms radial error=151.448, avgs=0 155/300: dt: 0.9000, rms radial error=150.595, avgs=0 160/300: dt: 0.9000, rms radial error=149.748, avgs=0 165/300: dt: 0.9000, rms radial error=148.904, avgs=0 170/300: dt: 0.9000, rms radial error=148.066, avgs=0 175/300: dt: 0.9000, rms radial error=147.232, avgs=0 180/300: dt: 0.9000, rms radial error=146.402, avgs=0 185/300: dt: 0.9000, rms radial error=145.577, avgs=0 190/300: dt: 0.9000, rms radial error=144.756, avgs=0 195/300: dt: 0.9000, rms radial error=143.939, avgs=0 200/300: dt: 0.9000, rms radial error=143.127, avgs=0 205/300: dt: 0.9000, rms radial error=142.320, avgs=0 210/300: dt: 0.9000, rms radial error=141.516, avgs=0 215/300: dt: 0.9000, rms radial error=140.717, avgs=0 220/300: dt: 0.9000, rms radial error=139.923, avgs=0 225/300: dt: 0.9000, rms radial error=139.133, avgs=0 230/300: dt: 0.9000, rms radial error=138.347, avgs=0 235/300: dt: 0.9000, rms radial error=137.566, avgs=0 240/300: dt: 0.9000, rms radial error=136.789, avgs=0 245/300: dt: 0.9000, rms radial error=136.016, avgs=0 250/300: dt: 0.9000, rms radial error=135.247, avgs=0 255/300: dt: 0.9000, rms radial error=134.483, avgs=0 260/300: dt: 0.9000, rms radial error=133.723, avgs=0 265/300: dt: 0.9000, rms radial error=132.968, avgs=0 270/300: dt: 0.9000, rms radial error=132.216, avgs=0 275/300: dt: 0.9000, rms radial error=131.469, avgs=0 280/300: dt: 0.9000, rms radial error=130.726, avgs=0 285/300: dt: 0.9000, rms radial error=129.986, avgs=0 290/300: dt: 0.9000, rms radial error=129.252, avgs=0 295/300: dt: 0.9000, rms radial error=128.521, avgs=0 300/300: dt: 0.9000, rms radial error=127.794, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15314.12 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 2819.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 423.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00289 epoch 4 (K=640.0), pass 1, starting sse = 66.21 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00544 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 1.77 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Sat Dec 7 01:29:42 CST 2013 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS3007-1 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=-514 (nv=128200, nf=257428, ne=386142, g=258) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 39503 ambiguous faces found in tessellation segmenting defects... 156 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 8 into 0 -merging segment 20 into 0 -merging segment 9 into 3 -merging segment 21 into 3 -merging segment 19 into 3 -merging segment 31 into 28 -merging segment 39 into 28 -merging segment 62 into 40 -merging segment 53 into 46 -merging segment 54 into 46 -merging segment 64 into 46 -merging segment 86 into 48 -merging segment 114 into 79 -merging segment 92 into 82 -merging segment 109 into 104 -merging segment 118 into 116 -merging segment 127 into 125 138 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2407 (-4.6203) -vertex loglikelihood: -6.5348 (-3.2674) -normal dot loglikelihood: -3.5506 (-3.5506) -quad curv loglikelihood: -6.0732 (-3.0366) Total Loglikelihood : -25.3993 CORRECTING DEFECT 0 (vertices=1215, convex hull=764) After retessellation of defect 0, euler #=-135 (105712,310629,204782) : difference with theory (-135) = 0 CORRECTING DEFECT 1 (vertices=47, convex hull=75) After retessellation of defect 1, euler #=-134 (105728,310708,204846) : difference with theory (-134) = 0 CORRECTING DEFECT 2 (vertices=734, convex hull=493) After retessellation of defect 2, euler #=-130 (105880,311426,205416) : difference with theory (-133) = -3 CORRECTING DEFECT 3 (vertices=36, convex hull=75) After retessellation of defect 3, euler #=-129 (105896,311502,205477) : difference with theory (-132) = -3 CORRECTING DEFECT 4 (vertices=67, convex hull=62) After retessellation of defect 4, euler #=-128 (105902,311549,205519) : difference with theory (-131) = -3 CORRECTING DEFECT 5 (vertices=194, convex hull=77) After retessellation of defect 5, euler #=-127 (105941,311704,205636) : difference with theory (-130) = -3 CORRECTING DEFECT 6 (vertices=71, convex hull=56) After retessellation of defect 6, euler #=-126 (105955,311768,205687) : difference with theory (-129) = -3 CORRECTING DEFECT 7 (vertices=38, convex hull=21) After retessellation of defect 7, euler #=-125 (105958,311784,205701) : difference with theory (-128) = -3 CORRECTING DEFECT 8 (vertices=31, convex hull=35) After retessellation of defect 8, euler #=-124 (105961,311810,205725) : difference with theory (-127) = -3 CORRECTING DEFECT 9 (vertices=308, convex hull=256) After retessellation of defect 9, euler #=-123 (106067,312250,206060) : difference with theory (-126) = -3 CORRECTING DEFECT 10 (vertices=24, convex hull=34) After retessellation of defect 10, euler #=-122 (106070,312271,206079) : difference with theory (-125) = -3 CORRECTING DEFECT 11 (vertices=29, convex hull=49) After retessellation of defect 11, euler #=-121 (106078,312311,206112) : difference with theory (-124) = -3 CORRECTING DEFECT 12 (vertices=94, convex hull=58) After retessellation of defect 12, euler #=-120 (106096,312382,206166) : difference with theory (-123) = -3 CORRECTING DEFECT 13 (vertices=1245, convex hull=545) After retessellation of defect 13, euler #=-120 (106314,313311,206877) : difference with theory (-122) = -2 CORRECTING DEFECT 14 (vertices=414, convex hull=132) After retessellation of defect 14, euler #=-119 (106366,313530,207045) : difference with theory (-121) = -2 CORRECTING DEFECT 15 (vertices=102, convex hull=101) After retessellation of defect 15, euler #=-118 (106381,313621,207122) : difference with theory (-120) = -2 CORRECTING DEFECT 16 (vertices=93, convex hull=57) After retessellation of defect 16, euler #=-117 (106390,313670,207163) : difference with theory (-119) = -2 CORRECTING DEFECT 17 (vertices=27, convex hull=69) After retessellation of defect 17, euler #=-116 (106405,313742,207221) : difference with theory (-118) = -2 CORRECTING DEFECT 18 (vertices=6, convex hull=23) After retessellation of defect 18, euler #=-115 (106407,313755,207233) : difference with theory (-117) = -2 CORRECTING DEFECT 19 (vertices=370, convex hull=236) After retessellation of defect 19, euler #=-114 (106454,314012,207444) : difference with theory (-116) = -2 CORRECTING DEFECT 20 (vertices=335, convex hull=85) After retessellation of defect 20, euler #=-113 (106463,314073,207497) : difference with theory (-115) = -2 CORRECTING DEFECT 21 (vertices=39, convex hull=93) After retessellation of defect 21, euler #=-112 (106491,314194,207591) : difference with theory (-114) = -2 CORRECTING DEFECT 22 (vertices=495, convex hull=336) After retessellation of defect 22, euler #=-109 (106517,314459,207833) : difference with theory (-113) = -4 CORRECTING DEFECT 23 (vertices=520, convex hull=252) After retessellation of defect 23, euler #=-108 (106678,315067,208281) : difference with theory (-112) = -4 CORRECTING DEFECT 24 (vertices=20, convex hull=17) After retessellation of defect 24, euler #=-107 (106679,315075,208289) : difference with theory (-111) = -4 CORRECTING DEFECT 25 (vertices=52, convex hull=81) After retessellation of defect 25, euler #=-106 (106694,315162,208362) : difference with theory (-110) = -4 CORRECTING DEFECT 26 (vertices=86, convex hull=112) After retessellation of defect 26, euler #=-105 (106733,315330,208492) : difference with theory (-109) = -4 CORRECTING DEFECT 27 (vertices=45, convex hull=32) After retessellation of defect 27, euler #=-104 (106735,315343,208504) : difference with theory (-108) = -4 CORRECTING DEFECT 28 (vertices=18, convex hull=49) After retessellation of defect 28, euler #=-103 (106740,315375,208532) : difference with theory (-107) = -4 CORRECTING DEFECT 29 (vertices=39, convex hull=55) After retessellation of defect 29, euler #=-102 (106756,315450,208592) : difference with theory (-106) = -4 CORRECTING DEFECT 30 (vertices=8, convex hull=24) After retessellation of defect 30, euler #=-101 (106756,315457,208600) : difference with theory (-105) = -4 CORRECTING DEFECT 31 (vertices=20, convex hull=35) After retessellation of defect 31, euler #=-100 (106760,315480,208620) : difference with theory (-104) = -4 CORRECTING DEFECT 32 (vertices=741, convex hull=391) After retessellation of defect 32, euler #=-99 (106929,316202,209174) : difference with theory (-103) = -4 CORRECTING DEFECT 33 (vertices=70, convex hull=95) After retessellation of defect 33, euler #=-98 (106958,316332,209276) : difference with theory (-102) = -4 CORRECTING DEFECT 34 (vertices=15, convex hull=27) After retessellation of defect 34, euler #=-97 (106959,316345,209289) : difference with theory (-101) = -4 CORRECTING DEFECT 35 (vertices=869, convex hull=145) After retessellation of defect 35, euler #=-96 (107069,316739,209574) : difference with theory (-100) = -4 CORRECTING DEFECT 36 (vertices=224, convex hull=209) After retessellation of defect 36, euler #=-95 (107094,316918,209729) : difference with theory (-99) = -4 CORRECTING DEFECT 37 (vertices=26, convex hull=34) After retessellation of defect 37, euler #=-94 (107100,316955,209761) : difference with theory (-98) = -4 CORRECTING DEFECT 38 (vertices=444, convex hull=417) After retessellation of defect 38, euler #=-90 (107154,317333,210089) : difference with theory (-97) = -7 CORRECTING DEFECT 39 (vertices=22, convex hull=43) After retessellation of defect 39, euler #=-89 (107160,317364,210115) : difference with theory (-96) = -7 CORRECTING DEFECT 40 (vertices=2541, convex hull=776) After retessellation of defect 40, euler #=-89 (107713,319454,211652) : difference with theory (-95) = -6 CORRECTING DEFECT 41 (vertices=126, convex hull=100) After retessellation of defect 41, euler #=-88 (107736,319568,211744) : difference with theory (-94) = -6 CORRECTING DEFECT 42 (vertices=17, convex hull=15) After retessellation of defect 42, euler #=-87 (107737,319577,211753) : difference with theory (-93) = -6 CORRECTING DEFECT 43 (vertices=30, convex hull=23) After retessellation of defect 43, euler #=-86 (107742,319602,211774) : difference with theory (-92) = -6 CORRECTING DEFECT 44 (vertices=37, convex hull=63) After retessellation of defect 44, euler #=-85 (107761,319682,211836) : difference with theory (-91) = -6 CORRECTING DEFECT 45 (vertices=69, convex hull=82) After retessellation of defect 45, euler #=-84 (107774,319760,211902) : difference with theory (-90) = -6 CORRECTING DEFECT 46 (vertices=25, convex hull=90) After retessellation of defect 46, euler #=-83 (107785,319830,211962) : difference with theory (-89) = -6 CORRECTING DEFECT 47 (vertices=148, convex hull=165) After retessellation of defect 47, euler #=-82 (107804,319970,212084) : difference with theory (-88) = -6 CORRECTING DEFECT 48 (vertices=6, convex hull=11) After retessellation of defect 48, euler #=-81 (107805,319976,212090) : difference with theory (-87) = -6 CORRECTING DEFECT 49 (vertices=33, convex hull=51) After retessellation of defect 49, euler #=-80 (107814,320019,212125) : difference with theory (-86) = -6 CORRECTING DEFECT 50 (vertices=16, convex hull=36) After retessellation of defect 50, euler #=-79 (107816,320035,212140) : difference with theory (-85) = -6 CORRECTING DEFECT 51 (vertices=205, convex hull=35) After retessellation of defect 51, euler #=-78 (107828,320084,212178) : difference with theory (-84) = -6 CORRECTING DEFECT 52 (vertices=100, convex hull=106) After retessellation of defect 52, euler #=-77 (107840,320171,212254) : difference with theory (-83) = -6 CORRECTING DEFECT 53 (vertices=48, convex hull=67) After retessellation of defect 53, euler #=-76 (107860,320256,212320) : difference with theory (-82) = -6 CORRECTING DEFECT 54 (vertices=53, convex hull=52) After retessellation of defect 54, euler #=-75 (107874,320321,212372) : difference with theory (-81) = -6 CORRECTING DEFECT 55 (vertices=13, convex hull=17) After retessellation of defect 55, euler #=-74 (107876,320332,212382) : difference with theory (-80) = -6 CORRECTING DEFECT 56 (vertices=75, convex hull=68) After retessellation of defect 56, euler #=-73 (107918,320492,212501) : difference with theory (-79) = -6 CORRECTING DEFECT 57 (vertices=24, convex hull=31) After retessellation of defect 57, euler #=-72 (107922,320512,212518) : difference with theory (-78) = -6 CORRECTING DEFECT 58 (vertices=587, convex hull=270) After retessellation of defect 58, euler #=-73 (107981,320843,212789) : difference with theory (-77) = -4 CORRECTING DEFECT 59 (vertices=24, convex hull=21) After retessellation of defect 59, euler #=-72 (107981,320848,212795) : difference with theory (-76) = -4 CORRECTING DEFECT 60 (vertices=83, convex hull=40) After retessellation of defect 60, euler #=-71 (107988,320884,212825) : difference with theory (-75) = -4 CORRECTING DEFECT 61 (vertices=52, convex hull=87) After retessellation of defect 61, euler #=-70 (107997,320949,212882) : difference with theory (-74) = -4 CORRECTING DEFECT 62 (vertices=590, convex hull=151) After retessellation of defect 62, euler #=-69 (108082,321282,213131) : difference with theory (-73) = -4 CORRECTING DEFECT 63 (vertices=67, convex hull=95) After retessellation of defect 63, euler #=-69 (108110,321408,213229) : difference with theory (-72) = -3 CORRECTING DEFECT 64 (vertices=54, convex hull=71) After retessellation of defect 64, euler #=-68 (108142,321532,213322) : difference with theory (-71) = -3 CORRECTING DEFECT 65 (vertices=171, convex hull=120) After retessellation of defect 65, euler #=-68 (108151,321624,213405) : difference with theory (-70) = -2 CORRECTING DEFECT 66 (vertices=110, convex hull=87) After retessellation of defect 66, euler #=-68 (108188,321783,213527) : difference with theory (-69) = -1 CORRECTING DEFECT 67 (vertices=3570, convex hull=1414) After retessellation of defect 67, euler #=-69 (109378,326164,216717) : difference with theory (-68) = 1 CORRECTING DEFECT 68 (vertices=6, convex hull=28) v 120811 (75409) --> 120951 (72875), len = 85.150 INFLATED: (-48.5, -16.5, -3.5) --> (-44.5, -18.5, 11.5), len = 15.65 CANON: (-59.4, -11.6, -79.6) --> (-82.4, -6.2, -56.4), len = 33.11 CURRENT: (-48.5, -16.5, -3.5) --> (-44.5, -18.5, 11.5), len = 15.65 ORIG: (-48.4, -16.5, -3.4) --> (-44.2, -18.0, 11.1), len = 15.14 After retessellation of defect 68, euler #=-68 (109381,326181,216732) : difference with theory (-67) = 1 CORRECTING DEFECT 69 (vertices=238, convex hull=176) After retessellation of defect 69, euler #=-67 (109437,326432,216928) : difference with theory (-66) = 1 CORRECTING DEFECT 70 (vertices=213, convex hull=212) After retessellation of defect 70, euler #=-65 (109467,326629,217097) : difference with theory (-65) = 0 CORRECTING DEFECT 71 (vertices=62, convex hull=78) After retessellation of defect 71, euler #=-64 (109493,326744,217187) : difference with theory (-64) = 0 CORRECTING DEFECT 72 (vertices=171, convex hull=199) After retessellation of defect 72, euler #=-63 (109558,327038,217417) : difference with theory (-63) = 0 CORRECTING DEFECT 73 (vertices=43, convex hull=21) After retessellation of defect 73, euler #=-62 (109560,327048,217426) : difference with theory (-62) = 0 CORRECTING DEFECT 74 (vertices=61, convex hull=94) After retessellation of defect 74, euler #=-61 (109573,327126,217492) : difference with theory (-61) = 0 CORRECTING DEFECT 75 (vertices=15, convex hull=24) After retessellation of defect 75, euler #=-60 (109577,327146,217509) : difference with theory (-60) = 0 CORRECTING DEFECT 76 (vertices=5, convex hull=22) After retessellation of defect 76, euler #=-59 (109579,327158,217520) : difference with theory (-59) = 0 CORRECTING DEFECT 77 (vertices=14, convex hull=25) After retessellation of defect 77, euler #=-58 (109582,327175,217535) : difference with theory (-58) = 0 CORRECTING DEFECT 78 (vertices=235, convex hull=65) After retessellation of defect 78, euler #=-57 (109603,327263,217603) : difference with theory (-57) = 0 CORRECTING DEFECT 79 (vertices=23, convex hull=32) After retessellation of defect 79, euler #=-56 (109607,327282,217619) : difference with theory (-56) = 0 CORRECTING DEFECT 80 (vertices=126, convex hull=83) After retessellation of defect 80, euler #=-55 (109638,327406,217713) : difference with theory (-55) = 0 CORRECTING DEFECT 81 (vertices=40, convex hull=78) After retessellation of defect 81, euler #=-54 (109652,327479,217773) : difference with theory (-54) = 0 CORRECTING DEFECT 82 (vertices=27, convex hull=34) After retessellation of defect 82, euler #=-53 (109661,327518,217804) : difference with theory (-53) = 0 CORRECTING DEFECT 83 (vertices=55, convex hull=30) After retessellation of defect 83, euler #=-52 (109669,327554,217833) : difference with theory (-52) = 0 CORRECTING DEFECT 84 (vertices=51, convex hull=37) After retessellation of defect 84, euler #=-51 (109676,327590,217863) : difference with theory (-51) = 0 CORRECTING DEFECT 85 (vertices=6, convex hull=15) After retessellation of defect 85, euler #=-50 (109677,327595,217868) : difference with theory (-50) = 0 CORRECTING DEFECT 86 (vertices=36, convex hull=22) After retessellation of defect 86, euler #=-49 (109683,327616,217884) : difference with theory (-49) = 0 CORRECTING DEFECT 87 (vertices=22, convex hull=57) After retessellation of defect 87, euler #=-48 (109694,327667,217925) : difference with theory (-48) = 0 CORRECTING DEFECT 88 (vertices=49, convex hull=93) After retessellation of defect 88, euler #=-47 (109709,327748,217992) : difference with theory (-47) = 0 CORRECTING DEFECT 89 (vertices=47, convex hull=62) After retessellation of defect 89, euler #=-46 (109734,327848,218068) : difference with theory (-46) = 0 CORRECTING DEFECT 90 (vertices=144, convex hull=236) normal vector of length zero at vertex 124955 with 3 faces normal vector of length zero at vertex 124955 with 3 faces normal vector of length zero at vertex 124955 with 3 faces After retessellation of defect 90, euler #=-44 (109746,327997,218207) : difference with theory (-45) = -1 CORRECTING DEFECT 91 (vertices=145, convex hull=152) After retessellation of defect 91, euler #=-43 (109816,328278,218419) : difference with theory (-44) = -1 CORRECTING DEFECT 92 (vertices=11, convex hull=43) After retessellation of defect 92, euler #=-42 (109820,328304,218442) : difference with theory (-43) = -1 CORRECTING DEFECT 93 (vertices=42, convex hull=48) After retessellation of defect 93, euler #=-41 (109842,328390,218507) : difference with theory (-42) = -1 CORRECTING DEFECT 94 (vertices=35, convex hull=35) After retessellation of defect 94, euler #=-40 (109848,328421,218533) : difference with theory (-41) = -1 CORRECTING DEFECT 95 (vertices=6, convex hull=22) After retessellation of defect 95, euler #=-39 (109849,328428,218540) : difference with theory (-40) = -1 CORRECTING DEFECT 96 (vertices=43, convex hull=78) After retessellation of defect 96, euler #=-38 (109880,328552,218634) : difference with theory (-39) = -1 CORRECTING DEFECT 97 (vertices=23, convex hull=18) After retessellation of defect 97, euler #=-37 (109882,328560,218641) : difference with theory (-38) = -1 CORRECTING DEFECT 98 (vertices=48, convex hull=46) After retessellation of defect 98, euler #=-37 (109898,328629,218694) : difference with theory (-37) = 0 CORRECTING DEFECT 99 (vertices=45, convex hull=63) After retessellation of defect 99, euler #=-36 (109922,328726,218768) : difference with theory (-36) = 0 CORRECTING DEFECT 100 (vertices=61, convex hull=101) After retessellation of defect 100, euler #=-34 (109946,328848,218868) : difference with theory (-35) = -1 CORRECTING DEFECT 101 (vertices=63, convex hull=75) After retessellation of defect 101, euler #=-34 (109974,328967,218959) : difference with theory (-34) = 0 CORRECTING DEFECT 102 (vertices=42, convex hull=75) After retessellation of defect 102, euler #=-33 (109997,329063,219033) : difference with theory (-33) = 0 CORRECTING DEFECT 103 (vertices=57, convex hull=62) After retessellation of defect 103, euler #=-32 (110019,329151,219100) : difference with theory (-32) = 0 CORRECTING DEFECT 104 (vertices=13, convex hull=36) After retessellation of defect 104, euler #=-31 (110023,329176,219122) : difference with theory (-31) = 0 CORRECTING DEFECT 105 (vertices=34, convex hull=64) After retessellation of defect 105, euler #=-30 (110044,329264,219190) : difference with theory (-30) = 0 CORRECTING DEFECT 106 (vertices=9, convex hull=18) After retessellation of defect 106, euler #=-29 (110046,329277,219202) : difference with theory (-29) = 0 CORRECTING DEFECT 107 (vertices=26, convex hull=58) After retessellation of defect 107, euler #=-28 (110054,329320,219238) : difference with theory (-28) = 0 CORRECTING DEFECT 108 (vertices=482, convex hull=257) After retessellation of defect 108, euler #=-26 (110081,329547,219440) : difference with theory (-27) = -1 CORRECTING DEFECT 109 (vertices=91, convex hull=146) After retessellation of defect 109, euler #=-25 (110147,329820,219648) : difference with theory (-26) = -1 CORRECTING DEFECT 110 (vertices=23, convex hull=68) After retessellation of defect 110, euler #=-24 (110162,329889,219703) : difference with theory (-25) = -1 CORRECTING DEFECT 111 (vertices=21, convex hull=34) After retessellation of defect 111, euler #=-23 (110167,329910,219720) : difference with theory (-24) = -1 CORRECTING DEFECT 112 (vertices=494, convex hull=206) After retessellation of defect 112, euler #=-22 (110290,330377,220065) : difference with theory (-23) = -1 CORRECTING DEFECT 113 (vertices=11, convex hull=32) After retessellation of defect 113, euler #=-21 (110291,330389,220077) : difference with theory (-22) = -1 CORRECTING DEFECT 114 (vertices=43, convex hull=69) After retessellation of defect 114, euler #=-20 (110310,330472,220142) : difference with theory (-21) = -1 CORRECTING DEFECT 115 (vertices=43, convex hull=78) After retessellation of defect 115, euler #=-19 (110335,330578,220224) : difference with theory (-20) = -1 CORRECTING DEFECT 116 (vertices=45, convex hull=40) After retessellation of defect 116, euler #=-18 (110343,330618,220257) : difference with theory (-19) = -1 CORRECTING DEFECT 117 (vertices=192, convex hull=46) After retessellation of defect 117, euler #=-17 (110358,330682,220307) : difference with theory (-18) = -1 CORRECTING DEFECT 118 (vertices=26, convex hull=64) After retessellation of defect 118, euler #=-16 (110371,330747,220360) : difference with theory (-17) = -1 CORRECTING DEFECT 119 (vertices=51, convex hull=32) After retessellation of defect 119, euler #=-15 (110375,330771,220381) : difference with theory (-16) = -1 CORRECTING DEFECT 120 (vertices=21, convex hull=16) After retessellation of defect 120, euler #=-14 (110380,330789,220395) : difference with theory (-15) = -1 CORRECTING DEFECT 121 (vertices=46, convex hull=27) After retessellation of defect 121, euler #=-14 (110385,330820,220421) : difference with theory (-14) = 0 CORRECTING DEFECT 122 (vertices=41, convex hull=48) After retessellation of defect 122, euler #=-13 (110409,330910,220488) : difference with theory (-13) = 0 CORRECTING DEFECT 123 (vertices=24, convex hull=52) After retessellation of defect 123, euler #=-12 (110421,330962,220529) : difference with theory (-12) = 0 CORRECTING DEFECT 124 (vertices=32, convex hull=47) After retessellation of defect 124, euler #=-11 (110439,331034,220584) : difference with theory (-11) = 0 CORRECTING DEFECT 125 (vertices=45, convex hull=89) After retessellation of defect 125, euler #=-10 (110463,331140,220667) : difference with theory (-10) = 0 CORRECTING DEFECT 126 (vertices=21, convex hull=26) After retessellation of defect 126, euler #=-9 (110466,331158,220683) : difference with theory (-9) = 0 CORRECTING DEFECT 127 (vertices=63, convex hull=56) After retessellation of defect 127, euler #=-8 (110483,331234,220743) : difference with theory (-8) = 0 CORRECTING DEFECT 128 (vertices=24, convex hull=45) After retessellation of defect 128, euler #=-7 (110493,331280,220780) : difference with theory (-7) = 0 CORRECTING DEFECT 129 (vertices=78, convex hull=50) After retessellation of defect 129, euler #=-6 (110503,331326,220817) : difference with theory (-6) = 0 CORRECTING DEFECT 130 (vertices=188, convex hull=91) After retessellation of defect 130, euler #=-5 (110524,331431,220902) : difference with theory (-5) = 0 CORRECTING DEFECT 131 (vertices=61, convex hull=48) After retessellation of defect 131, euler #=-4 (110531,331467,220932) : difference with theory (-4) = 0 CORRECTING DEFECT 132 (vertices=31, convex hull=50) After retessellation of defect 132, euler #=-3 (110545,331527,220979) : difference with theory (-3) = 0 CORRECTING DEFECT 133 (vertices=6, convex hull=20) After retessellation of defect 133, euler #=-2 (110546,331537,220989) : difference with theory (-2) = 0 CORRECTING DEFECT 134 (vertices=43, convex hull=104) After retessellation of defect 134, euler #=-1 (110555,331608,221052) : difference with theory (-1) = 0 CORRECTING DEFECT 135 (vertices=23, convex hull=61) After retessellation of defect 135, euler #=0 (110566,331664,221098) : difference with theory (0) = 0 CORRECTING DEFECT 136 (vertices=20, convex hull=51) After retessellation of defect 136, euler #=1 (110574,331708,221135) : difference with theory (1) = 0 CORRECTING DEFECT 137 (vertices=115, convex hull=28) After retessellation of defect 137, euler #=2 (110583,331743,221162) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.35 (0.01-->14.26) (max @ vno 73374 --> 80681) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.35 (0.01-->14.26) (max @ vno 73374 --> 80681) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 452 mutations (34.2%), 870 crossovers (65.8%), 1428 vertices were eliminated building final representation... 17617 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=110583, nf=221162, ne=331743, g=0) writing corrected surface to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 328.0 minutes 0 defective edges removing intersecting faces 000: 2339 intersecting 001: 249 intersecting 002: 118 intersecting 003: 72 intersecting 004: 69 intersecting 005: 30 intersecting 006: 17 intersecting 007: 2 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 110583 - 331743 + 221162 = 2 --> 0 holes F =2V-4: 221162 = 221166-4 (0) 2E=3F: 663486 = 663486 (0) total defect index = 0 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.01 hours removing intersecting faces 000: 870 intersecting 001: 245 intersecting 002: 104 intersecting 003: 85 intersecting 004: 63 intersecting 005: 43 intersecting 006: 27 intersecting 007: 11 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Dec 7 07:00:19 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... 9465 bright wm thresholded. 59 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.orig... computing class statistics... border white: 236071 voxels (1.41%) border gray 269932 voxels (1.61%) WM (90.0): 91.4 +- 8.2 [70.0 --> 110.0] GM (80.0) : 78.5 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.0 (was 70) setting MAX_BORDER_WHITE to 102.2 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 52.1 (was 40) setting MAX_GRAY to 85.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.01-->7.38) (max @ vno 70035 --> 108348) face area 0.27 +- 0.16 (0.00-->6.80) mean absolute distance = 0.92 +- 1.12 3552 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=94, GM=74 mean inside = 90.9, mean outside = 76.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=81.5, 1371 (1371) missing vertices, mean dist 0.3 [1.0 (%30.4)->0.9 (%69.6))] %49 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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 0.88 +- 0.31 (0.05-->7.36) (max @ vno 70035 --> 108348) face area 0.27 +- 0.16 (0.00-->6.48) mean absolute distance = 0.49 +- 0.69 3370 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3752492.2, rms=7.95 001: dt: 0.5000, sse=4815609.5, rms=5.731 (0.000%) 002: dt: 0.5000, sse=5126396.5, rms=4.596 (0.000%) 003: dt: 0.5000, sse=5509205.5, rms=4.031 (0.000%) 004: dt: 0.5000, sse=5603826.0, rms=3.699 (0.000%) 005: dt: 0.5000, sse=5740956.0, rms=3.495 (0.000%) 006: dt: 0.5000, sse=5742222.5, rms=3.356 (0.000%) 007: dt: 0.5000, sse=5841070.0, rms=3.264 (0.000%) 008: dt: 0.5000, sse=5803785.5, rms=3.204 (0.000%) rms = 3.17, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5882335.5, rms=3.169 (0.000%) 010: dt: 0.2500, sse=4338603.5, rms=2.726 (0.000%) 011: dt: 0.2500, sse=4180551.0, rms=2.633 (0.000%) rms = 2.61, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4088523.5, rms=2.612 (0.000%) rms = 2.58, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4036377.5, rms=2.575 (0.000%) positioning took 2.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.4, 1281 (629) missing vertices, mean dist -0.3 [0.5 (%71.0)->0.4 (%29.0))] %72 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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 0.88 +- 0.30 (0.06-->7.34) (max @ vno 70035 --> 108348) face area 0.32 +- 0.20 (0.00-->7.76) mean absolute distance = 0.34 +- 0.48 2911 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4394516.0, rms=4.60 014: dt: 0.5000, sse=4715727.5, rms=3.158 (0.000%) 015: dt: 0.5000, sse=5131054.5, rms=2.897 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=5363302.5, rms=2.850 (0.000%) 017: dt: 0.2500, sse=4494373.0, rms=2.297 (0.000%) 018: dt: 0.2500, sse=4382522.5, rms=2.164 (0.000%) rms = 2.15, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4287479.5, rms=2.152 (0.000%) 020: dt: 0.1250, sse=4230864.5, rms=2.094 (0.000%) rms = 2.08, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4209280.0, rms=2.080 (0.000%) positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.1, 1113 (448) missing vertices, mean dist -0.1 [0.4 (%66.1)->0.3 (%33.9))] %82 local maxima, % 9 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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 0.88 +- 0.30 (0.06-->7.42) (max @ vno 80680 --> 81210) face area 0.32 +- 0.19 (0.00-->7.67) mean absolute distance = 0.27 +- 0.41 2701 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4334767.5, rms=3.28 022: dt: 0.5000, sse=4710801.5, rms=2.519 (0.000%) rms = 2.62, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4472456.5, rms=2.145 (0.000%) 024: dt: 0.2500, sse=4477056.0, rms=1.976 (0.000%) rms = 1.94, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4474796.0, rms=1.935 (0.000%) 026: dt: 0.1250, sse=4396368.5, rms=1.883 (0.000%) rms = 1.87, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4371961.0, rms=1.871 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=86.7, 1196 (404) missing vertices, mean dist -0.0 [0.3 (%54.5)->0.3 (%45.5))] %85 local maxima, % 7 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4379601.0, rms=1.98 028: dt: 0.5000, sse=5778106.0, rms=1.731 (0.000%) rms = 2.17, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5289762.0, rms=1.521 (0.000%) rms = 1.54, time step reduction 2 of 3 to 0.125... rms = 1.50, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5236056.5, rms=1.497 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 27 non-cortical segments detected only using segment with 1974 vertices erasing segment 0 (vno[0] = 42343) erasing segment 2 (vno[0] = 48042) erasing segment 3 (vno[0] = 48168) erasing segment 4 (vno[0] = 49323) erasing segment 5 (vno[0] = 50368) erasing segment 6 (vno[0] = 51427) erasing segment 7 (vno[0] = 52481) erasing segment 8 (vno[0] = 55314) erasing segment 9 (vno[0] = 55330) erasing segment 10 (vno[0] = 60187) erasing segment 11 (vno[0] = 60232) erasing segment 12 (vno[0] = 61277) erasing segment 13 (vno[0] = 61309) erasing segment 14 (vno[0] = 62386) erasing segment 15 (vno[0] = 65936) erasing segment 16 (vno[0] = 68529) erasing segment 17 (vno[0] = 75251) erasing segment 18 (vno[0] = 78074) erasing segment 19 (vno[0] = 78587) erasing segment 20 (vno[0] = 80675) erasing segment 21 (vno[0] = 81715) erasing segment 22 (vno[0] = 81725) erasing segment 23 (vno[0] = 82747) erasing segment 24 (vno[0] = 82760) erasing segment 25 (vno[0] = 83752) erasing segment 26 (vno[0] = 84706) writing cortex label to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/lh.cortex.label... writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.area vertex spacing 0.88 +- 0.30 (0.04-->7.56) (max @ vno 80680 --> 81207) face area 0.32 +- 0.19 (0.00-->7.10) refinement took 9.7 minutes #-------------------------------------------- #@# Smooth2 lh Sat Dec 7 07:10:04 CST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 Sat Dec 7 07:10:10 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 44.9 mm, total surface area = 64241 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.131 (target=0.015) step 005: RMS=0.095 (target=0.015) step 010: RMS=0.076 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.044 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.9 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 121 vertices thresholded to be in k1 ~ [-1.19 0.76], k2 ~ [-0.18 0.75] total integrated curvature = 0.099*4pi (1.239) --> 1 handles ICI = 1.3, FI = 9.7, variation=164.635 88 vertices thresholded to be in [-0.11 0.05] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.003 97 vertices thresholded to be in [-0.38 0.29] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.022, std = 0.028 done. #----------------------------------------- #@# Curvature Stats lh Sat Dec 7 07:13:56 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm MPS3007-1 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 [ MPS3007-1/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 [ 232 ] Gb_filter = 0 WARN: S lookup min: -0.348171 WARN: S explicit min: 0.000000 vertex = 485 #-------------------------------------------- #@# Sphere lh Sat Dec 7 07:14:05 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 0.309... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=node1, 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 %22.15 pass 1: epoch 2 of 3 starting distance error %22.05 unfolding complete - removing small folds... starting distance error %21.80 removing remaining folds... final distance error %21.84 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.61 hours #-------------------------------------------- #@# Surf Reg lh Sat Dec 7 08:50:42 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_register -curv ../surf/lh.sphere /soft/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 /soft/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=node1, 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=node1, 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 = 0.584 curvature mean = 0.051, std = 0.927 curvature mean = 0.023, std = 0.884 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 288359.0, tmin=1.4743 d=32.00 min @ (8.00, 8.00, 8.00) sse = 221000.7, tmin=2.9511 d=16.00 min @ (0.00, 0.00, -4.00) sse = 214403.3, tmin=4.4649 d=4.00 min @ (-1.00, 0.00, 1.00) sse = 213491.8, tmin=7.7454 d=2.00 min @ (0.50, -0.50, 0.00) sse = 213227.1, tmin=9.2450 d=1.00 min @ (-0.25, 0.25, 0.00) sse = 213150.1, tmin=10.7381 d=0.50 min @ (0.00, -0.12, 0.12) sse = 213122.7, tmin=12.2748 tol=1.0e+00, sigma=0.5, host=node1, 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 12.27 min curvature mean = 0.015, std = 0.970 curvature mean = 0.012, std = 0.947 curvature mean = 0.014, std = 0.983 curvature mean = 0.005, std = 0.974 curvature mean = 0.014, std = 0.987 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.042, std = 0.493 curvature mean = 0.005, std = 0.067 curvature mean = 0.053, std = 0.215 curvature mean = 0.003, std = 0.080 curvature mean = 0.029, std = 0.319 curvature mean = 0.002, std = 0.086 curvature mean = 0.017, std = 0.423 curvature mean = 0.002, std = 0.090 curvature mean = 0.006, std = 0.535 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Sat Dec 7 09:38:43 CST 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Sat Dec 7 09:38:47 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mrisp_paint -a 5 /soft/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 /soft/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Sat Dec 7 09:38:51 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 lh ../surf/lh.sphere.reg /soft/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 /soft/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... 951 labels changed using aseg relabeling using gibbs priors... 000: 2387 changed, 110583 examined... 001: 557 changed, 10566 examined... 002: 134 changed, 3073 examined... 003: 33 changed, 800 examined... 004: 11 changed, 204 examined... 005: 6 changed, 70 examined... 006: 0 changed, 32 examined... 177 labels changed using aseg 000: 116 total segments, 71 labels (392 vertices) changed 001: 43 total segments, 4 labels (20 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 41 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1237 vertices marked for relabeling... 1237 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 6 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sat Dec 7 09:39:58 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... 9465 bright wm thresholded. 59 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.orig... computing class statistics... border white: 236071 voxels (1.41%) border gray 269932 voxels (1.61%) WM (90.0): 91.4 +- 8.2 [70.0 --> 110.0] GM (80.0) : 78.5 +- 11.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.0 (was 70) setting MAX_BORDER_WHITE to 102.2 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 52.1 (was 40) setting MAX_GRAY to 85.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.1 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=94, GM=74 mean inside = 90.9, mean outside = 76.7 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.01-->7.38) (max @ vno 70035 --> 108348) face area 0.27 +- 0.16 (0.00-->6.80) mean absolute distance = 0.92 +- 1.12 3566 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 45 points - only 0.00% unknown deleting segment 2 with 173 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown mean border=81.5, 1386 (1373) missing vertices, mean dist 0.3 [1.0 (%30.5)->0.9 (%69.5))] %50 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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 0.88 +- 0.31 (0.05-->7.36) (max @ vno 70035 --> 108348) face area 0.27 +- 0.16 (0.00-->6.48) mean absolute distance = 0.49 +- 0.69 3371 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3757634.8, rms=7.95 001: dt: 0.5000, sse=4822115.0, rms=5.733 (0.000%) 002: dt: 0.5000, sse=5134127.5, rms=4.597 (0.000%) 003: dt: 0.5000, sse=5516999.5, rms=4.031 (0.000%) 004: dt: 0.5000, sse=5611654.0, rms=3.699 (0.000%) 005: dt: 0.5000, sse=5752293.5, rms=3.495 (0.000%) 006: dt: 0.5000, sse=5753842.5, rms=3.357 (0.000%) 007: dt: 0.5000, sse=5853524.0, rms=3.265 (0.000%) 008: dt: 0.5000, sse=5814691.5, rms=3.205 (0.000%) rms = 3.17, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5895181.0, rms=3.170 (0.000%) 010: dt: 0.2500, sse=4343500.0, rms=2.726 (0.000%) 011: dt: 0.2500, sse=4185737.5, rms=2.633 (0.000%) rms = 2.61, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4093824.8, rms=2.613 (0.000%) rms = 2.58, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4040784.2, rms=2.575 (0.000%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 65 points - only 0.00% unknown deleting segment 2 with 180 points - only 0.00% unknown removing 4 vertex label from ripped group mean border=84.4, 1295 (632) missing vertices, mean dist -0.3 [0.5 (%71.0)->0.4 (%29.0))] %72 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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 0.88 +- 0.30 (0.06-->7.34) (max @ vno 70035 --> 108348) face area 0.33 +- 0.20 (0.00-->7.76) mean absolute distance = 0.34 +- 0.48 2910 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4399395.0, rms=4.60 014: dt: 0.5000, sse=4720885.5, rms=3.158 (0.000%) 015: dt: 0.5000, sse=5139768.5, rms=2.898 (0.000%) rms = 2.85, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=5368952.0, rms=2.851 (0.000%) 017: dt: 0.2500, sse=4499729.5, rms=2.297 (0.000%) 018: dt: 0.2500, sse=4387038.0, rms=2.164 (0.000%) rms = 2.15, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=4290918.0, rms=2.151 (0.000%) 020: dt: 0.1250, sse=4233886.0, rms=2.094 (0.000%) rms = 2.08, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4212158.5, rms=2.080 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 65 points - only 0.00% unknown deleting segment 1 with 183 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 5 points - only 0.00% unknown mean border=86.1, 1110 (447) missing vertices, mean dist -0.1 [0.4 (%66.1)->0.3 (%33.9))] %83 local maxima, % 9 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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 0.88 +- 0.30 (0.06-->7.42) (max @ vno 80680 --> 81210) face area 0.32 +- 0.19 (0.00-->7.66) mean absolute distance = 0.27 +- 0.41 2711 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4338570.5, rms=3.28 022: dt: 0.5000, sse=4712047.5, rms=2.523 (0.000%) rms = 2.62, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4473857.5, rms=2.147 (0.000%) 024: dt: 0.2500, sse=4479210.5, rms=1.976 (0.000%) rms = 1.93, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4476845.5, rms=1.935 (0.000%) 026: dt: 0.1250, sse=4397727.5, rms=1.883 (0.000%) rms = 1.87, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4373479.5, rms=1.870 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 66 points - only 0.00% unknown deleting segment 1 with 182 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 27 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown deleting segment 6 with 5 points - only 0.00% unknown mean border=86.7, 1198 (404) missing vertices, mean dist -0.0 [0.3 (%54.5)->0.3 (%45.5))] %85 local maxima, % 7 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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=4383144.0, rms=1.98 028: dt: 0.5000, sse=5783849.5, rms=1.730 (0.000%) rms = 2.17, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5294467.0, rms=1.520 (0.000%) rms = 1.54, time step reduction 2 of 3 to 0.125... rms = 1.50, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5240676.5, rms=1.495 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=62.2, 1039 (1039) missing vertices, mean dist 2.5 [1.4 (%0.2)->3.1 (%99.8))] %37 local maxima, %40 large gradients and %18 min vals, 852 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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=14942448.0, rms=24.70 001: dt: 0.5000, sse=12316106.0, rms=21.877 (0.000%) 002: dt: 0.5000, sse=10492994.0, rms=19.632 (0.000%) 003: dt: 0.5000, sse=9231357.0, rms=17.877 (0.000%) 004: dt: 0.5000, sse=8428625.0, rms=16.422 (0.000%) 005: dt: 0.5000, sse=7957032.5, rms=15.199 (0.000%) 006: dt: 0.5000, sse=7686534.0, rms=14.162 (0.000%) 007: dt: 0.5000, sse=7539650.5, rms=13.289 (0.000%) 008: dt: 0.5000, sse=7371002.0, rms=12.477 (0.000%) 009: dt: 0.5000, sse=7278233.0, rms=11.761 (0.000%) 010: dt: 0.5000, sse=7144839.5, rms=11.115 (0.000%) 011: dt: 0.5000, sse=7149535.0, rms=10.584 (0.000%) 012: dt: 0.5000, sse=7106123.0, rms=10.094 (0.000%) 013: dt: 0.5000, sse=7160687.0, rms=9.676 (0.000%) 014: dt: 0.5000, sse=7110679.0, rms=9.243 (0.000%) 015: dt: 0.5000, sse=7129135.0, rms=8.886 (0.000%) 016: dt: 0.5000, sse=7088590.0, rms=8.495 (0.000%) 017: dt: 0.5000, sse=7092451.0, rms=8.150 (0.000%) 018: dt: 0.5000, sse=7038182.0, rms=7.758 (0.000%) 019: dt: 0.5000, sse=7034354.5, rms=7.445 (0.000%) 020: dt: 0.5000, sse=6966753.5, rms=7.107 (0.000%) 021: dt: 0.5000, sse=7017304.5, rms=6.882 (0.000%) 022: dt: 0.5000, sse=6970407.0, rms=6.630 (0.000%) 023: dt: 0.5000, sse=7014723.0, rms=6.475 (0.000%) 024: dt: 0.5000, sse=6990853.0, rms=6.310 (0.000%) 025: dt: 0.5000, sse=7028208.0, rms=6.253 (0.000%) 026: dt: 0.5000, sse=6959093.0, rms=6.128 (0.000%) rms = 6.09, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=7043008.0, rms=6.087 (0.000%) 028: dt: 0.2500, sse=5193186.5, rms=5.154 (0.000%) 029: dt: 0.2500, sse=5012310.5, rms=4.882 (0.000%) rms = 4.85, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4884323.5, rms=4.853 (0.000%) positioning took 4.9 minutes mean border=58.2, 1264 (117) missing vertices, mean dist 0.3 [0.2 (%30.1)->0.5 (%69.9))] %55 local maxima, %26 large gradients and %12 min vals, 424 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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=5936063.5, rms=7.61 031: dt: 0.5000, sse=6362574.0, rms=6.605 (0.000%) 032: dt: 0.5000, sse=7078540.0, rms=6.445 (0.000%) rms = 6.49, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5853369.5, rms=5.362 (0.000%) 034: dt: 0.2500, sse=5492225.0, rms=5.073 (0.000%) rms = 5.10, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=5300769.0, rms=4.879 (0.000%) 036: dt: 0.1250, sse=5036259.5, rms=4.595 (0.000%) 037: dt: 0.1250, sse=4958203.0, rms=4.487 (0.000%) rms = 4.45, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4932325.5, rms=4.445 (0.000%) positioning took 1.6 minutes mean border=56.3, 1538 (84) missing vertices, mean dist 0.1 [0.2 (%32.2)->0.3 (%67.8))] %63 local maxima, %19 large gradients and %12 min vals, 472 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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=5070012.0, rms=5.08 rms = 6.29, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=4914242.5, rms=4.540 (0.000%) 040: dt: 0.2500, sse=5017276.0, rms=4.475 (0.000%) rms = 4.53, time step reduction 2 of 3 to 0.125... 041: dt: 0.1250, sse=4943185.0, rms=4.376 (0.000%) 042: dt: 0.1250, sse=4884982.5, rms=4.251 (0.000%) 043: dt: 0.1250, sse=4887577.0, rms=4.168 (0.000%) rms = 4.13, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4914974.0, rms=4.131 (0.000%) positioning took 1.2 minutes mean border=55.6, 2550 (78) missing vertices, mean dist 0.1 [0.2 (%42.7)->0.3 (%57.3))] %64 local maxima, %17 large gradients and %12 min vals, 427 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4922976.5, rms=4.17 rms = 5.14, time step reduction 1 of 3 to 0.250... 045: dt: 0.2500, sse=4920550.5, rms=3.999 (0.000%) rms = 3.95, time step reduction 2 of 3 to 0.125... 046: dt: 0.2500, sse=5179884.0, rms=3.951 (0.000%) 047: dt: 0.1250, sse=5092796.0, rms=3.830 (0.000%) 048: dt: 0.1250, sse=5118635.0, rms=3.750 (0.000%) rms = 3.72, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=5144653.5, rms=3.716 (0.000%) positioning took 1.0 minutes writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.area.pial vertex spacing 1.08 +- 0.55 (0.03-->9.05) (max @ vno 88265 --> 88261) face area 0.46 +- 0.43 (0.00-->10.67) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 110583 vertices processed 25000 of 110583 vertices processed 50000 of 110583 vertices processed 75000 of 110583 vertices processed 100000 of 110583 vertices processed 0 of 110583 vertices processed 25000 of 110583 vertices processed 50000 of 110583 vertices processed 75000 of 110583 vertices processed 100000 of 110583 vertices processed thickness calculation complete, 2593:11328 truncations. 18807 vertices at 0 distance 52134 vertices at 1 distance 59513 vertices at 2 distance 43374 vertices at 3 distance 21612 vertices at 4 distance 8567 vertices at 5 distance 3192 vertices at 6 distance 1306 vertices at 7 distance 645 vertices at 8 distance 356 vertices at 9 distance 231 vertices at 10 distance 172 vertices at 11 distance 90 vertices at 12 distance 54 vertices at 13 distance 56 vertices at 14 distance 47 vertices at 15 distance 44 vertices at 16 distance 39 vertices at 17 distance 37 vertices at 18 distance 35 vertices at 19 distance 35 vertices at 20 distance writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.thickness positioning took 18.9 minutes #-------------------------------------------- #@# Surf Volume lh Sat Dec 7 09:58:51 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 Sat Dec 7 09:58:52 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts pctsurfcon --s MPS3007-1 --lh-only Log file is /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts/pctsurfcon.log Sat Dec 7 09:58:52 CST 2013 setenv SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post cd /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts /soft/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node1109 2.6.32-358.14.1.el6.x86_64 #1 SMP Tue Jul 16 23:51:20 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /soft/freesurfer/5.3.0 mri_vol2surf --mov /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.45079/lh.wm.mgh --regheader MPS3007-1 --cortex srcvol = /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/lh.cortex.label Reading surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 = 57946 Masking with /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/lh.cortex.label Writing to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.45079/lh.wm.mgh Dim: 110583 1 1 mri_vol2surf --mov /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.45079/lh.gm.mgh --projfrac 0.3 --regheader MPS3007-1 --cortex srcvol = /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/lh.cortex.label Reading surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Done reading source surface Reading thickness /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 = 69483 Masking with /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/lh.cortex.label Writing to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.45079/lh.gm.mgh Dim: 110583 1 1 mri_concat /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.45079/lh.wm.mgh /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.45079/lh.gm.mgh --paired-diff-norm --mul 100 --o /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.w-g.pct.mgh mri_segstats --in /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.w-g.pct.mgh --annot MPS3007-1 lh aparc --sum /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.w-g.pct.mgh --annot MPS3007-1 lh aparc --sum /lustre/kovacv/FS/MPSIII-post/MPS3007-1/stats/lh.w-g.pct.stats --snr sysname Linux hostname node1109 machine x86_64 user kovacv 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.w-g.pct.mgh Vertex Area is 0.648267 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1071 702.001 2 1002 caudalanteriorcingulate 698 451.346 3 1003 caudalmiddlefrontal 2976 2014.642 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2454 1577.916 6 1006 entorhinal 480 334.265 7 1007 fusiform 3449 2294.828 8 1008 inferiorparietal 4101 2592.995 9 1009 inferiortemporal 2991 2080.530 10 1010 isthmuscingulate 1343 887.597 11 1011 lateraloccipital 8357 4828.579 12 1012 lateralorbitofrontal 2244 1516.418 13 1013 lingual 3359 2188.729 14 1014 medialorbitofrontal 2180 1507.985 15 1015 middletemporal 2933 1886.935 16 1016 parahippocampal 1293 890.821 17 1017 paracentral 1966 1221.555 18 1018 parsopercularis 1728 1175.377 19 1019 parsorbitalis 802 540.227 20 1020 parstriangularis 1261 883.343 21 1021 pericalcarine 1953 1379.980 22 1022 postcentral 5527 3534.845 23 1023 posteriorcingulate 1364 939.944 24 1024 precentral 6005 4054.608 25 1025 precuneus 4371 2838.590 26 1026 rostralanteriorcingulate 700 440.722 27 1027 rostralmiddlefrontal 5618 3784.261 28 1028 superiorfrontal 8292 5670.292 29 1029 superiorparietal 8539 5143.541 30 1030 superiortemporal 5032 3120.698 31 1031 supramarginal 5922 3741.898 32 1032 frontalpole 397 246.033 33 1033 temporalpole 426 272.947 34 1034 transversetemporal 692 423.189 35 1035 insula 2352 1656.375 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Sat Dec 7 09:59:07 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 MPS3007-1 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 1071 702 1939 2.825 0.579 0.136 0.066 21 3.0 bankssts 698 451 1784 3.549 0.886 0.110 0.040 6 1.3 caudalanteriorcingulate 2976 2015 8210 3.073 0.811 0.158 0.092 80 11.3 caudalmiddlefrontal 2454 1578 3871 2.219 0.714 0.202 0.234 1184 14.0 cuneus 480 334 2274 3.842 1.038 0.218 0.158 19 3.0 entorhinal 3449 2295 9094 3.039 0.947 0.215 0.288 424 31.1 fusiform 4101 2593 8537 2.832 0.795 0.214 0.232 256 39.0 inferiorparietal 2991 2081 9187 3.214 0.894 0.208 0.155 147 17.6 inferiortemporal 1343 888 3166 3.023 1.526 0.191 0.123 53 6.8 isthmuscingulate 8357 4829 10949 2.120 0.649 0.216 0.219 848 90.2 lateraloccipital 2244 1516 7211 3.397 0.919 0.154 0.088 55 6.8 lateralorbitofrontal 3359 2189 6650 2.521 0.885 0.200 0.179 208 21.6 lingual 2180 1508 6757 3.202 0.995 0.172 0.113 95 9.7 medialorbitofrontal 2933 1887 9222 3.320 0.851 0.188 0.136 151 17.3 middletemporal 1293 891 3477 3.226 0.791 0.198 0.161 263 7.0 parahippocampal 1966 1222 4027 2.849 0.707 0.143 0.101 62 10.3 paracentral 1728 1175 5344 3.176 0.820 0.149 0.107 34 5.1 parsopercularis 802 540 2705 3.303 0.835 0.205 0.155 36 4.0 parsorbitalis 1261 883 3521 2.941 0.803 0.183 0.101 41 5.2 parstriangularis 1953 1380 2715 1.958 0.683 0.178 1.098 1629 8.3 pericalcarine 5527 3535 11519 2.595 0.907 0.177 0.149 492 32.9 postcentral 1364 940 3539 3.240 0.860 0.180 0.112 59 6.8 posteriorcingulate 6005 4055 17078 3.174 0.969 0.182 0.252 980 39.8 precentral 4371 2839 10216 2.816 0.906 0.170 0.151 356 29.7 precuneus 700 441 2194 3.948 0.832 0.141 0.082 15 2.7 rostralanteriorcingulate 5618 3784 14430 2.947 0.783 0.166 0.090 152 19.8 rostralmiddlefrontal 8292 5670 27077 3.462 0.796 0.167 0.102 259 34.7 superiorfrontal 8539 5144 15696 2.525 0.733 0.200 0.342 997 94.7 superiorparietal 5032 3121 10982 2.860 1.011 0.213 0.446 798 125.6 superiortemporal 5922 3742 15619 3.144 0.824 0.192 0.154 342 38.3 supramarginal 397 246 1456 3.467 0.833 0.273 0.244 54 4.0 frontalpole 426 273 1380 3.174 0.864 0.274 0.312 48 4.4 temporalpole 692 423 1478 2.705 0.774 0.208 0.239 45 5.1 transversetemporal 2352 1656 7358 3.744 1.123 0.142 0.265 210 23.6 insula #----------------------------------------- #@# Cortical Parc 2 lh Sat Dec 7 09:59:29 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 lh ../surf/lh.sphere.reg /soft/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 /soft/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... 9 labels changed using aseg relabeling using gibbs priors... 000: 7439 changed, 110583 examined... 001: 1770 changed, 28757 examined... 002: 582 changed, 9132 examined... 003: 247 changed, 3272 examined... 004: 121 changed, 1383 examined... 005: 64 changed, 672 examined... 006: 39 changed, 324 examined... 007: 16 changed, 193 examined... 008: 6 changed, 101 examined... 009: 4 changed, 34 examined... 010: 3 changed, 23 examined... 011: 3 changed, 21 examined... 012: 2 changed, 21 examined... 013: 2 changed, 16 examined... 014: 0 changed, 12 examined... 6 labels changed using aseg 000: 284 total segments, 203 labels (2366 vertices) changed 001: 87 total segments, 8 labels (32 vertices) changed 002: 80 total segments, 1 labels (3 vertices) changed 003: 79 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 117 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 960 vertices marked for relabeling... 960 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 19 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sat Dec 7 10:00:48 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 MPS3007-1 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 904 600 2574 3.235 0.877 0.189 0.105 29 4.2 G_and_S_frontomargin 2326 1364 3736 2.368 0.786 0.230 0.438 548 39.5 G_and_S_occipital_inf 1441 843 3326 2.753 0.926 0.201 0.216 130 16.0 G_and_S_paracentral 1368 895 4422 3.511 0.893 0.201 0.286 381 12.3 G_and_S_subcentral 500 332 1697 3.255 0.707 0.224 0.194 51 3.7 G_and_S_transv_frontopol 1720 1137 4506 3.359 0.845 0.139 0.075 30 4.8 G_and_S_cingul-Ant 993 686 2485 3.210 0.759 0.116 0.048 10 2.1 G_and_S_cingul-Mid-Ant 1056 728 2485 3.151 0.738 0.119 0.037 15 1.8 G_and_S_cingul-Mid-Post 342 217 1170 3.558 0.992 0.288 0.258 31 4.3 G_cingul-Post-dorsal 507 331 1022 2.396 1.832 0.197 0.116 18 2.7 G_cingul-Post-ventral 2143 1372 3315 2.097 0.713 0.216 0.265 1188 13.6 G_cuneus 1163 824 5110 3.701 0.679 0.180 0.117 32 4.9 G_front_inf-Opercular 206 145 946 3.611 0.631 0.217 0.145 9 1.1 G_front_inf-Orbital 685 471 2538 3.405 0.715 0.217 0.143 32 4.0 G_front_inf-Triangul 3137 2151 11039 3.301 0.799 0.189 0.126 129 14.3 G_front_middle 6303 4306 23112 3.613 0.769 0.189 0.123 256 32.8 G_front_sup 306 231 1287 4.421 0.756 0.280 0.469 64 5.8 G_Ins_lg_and_S_cent_ins 326 245 1763 4.791 0.395 0.048 0.009 1 0.1 G_insular_short 2394 1259 3657 2.296 0.754 0.256 0.332 333 36.6 G_occipital_middle 1771 1071 3671 2.646 0.739 0.192 0.164 173 13.0 G_occipital_sup 1168 800 3707 3.355 0.703 0.213 0.120 55 5.9 G_oc-temp_lat-fusifor 2009 1249 3739 2.318 0.823 0.218 0.262 385 17.0 G_oc-temp_med-Lingual 1217 848 4512 3.626 0.960 0.184 0.162 52 11.5 G_oc-temp_med-Parahip 1933 1322 7634 3.682 0.837 0.197 0.140 78 8.9 G_orbital 1545 893 3790 2.835 0.983 0.276 0.343 175 26.0 G_pariet_inf-Angular 3343 2032 10200 3.415 0.801 0.214 0.180 211 25.4 G_pariet_inf-Supramar 2876 1590 5643 2.610 0.776 0.239 0.678 412 47.2 G_parietal_sup 2163 1344 5066 2.709 0.741 0.188 0.141 81 13.1 G_postcentral 2103 1456 8384 3.661 0.785 0.213 0.180 307 18.7 G_precentral 2115 1294 5944 2.899 0.911 0.215 0.271 418 28.0 G_precuneus 762 527 3381 3.848 0.721 0.236 0.182 62 6.3 G_rectus 140 89 380 3.764 0.758 0.076 0.049 1 0.1 G_subcallosal 568 321 1392 3.020 0.707 0.275 0.357 163 6.7 G_temp_sup-G_T_transv 1997 1223 5457 2.800 1.136 0.287 0.917 532 107.2 G_temp_sup-Lateral 357 230 851 3.064 0.917 0.304 0.896 119 6.4 G_temp_sup-Plan_polar 1122 718 2630 3.144 0.768 0.156 0.108 39 5.3 G_temp_sup-Plan_tempo 1807 1234 6576 3.501 0.840 0.234 0.200 122 13.4 G_temporal_inf 2016 1274 7071 3.534 0.757 0.201 0.158 127 13.6 G_temporal_middle 251 176 595 2.800 0.810 0.168 0.060 7 0.6 Lat_Fis-ant-Horizont 180 118 330 2.576 0.597 0.109 0.044 1 0.3 Lat_Fis-ant-Vertical 1587 1035 2527 2.624 0.654 0.143 0.075 66 4.9 Lat_Fis-post 2491 1412 2746 1.843 0.610 0.213 0.159 114 18.2 Pole_occipital 1183 782 3370 2.848 1.000 0.244 0.342 182 16.1 Pole_temporal 2404 1673 3743 2.360 0.992 0.156 0.887 1619 7.7 S_calcarine 2848 1883 3893 2.314 0.800 0.157 0.310 582 10.9 S_central 1155 780 1994 2.607 0.591 0.104 0.036 8 1.9 S_cingul-Marginalis 402 254 825 3.368 0.812 0.101 0.043 3 0.8 S_circular_insula_ant 882 616 2260 3.927 1.086 0.105 0.043 10 1.2 S_circular_insula_inf 1379 910 2425 2.792 0.830 0.127 0.122 39 9.1 S_circular_insula_sup 504 324 1304 2.793 1.007 0.152 0.081 12 1.8 S_collat_transv_ant 244 161 477 2.704 0.519 0.133 0.061 8 0.6 S_collat_transv_post 1703 1141 3073 2.646 0.592 0.139 0.088 26 4.3 S_front_inf 891 593 1555 2.499 0.530 0.124 0.051 11 1.9 S_front_middle 2058 1390 3975 2.824 0.639 0.126 0.056 25 5.3 S_front_sup 126 76 297 2.738 0.668 0.199 0.158 4 1.0 S_interm_prim-Jensen 3170 2070 5245 2.464 0.645 0.146 0.097 117 13.9 S_intrapariet_and_P_trans 988 622 1572 2.455 0.596 0.192 0.103 32 4.8 S_oc_middle_and_Lunatus 1478 972 2222 2.373 0.644 0.170 0.096 40 5.8 S_oc_sup_and_transversal 460 321 775 2.405 0.659 0.161 0.080 18 1.2 S_occipital_ant 407 293 1235 3.676 0.923 0.254 0.162 18 2.7 S_oc-temp_lat 2277 1626 5364 2.936 0.828 0.198 0.124 105 11.5 S_oc-temp_med_and_Lingual 229 152 378 2.537 0.685 0.154 0.056 3 0.7 S_orbital_lateral 502 334 1593 3.587 0.996 0.106 0.065 9 0.6 S_orbital_med-olfact 733 508 1643 2.743 0.807 0.135 0.051 9 1.7 S_orbital-H_Shaped 2217 1487 3936 2.552 0.881 0.153 0.106 97 8.2 S_parieto_occipital 818 534 1968 3.574 1.228 0.188 0.119 36 3.7 S_pericallosal 2492 1666 4610 2.558 0.753 0.170 0.166 168 20.1 S_postcentral 1092 713 2310 2.899 0.926 0.124 0.058 11 2.9 S_precentral-inf-part 1003 664 1609 2.598 0.677 0.131 0.062 13 2.9 S_precentral-sup-part 568 399 1177 2.481 0.920 0.146 0.062 11 1.5 S_suborbital 747 476 1628 2.977 0.725 0.186 0.155 35 4.6 S_subparietal 843 568 1487 2.704 0.616 0.150 0.107 19 4.5 S_temporal_inf 3325 2178 5751 2.724 0.666 0.167 0.137 157 17.3 S_temporal_sup 407 263 555 2.220 0.487 0.139 0.061 5 1.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Sat Dec 7 10:01:10 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 lh ../surf/lh.sphere.reg /soft/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 /soft/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... 459 labels changed using aseg relabeling using gibbs priors... 000: 2414 changed, 110583 examined... 001: 568 changed, 10333 examined... 002: 154 changed, 3111 examined... 003: 56 changed, 923 examined... 004: 25 changed, 289 examined... 005: 12 changed, 158 examined... 006: 4 changed, 77 examined... 007: 2 changed, 15 examined... 008: 1 changed, 12 examined... 009: 0 changed, 7 examined... 47 labels changed using aseg 000: 78 total segments, 45 labels (425 vertices) changed 001: 34 total segments, 1 labels (1 vertices) changed 002: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 52 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 691 vertices marked for relabeling... 691 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 1 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Sat Dec 7 10:02:11 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 MPS3007-1 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 1259 826 3041 3.412 0.830 0.127 0.078 31 4.7 caudalanteriorcingulate 3131 2110 8790 3.095 0.821 0.157 0.090 82 11.5 caudalmiddlefrontal 3260 2091 5458 2.269 0.717 0.186 0.190 1198 15.7 cuneus 509 355 2409 3.847 1.033 0.215 0.154 19 3.0 entorhinal 2865 1973 8300 3.253 0.844 0.202 0.124 133 14.7 fusiform 3964 2481 8310 2.825 0.827 0.215 0.246 269 38.9 inferiorparietal 3255 2217 9555 3.106 0.949 0.214 0.212 330 30.0 inferiortemporal 1357 896 3195 3.022 1.520 0.190 0.122 53 6.9 isthmuscingulate 8900 5111 11960 2.141 0.680 0.221 0.262 998 98.2 lateraloccipital 2539 1706 8741 3.515 0.925 0.160 0.131 90 14.9 lateralorbitofrontal 3390 2208 6666 2.505 0.883 0.200 0.178 208 21.7 lingual 1970 1361 6545 3.286 0.984 0.193 0.131 105 10.8 medialorbitofrontal 3705 2411 10402 3.167 0.842 0.181 0.130 164 21.0 middletemporal 1262 869 3350 3.219 0.786 0.200 0.163 263 6.9 parahippocampal 2099 1319 4565 2.906 0.762 0.142 0.099 63 10.8 paracentral 1478 1004 4632 3.196 0.825 0.152 0.116 30 4.6 parsopercularis 793 540 2473 3.130 0.716 0.185 0.126 31 2.9 parsorbitalis 1564 1082 3969 2.869 0.786 0.167 0.088 39 5.7 parstriangularis 1924 1370 2689 1.958 0.688 0.178 1.114 1627 8.3 pericalcarine 6133 3893 12675 2.637 0.904 0.179 0.158 609 37.8 postcentral 1484 1019 3669 3.188 0.860 0.174 0.106 59 7.0 posteriorcingulate 5860 3959 16361 3.160 0.966 0.182 0.255 975 39.2 precentral 4255 2762 10146 2.867 0.890 0.175 0.159 360 30.5 precuneus 990 628 2685 3.673 0.946 0.140 0.082 19 3.5 rostralanteriorcingulate 4277 2915 12097 3.046 0.822 0.180 0.104 136 17.5 rostralmiddlefrontal 8816 6000 27995 3.356 0.826 0.166 0.099 284 35.0 superiorfrontal 6934 4176 12355 2.489 0.723 0.202 0.378 820 83.6 superiorparietal 6461 4082 14696 2.904 0.968 0.210 0.412 954 136.0 superiortemporal 5764 3652 15254 3.156 0.804 0.190 0.144 319 35.9 supramarginal 692 423 1458 2.673 0.771 0.206 0.239 45 5.0 transversetemporal 1986 1385 6221 3.780 1.135 0.129 0.144 97 12.6 insula #-------------------------------------------- #@# Tessellate rh Sat Dec 7 10:02:33 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 7 found - 7 modified | TOTAL: 11 pass 2 (yz+): 0 found - 7 modified | TOTAL: 11 pass 1 (yz-): 0 found - 0 modified | TOTAL: 11 pass 1 (xz+): 4 found - 4 modified | TOTAL: 15 pass 2 (xz+): 0 found - 4 modified | TOTAL: 15 pass 1 (xz-): 1 found - 1 modified | TOTAL: 16 pass 2 (xz-): 0 found - 1 modified | TOTAL: 16 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 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 = 19 (out of 186023: 0.010214) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 118 vertices, 149 faces slice 50: 3197 vertices, 3355 faces slice 60: 9068 vertices, 9368 faces slice 70: 15637 vertices, 15978 faces slice 80: 24096 vertices, 24582 faces slice 90: 34357 vertices, 34937 faces slice 100: 46454 vertices, 47185 faces slice 110: 60903 vertices, 61738 faces slice 120: 75335 vertices, 76221 faces slice 130: 89568 vertices, 90481 faces slice 140: 98875 vertices, 99605 faces slice 150: 105039 vertices, 105738 faces slice 160: 110817 vertices, 111554 faces slice 170: 117836 vertices, 118576 faces slice 180: 123014 vertices, 123755 faces slice 190: 127740 vertices, 128382 faces slice 200: 129584 vertices, 130139 faces slice 210: 129598 vertices, 130146 faces slice 220: 129598 vertices, 130146 faces slice 230: 129598 vertices, 130146 faces slice 240: 129598 vertices, 130146 faces slice 250: 129598 vertices, 130146 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... 129598 voxel in cpt #1: X=-548 [v=129598,e=390438,f=260292] located at (29.308508, -14.389342, 22.674725) For the whole surface: X=-548 [v=129598,e=390438,f=260292] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Sat Dec 7 10:02:47 CST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 Sat Dec 7 10:02:56 CST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts avg radius = 43.6 mm, total surface area = 63063 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.0 minutes Not saving sulc step 000: RMS=0.141 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.099 (target=0.015) step 015: RMS=0.092 (target=0.015) step 020: RMS=0.088 (target=0.015) step 025: RMS=0.085 (target=0.015) step 030: RMS=0.083 (target=0.015) step 035: RMS=0.082 (target=0.015) step 040: RMS=0.080 (target=0.015) step 045: RMS=0.080 (target=0.015) step 050: RMS=0.079 (target=0.015) step 055: RMS=0.079 (target=0.015) step 060: RMS=0.079 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Sat Dec 7 10:03:54 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 +- 0.71 (0.00-->8.63) (max @ vno 83673 --> 83674) face area 0.02 +- 0.03 (-0.31-->0.59) scaling brain by 0.314... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=178.285, avgs=0 005/300: dt: 0.9000, rms radial error=178.023, avgs=0 010/300: dt: 0.9000, rms radial error=177.459, avgs=0 015/300: dt: 0.9000, rms radial error=176.720, avgs=0 020/300: dt: 0.9000, rms radial error=175.879, avgs=0 025/300: dt: 0.9000, rms radial error=174.980, avgs=0 030/300: dt: 0.9000, rms radial error=174.050, avgs=0 035/300: dt: 0.9000, rms radial error=173.102, avgs=0 040/300: dt: 0.9000, rms radial error=172.146, avgs=0 045/300: dt: 0.9000, rms radial error=171.188, avgs=0 050/300: dt: 0.9000, rms radial error=170.230, avgs=0 055/300: dt: 0.9000, rms radial error=169.274, avgs=0 060/300: dt: 0.9000, rms radial error=168.326, avgs=0 065/300: dt: 0.9000, rms radial error=167.383, avgs=0 070/300: dt: 0.9000, rms radial error=166.445, avgs=0 075/300: dt: 0.9000, rms radial error=165.511, avgs=0 080/300: dt: 0.9000, rms radial error=164.582, avgs=0 085/300: dt: 0.9000, rms radial error=163.657, avgs=0 090/300: dt: 0.9000, rms radial error=162.738, avgs=0 095/300: dt: 0.9000, rms radial error=161.823, avgs=0 100/300: dt: 0.9000, rms radial error=160.913, avgs=0 105/300: dt: 0.9000, rms radial error=160.008, avgs=0 110/300: dt: 0.9000, rms radial error=159.108, avgs=0 115/300: dt: 0.9000, rms radial error=158.212, avgs=0 120/300: dt: 0.9000, rms radial error=157.321, avgs=0 125/300: dt: 0.9000, rms radial error=156.434, avgs=0 130/300: dt: 0.9000, rms radial error=155.553, avgs=0 135/300: dt: 0.9000, rms radial error=154.676, avgs=0 140/300: dt: 0.9000, rms radial error=153.804, avgs=0 145/300: dt: 0.9000, rms radial error=152.936, avgs=0 150/300: dt: 0.9000, rms radial error=152.073, avgs=0 155/300: dt: 0.9000, rms radial error=151.215, avgs=0 160/300: dt: 0.9000, rms radial error=150.362, avgs=0 165/300: dt: 0.9000, rms radial error=149.514, avgs=0 170/300: dt: 0.9000, rms radial error=148.670, avgs=0 175/300: dt: 0.9000, rms radial error=147.831, avgs=0 180/300: dt: 0.9000, rms radial error=146.996, avgs=0 185/300: dt: 0.9000, rms radial error=146.166, avgs=0 190/300: dt: 0.9000, rms radial error=145.340, avgs=0 195/300: dt: 0.9000, rms radial error=144.520, avgs=0 200/300: dt: 0.9000, rms radial error=143.703, avgs=0 205/300: dt: 0.9000, rms radial error=142.892, avgs=0 210/300: dt: 0.9000, rms radial error=142.084, avgs=0 215/300: dt: 0.9000, rms radial error=141.281, avgs=0 220/300: dt: 0.9000, rms radial error=140.482, avgs=0 225/300: dt: 0.9000, rms radial error=139.688, avgs=0 230/300: dt: 0.9000, rms radial error=138.898, avgs=0 235/300: dt: 0.9000, rms radial error=138.113, avgs=0 240/300: dt: 0.9000, rms radial error=137.332, avgs=0 245/300: dt: 0.9000, rms radial error=136.555, avgs=0 250/300: dt: 0.9000, rms radial error=135.783, avgs=0 255/300: dt: 0.9000, rms radial error=135.014, avgs=0 260/300: dt: 0.9000, rms radial error=134.251, avgs=0 265/300: dt: 0.9000, rms radial error=133.492, avgs=0 270/300: dt: 0.9000, rms radial error=132.737, avgs=0 275/300: dt: 0.9000, rms radial error=131.986, avgs=0 280/300: dt: 0.9000, rms radial error=131.240, avgs=0 285/300: dt: 0.9000, rms radial error=130.497, avgs=0 290/300: dt: 0.9000, rms radial error=129.759, avgs=0 295/300: dt: 0.9000, rms radial error=129.025, avgs=0 300/300: dt: 0.9000, rms radial error=128.295, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15461.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00018 epoch 2 (K=40.0), pass 1, starting sse = 2798.93 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 = 422.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00282 epoch 4 (K=640.0), pass 1, starting sse = 70.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/12 = 0.00491 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.13 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Sat Dec 7 10:11:25 CST 2013 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS3007-1 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=-548 (nv=129598, nf=260292, ne=390438, g=275) 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 12 iterations marking ambiguous vertices... 41337 ambiguous faces found in tessellation segmenting defects... 155 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 1 -merging segment 5 into 1 -merging segment 14 into 1 -merging segment 1 into 6 -merging segment 17 into 11 -merging segment 34 into 33 -merging segment 58 into 53 -merging segment 62 into 53 -merging segment 68 into 66 -merging segment 76 into 66 -merging segment 69 into 70 -merging segment 104 into 75 -merging segment 106 into 75 -merging segment 109 into 75 -merging segment 110 into 75 -merging segment 119 into 75 -merging segment 117 into 116 138 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2087 (-4.6043) -vertex loglikelihood: -6.4121 (-3.2060) -normal dot loglikelihood: -3.4935 (-3.4935) -quad curv loglikelihood: -6.1343 (-3.0671) Total Loglikelihood : -25.2485 CORRECTING DEFECT 0 (vertices=161, convex hull=124) After retessellation of defect 0, euler #=-123 (105633,310042,204286) : difference with theory (-135) = -12 CORRECTING DEFECT 1 (vertices=180, convex hull=92) After retessellation of defect 1, euler #=-122 (105645,310115,204348) : difference with theory (-134) = -12 CORRECTING DEFECT 2 (vertices=578, convex hull=257) After retessellation of defect 2, euler #=-122 (105835,310815,204858) : difference with theory (-133) = -11 CORRECTING DEFECT 3 (vertices=2263, convex hull=1357) After retessellation of defect 3, euler #=-123 (106596,313919,207200) : difference with theory (-132) = -9 CORRECTING DEFECT 4 (vertices=322, convex hull=336) After retessellation of defect 4, euler #=-123 (106764,314586,207699) : difference with theory (-131) = -8 CORRECTING DEFECT 5 (vertices=11, convex hull=23) After retessellation of defect 5, euler #=-122 (106764,314593,207707) : difference with theory (-130) = -8 CORRECTING DEFECT 6 (vertices=29, convex hull=28) After retessellation of defect 6, euler #=-121 (106767,314610,207722) : difference with theory (-129) = -8 CORRECTING DEFECT 7 (vertices=482, convex hull=267) After retessellation of defect 7, euler #=-120 (106893,315122,208109) : difference with theory (-128) = -8 CORRECTING DEFECT 8 (vertices=150, convex hull=118) After retessellation of defect 8, euler #=-118 (106929,315287,208240) : difference with theory (-127) = -9 CORRECTING DEFECT 9 (vertices=8, convex hull=22) After retessellation of defect 9, euler #=-117 (106931,315299,208251) : difference with theory (-126) = -9 CORRECTING DEFECT 10 (vertices=35, convex hull=53) After retessellation of defect 10, euler #=-116 (106941,315348,208291) : difference with theory (-125) = -9 CORRECTING DEFECT 11 (vertices=13, convex hull=17) After retessellation of defect 11, euler #=-115 (106942,315356,208299) : difference with theory (-124) = -9 CORRECTING DEFECT 12 (vertices=23, convex hull=64) After retessellation of defect 12, euler #=-114 (106951,315408,208343) : difference with theory (-123) = -9 CORRECTING DEFECT 13 (vertices=19, convex hull=35) After retessellation of defect 13, euler #=-113 (106952,315425,208360) : difference with theory (-122) = -9 CORRECTING DEFECT 14 (vertices=72, convex hull=95) After retessellation of defect 14, euler #=-112 (106992,315588,208484) : difference with theory (-121) = -9 CORRECTING DEFECT 15 (vertices=38, convex hull=39) After retessellation of defect 15, euler #=-111 (106997,315617,208509) : difference with theory (-120) = -9 CORRECTING DEFECT 16 (vertices=33, convex hull=62) After retessellation of defect 16, euler #=-110 (107020,315703,208573) : difference with theory (-119) = -9 CORRECTING DEFECT 17 (vertices=727, convex hull=304) After retessellation of defect 17, euler #=-110 (107254,316589,209225) : difference with theory (-118) = -8 CORRECTING DEFECT 18 (vertices=33, convex hull=63) After retessellation of defect 18, euler #=-109 (107264,316643,209270) : difference with theory (-117) = -8 CORRECTING DEFECT 19 (vertices=6, convex hull=31) After retessellation of defect 19, euler #=-108 (107265,316658,209285) : difference with theory (-116) = -8 CORRECTING DEFECT 20 (vertices=50, convex hull=69) After retessellation of defect 20, euler #=-107 (107283,316738,209348) : difference with theory (-115) = -8 CORRECTING DEFECT 21 (vertices=34, convex hull=77) After retessellation of defect 21, euler #=-106 (107301,316821,209414) : difference with theory (-114) = -8 CORRECTING DEFECT 22 (vertices=120, convex hull=133) After retessellation of defect 22, euler #=-105 (107343,317011,209563) : difference with theory (-113) = -8 CORRECTING DEFECT 23 (vertices=46, convex hull=82) After retessellation of defect 23, euler #=-104 (107355,317074,209615) : difference with theory (-112) = -8 CORRECTING DEFECT 24 (vertices=45, convex hull=48) After retessellation of defect 24, euler #=-103 (107367,317127,209657) : difference with theory (-111) = -8 CORRECTING DEFECT 25 (vertices=105, convex hull=104) After retessellation of defect 25, euler #=-102 (107395,317260,209763) : difference with theory (-110) = -8 CORRECTING DEFECT 26 (vertices=16, convex hull=56) After retessellation of defect 26, euler #=-101 (107403,317303,209799) : difference with theory (-109) = -8 CORRECTING DEFECT 27 (vertices=971, convex hull=272) After retessellation of defect 27, euler #=-101 (107582,317996,210313) : difference with theory (-108) = -7 CORRECTING DEFECT 28 (vertices=259, convex hull=184) After retessellation of defect 28, euler #=-99 (107647,318281,210535) : difference with theory (-107) = -8 CORRECTING DEFECT 29 (vertices=26, convex hull=62) After retessellation of defect 29, euler #=-98 (107656,318331,210577) : difference with theory (-106) = -8 CORRECTING DEFECT 30 (vertices=74, convex hull=87) After retessellation of defect 30, euler #=-97 (107677,318431,210657) : difference with theory (-105) = -8 CORRECTING DEFECT 31 (vertices=73, convex hull=64) After retessellation of defect 31, euler #=-96 (107715,318570,210759) : difference with theory (-104) = -8 CORRECTING DEFECT 32 (vertices=55, convex hull=59) After retessellation of defect 32, euler #=-95 (107730,318638,210813) : difference with theory (-103) = -8 CORRECTING DEFECT 33 (vertices=59, convex hull=71) After retessellation of defect 33, euler #=-94 (107748,318718,210876) : difference with theory (-102) = -8 CORRECTING DEFECT 34 (vertices=79, convex hull=110) After retessellation of defect 34, euler #=-94 (107784,318878,211000) : difference with theory (-101) = -7 CORRECTING DEFECT 35 (vertices=73, convex hull=46) After retessellation of defect 35, euler #=-93 (107788,318907,211026) : difference with theory (-100) = -7 CORRECTING DEFECT 36 (vertices=53, convex hull=65) After retessellation of defect 36, euler #=-92 (107797,318957,211068) : difference with theory (-99) = -7 CORRECTING DEFECT 37 (vertices=10, convex hull=28) After retessellation of defect 37, euler #=-91 (107799,318971,211081) : difference with theory (-98) = -7 CORRECTING DEFECT 38 (vertices=70, convex hull=98) After retessellation of defect 38, euler #=-90 (107827,319097,211180) : difference with theory (-97) = -7 CORRECTING DEFECT 39 (vertices=839, convex hull=129) After retessellation of defect 39, euler #=-89 (107921,319436,211426) : difference with theory (-96) = -7 CORRECTING DEFECT 40 (vertices=30, convex hull=47) After retessellation of defect 40, euler #=-88 (107938,319506,211480) : difference with theory (-95) = -7 CORRECTING DEFECT 41 (vertices=82, convex hull=33) After retessellation of defect 41, euler #=-87 (107947,319544,211510) : difference with theory (-94) = -7 CORRECTING DEFECT 42 (vertices=39, convex hull=77) After retessellation of defect 42, euler #=-86 (107972,319646,211588) : difference with theory (-93) = -7 CORRECTING DEFECT 43 (vertices=7, convex hull=28) After retessellation of defect 43, euler #=-85 (107973,319658,211600) : difference with theory (-92) = -7 CORRECTING DEFECT 44 (vertices=105, convex hull=48) After retessellation of defect 44, euler #=-84 (107986,319717,211647) : difference with theory (-91) = -7 CORRECTING DEFECT 45 (vertices=122, convex hull=70) After retessellation of defect 45, euler #=-83 (108010,319821,211728) : difference with theory (-90) = -7 CORRECTING DEFECT 46 (vertices=30, convex hull=51) After retessellation of defect 46, euler #=-82 (108019,319865,211764) : difference with theory (-89) = -7 CORRECTING DEFECT 47 (vertices=1164, convex hull=686) After retessellation of defect 47, euler #=-79 (108467,321597,213051) : difference with theory (-88) = -9 CORRECTING DEFECT 48 (vertices=15, convex hull=25) After retessellation of defect 48, euler #=-78 (108468,321608,213062) : difference with theory (-87) = -9 CORRECTING DEFECT 49 (vertices=105, convex hull=34) After retessellation of defect 49, euler #=-77 (108481,321659,213101) : difference with theory (-86) = -9 CORRECTING DEFECT 50 (vertices=11, convex hull=24) After retessellation of defect 50, euler #=-76 (108483,321671,213112) : difference with theory (-85) = -9 CORRECTING DEFECT 51 (vertices=560, convex hull=250) After retessellation of defect 51, euler #=-76 (108632,322250,213542) : difference with theory (-84) = -8 CORRECTING DEFECT 52 (vertices=1564, convex hull=533) After retessellation of defect 52, euler #=-79 (109091,323962,214792) : difference with theory (-83) = -4 CORRECTING DEFECT 53 (vertices=32, convex hull=75) After retessellation of defect 53, euler #=-78 (109111,324053,214864) : difference with theory (-82) = -4 CORRECTING DEFECT 54 (vertices=105, convex hull=36) After retessellation of defect 54, euler #=-77 (109118,324088,214893) : difference with theory (-81) = -4 CORRECTING DEFECT 55 (vertices=51, convex hull=44) After retessellation of defect 55, euler #=-76 (109123,324115,214916) : difference with theory (-80) = -4 CORRECTING DEFECT 56 (vertices=39, convex hull=34) After retessellation of defect 56, euler #=-75 (109131,324151,214945) : difference with theory (-79) = -4 CORRECTING DEFECT 57 (vertices=71, convex hull=92) After retessellation of defect 57, euler #=-74 (109173,324315,215068) : difference with theory (-78) = -4 CORRECTING DEFECT 58 (vertices=283, convex hull=214) After retessellation of defect 58, euler #=-71 (109258,324702,215373) : difference with theory (-77) = -6 CORRECTING DEFECT 59 (vertices=85, convex hull=84) After retessellation of defect 59, euler #=-70 (109277,324797,215450) : difference with theory (-76) = -6 CORRECTING DEFECT 60 (vertices=99, convex hull=138) After retessellation of defect 60, euler #=-68 (109327,325013,215618) : difference with theory (-75) = -7 CORRECTING DEFECT 61 (vertices=39, convex hull=68) After retessellation of defect 61, euler #=-67 (109337,325069,215665) : difference with theory (-74) = -7 CORRECTING DEFECT 62 (vertices=76, convex hull=22) After retessellation of defect 62, euler #=-66 (109346,325100,215688) : difference with theory (-73) = -7 CORRECTING DEFECT 63 (vertices=27, convex hull=67) After retessellation of defect 63, euler #=-65 (109356,325154,215733) : difference with theory (-72) = -7 CORRECTING DEFECT 64 (vertices=284, convex hull=186) After retessellation of defect 64, euler #=-65 (109403,325393,215925) : difference with theory (-71) = -6 CORRECTING DEFECT 65 (vertices=6015, convex hull=2113) After retessellation of defect 65, euler #=-67 (111439,332765,221259) : difference with theory (-70) = -3 CORRECTING DEFECT 66 (vertices=573, convex hull=86) After retessellation of defect 66, euler #=-66 (111479,332924,221379) : difference with theory (-69) = -3 CORRECTING DEFECT 67 (vertices=26, convex hull=47) After retessellation of defect 67, euler #=-65 (111495,332988,221428) : difference with theory (-68) = -3 CORRECTING DEFECT 68 (vertices=14, convex hull=24) After retessellation of defect 68, euler #=-64 (111498,333003,221441) : difference with theory (-67) = -3 CORRECTING DEFECT 69 (vertices=9, convex hull=20) After retessellation of defect 69, euler #=-63 (111499,333012,221450) : difference with theory (-66) = -3 CORRECTING DEFECT 70 (vertices=22, convex hull=27) After retessellation of defect 70, euler #=-62 (111503,333037,221472) : difference with theory (-65) = -3 CORRECTING DEFECT 71 (vertices=5, convex hull=14) After retessellation of defect 71, euler #=-61 (111503,333041,221477) : difference with theory (-64) = -3 CORRECTING DEFECT 72 (vertices=70, convex hull=98) After retessellation of defect 72, euler #=-60 (111532,333168,221576) : difference with theory (-63) = -3 CORRECTING DEFECT 73 (vertices=23, convex hull=48) After retessellation of defect 73, euler #=-59 (111544,333221,221618) : difference with theory (-62) = -3 CORRECTING DEFECT 74 (vertices=24, convex hull=69) After retessellation of defect 74, euler #=-58 (111553,333275,221664) : difference with theory (-61) = -3 CORRECTING DEFECT 75 (vertices=100, convex hull=39) After retessellation of defect 75, euler #=-57 (111562,333316,221697) : difference with theory (-60) = -3 CORRECTING DEFECT 76 (vertices=62, convex hull=47) After retessellation of defect 76, euler #=-56 (111573,333371,221742) : difference with theory (-59) = -3 CORRECTING DEFECT 77 (vertices=162, convex hull=101) After retessellation of defect 77, euler #=-55 (111598,333491,221838) : difference with theory (-58) = -3 CORRECTING DEFECT 78 (vertices=244, convex hull=71) After retessellation of defect 78, euler #=-54 (111612,333561,221895) : difference with theory (-57) = -3 CORRECTING DEFECT 79 (vertices=46, convex hull=56) After retessellation of defect 79, euler #=-53 (111624,333620,221943) : difference with theory (-56) = -3 CORRECTING DEFECT 80 (vertices=53, convex hull=93) After retessellation of defect 80, euler #=-52 (111658,333764,222054) : difference with theory (-55) = -3 CORRECTING DEFECT 81 (vertices=47, convex hull=68) After retessellation of defect 81, euler #=-51 (111667,333818,222100) : difference with theory (-54) = -3 CORRECTING DEFECT 82 (vertices=17, convex hull=19) After retessellation of defect 82, euler #=-50 (111674,333843,222119) : difference with theory (-53) = -3 CORRECTING DEFECT 83 (vertices=61, convex hull=88) After retessellation of defect 83, euler #=-49 (111701,333967,222217) : difference with theory (-52) = -3 CORRECTING DEFECT 84 (vertices=19, convex hull=18) After retessellation of defect 84, euler #=-48 (111704,333979,222227) : difference with theory (-51) = -3 CORRECTING DEFECT 85 (vertices=39, convex hull=26) After retessellation of defect 85, euler #=-47 (111709,334002,222246) : difference with theory (-50) = -3 CORRECTING DEFECT 86 (vertices=22, convex hull=67) After retessellation of defect 86, euler #=-46 (111719,334054,222289) : difference with theory (-49) = -3 CORRECTING DEFECT 87 (vertices=36, convex hull=57) After retessellation of defect 87, euler #=-45 (111743,334146,222358) : difference with theory (-48) = -3 CORRECTING DEFECT 88 (vertices=34, convex hull=24) After retessellation of defect 88, euler #=-44 (111747,334167,222376) : difference with theory (-47) = -3 CORRECTING DEFECT 89 (vertices=28, convex hull=25) After retessellation of defect 89, euler #=-43 (111750,334183,222390) : difference with theory (-46) = -3 CORRECTING DEFECT 90 (vertices=107, convex hull=20) After retessellation of defect 90, euler #=-42 (111754,334201,222405) : difference with theory (-45) = -3 CORRECTING DEFECT 91 (vertices=45, convex hull=50) After retessellation of defect 91, euler #=-41 (111774,334280,222465) : difference with theory (-44) = -3 CORRECTING DEFECT 92 (vertices=464, convex hull=288) After retessellation of defect 92, euler #=-42 (111934,334912,222936) : difference with theory (-43) = -1 CORRECTING DEFECT 93 (vertices=11, convex hull=22) After retessellation of defect 93, euler #=-41 (111935,334920,222944) : difference with theory (-42) = -1 CORRECTING DEFECT 94 (vertices=33, convex hull=43) After retessellation of defect 94, euler #=-40 (111958,335005,223007) : difference with theory (-41) = -1 CORRECTING DEFECT 95 (vertices=115, convex hull=146) After retessellation of defect 95, euler #=-39 (111975,335125,223111) : difference with theory (-40) = -1 CORRECTING DEFECT 96 (vertices=24, convex hull=20) After retessellation of defect 96, euler #=-38 (111977,335136,223121) : difference with theory (-39) = -1 CORRECTING DEFECT 97 (vertices=83, convex hull=47) After retessellation of defect 97, euler #=-37 (111988,335191,223166) : difference with theory (-38) = -1 CORRECTING DEFECT 98 (vertices=45, convex hull=64) After retessellation of defect 98, euler #=-36 (112005,335264,223223) : difference with theory (-37) = -1 CORRECTING DEFECT 99 (vertices=29, convex hull=24) After retessellation of defect 99, euler #=-35 (112008,335279,223236) : difference with theory (-36) = -1 CORRECTING DEFECT 100 (vertices=9, convex hull=35) After retessellation of defect 100, euler #=-34 (112010,335296,223252) : difference with theory (-35) = -1 CORRECTING DEFECT 101 (vertices=90, convex hull=91) After retessellation of defect 101, euler #=-32 (112043,335446,223371) : difference with theory (-34) = -2 CORRECTING DEFECT 102 (vertices=36, convex hull=25) After retessellation of defect 102, euler #=-31 (112047,335465,223387) : difference with theory (-33) = -2 CORRECTING DEFECT 103 (vertices=10, convex hull=31) After retessellation of defect 103, euler #=-30 (112049,335482,223403) : difference with theory (-32) = -2 CORRECTING DEFECT 104 (vertices=5, convex hull=24) After retessellation of defect 104, euler #=-29 (112050,335492,223413) : difference with theory (-31) = -2 CORRECTING DEFECT 105 (vertices=39, convex hull=79) After retessellation of defect 105, euler #=-28 (112059,335554,223467) : difference with theory (-30) = -2 CORRECTING DEFECT 106 (vertices=8, convex hull=21) After retessellation of defect 106, euler #=-27 (112060,335562,223475) : difference with theory (-29) = -2 CORRECTING DEFECT 107 (vertices=9, convex hull=21) After retessellation of defect 107, euler #=-26 (112060,335568,223482) : difference with theory (-28) = -2 CORRECTING DEFECT 108 (vertices=23, convex hull=23) After retessellation of defect 108, euler #=-25 (112063,335583,223495) : difference with theory (-27) = -2 CORRECTING DEFECT 109 (vertices=57, convex hull=75) After retessellation of defect 109, euler #=-24 (112077,335664,223563) : difference with theory (-26) = -2 CORRECTING DEFECT 110 (vertices=22, convex hull=29) After retessellation of defect 110, euler #=-23 (112082,335686,223581) : difference with theory (-25) = -2 CORRECTING DEFECT 111 (vertices=54, convex hull=79) After retessellation of defect 111, euler #=-22 (112111,335805,223672) : difference with theory (-24) = -2 CORRECTING DEFECT 112 (vertices=16, convex hull=24) After retessellation of defect 112, euler #=-21 (112114,335821,223686) : difference with theory (-23) = -2 CORRECTING DEFECT 113 (vertices=49, convex hull=63) After retessellation of defect 113, euler #=-20 (112122,335873,223731) : difference with theory (-22) = -2 CORRECTING DEFECT 114 (vertices=15, convex hull=16) After retessellation of defect 114, euler #=-19 (112125,335886,223742) : difference with theory (-21) = -2 CORRECTING DEFECT 115 (vertices=48, convex hull=53) After retessellation of defect 115, euler #=-18 (112146,335970,223806) : difference with theory (-20) = -2 CORRECTING DEFECT 116 (vertices=155, convex hull=39) After retessellation of defect 116, euler #=-17 (112155,336012,223840) : difference with theory (-19) = -2 CORRECTING DEFECT 117 (vertices=124, convex hull=43) After retessellation of defect 117, euler #=-16 (112170,336074,223888) : difference with theory (-18) = -2 CORRECTING DEFECT 118 (vertices=41, convex hull=52) After retessellation of defect 118, euler #=-15 (112179,336120,223926) : difference with theory (-17) = -2 CORRECTING DEFECT 119 (vertices=61, convex hull=48) After retessellation of defect 119, euler #=-14 (112187,336160,223959) : difference with theory (-16) = -2 CORRECTING DEFECT 120 (vertices=136, convex hull=104) After retessellation of defect 120, euler #=-13 (112215,336292,224064) : difference with theory (-15) = -2 CORRECTING DEFECT 121 (vertices=17, convex hull=19) After retessellation of defect 121, euler #=-13 (112221,336319,224085) : difference with theory (-14) = -1 CORRECTING DEFECT 122 (vertices=45, convex hull=35) After retessellation of defect 122, euler #=-12 (112229,336351,224110) : difference with theory (-13) = -1 CORRECTING DEFECT 123 (vertices=35, convex hull=60) After retessellation of defect 123, euler #=-11 (112252,336443,224180) : difference with theory (-12) = -1 CORRECTING DEFECT 124 (vertices=67, convex hull=38) After retessellation of defect 124, euler #=-11 (112260,336483,224212) : difference with theory (-11) = 0 CORRECTING DEFECT 125 (vertices=28, convex hull=55) After retessellation of defect 125, euler #=-10 (112274,336548,224264) : difference with theory (-10) = 0 CORRECTING DEFECT 126 (vertices=62, convex hull=78) After retessellation of defect 126, euler #=-9 (112292,336637,224336) : difference with theory (-9) = 0 CORRECTING DEFECT 127 (vertices=77, convex hull=103) After retessellation of defect 127, euler #=-8 (112314,336747,224425) : difference with theory (-8) = 0 CORRECTING DEFECT 128 (vertices=20, convex hull=48) After retessellation of defect 128, euler #=-7 (112324,336793,224462) : difference with theory (-7) = 0 CORRECTING DEFECT 129 (vertices=36, convex hull=75) After retessellation of defect 129, euler #=-6 (112338,336866,224522) : difference with theory (-6) = 0 CORRECTING DEFECT 130 (vertices=18, convex hull=26) After retessellation of defect 130, euler #=-5 (112339,336879,224535) : difference with theory (-5) = 0 CORRECTING DEFECT 131 (vertices=37, convex hull=68) After retessellation of defect 131, euler #=-4 (112351,336945,224590) : difference with theory (-4) = 0 CORRECTING DEFECT 132 (vertices=260, convex hull=59) After retessellation of defect 132, euler #=-3 (112375,337040,224662) : difference with theory (-3) = 0 CORRECTING DEFECT 133 (vertices=60, convex hull=51) After retessellation of defect 133, euler #=-2 (112380,337076,224694) : difference with theory (-2) = 0 CORRECTING DEFECT 134 (vertices=136, convex hull=49) After retessellation of defect 134, euler #=-1 (112385,337113,224727) : difference with theory (-1) = 0 CORRECTING DEFECT 135 (vertices=79, convex hull=55) After retessellation of defect 135, euler #=0 (112388,337145,224757) : difference with theory (0) = 0 CORRECTING DEFECT 136 (vertices=11, convex hull=25) After retessellation of defect 136, euler #=1 (112391,337159,224769) : difference with theory (1) = 0 CORRECTING DEFECT 137 (vertices=7, convex hull=23) After retessellation of defect 137, euler #=2 (112392,337170,224780) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.31 (0.03-->11.80) (max @ vno 5422 --> 6363) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.31 (0.03-->11.80) (max @ vno 5422 --> 6363) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 454 mutations (34.7%), 854 crossovers (65.3%), 563 vertices were eliminated building final representation... 17206 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=112392, nf=224780, ne=337170, g=0) writing corrected surface to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 127.8 minutes 0 defective edges removing intersecting faces 000: 2055 intersecting 001: 137 intersecting 002: 18 intersecting 003: 13 intersecting expanding nbhd size to 2 004: 14 intersecting 005: 13 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 112392 - 337170 + 224780 = 2 --> 0 holes F =2V-4: 224780 = 224784-4 (0) 2E=3F: 674340 = 674340 (0) total defect index = 0 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 882 intersecting 001: 91 intersecting 002: 13 intersecting expanding nbhd size to 2 003: 13 intersecting expanding nbhd size to 3 004: 14 intersecting 005: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sat Dec 7 12:19:23 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... 8936 bright wm thresholded. 59 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.orig... computing class statistics... border white: 236071 voxels (1.41%) border gray 269932 voxels (1.61%) WM (91.0): 91.4 +- 8.0 [70.0 --> 110.0] GM (80.0) : 78.4 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70) setting MAX_BORDER_WHITE to 102.0 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 50.8 (was 40) setting MAX_GRAY to 86.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.26 (0.01-->4.99) (max @ vno 109667 --> 110334) face area 0.27 +- 0.14 (0.00-->3.96) mean absolute distance = 0.95 +- 1.16 3945 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=94, GM=73 mean inside = 90.5, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=81.3, 766 (766) missing vertices, mean dist 0.3 [1.0 (%30.6)->0.9 (%69.4))] %58 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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 0.88 +- 0.30 (0.04-->5.07) (max @ vno 109667 --> 110334) face area 0.27 +- 0.16 (0.00-->4.22) mean absolute distance = 0.53 +- 0.77 3609 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3574402.8, rms=7.50 001: dt: 0.5000, sse=4824757.0, rms=5.516 (0.000%) 002: dt: 0.5000, sse=5194365.5, rms=4.495 (0.000%) 003: dt: 0.5000, sse=5517697.5, rms=3.951 (0.000%) 004: dt: 0.5000, sse=5636841.5, rms=3.647 (0.000%) 005: dt: 0.5000, sse=5769381.5, rms=3.439 (0.000%) 006: dt: 0.5000, sse=5825981.5, rms=3.298 (0.000%) 007: dt: 0.5000, sse=5883011.0, rms=3.187 (0.000%) 008: dt: 0.5000, sse=5888509.0, rms=3.108 (0.000%) 009: dt: 0.5000, sse=5937002.5, rms=3.048 (0.000%) rms = 3.00, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=5904396.5, rms=3.002 (0.000%) 011: dt: 0.2500, sse=4432849.0, rms=2.571 (0.000%) 012: dt: 0.2500, sse=4279717.0, rms=2.484 (0.000%) rms = 2.47, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=4224312.0, rms=2.468 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=4160461.0, rms=2.430 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 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 removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=84.1, 810 (254) missing vertices, mean dist -0.3 [0.6 (%71.2)->0.4 (%28.8))] %76 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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 0.87 +- 0.30 (0.07-->4.85) (max @ vno 109667 --> 110334) face area 0.32 +- 0.19 (0.00-->5.22) mean absolute distance = 0.35 +- 0.50 2763 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4514030.5, rms=4.37 015: dt: 0.5000, sse=4902109.0, rms=3.024 (0.000%) 016: dt: 0.5000, sse=5323216.0, rms=2.754 (0.000%) rms = 2.70, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=5489683.0, rms=2.704 (0.000%) 018: dt: 0.2500, sse=4679129.5, rms=2.184 (0.000%) 019: dt: 0.2500, sse=4524089.5, rms=2.061 (0.000%) rms = 2.05, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4437545.5, rms=2.048 (0.000%) 021: dt: 0.1250, sse=4388366.0, rms=1.997 (0.000%) rms = 1.99, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4364879.0, rms=1.987 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group mean border=85.7, 851 (175) missing vertices, mean dist -0.1 [0.4 (%65.4)->0.3 (%34.6))] %85 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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 0.88 +- 0.30 (0.03-->4.75) (max @ vno 109667 --> 110334) face area 0.32 +- 0.18 (0.00-->4.90) mean absolute distance = 0.28 +- 0.42 3021 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4470057.5, rms=3.08 023: dt: 0.5000, sse=4883080.5, rms=2.375 (0.000%) rms = 2.46, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4655754.0, rms=2.029 (0.000%) 025: dt: 0.2500, sse=4639060.5, rms=1.879 (0.000%) rms = 1.84, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4601916.5, rms=1.845 (0.000%) rms = 1.80, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4539387.5, rms=1.803 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=86.2, 971 (147) missing vertices, mean dist -0.0 [0.3 (%54.1)->0.3 (%45.9))] %87 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4550493.0, rms=1.94 028: dt: 0.5000, sse=5981820.0, rms=1.671 (0.000%) rms = 2.09, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5532790.0, rms=1.495 (0.000%) rms = 1.52, time step reduction 2 of 3 to 0.125... rms = 1.47, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5479685.5, rms=1.474 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group generating cortex label... 27 non-cortical segments detected only using segment with 1666 vertices erasing segment 1 (vno[0] = 36136) erasing segment 2 (vno[0] = 38213) erasing segment 3 (vno[0] = 63864) erasing segment 4 (vno[0] = 69014) erasing segment 5 (vno[0] = 69853) erasing segment 6 (vno[0] = 69885) erasing segment 7 (vno[0] = 71561) erasing segment 8 (vno[0] = 71600) erasing segment 9 (vno[0] = 71604) erasing segment 10 (vno[0] = 72354) erasing segment 11 (vno[0] = 73083) erasing segment 12 (vno[0] = 73838) erasing segment 13 (vno[0] = 74487) erasing segment 14 (vno[0] = 74558) erasing segment 15 (vno[0] = 75071) erasing segment 16 (vno[0] = 75104) erasing segment 17 (vno[0] = 75105) erasing segment 18 (vno[0] = 76148) erasing segment 19 (vno[0] = 76744) erasing segment 20 (vno[0] = 77377) erasing segment 21 (vno[0] = 78634) erasing segment 22 (vno[0] = 78638) erasing segment 23 (vno[0] = 79431) erasing segment 24 (vno[0] = 81090) erasing segment 25 (vno[0] = 81620) erasing segment 26 (vno[0] = 111037) writing cortex label to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/rh.cortex.label... writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.curv writing smoothed area to rh.area writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.area vertex spacing 0.88 +- 0.29 (0.05-->4.71) (max @ vno 109667 --> 110334) face area 0.32 +- 0.18 (0.00-->4.55) refinement took 4.2 minutes #-------------------------------------------- #@# Smooth2 rh Sat Dec 7 12:23:33 CST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 Sat Dec 7 12:23:36 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 43.4 mm, total surface area = 64330 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.133 (target=0.015) step 005: RMS=0.095 (target=0.015) step 010: RMS=0.077 (target=0.015) step 015: RMS=0.067 (target=0.015) step 020: RMS=0.058 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.028 (target=0.015) step 060: RMS=0.026 (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 103 vertices thresholded to be in k1 ~ [-0.44 3.32], k2 ~ [-0.20 0.14] total integrated curvature = 0.234*4pi (2.939) --> 1 handles ICI = 1.4, FI = 10.5, variation=175.708 107 vertices thresholded to be in [-0.13 0.03] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 87 vertices thresholded to be in [-0.23 0.96] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.021, std = 0.029 done. #----------------------------------------- #@# Curvature Stats rh Sat Dec 7 12:25:04 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm MPS3007-1 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 [ MPS3007-1/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 [ 246 ] Gb_filter = 0 #-------------------------------------------- #@# Sphere rh Sat Dec 7 12:25:07 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 0.306... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=node1, 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 %22.66 pass 1: epoch 2 of 3 starting distance error %22.58 unfolding complete - removing small folds... starting distance error %22.38 removing remaining folds... final distance error %22.42 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.67 hours #-------------------------------------------- #@# Surf Reg rh Sat Dec 7 13:05:02 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_register -curv ../surf/rh.sphere /soft/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 /soft/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=node1, 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=node1, 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 = 0.595 curvature mean = 0.016, std = 0.935 curvature mean = 0.023, std = 0.891 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 32.00) sse = 307413.4, tmin=0.8066 d=32.00 min @ (8.00, 0.00, -8.00) sse = 257685.7, tmin=1.6189 d=16.00 min @ (-4.00, -4.00, 4.00) sse = 236478.7, tmin=2.4348 d=8.00 min @ (2.00, 0.00, 0.00) sse = 234942.0, tmin=3.3001 d=4.00 min @ (0.00, 1.00, 0.00) sse = 234287.2, tmin=4.1753 d=2.00 min @ (-0.50, -0.50, 0.50) sse = 234002.7, tmin=5.0479 d=1.00 min @ (0.25, 0.00, 0.00) sse = 233969.3, tmin=5.8878 tol=1.0e+00, sigma=0.5, host=node1, 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 singular matrix in quadratic form MRISrigidBodyAlignGlobal() done 6.71 min curvature mean = -0.009, std = 0.975 curvature mean = 0.010, std = 0.953 curvature mean = -0.010, std = 0.988 curvature mean = 0.004, std = 0.979 curvature mean = -0.011, std = 0.991 curvature mean = 0.001, std = 0.991 2 Reading smoothwm curvature mean = -0.041, std = 0.438 curvature mean = 0.004, std = 0.071 curvature mean = 0.061, std = 0.245 curvature mean = 0.003, std = 0.085 curvature mean = 0.035, std = 0.362 curvature mean = 0.003, std = 0.092 curvature mean = 0.020, std = 0.476 curvature mean = 0.003, std = 0.094 curvature mean = 0.007, std = 0.593 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Sat Dec 7 13:25:49 CST 2013 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Sat Dec 7 13:25:51 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mrisp_paint -a 5 /soft/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 /soft/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Sat Dec 7 13:25:52 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 rh ../surf/rh.sphere.reg /soft/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 /soft/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... 1283 labels changed using aseg relabeling using gibbs priors... 000: 2590 changed, 112392 examined... 001: 601 changed, 11248 examined... 002: 156 changed, 3324 examined... 003: 54 changed, 919 examined... 004: 24 changed, 303 examined... 005: 11 changed, 159 examined... 006: 3 changed, 55 examined... 007: 3 changed, 26 examined... 008: 1 changed, 15 examined... 009: 1 changed, 5 examined... 010: 0 changed, 11 examined... 200 labels changed using aseg 000: 110 total segments, 73 labels (651 vertices) changed 001: 37 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... 1032 vertices marked for relabeling... 1032 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 30 seconds. #-------------------------------------------- #@# Make Pial Surf rh Sat Dec 7 13:26:22 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... 8936 bright wm thresholded. 59 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.orig... computing class statistics... border white: 236071 voxels (1.41%) border gray 269932 voxels (1.61%) WM (91.0): 91.4 +- 8.0 [70.0 --> 110.0] GM (80.0) : 78.4 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 61.9 (was 70) setting MAX_BORDER_WHITE to 102.0 (was 105) setting MIN_BORDER_WHITE to 73.0 (was 85) setting MAX_CSF to 50.8 (was 40) setting MAX_GRAY to 86.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 67.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=94, GM=73 mean inside = 90.5, 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.26 (0.01-->4.99) (max @ vno 109667 --> 110334) face area 0.27 +- 0.14 (0.00-->3.96) mean absolute distance = 0.95 +- 1.16 3945 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 5 points - only 0.00% unknown deleting segment 7 with 6 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown mean border=81.3, 766 (766) missing vertices, mean dist 0.3 [1.0 (%30.6)->0.9 (%69.4))] %58 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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 0.88 +- 0.30 (0.04-->5.07) (max @ vno 109667 --> 110334) face area 0.27 +- 0.16 (0.00-->4.22) mean absolute distance = 0.53 +- 0.77 3607 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3574616.5, rms=7.50 001: dt: 0.5000, sse=4826161.0, rms=5.515 (0.000%) 002: dt: 0.5000, sse=5195391.0, rms=4.495 (0.000%) 003: dt: 0.5000, sse=5519478.5, rms=3.950 (0.000%) 004: dt: 0.5000, sse=5638612.0, rms=3.646 (0.000%) 005: dt: 0.5000, sse=5769803.5, rms=3.438 (0.000%) 006: dt: 0.5000, sse=5827710.0, rms=3.298 (0.000%) 007: dt: 0.5000, sse=5883393.5, rms=3.187 (0.000%) 008: dt: 0.5000, sse=5890739.5, rms=3.108 (0.000%) 009: dt: 0.5000, sse=5938549.5, rms=3.048 (0.000%) rms = 3.00, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=5907217.5, rms=3.001 (0.000%) 011: dt: 0.2500, sse=4432960.5, rms=2.571 (0.000%) 012: dt: 0.2500, sse=4280166.0, rms=2.484 (0.000%) rms = 2.47, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=4224384.0, rms=2.468 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 014: dt: 0.1250, sse=4161203.0, rms=2.429 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 9 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 50.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 11 with 11 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 19 with 4 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 20 with 1 points - only 0.00% unknown mean border=84.1, 811 (254) missing vertices, mean dist -0.3 [0.6 (%71.2)->0.4 (%28.8))] %76 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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 0.87 +- 0.30 (0.07-->4.85) (max @ vno 109667 --> 110334) face area 0.32 +- 0.19 (0.00-->5.22) mean absolute distance = 0.35 +- 0.50 2767 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4519882.0, rms=4.37 015: dt: 0.5000, sse=4906273.0, rms=3.025 (0.000%) 016: dt: 0.5000, sse=5327947.5, rms=2.755 (0.000%) rms = 2.71, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=5495698.0, rms=2.705 (0.000%) 018: dt: 0.2500, sse=4683456.0, rms=2.186 (0.000%) 019: dt: 0.2500, sse=4528880.5, rms=2.062 (0.000%) rms = 2.05, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4440925.0, rms=2.049 (0.000%) 021: dt: 0.1250, sse=4391948.0, rms=1.999 (0.000%) rms = 1.99, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4369416.0, rms=1.989 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 9 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group 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 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 points - only 0.00% unknown mean border=85.7, 854 (175) missing vertices, mean dist -0.1 [0.4 (%65.5)->0.3 (%34.5))] %85 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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 0.88 +- 0.30 (0.03-->4.75) (max @ vno 109667 --> 110334) face area 0.32 +- 0.18 (0.00-->4.90) mean absolute distance = 0.28 +- 0.42 3014 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4474660.0, rms=3.08 023: dt: 0.5000, sse=4885389.5, rms=2.377 (0.000%) rms = 2.46, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4659137.0, rms=2.030 (0.000%) 025: dt: 0.2500, sse=4642664.5, rms=1.881 (0.000%) rms = 1.85, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4605958.0, rms=1.847 (0.000%) rms = 1.81, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=4544349.0, rms=1.806 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 15 points - only 0.00% unknown deleting segment 1 with 8 points - only 0.00% unknown deleting segment 2 with 6 points - only 0.00% unknown deleting segment 4 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 7 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 5 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown mean border=86.2, 973 (147) missing vertices, mean dist -0.0 [0.3 (%54.1)->0.3 (%45.9))] %87 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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=4555496.0, rms=1.95 028: dt: 0.5000, sse=5989410.0, rms=1.673 (0.000%) rms = 2.09, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5539688.5, rms=1.496 (0.000%) rms = 1.52, time step reduction 2 of 3 to 0.125... rms = 1.48, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5486370.0, rms=1.475 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 6 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=62.4, 842 (842) missing vertices, mean dist 2.4 [2.2 (%0.1)->3.2 (%99.9))] %29 local maxima, %40 large gradients and %25 min vals, 754 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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=14804864.0, rms=24.24 001: dt: 0.5000, sse=12340520.0, rms=21.591 (0.000%) 002: dt: 0.5000, sse=10578271.0, rms=19.462 (0.000%) 003: dt: 0.5000, sse=9316506.0, rms=17.737 (0.000%) 004: dt: 0.5000, sse=8439935.0, rms=16.292 (0.000%) 005: dt: 0.5000, sse=7855486.5, rms=15.050 (0.000%) 006: dt: 0.5000, sse=7544733.0, rms=13.992 (0.000%) 007: dt: 0.5000, sse=7333913.5, rms=13.088 (0.000%) 008: dt: 0.5000, sse=7214375.0, rms=12.277 (0.000%) 009: dt: 0.5000, sse=7158580.0, rms=11.575 (0.000%) 010: dt: 0.5000, sse=7126893.0, rms=10.983 (0.000%) 011: dt: 0.5000, sse=7127176.5, rms=10.448 (0.000%) 012: dt: 0.5000, sse=7146392.5, rms=9.964 (0.000%) 013: dt: 0.5000, sse=7155839.5, rms=9.527 (0.000%) 014: dt: 0.5000, sse=7161491.5, rms=9.119 (0.000%) 015: dt: 0.5000, sse=7164488.5, rms=8.727 (0.000%) 016: dt: 0.5000, sse=7193373.5, rms=8.342 (0.000%) 017: dt: 0.5000, sse=7193881.5, rms=7.968 (0.000%) 018: dt: 0.5000, sse=7171791.5, rms=7.608 (0.000%) 019: dt: 0.5000, sse=7169802.0, rms=7.270 (0.000%) 020: dt: 0.5000, sse=7157275.5, rms=6.974 (0.000%) 021: dt: 0.5000, sse=7159879.5, rms=6.714 (0.000%) 022: dt: 0.5000, sse=7111126.5, rms=6.507 (0.000%) 023: dt: 0.5000, sse=7147564.5, rms=6.334 (0.000%) 024: dt: 0.5000, sse=7105324.0, rms=6.207 (0.000%) 025: dt: 0.5000, sse=7126065.5, rms=6.100 (0.000%) 026: dt: 0.5000, sse=7086017.5, rms=5.986 (0.000%) 027: dt: 0.5000, sse=7069483.0, rms=5.899 (0.000%) 028: dt: 0.5000, sse=7044480.5, rms=5.833 (0.000%) 029: dt: 0.5000, sse=7071013.5, rms=5.773 (0.000%) rms = 5.74, time step reduction 1 of 3 to 0.250... 030: dt: 0.5000, sse=7018136.5, rms=5.743 (0.000%) positioning took 2.1 minutes mean border=58.7, 1510 (173) missing vertices, mean dist 0.3 [0.2 (%33.2)->0.6 (%66.8))] %52 local maxima, %24 large gradients and %18 min vals, 332 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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=8028374.0, rms=7.98 031: dt: 0.5000, sse=7236457.5, rms=6.445 (0.000%) rms = 6.40, time step reduction 1 of 3 to 0.250... 032: dt: 0.5000, sse=7965885.5, rms=6.396 (0.000%) 033: dt: 0.2500, sse=6017570.0, rms=5.426 (0.000%) 034: dt: 0.2500, sse=5939108.0, rms=5.144 (0.000%) 035: dt: 0.2500, sse=5880419.5, rms=5.093 (0.000%) 036: dt: 0.2500, sse=5926205.5, rms=5.026 (0.000%) rms = 4.98, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5889726.5, rms=4.980 (0.000%) 038: dt: 0.1250, sse=5414662.5, rms=4.503 (0.000%) 039: dt: 0.1250, sse=5407886.0, rms=4.407 (0.000%) rms = 4.38, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5377039.0, rms=4.385 (0.000%) positioning took 0.7 minutes mean border=57.2, 1965 (113) missing vertices, mean dist 0.1 [0.2 (%36.2)->0.4 (%63.8))] %61 local maxima, %15 large gradients and %17 min vals, 353 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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=5473642.0, rms=4.89 rms = 5.87, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=5326383.0, rms=4.475 (0.000%) rms = 4.43, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5424300.5, rms=4.428 (0.000%) 043: dt: 0.1250, sse=5297323.5, rms=4.276 (0.000%) 044: dt: 0.1250, sse=5310957.0, rms=4.207 (0.000%) rms = 4.18, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=5333323.0, rms=4.183 (0.000%) positioning took 0.4 minutes mean border=56.5, 3529 (97) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.3 (%55.9))] %61 local maxima, %15 large gradients and %17 min vals, 288 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5339814.0, rms=4.22 rms = 5.03, time step reduction 1 of 3 to 0.250... 046: dt: 0.2500, sse=5331100.0, rms=4.072 (0.000%) rms = 4.03, time step reduction 2 of 3 to 0.125... 047: dt: 0.2500, sse=5588381.5, rms=4.029 (0.000%) 048: dt: 0.1250, sse=5489830.0, rms=3.928 (0.000%) 049: dt: 0.1250, sse=5513522.0, rms=3.871 (0.000%) rms = 3.85, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=5568101.5, rms=3.847 (0.000%) positioning took 0.4 minutes writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.area.pial vertex spacing 1.07 +- 0.56 (0.03-->14.99) (max @ vno 109666 --> 110334) face area 0.45 +- 0.44 (0.00-->27.15) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 112392 vertices processed 25000 of 112392 vertices processed 50000 of 112392 vertices processed 75000 of 112392 vertices processed 100000 of 112392 vertices processed 0 of 112392 vertices processed 25000 of 112392 vertices processed 50000 of 112392 vertices processed 75000 of 112392 vertices processed 100000 of 112392 vertices processed thickness calculation complete, 2791:12215 truncations. 16895 vertices at 0 distance 49465 vertices at 1 distance 59057 vertices at 2 distance 45180 vertices at 3 distance 24820 vertices at 4 distance 10806 vertices at 5 distance 4345 vertices at 6 distance 1753 vertices at 7 distance 835 vertices at 8 distance 417 vertices at 9 distance 243 vertices at 10 distance 163 vertices at 11 distance 136 vertices at 12 distance 101 vertices at 13 distance 83 vertices at 14 distance 66 vertices at 15 distance 76 vertices at 16 distance 60 vertices at 17 distance 39 vertices at 18 distance 26 vertices at 19 distance 64 vertices at 20 distance writing curvature file /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.thickness positioning took 8.0 minutes #-------------------------------------------- #@# Surf Volume rh Sat Dec 7 13:34:21 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 Sat Dec 7 13:34:21 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts pctsurfcon --s MPS3007-1 --rh-only Log file is /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts/pctsurfcon.log Sat Dec 7 13:34:21 CST 2013 setenv SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post cd /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts /soft/freesurfer/5.3.0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node1109 2.6.32-358.14.1.el6.x86_64 #1 SMP Tue Jul 16 23:51:20 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /soft/freesurfer/5.3.0 mri_vol2surf --mov /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.6232/rh.wm.mgh --regheader MPS3007-1 --cortex srcvol = /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/rh.cortex.label Reading surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 = 58544 Masking with /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/rh.cortex.label Writing to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.6232/rh.wm.mgh Dim: 112392 1 1 mri_vol2surf --mov /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.6232/rh.gm.mgh --projfrac 0.3 --regheader MPS3007-1 --cortex srcvol = /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/rh.cortex.label Reading surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Done reading source surface Reading thickness /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 = 70266 Masking with /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/rh.cortex.label Writing to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.6232/rh.gm.mgh Dim: 112392 1 1 mri_concat /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.6232/rh.wm.mgh /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/tmp.pctsurfcon.6232/rh.gm.mgh --paired-diff-norm --mul 100 --o /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.w-g.pct.mgh mri_segstats --in /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.w-g.pct.mgh --annot MPS3007-1 rh aparc --sum /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.w-g.pct.mgh --annot MPS3007-1 rh aparc --sum /lustre/kovacv/FS/MPSIII-post/MPS3007-1/stats/rh.w-g.pct.stats --snr sysname Linux hostname node1109 machine x86_64 user kovacv 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.w-g.pct.mgh Vertex Area is 0.64118 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1473 912.383 2 2002 caudalanteriorcingulate 1022 685.012 3 2003 caudalmiddlefrontal 2568 1747.388 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2232 1403.018 6 2006 entorhinal 338 230.388 7 2007 fusiform 3741 2512.800 8 2008 inferiorparietal 6189 4104.021 9 2009 inferiortemporal 2632 1825.251 10 2010 isthmuscingulate 1083 698.758 11 2011 lateraloccipital 6243 3964.792 12 2012 lateralorbitofrontal 2337 1597.269 13 2013 lingual 3643 2371.617 14 2014 medialorbitofrontal 2158 1498.012 15 2015 middletemporal 2885 1833.388 16 2016 parahippocampal 868 564.416 17 2017 paracentral 2065 1299.038 18 2018 parsopercularis 1652 1122.485 19 2019 parsorbitalis 839 561.547 20 2020 parstriangularis 1580 1096.592 21 2021 pericalcarine 2356 1565.833 22 2022 postcentral 7582 4319.805 23 2023 posteriorcingulate 1577 1103.039 24 2024 precentral 6805 4464.187 25 2025 precuneus 5200 3407.270 26 2026 rostralanteriorcingulate 935 598.625 27 2027 rostralmiddlefrontal 6608 4253.565 28 2028 superiorfrontal 7896 5281.518 29 2029 superiorparietal 6926 4256.824 30 2030 superiortemporal 5371 3242.134 31 2031 supramarginal 4775 2802.537 32 2032 frontalpole 340 238.242 33 2033 temporalpole 450 322.006 34 2034 transversetemporal 616 369.350 35 2035 insula 2392 1548.267 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Sat Dec 7 13:34:28 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 MPS3007-1 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 1473 912 3053 2.870 0.836 0.202 0.177 101 13.1 bankssts 1022 685 3406 3.747 0.965 0.154 0.071 59 3.3 caudalanteriorcingulate 2568 1747 7209 3.205 0.755 0.157 0.089 64 9.5 caudalmiddlefrontal 2232 1403 3850 2.269 0.700 0.207 1.368 390 15.2 cuneus 338 230 1668 3.877 0.837 0.199 0.112 9 1.7 entorhinal 3741 2513 9169 3.172 0.887 0.215 0.225 217 35.2 fusiform 6189 4104 17495 3.088 0.885 0.209 0.250 784 55.7 inferiorparietal 2632 1825 8774 3.432 0.833 0.223 0.191 195 20.9 inferiortemporal 1083 699 2827 3.216 1.111 0.179 0.207 71 5.5 isthmuscingulate 6243 3965 13804 2.713 0.987 0.227 0.214 599 62.5 lateraloccipital 2337 1597 7872 3.619 0.961 0.160 0.115 63 11.5 lateralorbitofrontal 3643 2372 7069 2.584 0.777 0.197 0.159 175 24.7 lingual 2158 1498 7318 3.533 0.862 0.179 0.095 107 8.3 medialorbitofrontal 2885 1833 10047 3.562 0.890 0.197 0.164 322 17.0 middletemporal 868 564 2149 2.847 0.742 0.139 0.068 18 2.5 parahippocampal 2065 1299 4603 3.038 0.896 0.164 0.130 98 12.4 paracentral 1652 1122 4586 3.165 0.736 0.147 0.076 38 5.2 parsopercularis 839 562 3080 3.690 0.972 0.215 0.344 93 14.8 parsorbitalis 1580 1097 5274 3.379 0.903 0.170 0.091 46 6.3 parstriangularis 2356 1566 3226 1.908 0.640 0.220 0.192 436 21.1 pericalcarine 7582 4320 11507 2.315 0.823 0.218 0.263 707 81.0 postcentral 1577 1103 4457 3.110 1.102 0.165 0.100 71 7.8 posteriorcingulate 6805 4464 16792 3.098 0.867 0.162 0.109 197 32.9 precentral 5200 3407 12760 2.927 0.868 0.182 0.177 312 39.8 precuneus 935 599 2597 3.641 0.605 0.159 0.094 22 4.1 rostralanteriorcingulate 6608 4254 16172 2.870 0.795 0.169 0.206 298 29.9 rostralmiddlefrontal 7896 5282 23863 3.463 0.761 0.162 0.491 1026 37.5 superiorfrontal 6926 4257 13309 2.578 0.718 0.175 0.162 375 43.3 superiorparietal 5371 3242 11016 2.766 1.009 0.217 2.451 2369 54.1 superiortemporal 4775 2803 8282 2.769 0.976 0.211 0.281 333 50.8 supramarginal 340 238 1569 4.115 0.537 0.259 0.242 21 2.5 frontalpole 450 322 2166 3.582 1.161 0.375 0.384 385 7.8 temporalpole 616 369 1237 2.905 0.774 0.169 0.170 36 5.4 transversetemporal 2392 1548 6256 3.465 1.056 0.130 0.128 115 11.9 insula #----------------------------------------- #@# Cortical Parc 2 rh Sat Dec 7 13:34:37 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 rh ../surf/rh.sphere.reg /soft/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 /soft/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... 47 labels changed using aseg relabeling using gibbs priors... 000: 7975 changed, 112392 examined... 001: 1878 changed, 30466 examined... 002: 564 changed, 9714 examined... 003: 263 changed, 3193 examined... 004: 123 changed, 1470 examined... 005: 65 changed, 718 examined... 006: 24 changed, 366 examined... 007: 8 changed, 130 examined... 008: 7 changed, 54 examined... 009: 2 changed, 30 examined... 010: 0 changed, 15 examined... 24 labels changed using aseg 000: 248 total segments, 166 labels (1593 vertices) changed 001: 90 total segments, 8 labels (53 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 101 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1027 vertices marked for relabeling... 1027 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 37 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Sat Dec 7 13:35:14 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 MPS3007-1 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 778 527 2282 3.137 0.983 0.188 0.141 32 3.4 G_and_S_frontomargin 956 636 3020 3.390 1.028 0.231 0.190 66 7.8 G_and_S_occipital_inf 1314 768 2735 2.673 0.686 0.192 0.181 76 9.7 G_and_S_paracentral 1486 892 3315 3.180 0.910 0.190 0.146 58 9.6 G_and_S_subcentral 768 476 2241 3.118 0.809 0.188 0.124 26 4.6 G_and_S_transv_frontopol 2582 1720 6821 3.301 0.790 0.162 0.086 85 9.4 G_and_S_cingul-Ant 1331 895 3911 3.529 0.732 0.156 0.167 467 12.7 G_and_S_cingul-Mid-Ant 1122 773 3276 3.446 0.764 0.146 0.092 42 5.4 G_and_S_cingul-Mid-Post 442 290 1798 3.831 0.757 0.249 0.190 30 3.3 G_cingul-Post-dorsal 242 149 944 4.118 0.560 0.249 0.654 40 2.4 G_cingul-Post-ventral 1971 1208 3427 2.216 0.725 0.227 1.555 397 15.4 G_cuneus 1157 807 4733 3.656 0.620 0.185 0.123 46 5.6 G_front_inf-Opercular 261 179 1012 3.630 0.628 0.230 0.141 18 1.9 G_front_inf-Orbital 975 642 4037 3.814 0.767 0.198 0.122 36 4.9 G_front_inf-Triangul 3628 2271 11700 3.292 0.789 0.201 0.333 242 23.4 G_front_middle 5463 3637 19937 3.734 0.733 0.191 0.693 677 31.3 G_front_sup 295 188 1129 3.983 1.234 0.101 0.147 14 2.7 G_Ins_lg_and_S_cent_ins 447 280 1558 3.823 1.134 0.134 0.162 43 2.6 G_insular_short 2477 1543 7541 3.164 0.969 0.275 0.343 397 42.6 G_occipital_middle 1660 901 3200 2.674 0.662 0.188 0.223 87 12.8 G_occipital_sup 1348 856 4119 3.358 0.634 0.182 0.109 65 7.1 G_oc-temp_lat-fusifor 2274 1441 4981 2.590 0.869 0.233 0.223 159 21.4 G_oc-temp_med-Lingual 927 615 3176 3.343 0.929 0.166 0.137 27 3.9 G_oc-temp_med-Parahip 1869 1308 8558 4.074 0.735 0.207 0.129 134 9.9 G_orbital 2643 1634 8287 3.344 1.029 0.265 0.317 530 35.5 G_pariet_inf-Angular 2688 1519 4783 2.615 1.040 0.243 0.314 217 34.0 G_pariet_inf-Supramar 2225 1346 4885 2.643 0.689 0.202 0.199 169 16.7 G_parietal_sup 3248 1677 4567 2.219 0.716 0.266 0.403 495 53.5 G_postcentral 2486 1549 7791 3.500 0.854 0.189 0.149 95 16.3 G_precentral 2499 1626 8022 3.173 0.818 0.225 0.262 178 30.7 G_precuneus 535 401 2480 3.851 0.704 0.222 0.107 38 2.3 G_rectus 146 88 437 4.163 0.905 0.091 0.209 2 2.1 G_subcallosal 436 255 1021 3.158 0.720 0.171 0.178 31 3.9 G_temp_sup-G_T_transv 2476 1378 5316 2.677 1.082 0.256 0.308 560 30.9 G_temp_sup-Lateral 461 292 1476 3.028 1.111 0.195 0.152 24 2.8 G_temp_sup-Plan_polar 575 337 681 2.067 0.808 0.206 0.224 79 6.9 G_temp_sup-Plan_tempo 1613 1131 6039 3.555 0.788 0.229 0.158 98 11.5 G_temporal_inf 1997 1248 7887 3.805 0.859 0.230 0.208 308 14.4 G_temporal_middle 279 205 544 2.579 0.506 0.124 0.040 2 0.5 Lat_Fis-ant-Horizont 225 146 675 3.528 0.708 0.133 0.057 3 0.5 Lat_Fis-ant-Vertical 1331 897 2140 2.783 0.703 0.153 0.259 65 10.2 Lat_Fis-post 2740 1745 4713 2.206 0.828 0.236 0.197 372 25.0 Pole_occipital 1176 767 4898 3.571 0.863 0.270 0.330 431 18.2 Pole_temporal 2549 1692 3607 2.190 0.813 0.177 0.123 245 14.4 S_calcarine 3313 2164 4294 2.158 0.755 0.151 0.104 80 14.6 S_central 1150 802 2204 2.575 0.764 0.117 0.038 9 1.9 S_cingul-Marginalis 526 343 1182 3.461 0.815 0.108 0.110 7 1.1 S_circular_insula_ant 980 659 2218 3.283 1.004 0.175 11.456 1531 5.7 S_circular_insula_inf 1309 885 2436 2.936 0.671 0.128 0.075 22 4.6 S_circular_insula_sup 867 648 2000 2.912 1.244 0.275 0.260 62 9.3 S_collat_transv_ant 319 207 415 2.304 0.442 0.130 0.076 4 1.3 S_collat_transv_post 1330 890 2220 2.470 0.546 0.125 0.043 17 2.2 S_front_inf 1609 1072 2760 2.533 0.557 0.137 0.064 34 4.2 S_front_middle 1769 1216 3623 3.018 0.608 0.127 0.049 16 3.7 S_front_sup 121 78 267 3.153 0.598 0.140 0.056 1 0.3 S_interm_prim-Jensen 2286 1498 3890 2.600 0.721 0.147 0.106 105 12.6 S_intrapariet_and_P_trans 955 679 1868 2.535 0.700 0.132 0.052 11 1.8 S_oc_middle_and_Lunatus 1396 926 2169 2.373 0.662 0.139 0.078 56 3.5 S_oc_sup_and_transversal 450 319 1266 2.901 0.890 0.173 0.099 13 2.0 S_occipital_ant 721 473 1614 3.483 0.957 0.256 0.298 78 7.7 S_oc-temp_lat 1748 1187 2896 2.777 0.590 0.157 0.102 42 7.6 S_oc-temp_med_and_Lingual 396 250 724 2.681 0.677 0.160 0.548 37 12.1 S_orbital_lateral 495 331 1345 3.199 1.096 0.116 0.091 13 2.2 S_orbital_med-olfact 665 453 1720 3.295 1.025 0.146 0.058 10 1.7 S_orbital-H_Shaped 2189 1467 4077 2.763 0.910 0.141 0.097 44 6.1 S_parieto_occipital 1468 959 2491 2.849 1.253 0.132 0.055 40 3.3 S_pericallosal 1996 1279 3368 2.767 0.705 0.169 0.123 93 9.3 S_postcentral 1369 957 2848 2.936 0.619 0.124 0.038 12 2.3 S_precentral-inf-part 1208 810 2038 2.803 0.601 0.116 0.041 8 2.2 S_precentral-sup-part 82 57 204 2.943 0.489 0.128 0.037 1 0.1 S_suborbital 902 591 1645 2.543 0.582 0.177 0.117 55 4.7 S_subparietal 623 401 1222 2.913 0.654 0.179 0.243 42 6.1 S_temporal_inf 4734 3063 9248 2.794 0.766 0.168 0.392 499 36.4 S_temporal_sup 300 200 510 2.679 0.757 0.113 0.038 2 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Sat Dec 7 13:35:23 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 rh ../surf/rh.sphere.reg /soft/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 /soft/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... 702 labels changed using aseg relabeling using gibbs priors... 000: 2346 changed, 112392 examined... 001: 513 changed, 10267 examined... 002: 97 changed, 2850 examined... 003: 27 changed, 584 examined... 004: 16 changed, 154 examined... 005: 14 changed, 94 examined... 006: 10 changed, 76 examined... 007: 6 changed, 43 examined... 008: 5 changed, 32 examined... 009: 4 changed, 23 examined... 010: 3 changed, 14 examined... 011: 5 changed, 17 examined... 012: 3 changed, 19 examined... 013: 2 changed, 11 examined... 014: 4 changed, 12 examined... 015: 3 changed, 17 examined... 016: 1 changed, 16 examined... 017: 1 changed, 7 examined... 018: 0 changed, 7 examined... 158 labels changed using aseg 000: 79 total segments, 46 labels (384 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 27 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 731 vertices marked for relabeling... 731 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 31 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Sat Dec 7 13:35:54 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 MPS3007-1 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 1031 691 3428 3.747 0.919 0.155 0.071 60 3.3 caudalanteriorcingulate 2635 1781 7166 3.166 0.759 0.154 0.083 62 9.4 caudalmiddlefrontal 2728 1738 4665 2.262 0.695 0.193 1.126 395 15.9 cuneus 332 224 1632 3.904 0.826 0.213 0.223 16 2.0 entorhinal 3196 2181 8010 3.211 0.868 0.204 0.166 151 22.8 fusiform 5743 3796 16398 3.096 0.892 0.209 0.236 486 48.8 inferiorparietal 3124 2112 9680 3.306 0.906 0.233 0.260 263 33.6 inferiortemporal 1118 727 2845 3.175 1.103 0.175 0.198 70 5.2 isthmuscingulate 6640 4224 14749 2.728 0.981 0.227 0.211 613 64.6 lateraloccipital 2595 1772 9394 3.688 0.963 0.173 0.141 94 13.8 lateralorbitofrontal 3668 2387 7103 2.577 0.784 0.196 0.158 176 24.7 lingual 1555 1091 5795 3.591 0.895 0.180 0.105 73 6.4 medialorbitofrontal 3483 2230 11374 3.464 0.902 0.189 0.147 331 18.9 middletemporal 884 577 2151 2.862 0.736 0.147 0.084 21 3.1 parahippocampal 2161 1340 4859 3.083 0.910 0.167 0.146 120 13.3 paracentral 1723 1171 4829 3.170 0.728 0.152 0.084 41 5.9 parsopercularis 985 656 3130 3.434 0.942 0.204 0.301 96 15.4 parsorbitalis 1713 1178 5322 3.264 0.936 0.162 0.080 45 6.0 parstriangularis 2339 1550 3230 1.919 0.640 0.220 0.193 435 21.1 pericalcarine 7872 4539 12046 2.322 0.824 0.214 0.251 687 81.1 postcentral 1604 1122 4477 3.102 1.099 0.164 0.099 70 7.9 posteriorcingulate 6559 4312 16439 3.108 0.868 0.164 0.113 199 33.0 precentral 5397 3492 13687 2.968 0.857 0.188 0.186 334 42.6 precuneus 1111 729 3274 3.695 0.616 0.176 0.096 48 5.0 rostralanteriorcingulate 4079 2686 10430 2.906 0.790 0.168 0.113 161 17.1 rostralmiddlefrontal 10688 7012 30164 3.316 0.810 0.164 0.449 1168 51.2 superiorfrontal 5689 3488 10830 2.586 0.712 0.175 0.169 341 37.9 superiorparietal 7190 4405 15760 2.803 1.021 0.226 1.900 2852 76.8 superiortemporal 4614 2712 8033 2.781 0.957 0.211 0.292 604 51.7 supramarginal 583 348 1183 2.944 0.771 0.166 0.170 34 5.2 transversetemporal 2338 1530 6381 3.550 1.025 0.131 0.122 103 11.5 insula #-------------------------------------------- #@# Cortical ribbon mask Sat Dec 7 13:36:02 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon MPS3007-1 SUBJECTS_DIR is /lustre/kovacv/FS/MPSIII-post 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 = 0 writing volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Sat Dec 7 13:43:45 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1 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 /soft/freesurfer/5.3.0/ASegStatsLUT.txt --subject MPS3007-1 $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 /soft/freesurfer/5.3.0/ASegStatsLUT.txt --subject MPS3007-1 sysname Linux hostname node1109 machine x86_64 user kovacv UseRobust 0 atlas_icv (eTIV) = 1454913 mm^3 (det: 1.338984 ) Computing euler number orig.nofix lheno = -514, rheno = -548 orig.nofix lhholes = 258, rhholes = 275 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 255017.378 254742.000 diff= 275.4 pctdiff= 0.108 rhCtxGM: 263067.004 262552.000 diff= 515.0 pctdiff= 0.196 lhCtxWM: 143715.083 145024.500 diff=-1309.4 pctdiff=-0.911 rhCtxWM: 148387.282 148216.500 diff= 170.8 pctdiff= 0.115 SubCortGMVol 49329.000 SupraTentVol 883623.747 (882483.000) diff=1140.747 pctdiff=0.129 SupraTentVolNotVent 861028.747 (859888.000) diff=1140.747 pctdiff=0.132 BrainSegVol 1041360.000 (1037755.000) diff=3605.000 pctdiff=0.346 BrainSegVolNotVent 1013696.000 (1013129.747) diff=566.253 pctdiff=0.056 BrainSegVolNotVent 1013696.000 CerebellumVol 153590.000 VentChorVol 22595.000 3rd4th5thCSF 5069.000 CSFVol 1491.000, OptChiasmVol 191.000 MaskVol 1475307.000 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 11998 11998.180 4 5 Left-Inf-Lat-Vent 1325 1324.824 5 7 Left-Cerebellum-White-Matter 10794 10793.757 6 8 Left-Cerebellum-Cortex 64839 64839.086 7 10 Left-Thalamus-Proper 7191 7190.803 8 11 Left-Caudate 3338 3337.991 9 12 Left-Putamen 4427 4426.863 10 13 Left-Pallidum 1353 1353.217 11 14 3rd-Ventricle 1938 1938.149 12 15 4th-Ventricle 1749 1749.002 13 16 Brain-Stem 17519 17518.639 14 17 Left-Hippocampus 3529 3528.835 15 18 Left-Amygdala 1306 1306.276 16 24 CSF 1412 1411.931 17 26 Left-Accumbens-area 491 491.212 18 28 Left-VentralDC 3040 3040.054 19 30 Left-vessel 18 17.971 20 31 Left-choroid-plexus 1353 1352.559 23 43 Right-Lateral-Ventricle 5844 5843.683 24 44 Right-Inf-Lat-Vent 400 400.260 25 46 Right-Cerebellum-White-Matter 11672 11672.431 26 47 Right-Cerebellum-Cortex 68133 68132.797 27 49 Right-Thalamus-Proper 5721 5721.199 28 50 Right-Caudate 3156 3155.564 29 51 Right-Putamen 4491 4491.408 30 52 Right-Pallidum 1661 1660.954 31 53 Right-Hippocampus 3280 3279.569 32 54 Right-Amygdala 1363 1362.579 33 58 Right-Accumbens-area 641 640.746 34 60 Right-VentralDC 3368 3367.893 35 62 Right-vessel 11 11.406 36 63 Right-choroid-plexus 1579 1579.252 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 5050 5049.643 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 19 19.226 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 198 198.276 45 251 CC_Posterior 362 362.054 46 252 CC_Mid_Posterior 130 130.173 47 253 CC_Central 212 212.204 48 254 CC_Mid_Anterior 211 211.404 49 255 CC_Anterior 406 405.633 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Sat Dec 7 13:46:09 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1 mri_aparc2aseg --s MPS3007-1 --volmask SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post subject MPS3007-1 outvol /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 = 515153 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aparc+aseg.mgz /lustre/kovacv/FS/MPSIII-post/MPS3007-1 mri_aparc2aseg --s MPS3007-1 --volmask --a2009s SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post subject MPS3007-1 outvol /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 = 515153 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Sat Dec 7 13:48:14 CST 2013 /lustre/kovacv/FS/MPSIII-post/MPS3007-1 mri_aparc2aseg --s MPS3007-1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post subject MPS3007-1 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aparc+aseg.mgz Reading lh white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/ribbon.mgz Loading filled from /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7707 vertices from left hemi Ripped 7015 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/aseg.mgz Loading Ctx Seg File /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 = 808995 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 21 clusters 0 k 1.000000 1 k 7.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 6.000000 9 k 2.000000 10 k 1.000000 11 k 3.000000 12 k 2.000000 13 k 1.000000 14 k 4.000000 15 k 1.000000 16 k 1.000000 17 k 1059.000000 18 k 2.000000 19 k 5.000000 20 k 1.000000 Fixing Parahip RH WM Found 5 clusters 0 k 757.000000 1 k 1.000000 2 k 1.000000 3 k 3.000000 4 k 1.000000 Writing output aseg to mri/wmparc.mgz /lustre/kovacv/FS/MPSIII-post/MPS3007-1 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 MPS3007-1 --surf-wm-vol --ctab /soft/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 MPS3007-1 --surf-wm-vol --ctab /soft/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv sysname Linux hostname node1109 machine x86_64 user kovacv UseRobust 0 atlas_icv (eTIV) = 1454913 mm^3 (det: 1.338984 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 255017.378 254742.000 diff= 275.4 pctdiff= 0.108 rhCtxGM: 263067.004 262552.000 diff= 515.0 pctdiff= 0.196 lhCtxWM: 143715.083 145024.500 diff=-1309.4 pctdiff=-0.911 rhCtxWM: 148387.282 148216.500 diff= 170.8 pctdiff= 0.115 SubCortGMVol 49329.000 SupraTentVol 883623.747 (882483.000) diff=1140.747 pctdiff=0.129 SupraTentVolNotVent 861028.747 (859888.000) diff=1140.747 pctdiff=0.132 BrainSegVol 1041360.000 (1037755.000) diff=3605.000 pctdiff=0.346 BrainSegVolNotVent 1013696.000 (1013129.747) diff=566.253 pctdiff=0.056 BrainSegVolNotVent 1013696.000 CerebellumVol 153590.000 VentChorVol 22595.000 3rd4th5thCSF 5069.000 CSFVol 1491.000, OptChiasmVol 191.000 MaskVol 1475307.000 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 1963 1963.239 2 3002 wm-lh-caudalanteriorcingulate 1980 1979.701 3 3003 wm-lh-caudalmiddlefrontal 4937 4936.869 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2236 2236.412 6 3006 wm-lh-entorhinal 350 350.062 7 3007 wm-lh-fusiform 4306 4305.867 8 3008 wm-lh-inferiorparietal 4805 4804.834 9 3009 wm-lh-inferiortemporal 3668 3668.316 10 3010 wm-lh-isthmuscingulate 2911 2911.450 11 3011 wm-lh-lateraloccipital 7560 7560.041 12 3012 wm-lh-lateralorbitofrontal 3985 3984.854 13 3013 wm-lh-lingual 2723 2723.209 14 3014 wm-lh-medialorbitofrontal 2547 2546.851 15 3015 wm-lh-middletemporal 3138 3137.571 16 3016 wm-lh-parahippocampal 1248 1247.845 17 3017 wm-lh-paracentral 2780 2779.818 18 3018 wm-lh-parsopercularis 2226 2226.151 19 3019 wm-lh-parsorbitalis 862 861.523 20 3020 wm-lh-parstriangularis 1892 1892.299 21 3021 wm-lh-pericalcarine 2407 2407.476 22 3022 wm-lh-postcentral 5639 5638.543 23 3023 wm-lh-posteriorcingulate 3021 3021.353 24 3024 wm-lh-precentral 9686 9686.462 25 3025 wm-lh-precuneus 5219 5218.866 26 3026 wm-lh-rostralanteriorcingulate 1736 1735.638 27 3027 wm-lh-rostralmiddlefrontal 7823 7823.329 28 3028 wm-lh-superiorfrontal 12384 12383.895 29 3029 wm-lh-superiorparietal 8515 8515.188 30 3030 wm-lh-superiortemporal 6018 6018.410 31 3031 wm-lh-supramarginal 6643 6642.737 32 3032 wm-lh-frontalpole 195 194.677 33 3033 wm-lh-temporalpole 336 335.685 34 3034 wm-lh-transversetemporal 974 973.736 35 3035 wm-lh-insula 5884 5883.842 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 2039 2038.531 120 4002 wm-rh-caudalanteriorcingulate 2056 2055.659 121 4003 wm-rh-caudalmiddlefrontal 3754 3753.513 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 1853 1853.483 124 4006 wm-rh-entorhinal 340 340.303 125 4007 wm-rh-fusiform 4928 4928.494 126 4008 wm-rh-inferiorparietal 7858 7857.748 127 4009 wm-rh-inferiortemporal 3389 3389.159 128 4010 wm-rh-isthmuscingulate 2158 2157.756 129 4011 wm-rh-lateraloccipital 6059 6059.263 130 4012 wm-rh-lateralorbitofrontal 4047 4046.544 131 4013 wm-rh-lingual 3150 3149.842 132 4014 wm-rh-medialorbitofrontal 2615 2614.848 133 4015 wm-rh-middletemporal 2950 2950.009 134 4016 wm-rh-parahippocampal 837 836.931 135 4017 wm-rh-paracentral 3419 3419.341 136 4018 wm-rh-parsopercularis 2689 2689.234 137 4019 wm-rh-parsorbitalis 880 880.474 138 4020 wm-rh-parstriangularis 2272 2271.614 139 4021 wm-rh-pericalcarine 2453 2452.503 140 4022 wm-rh-postcentral 6322 6321.675 141 4023 wm-rh-posteriorcingulate 3245 3245.228 142 4024 wm-rh-precentral 10601 10600.647 143 4025 wm-rh-precuneus 6611 6611.478 144 4026 wm-rh-rostralanteriorcingulate 2029 2029.195 145 4027 wm-rh-rostralmiddlefrontal 7484 7483.637 146 4028 wm-rh-superiorfrontal 12322 12321.623 147 4029 wm-rh-superiorparietal 7977 7976.708 148 4030 wm-rh-superiortemporal 6197 6197.187 149 4031 wm-rh-supramarginal 5128 5128.116 150 4032 wm-rh-frontalpole 206 206.365 151 4033 wm-rh-temporalpole 464 463.777 152 4034 wm-rh-transversetemporal 757 756.551 153 4035 wm-rh-insula 6105 6104.737 154 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 13423 13423.099 237 5002 Right-UnsegmentedWhiteMatter 14956 14956.413 238 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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label #-------------------------------------------- #@# BA Labels lh Sat Dec 7 13:54:58 CST 2013 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA1.label --trgsubject MPS3007-1 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 267 Checking for and removing duplicates Writing label file ./lh.BA1.label 4396 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA2.label --trgsubject MPS3007-1 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 493 Checking for and removing duplicates Writing label file ./lh.BA2.label 8402 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA3a.label --trgsubject MPS3007-1 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 244 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4321 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA3b.label --trgsubject MPS3007-1 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 462 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6445 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA4a.label --trgsubject MPS3007-1 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 320 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6104 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA4p.label --trgsubject MPS3007-1 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 264 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4334 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA6.label --trgsubject MPS3007-1 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 738 Checking for and removing duplicates Writing label file ./lh.BA6.label 14327 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA44.label --trgsubject MPS3007-1 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./lh.BA44.label 4373 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA45.label --trgsubject MPS3007-1 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./lh.BA45.label 3643 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.V1.label --trgsubject MPS3007-1 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 1428 Checking for and removing duplicates Writing label file ./lh.V1.label 6069 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.V2.label --trgsubject MPS3007-1 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 2916 Checking for and removing duplicates Writing label file ./lh.V2.label 11030 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.MT.label --trgsubject MPS3007-1 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 903 Checking for and removing duplicates Writing label file ./lh.MT.label 2921 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.perirhinal.label --trgsubject MPS3007-1 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 100 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1299 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA1.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 81 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1095 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA2.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 64 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2156 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA3a.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 40 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1544 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA3b.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2190 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA4a.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2447 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA4p.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 172 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1721 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA6.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 270 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7305 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA44.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2000 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA45.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1267 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.V1.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 914 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.V2.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 1412 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4746 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.MT.thresh.label --trgsubject MPS3007-1 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 110583 Number of reverse mapping hits = 370 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 883 mri_label2label: Done mris_label2annot --s MPS3007-1 --hemi lh --ctab /soft/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 /soft/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label cmdline mris_label2annot --s MPS3007-1 --hemi lh --ctab /soft/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 node1109 machine x86_64 user kovacv subject MPS3007-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post ColorTable /soft/freesurfer/5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 75399 unhit vertices Writing annot to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/lh.BA.annot mris_label2annot --s MPS3007-1 --hemi lh --ctab /soft/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 /soft/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label cmdline mris_label2annot --s MPS3007-1 --hemi lh --ctab /soft/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 node1109 machine x86_64 user kovacv subject MPS3007-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post ColorTable /soft/freesurfer/5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 90185 unhit vertices Writing annot to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab MPS3007-1 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /soft/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 931 541 2360 2.937 0.726 0.221 0.192 53 7.4 BA1 3237 2118 6656 2.710 0.798 0.171 0.164 195 23.9 BA2 933 640 991 1.931 0.439 0.152 0.065 15 2.5 BA3a 2346 1529 4696 2.426 0.909 0.174 0.108 71 11.7 BA3b 1319 848 3849 3.339 0.806 0.193 0.192 287 13.8 BA4a 1303 794 2186 2.860 0.803 0.189 0.704 626 12.1 BA4p 7011 4859 25117 3.523 0.885 0.181 0.115 200 34.9 BA6 1647 1166 6122 3.558 0.910 0.164 0.106 35 6.4 BA44 2114 1459 5778 2.913 0.790 0.172 0.115 59 8.2 BA45 3220 2181 4163 1.826 0.748 0.235 1.127 8673 16.9 V1 8030 4863 12027 2.216 0.743 0.200 0.182 1471 50.1 V2 2243 1314 3418 2.291 0.622 0.234 0.492 544 40.3 MT 850 604 3238 3.577 1.040 0.221 0.127 52 5.6 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab MPS3007-1 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /soft/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 613 334 1392 2.793 0.503 0.227 0.176 35 4.5 BA1 1190 821 2585 2.587 0.707 0.150 0.082 20 4.0 BA2 802 542 798 1.904 0.422 0.148 0.074 13 2.5 BA3a 1507 986 2168 1.986 0.533 0.153 0.088 37 6.5 BA3b 1256 813 3632 3.389 0.794 0.182 0.195 271 12.3 BA4a 1114 692 1801 2.708 0.793 0.198 0.729 604 10.5 BA4p 3667 2553 13727 3.554 0.933 0.188 0.118 117 18.5 BA6 1061 745 4294 3.697 0.912 0.180 0.124 28 4.6 BA44 940 655 3204 3.212 0.785 0.201 0.118 37 4.5 BA45 3387 2267 4275 1.801 0.743 0.232 1.081 8683 18.5 V1 4123 2488 5750 2.120 0.702 0.210 0.166 222 27.1 V2 738 397 1051 2.336 0.573 0.215 0.202 43 6.4 MT #-------------------------------------------- #@# BA Labels rh Sat Dec 7 13:57:37 CST 2013 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA1.label --trgsubject MPS3007-1 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 1060 Checking for and removing duplicates Writing label file ./rh.BA1.label 5022 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA2.label --trgsubject MPS3007-1 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 1087 Checking for and removing duplicates Writing label file ./rh.BA2.label 7774 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA3a.label --trgsubject MPS3007-1 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 318 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4298 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA3b.label --trgsubject MPS3007-1 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 903 Checking for and removing duplicates Writing label file ./rh.BA3b.label 5425 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA4a.label --trgsubject MPS3007-1 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 332 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6079 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA4p.label --trgsubject MPS3007-1 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4676 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA6.label --trgsubject MPS3007-1 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 885 Checking for and removing duplicates Writing label file ./rh.BA6.label 13141 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA44.label --trgsubject MPS3007-1 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 566 Checking for and removing duplicates Writing label file ./rh.BA44.label 7478 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA45.label --trgsubject MPS3007-1 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 462 Checking for and removing duplicates Writing label file ./rh.BA45.label 5817 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.V1.label --trgsubject MPS3007-1 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 1750 Checking for and removing duplicates Writing label file ./rh.V1.label 6477 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.V2.label --trgsubject MPS3007-1 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 2181 Checking for and removing duplicates Writing label file ./rh.V2.label 10197 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.MT.label --trgsubject MPS3007-1 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 369 Checking for and removing duplicates Writing label file ./rh.MT.label 2301 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.perirhinal.label --trgsubject MPS3007-1 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 68 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 820 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA1.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 244 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1120 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA2.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 429 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3117 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA3a.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 73 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1771 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA3b.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 513 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2696 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA4a.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 98 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1486 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA4p.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 99 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1588 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA6.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 465 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7424 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA44.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 87 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1099 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA45.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1290 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.V1.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 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 /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.V2.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 986 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4423 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.MT.thresh.label --trgsubject MPS3007-1 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/MPSIII-post/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/MPSIII-post FREESURFER_HOME /soft/freesurfer/5.3.0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/MPSIII-post/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 112392 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 300 mri_label2label: Done mris_label2annot --s MPS3007-1 --hemi rh --ctab /soft/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 /soft/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label cmdline mris_label2annot --s MPS3007-1 --hemi rh --ctab /soft/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 node1109 machine x86_64 user kovacv subject MPS3007-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post ColorTable /soft/freesurfer/5.3.0/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 75634 unhit vertices Writing annot to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/rh.BA.annot mris_label2annot --s MPS3007-1 --hemi rh --ctab /soft/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 /soft/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 /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label cmdline mris_label2annot --s MPS3007-1 --hemi rh --ctab /soft/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 node1109 machine x86_64 user kovacv subject MPS3007-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/MPSIII-post ColorTable /soft/freesurfer/5.3.0/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 91010 unhit vertices Writing annot to /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab MPS3007-1 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /soft/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 1313 616 1808 2.277 0.740 0.277 0.528 219 22.6 BA1 3025 1819 4885 2.551 0.724 0.196 0.194 283 27.8 BA2 1077 703 1102 1.927 0.584 0.155 0.146 47 6.1 BA3a 2657 1582 3323 1.936 0.538 0.211 0.200 148 23.7 BA3b 1310 826 3392 3.224 0.772 0.190 0.174 114 10.5 BA4a 1141 700 2015 2.953 0.834 0.152 0.105 26 5.5 BA4p 6555 4353 20425 3.492 0.848 0.173 0.595 1014 39.3 BA6 3237 2244 9310 3.222 0.763 0.150 0.070 64 9.4 BA44 3186 2152 9998 3.230 0.934 0.178 0.158 167 23.9 BA45 4067 2588 6006 1.997 0.713 0.223 0.205 526 38.8 V1 6918 4418 12658 2.465 0.761 0.207 0.547 712 44.3 V2 1700 1150 4722 3.140 0.888 0.200 0.147 105 11.1 MT 572 354 1789 3.231 1.148 0.266 0.675 269 7.4 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab MPS3007-1 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /soft/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 794 357 1151 2.278 0.649 0.268 0.650 113 14.1 BA1 2046 1159 3451 2.541 0.719 0.203 0.220 232 20.1 BA2 964 643 924 1.876 0.475 0.158 0.131 30 5.9 BA3a 2198 1317 2578 1.872 0.490 0.195 0.186 113 17.8 BA3b 816 513 2272 3.396 0.874 0.211 0.243 98 9.4 BA4a 964 589 1620 2.972 0.846 0.160 0.118 31 5.7 BA4p 4166 2727 12529 3.427 0.894 0.171 0.844 549 19.3 BA6 744 538 2601 3.370 0.678 0.168 0.092 23 3.2 BA44 908 603 3557 3.747 0.799 0.195 0.143 38 5.0 BA45 3924 2486 5641 1.989 0.710 0.219 0.205 516 37.4 V1 3648 2385 6445 2.310 0.749 0.225 0.916 538 26.8 V2 210 144 701 3.308 0.756 0.250 0.218 17 1.8 MT /lustre/kovacv/FS/MPSIII-post/MPS3007-1/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Sat Dec 7 14:00:13 CST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS3007-1 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject MPS3007-1. processing subject lh.EC_average... reading output surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 932 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label MPS3007-1 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 351 227 1652 3.916 0.726 0.179 0.154 13 2.7 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Sat Dec 7 14:00:24 CST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS3007-1 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject MPS3007-1. processing subject rh.EC_average... reading output surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 765 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label MPS3007-1 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/MPSIII-post/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/MPSIII-post/MPS3007-1/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 277 164 1155 3.330 1.036 0.275 1.145 252 4.8 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Dec 5 19:09:01 CST 2013 Ended at Sat Dec 7 14:00:33 CST 2013 #@#%# recon-all-run-time-hours 42.859 recon-all -s MPS3007-1 finished without error at Sat Dec 7 14:00:34 CST 2013 New invocation of recon-all Wed May 28 18:01:44 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1 /soft/freesurfer/5.1.0/bin/recon-all -autorecon2-cp -autorecon3 -subjid MPS3007-1 subjid MPS3007-1 setenv SUBJECTS_DIR /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Actual FREESURFER_HOME /panfs/roc/itascasoft/freesurfer/5.1.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux node1118 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize 3840000 kbytes stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse 3840000 kbytes vmemoryuse unlimited descriptors 32768 memorylocked unlimited maxproc 514922 total used free shared buffers cached Mem: 65932048 1293080 64638968 0 6992 40040 -/+ buffers/cache: 1246048 64686000 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2014/05/28-23:01:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:46-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/28-23:01:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: kovacv Machine: node1118 Platform: Linux PlatformVersion: 2.6.32-431.5.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /soft/freesurfer/5.1.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /soft/freesurfer/5.1.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /soft/freesurfer/5.1.0 Previous: /soft/freesurfer/5.3.0 #------------------------------------- #@# EM Registration Wed May 28 18:01:50 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /soft/freesurfer/5.1.0/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 '/soft/freesurfer/5.1.0/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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=27.9 skull bounding box = (57, 57, 39) --> (198, 162, 195) using (104, 92, 117) as brain centroid... mean wm in atlas = 107, using box (87,79,98) --> (121, 104,136) to find MRI wm before smoothing, mri peak at 102 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 initial log_p = -7484.3 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-4.0, -2.8, -9.7): log p = -7403.116 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7329.3, old_max_log_p =-7403.1 (thresh=-7395.7) 1.000 0.000 0.000 -3.977; 0.000 1.028 -0.275 32.969; 0.000 0.278 1.038 -47.933; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7329.3, old_max_log_p =-7329.3 (thresh=-7322.0) 1.000 0.000 0.000 -3.977; 0.000 1.028 -0.275 32.969; 0.000 0.278 1.038 -47.933; 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=-7297.6, old_max_log_p =-7329.3 (thresh=-7322.0) 1.015 0.077 0.024 -15.697; -0.069 1.100 -0.223 27.582; -0.030 0.209 1.033 -33.530; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7271.5, old_max_log_p =-7297.6 (thresh=-7290.3) 1.017 0.042 0.031 -12.757; -0.036 1.143 -0.230 17.330; -0.030 0.209 1.033 -33.530; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7271.5, old_max_log_p =-7271.5 (thresh=-7264.2) 1.017 0.042 0.031 -12.757; -0.036 1.143 -0.230 17.330; -0.030 0.209 1.033 -33.530; 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=-7258.6, old_max_log_p =-7271.5 (thresh=-7264.2) 1.017 0.042 0.031 -12.757; -0.036 1.140 -0.230 17.568; -0.030 0.208 1.030 -33.204; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7258.6, old_max_log_p =-7258.6 (thresh=-7251.4) 1.017 0.042 0.031 -12.757; -0.036 1.140 -0.230 17.568; -0.030 0.208 1.030 -33.204; 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 1.01688 0.04226 0.03074 -12.75739; -0.03574 1.14018 -0.22974 17.56750; -0.02959 0.20813 1.03037 -33.20419; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.01688 0.04226 0.03074 -12.75739; -0.03574 1.14018 -0.22974 17.56750; -0.02959 0.20813 1.03037 -33.20419; 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) = 7258.6 tol 0.000010 Resulting transform: 1.017 0.042 0.031 -12.757; -0.036 1.140 -0.230 17.568; -0.030 0.208 1.030 -33.204; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -7258.6 (old=-7484.3) transform before final EM align: 1.017 0.042 0.031 -12.757; -0.036 1.140 -0.230 17.568; -0.030 0.208 1.030 -33.204; 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 1.01688 0.04226 0.03074 -12.75739; -0.03574 1.14018 -0.22974 17.56750; -0.02959 0.20813 1.03037 -33.20419; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.01688 0.04226 0.03074 -12.75739; -0.03574 1.14018 -0.22974 17.56750; -0.02959 0.20813 1.03037 -33.20419; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 851839.8 after pass:transform: ( 1.02, 0.04, 0.03, -12.76) ( -0.04, 1.14, -0.23, 17.57) ( -0.03, 0.21, 1.03, -33.20) dfp_em_step_func: 011: -log(p) = 851839.2 after pass:transform: ( 1.02, 0.04, 0.03, -12.76) ( -0.04, 1.14, -0.23, 17.57) ( -0.03, 0.21, 1.03, -33.20) dfp_em_step_func: 012: -log(p) = 850757.4 after pass:transform: ( 1.02, 0.05, 0.04, -12.76) ( -0.03, 1.14, -0.23, 17.57) ( -0.03, 0.21, 1.03, -33.20) 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: 014: -log(p) = 850757.4 tol 0.000000 final transform: 1.020 0.045 0.035 -12.757; -0.032 1.145 -0.225 17.568; -0.029 0.207 1.030 -33.204; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 23 minutes and 36 seconds. #-------------------------------------- #@# CA Normalize Wed May 28 18:25:27 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri mri_ca_normalize -f /lustre/kovacv/FS/post-analysis/MPS3007-1/tmp/control.dat -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /soft/freesurfer/5.1.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz reading manually defined control points from /lustre/kovacv/FS/post-analysis/MPS3007-1/tmp/control.dat writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/soft/freesurfer/5.1.0/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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=27.9 skull bounding box = (57, 57, 39) --> (198, 162, 194) using (104, 92, 117) as brain centroid... mean wm in atlas = 107, using box (87,79,98) --> (121, 104,136) to find MRI wm before smoothing, mri peak at 102 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 using 244171 sample points... INFO: compute sample coordinates transform 1.020 0.045 0.035 -12.757; -0.032 1.145 -0.225 17.568; -0.029 0.207 1.030 -33.204; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 38) --> (192, 163, 199) Left_Cerebral_White_Matter: limiting intensities to 104.0 --> 186.0 0 of 13 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 55, 39) --> (128, 162, 198) Right_Cerebral_White_Matter: limiting intensities to 104.0 --> 186.0 0 of 9 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 122, 53) --> (175, 161, 106) Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 186.0 0 of 6 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 122, 51) --> (128, 161, 106) Right_Cerebellum_White_Matter: limiting intensities to 112.0 --> 186.0 0 of 11 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 122, 81) --> (142, 178, 117) Reading 314 control points... Brain_Stem: limiting intensities to 125.0 --> 186.0 5 of 6 (83.3%) samples deleted using 45 total control points for intensity normalization... bias field = 0.994 +- 0.095 0 of 354 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 38) --> (192, 163, 199) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 173.0 9 of 68 (13.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 55, 39) --> (128, 162, 198) Right_Cerebral_White_Matter: limiting intensities to 140.0 --> 173.0 63 of 67 (94.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 122, 53) --> (175, 161, 106) Left_Cerebellum_White_Matter: limiting intensities to 71.0 --> 173.0 0 of 49 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 122, 51) --> (128, 161, 106) Right_Cerebellum_White_Matter: limiting intensities to 75.0 --> 173.0 0 of 56 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 122, 81) --> (142, 178, 117) Reading 314 control points... Brain_Stem: limiting intensities to 68.0 --> 173.0 0 of 58 (0.0%) samples deleted using 298 total control points for intensity normalization... bias field = 1.010 +- 0.054 0 of 540 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 55, 38) --> (192, 163, 199) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 182.0 19 of 128 (14.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 55, 39) --> (128, 162, 198) Right_Cerebral_White_Matter: limiting intensities to 122.0 --> 182.0 91 of 103 (88.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 122, 53) --> (175, 161, 106) Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 182.0 0 of 86 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 122, 51) --> (128, 161, 106) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 182.0 0 of 45 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 122, 81) --> (142, 178, 117) Reading 314 control points... Brain_Stem: limiting intensities to 86.0 --> 182.0 49 of 109 (45.0%) samples deleted using 471 total control points for intensity normalization... bias field = 0.995 +- 0.045 2 of 626 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 48 seconds. #-------------------------------------- #@# CA Reg Wed May 28 18:27:15 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /soft/freesurfer/5.1.0/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 '/soft/freesurfer/5.1.0/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.25 (predicted orig area = 6.4) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.920, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20775.262 ms 0001: dt=129.472000, rms=0.824 (10.432%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21967.342 ms 0002: dt=129.472000, rms=0.803 (2.510%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20049.025 ms 0003: dt=369.920000, rms=0.774 (3.610%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21543.758 ms 0004: dt=32.368000, rms=0.773 (0.170%), neg=0, invalid=766 0005: dt=32.368000, rms=0.773 (0.043%), neg=0, invalid=766 0006: dt=32.368000, rms=0.773 (-0.061%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.773, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23012.969 ms 0007: dt=27.744000, rms=0.773 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23326.020 ms 0008: dt=129.472000, rms=0.772 (0.109%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24114.623 ms 0009: dt=517.888000, rms=0.762 (1.252%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21450.990 ms 0010: dt=8.092000, rms=0.762 (-0.008%), neg=0, invalid=766 0011: dt=8.092000, rms=0.762 (0.003%), neg=0, invalid=766 0012: dt=8.092000, rms=0.762 (0.004%), neg=0, invalid=766 0013: dt=8.092000, rms=0.762 (-0.008%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.764, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19612.824 ms 0014: dt=145.152000, rms=0.737 (3.482%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19773.668 ms 0015: dt=36.288000, rms=0.722 (2.048%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20830.590 ms 0016: dt=31.104000, rms=0.719 (0.500%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21039.842 ms 0017: dt=145.152000, rms=0.706 (1.822%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19972.670 ms 0018: dt=36.288000, rms=0.703 (0.406%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20366.814 ms 0019: dt=82.944000, rms=0.696 (0.896%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20475.889 ms 0020: dt=36.288000, rms=0.692 (0.617%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20602.852 ms 0021: dt=36.288000, rms=0.690 (0.240%), neg=0, invalid=766 0022: dt=36.288000, rms=0.688 (0.387%), neg=0, invalid=766 0023: dt=36.288000, rms=0.685 (0.432%), neg=0, invalid=766 0024: dt=36.288000, rms=0.681 (0.543%), neg=0, invalid=766 0025: dt=36.288000, rms=0.677 (0.588%), neg=0, invalid=766 0026: dt=36.288000, rms=0.672 (0.756%), neg=0, invalid=766 0027: dt=36.288000, rms=0.667 (0.756%), neg=0, invalid=766 0028: dt=36.288000, rms=0.663 (0.610%), neg=0, invalid=766 0029: dt=36.288000, rms=0.660 (0.468%), neg=0, invalid=766 0030: dt=36.288000, rms=0.657 (0.401%), neg=0, invalid=766 0031: dt=36.288000, rms=0.654 (0.528%), neg=0, invalid=766 0032: dt=36.288000, rms=0.651 (0.410%), neg=0, invalid=766 0033: dt=36.288000, rms=0.649 (0.325%), neg=0, invalid=766 0034: dt=36.288000, rms=0.647 (0.246%), neg=0, invalid=766 0035: dt=36.288000, rms=0.645 (0.341%), neg=0, invalid=766 0036: dt=36.288000, rms=0.643 (0.368%), neg=0, invalid=766 0037: dt=36.288000, rms=0.641 (0.245%), neg=0, invalid=766 0038: dt=36.288000, rms=0.640 (0.147%), neg=0, invalid=766 0039: dt=36.288000, rms=0.639 (0.118%), neg=0, invalid=766 0040: dt=36.288000, rms=0.638 (0.232%), neg=0, invalid=766 0041: dt=36.288000, rms=0.637 (0.205%), neg=0, invalid=766 0042: dt=36.288000, rms=0.636 (0.141%), neg=0, invalid=766 0043: dt=36.288000, rms=0.635 (0.063%), neg=0, invalid=766 0044: dt=36.288000, rms=0.634 (0.127%), neg=0, invalid=766 0045: dt=36.288000, rms=0.633 (0.188%), neg=0, invalid=766 0046: dt=36.288000, rms=0.632 (0.125%), neg=0, invalid=766 0047: dt=36.288000, rms=0.632 (0.081%), neg=0, invalid=766 0048: dt=36.288000, rms=0.632 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22328.801 ms 0049: dt=36.288000, rms=0.631 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22593.965 ms 0050: dt=9.072000, rms=0.631 (0.004%), neg=0, invalid=766 0051: dt=9.072000, rms=0.631 (0.001%), neg=0, invalid=766 0052: dt=9.072000, rms=0.631 (0.008%), neg=0, invalid=766 0053: dt=9.072000, rms=0.631 (0.010%), neg=0, invalid=766 0054: dt=9.072000, rms=0.631 (0.011%), neg=0, invalid=766 0055: dt=9.072000, rms=0.631 (0.017%), neg=0, invalid=766 0056: dt=9.072000, rms=0.631 (0.017%), neg=0, invalid=766 0057: dt=9.072000, rms=0.631 (0.018%), neg=0, invalid=766 0058: dt=9.072000, rms=0.630 (0.012%), neg=0, invalid=766 0059: dt=9.072000, rms=0.630 (0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.630, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21519.982 ms 0060: dt=82.944000, rms=0.629 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21616.762 ms 0061: dt=36.288000, rms=0.629 (0.035%), neg=0, invalid=766 0062: dt=36.288000, rms=0.629 (0.021%), neg=0, invalid=766 0063: dt=36.288000, rms=0.629 (0.023%), neg=0, invalid=766 0064: dt=36.288000, rms=0.629 (0.015%), neg=0, invalid=766 0065: dt=36.288000, rms=0.628 (0.010%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.660, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20872.936 ms 0066: dt=2.000000, rms=0.659 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20875.711 ms 0067: dt=0.150000, rms=0.659 (-0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.659, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20035.557 ms 0068: dt=0.000000, rms=0.659 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.749, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20746.586 ms 0069: dt=4.567426, rms=0.726 (3.107%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21748.322 ms 0070: dt=3.456000, rms=0.724 (0.333%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20495.742 ms 0071: dt=0.500000, rms=0.724 (0.004%), neg=0, invalid=766 0072: dt=0.500000, rms=0.724 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.724, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19442.682 ms 0073: dt=0.000000, rms=0.724 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.803, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21084.957 ms 0074: dt=1.032520, rms=0.798 (0.517%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21811.148 ms 0075: dt=1.792000, rms=0.792 (0.745%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20366.297 ms 0076: dt=0.827586, rms=0.792 (0.102%), neg=0, invalid=766 0077: dt=0.827586, rms=0.791 (0.109%), neg=0, invalid=766 0078: dt=0.827586, rms=0.790 (0.064%), neg=0, invalid=766 0079: dt=0.827586, rms=0.790 (-0.140%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.790, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21224.801 ms 0080: dt=0.912752, rms=0.789 (0.117%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20633.807 ms 0081: dt=0.000000, rms=0.789 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.733, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20908.604 ms 0082: dt=0.159410, rms=0.724 (1.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20661.637 ms 0083: dt=0.000000, rms=0.724 (0.003%), neg=0, invalid=766 0084: dt=0.050000, rms=0.724 (-0.027%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.724, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22116.688 ms 0085: dt=0.262584, rms=0.722 (0.330%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20283.141 ms 0086: dt=0.112000, rms=0.720 (0.172%), neg=0, invalid=766 0087: dt=0.112000, rms=0.720 (0.059%), neg=0, invalid=766 0088: dt=0.112000, rms=0.719 (0.097%), neg=0, invalid=766 0089: dt=0.112000, rms=0.718 (0.171%), neg=0, invalid=766 0090: dt=0.112000, rms=0.717 (0.166%), neg=0, invalid=766 0091: dt=0.112000, rms=0.716 (0.153%), neg=0, invalid=766 0092: dt=0.112000, rms=0.715 (0.129%), neg=0, invalid=766 0093: dt=0.112000, rms=0.714 (0.120%), neg=0, invalid=766 0094: dt=0.112000, rms=0.713 (0.113%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20605.607 ms 0095: dt=0.000000, rms=0.713 (0.001%), neg=0, invalid=766 0096: dt=0.050000, rms=0.713 (-0.009%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.15034 (10) Left_Lateral_Ventricle (4): linear fit = 0.32 x + 0.0 (1789 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1789 voxels, peak = 8), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.12944 (11) Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (844 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (844 voxels, peak = 7), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.06146 (89) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (397 voxels, overlap=0.900) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (397 voxels, peak = 90), gca=90.0 gca peak = 0.19192 (97) mri peak = 0.07552 (88) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (407 voxels, overlap=0.596) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (407 voxels, peak = 87), gca=87.3 gca peak = 0.24007 (63) mri peak = 0.07298 (77) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (794 voxels, overlap=0.039) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (794 voxels, peak = 76), gca=75.6 gca peak = 0.29892 (64) mri peak = 0.05565 (69) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (838 voxels, overlap=0.576) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (838 voxels, peak = 70), gca=70.4 gca peak = 0.12541 (104) mri peak = 0.04475 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (55559 voxels, overlap=0.972) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (55559 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.05695 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (50305 voxels, overlap=0.824) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (50305 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.04524 (77) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (23608 voxels, overlap=0.286) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (23608 voxels, peak = 76), gca=75.6 gca peak = 0.13270 (63) mri peak = 0.04285 (77) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (24354 voxels, overlap=0.361) Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (24354 voxels, peak = 76), gca=75.6 gca peak = 0.15182 (70) mri peak = 0.10472 (90) Right_Caudate (50): linear fit = 1.25 x + 0.0 (478 voxels, overlap=0.001) Right_Caudate (50): linear fit = 1.25 x + 0.0 (478 voxels, peak = 88), gca=87.5 gca peak = 0.14251 (76) mri peak = 0.10020 (78) Left_Caudate (11): linear fit = 0.98 x + 0.0 (499 voxels, overlap=0.865) Left_Caudate (11): linear fit = 0.98 x + 0.0 (499 voxels, peak = 74), gca=74.1 gca peak = 0.12116 (60) mri peak = 0.04204 (75) Left_Cerebellum_Cortex (8): linear fit = 1.20 x + 0.0 (20266 voxels, overlap=0.380) Left_Cerebellum_Cortex (8): linear fit = 1.20 x + 0.0 (20266 voxels, peak = 72), gca=72.0 gca peak = 0.12723 (61) mri peak = 0.05287 (72) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (24784 voxels, overlap=0.632) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (24784 voxels, peak = 70), gca=70.2 gca peak = 0.22684 (88) mri peak = 0.07198 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7538 voxels, overlap=0.769) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7538 voxels, peak = 92), gca=92.4 gca peak = 0.21067 (87) mri peak = 0.06281 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7302 voxels, overlap=0.867) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7302 voxels, peak = 91), gca=91.3 gca peak = 0.25455 (62) mri peak = 0.11111 (68) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (337 voxels, overlap=0.970) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (337 voxels, peak = 64), gca=63.5 gca peak = 0.39668 (62) mri peak = 0.12189 (70) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (355 voxels, overlap=0.779) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (355 voxels, peak = 67), gca=66.7 gca peak = 0.10129 (93) mri peak = 0.05128 (99) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (4087 voxels, overlap=0.801) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (4087 voxels, peak = 100), gca=100.0 gca peak = 0.12071 (89) mri peak = 0.03616 (91) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3639 voxels, overlap=0.914) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3639 voxels, peak = 93), gca=93.4 gca peak = 0.13716 (82) mri peak = 0.05197 (91) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2647 voxels, overlap=0.926) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2647 voxels, peak = 90), gca=90.2 gca peak = 0.15214 (84) mri peak = 0.05962 (92) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2489 voxels, overlap=0.554) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2489 voxels, peak = 94), gca=94.5 gca peak = 0.08983 (85) mri peak = 0.06039 (90) Brain_Stem (16): linear fit = 1.08 x + 0.0 (10265 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.08 x + 0.0 (10265 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.05691 (97) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (889 voxels, overlap=0.888) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (889 voxels, peak = 97), gca=96.6 gca peak = 0.12914 (94) mri peak = 0.05899 (99) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (904 voxels, overlap=0.926) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (904 voxels, peak = 96), gca=96.3 gca peak = 0.21100 (36) mri peak = 0.11892 (13) Third_Ventricle (14): linear fit = 0.40 x + 0.0 (91 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.40 x + 0.0 (91 voxels, peak = 14), gca=14.4 gca peak = 0.13542 (27) mri peak = 0.18492 ( 9) Fourth_Ventricle (15): linear fit = 0.30 x + 0.0 (316 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.30 x + 0.0 (316 voxels, peak = 8), gca=8.1 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) not using caudate to estimate GM means estimating mean gm scale to be 1.13 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.743, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22491.873 ms 0097: dt=73.984000, rms=0.732 (1.424%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23068.572 ms 0098: dt=73.984000, rms=0.731 (0.191%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22788.508 ms 0099: dt=129.472000, rms=0.728 (0.393%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25420.580 ms 0100: dt=443.904000, rms=0.723 (0.669%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24468.154 ms 0101: dt=369.920000, rms=0.719 (0.551%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23703.947 ms 0102: dt=32.368000, rms=0.718 (0.112%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23890.664 ms 0103: dt=32.368000, rms=0.718 (0.024%), neg=0, invalid=766 0104: dt=32.368000, rms=0.718 (0.024%), neg=0, invalid=766 0105: dt=32.368000, rms=0.718 (0.035%), neg=0, invalid=766 0106: dt=32.368000, rms=0.717 (0.062%), neg=0, invalid=766 0107: dt=32.368000, rms=0.716 (0.105%), neg=0, invalid=766 0108: dt=32.368000, rms=0.716 (0.134%), neg=0, invalid=766 0109: dt=32.368000, rms=0.715 (0.127%), neg=0, invalid=766 0110: dt=32.368000, rms=0.714 (0.112%), neg=0, invalid=766 0111: dt=32.368000, rms=0.713 (0.099%), neg=0, invalid=766 0112: dt=32.368000, rms=0.713 (0.083%), neg=0, invalid=766 0113: dt=32.368000, rms=0.712 (0.076%), neg=0, invalid=766 0114: dt=32.368000, rms=0.711 (0.095%), neg=0, invalid=766 0115: dt=32.368000, rms=0.710 (0.133%), neg=0, invalid=766 0116: dt=32.368000, rms=0.709 (0.151%), neg=0, invalid=766 0117: dt=32.368000, rms=0.708 (0.141%), neg=0, invalid=766 0118: dt=32.368000, rms=0.707 (0.120%), neg=0, invalid=766 0119: dt=32.368000, rms=0.707 (0.100%), neg=0, invalid=766 0120: dt=32.368000, rms=0.706 (0.086%), neg=0, invalid=766 0121: dt=32.368000, rms=0.706 (0.071%), neg=0, invalid=766 0122: dt=32.368000, rms=0.705 (0.067%), neg=0, invalid=766 0123: dt=32.368000, rms=0.705 (0.082%), neg=0, invalid=766 0124: dt=32.368000, rms=0.704 (0.100%), neg=0, invalid=766 0125: dt=32.368000, rms=0.703 (0.108%), neg=0, invalid=766 0126: dt=32.368000, rms=0.702 (0.107%), neg=0, invalid=766 0127: dt=32.368000, rms=0.702 (0.104%), neg=0, invalid=766 0128: dt=32.368000, rms=0.701 (0.097%), neg=0, invalid=766 0129: dt=32.368000, rms=0.700 (0.096%), neg=0, invalid=766 0130: dt=32.368000, rms=0.700 (0.089%), neg=0, invalid=766 0131: dt=32.368000, rms=0.699 (0.093%), neg=0, invalid=766 0132: dt=32.368000, rms=0.698 (0.098%), neg=0, invalid=766 0133: dt=32.368000, rms=0.698 (0.102%), neg=0, invalid=766 0134: dt=32.368000, rms=0.697 (0.098%), neg=0, invalid=766 0135: dt=32.368000, rms=0.696 (0.089%), neg=0, invalid=766 0136: dt=32.368000, rms=0.696 (0.085%), neg=0, invalid=766 0137: dt=32.368000, rms=0.695 (0.079%), neg=0, invalid=766 0138: dt=32.368000, rms=0.695 (0.069%), neg=0, invalid=766 0139: dt=32.368000, rms=0.694 (0.077%), neg=0, invalid=766 0140: dt=32.368000, rms=0.694 (0.081%), neg=0, invalid=766 0141: dt=32.368000, rms=0.693 (0.085%), neg=0, invalid=766 0142: dt=32.368000, rms=0.692 (0.080%), neg=0, invalid=766 0143: dt=32.368000, rms=0.692 (0.071%), neg=0, invalid=766 0144: dt=32.368000, rms=0.691 (0.067%), neg=0, invalid=766 0145: dt=32.368000, rms=0.691 (0.067%), neg=0, invalid=766 0146: dt=32.368000, rms=0.691 (0.066%), neg=0, invalid=766 0147: dt=32.368000, rms=0.690 (0.068%), neg=0, invalid=766 0148: dt=32.368000, rms=0.690 (0.066%), neg=0, invalid=766 0149: dt=32.368000, rms=0.689 (0.069%), neg=0, invalid=766 0150: dt=32.368000, rms=0.689 (0.064%), neg=0, invalid=766 0151: dt=32.368000, rms=0.688 (0.060%), neg=0, invalid=766 0152: dt=32.368000, rms=0.688 (0.056%), neg=0, invalid=766 0153: dt=32.368000, rms=0.687 (0.062%), neg=0, invalid=766 0154: dt=32.368000, rms=0.687 (0.063%), neg=0, invalid=766 0155: dt=32.368000, rms=0.687 (0.055%), neg=0, invalid=766 0156: dt=32.368000, rms=0.686 (0.048%), neg=0, invalid=766 0157: dt=32.368000, rms=0.686 (0.047%), neg=0, invalid=766 0158: dt=32.368000, rms=0.686 (0.042%), neg=0, invalid=766 0159: dt=32.368000, rms=0.685 (0.046%), neg=0, invalid=766 0160: dt=32.368000, rms=0.685 (0.051%), neg=0, invalid=766 0161: dt=32.368000, rms=0.685 (0.057%), neg=0, invalid=766 0162: dt=32.368000, rms=0.684 (0.060%), neg=0, invalid=766 0163: dt=32.368000, rms=0.684 (0.057%), neg=0, invalid=766 0164: dt=32.368000, rms=0.684 (0.051%), neg=0, invalid=766 0165: dt=32.368000, rms=0.683 (0.047%), neg=0, invalid=766 0166: dt=32.368000, rms=0.683 (0.043%), neg=0, invalid=766 0167: dt=32.368000, rms=0.683 (0.040%), neg=0, invalid=766 0168: dt=32.368000, rms=0.682 (0.039%), neg=0, invalid=766 0169: dt=32.368000, rms=0.682 (0.039%), neg=0, invalid=766 0170: dt=32.368000, rms=0.682 (0.042%), neg=0, invalid=766 0171: dt=32.368000, rms=0.681 (0.046%), neg=0, invalid=766 0172: dt=32.368000, rms=0.681 (0.048%), neg=0, invalid=766 0173: dt=32.368000, rms=0.681 (0.049%), neg=0, invalid=766 0174: dt=32.368000, rms=0.681 (0.044%), neg=0, invalid=766 0175: dt=32.368000, rms=0.680 (0.036%), neg=0, invalid=766 0176: dt=32.368000, rms=0.680 (0.032%), neg=0, invalid=766 0177: dt=32.368000, rms=0.680 (0.027%), neg=0, invalid=766 0178: dt=32.368000, rms=0.680 (0.025%), neg=0, invalid=766 0179: dt=32.368000, rms=0.680 (0.030%), neg=0, invalid=766 0180: dt=32.368000, rms=0.679 (0.033%), neg=0, invalid=766 0181: dt=32.368000, rms=0.679 (0.037%), neg=0, invalid=766 0182: dt=32.368000, rms=0.679 (0.040%), neg=0, invalid=766 0183: dt=32.368000, rms=0.678 (0.041%), neg=0, invalid=766 0184: dt=32.368000, rms=0.678 (0.036%), neg=0, invalid=766 0185: dt=32.368000, rms=0.678 (0.033%), neg=0, invalid=766 0186: dt=32.368000, rms=0.678 (0.029%), neg=0, invalid=766 0187: dt=32.368000, rms=0.678 (0.026%), neg=0, invalid=766 0188: dt=32.368000, rms=0.677 (0.031%), neg=0, invalid=766 0189: dt=32.368000, rms=0.677 (0.030%), neg=0, invalid=766 0190: dt=32.368000, rms=0.677 (0.031%), neg=0, invalid=766 0191: dt=32.368000, rms=0.677 (0.028%), neg=0, invalid=766 0192: dt=32.368000, rms=0.677 (0.019%), neg=0, invalid=766 0193: dt=32.368000, rms=0.677 (0.019%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22866.490 ms 0194: dt=2071.552000, rms=0.675 (0.224%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21997.576 ms 0195: dt=23.120000, rms=0.675 (0.011%), neg=0, invalid=766 0196: dt=23.120000, rms=0.675 (0.001%), neg=0, invalid=766 0197: dt=23.120000, rms=0.675 (-0.015%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.675, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22260.531 ms 0198: dt=129.472000, rms=0.674 (0.146%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23452.350 ms 0199: dt=221.952000, rms=0.672 (0.271%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21871.189 ms 0200: dt=27.744000, rms=0.672 (0.022%), neg=0, invalid=766 0201: dt=27.744000, rms=0.672 (0.005%), neg=0, invalid=766 0202: dt=27.744000, rms=0.672 (-0.013%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.673, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20698.742 ms 0203: dt=82.944000, rms=0.669 (0.650%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20751.139 ms 0204: dt=124.416000, rms=0.658 (1.635%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20743.064 ms 0205: dt=20.736000, rms=0.655 (0.494%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21020.418 ms 0206: dt=36.288000, rms=0.653 (0.297%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20702.525 ms 0207: dt=145.152000, rms=0.646 (1.145%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22229.926 ms 0208: dt=103.680000, rms=0.642 (0.546%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19056.225 ms 0209: dt=20.736000, rms=0.640 (0.248%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19301.123 ms 0210: dt=36.288000, rms=0.638 (0.356%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19872.273 ms 0211: dt=145.152000, rms=0.634 (0.686%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19956.219 ms 0212: dt=36.288000, rms=0.632 (0.250%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19610.912 ms 0213: dt=36.288000, rms=0.631 (0.155%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20402.254 ms 0214: dt=145.152000, rms=0.628 (0.574%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19397.814 ms 0215: dt=20.736000, rms=0.627 (0.154%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20780.635 ms 0216: dt=145.152000, rms=0.623 (0.520%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21592.676 ms 0217: dt=145.152000, rms=0.621 (0.349%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18098.305 ms 0218: dt=31.104000, rms=0.620 (0.190%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19621.703 ms 0219: dt=36.288000, rms=0.619 (0.136%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19804.197 ms 0220: dt=103.680000, rms=0.618 (0.166%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20719.412 ms 0221: dt=31.104000, rms=0.617 (0.195%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20404.846 ms 0222: dt=36.288000, rms=0.616 (0.101%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22695.688 ms 0223: dt=124.416000, rms=0.615 (0.214%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18418.783 ms 0224: dt=20.736000, rms=0.614 (0.149%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20281.059 ms 0225: dt=580.608000, rms=0.608 (0.995%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17752.316 ms 0226: dt=31.104000, rms=0.607 (0.220%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20326.008 ms 0227: dt=82.944000, rms=0.605 (0.222%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18695.025 ms 0228: dt=20.736000, rms=0.605 (0.063%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19921.613 ms 0229: dt=36.288000, rms=0.605 (0.043%), neg=0, invalid=766 0230: dt=36.288000, rms=0.604 (0.084%), neg=0, invalid=766 0231: dt=36.288000, rms=0.603 (0.111%), neg=0, invalid=766 0232: dt=36.288000, rms=0.603 (0.117%), neg=0, invalid=766 0233: dt=36.288000, rms=0.602 (0.168%), neg=0, invalid=766 0234: dt=36.288000, rms=0.600 (0.235%), neg=0, invalid=766 0235: dt=36.288000, rms=0.599 (0.222%), neg=0, invalid=766 0236: dt=36.288000, rms=0.598 (0.207%), neg=0, invalid=766 0237: dt=36.288000, rms=0.596 (0.234%), neg=0, invalid=766 0238: dt=36.288000, rms=0.595 (0.242%), neg=0, invalid=766 0239: dt=36.288000, rms=0.593 (0.237%), neg=0, invalid=766 0240: dt=36.288000, rms=0.592 (0.191%), neg=0, invalid=766 0241: dt=36.288000, rms=0.591 (0.169%), neg=0, invalid=766 0242: dt=36.288000, rms=0.590 (0.200%), neg=0, invalid=766 0243: dt=36.288000, rms=0.590 (0.066%), neg=0, invalid=766 0244: dt=36.288000, rms=0.589 (0.050%), neg=0, invalid=766 0245: dt=36.288000, rms=0.589 (0.022%), neg=0, invalid=766 0246: dt=36.288000, rms=0.589 (0.048%), neg=0, invalid=766 0247: dt=36.288000, rms=0.588 (0.116%), neg=0, invalid=766 0248: dt=36.288000, rms=0.588 (0.103%), neg=0, invalid=766 0249: dt=36.288000, rms=0.587 (0.089%), neg=0, invalid=766 0250: dt=36.288000, rms=0.587 (0.088%), neg=0, invalid=766 0251: dt=36.288000, rms=0.586 (0.123%), neg=0, invalid=766 0252: dt=36.288000, rms=0.585 (0.145%), neg=0, invalid=766 0253: dt=36.288000, rms=0.585 (0.098%), neg=0, invalid=766 0254: dt=36.288000, rms=0.584 (0.087%), neg=0, invalid=766 0255: dt=36.288000, rms=0.583 (0.121%), neg=0, invalid=766 0256: dt=36.288000, rms=0.583 (0.134%), neg=0, invalid=766 0257: dt=36.288000, rms=0.582 (0.113%), neg=0, invalid=766 0258: dt=36.288000, rms=0.581 (0.083%), neg=0, invalid=766 0259: dt=36.288000, rms=0.581 (0.089%), neg=0, invalid=766 0260: dt=36.288000, rms=0.580 (0.125%), neg=0, invalid=766 0261: dt=36.288000, rms=0.579 (0.121%), neg=0, invalid=766 0262: dt=36.288000, rms=0.579 (-0.025%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20384.252 ms 0263: dt=0.000000, rms=0.579 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19991.369 ms 0264: dt=36.288000, rms=0.577 (0.426%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21730.270 ms 0265: dt=124.416000, rms=0.575 (0.292%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 16290.411 ms 0266: dt=9.072000, rms=0.575 (0.065%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17885.598 ms 0267: dt=9.072000, rms=0.575 (0.043%), neg=0, invalid=766 0268: dt=9.072000, rms=0.575 (0.032%), neg=0, invalid=766 0269: dt=9.072000, rms=0.574 (0.019%), neg=0, invalid=766 0270: dt=2.268000, rms=0.574 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 16550.682 ms 0271: dt=0.567000, rms=0.574 (0.002%), neg=0, invalid=766 0272: dt=0.567000, rms=0.574 (0.001%), neg=0, invalid=766 0273: dt=0.283500, rms=0.574 (0.001%), neg=0, invalid=766 0274: dt=0.141750, rms=0.574 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.586, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19333.973 ms 0275: dt=11.200000, rms=0.584 (0.367%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19891.229 ms 0276: dt=11.200000, rms=0.582 (0.410%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20684.818 ms 0277: dt=44.800000, rms=0.575 (1.179%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17949.949 ms 0278: dt=11.200000, rms=0.573 (0.302%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20598.045 ms 0279: dt=32.000000, rms=0.568 (0.946%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18844.898 ms 0280: dt=6.400000, rms=0.568 (0.026%), neg=0, invalid=766 0281: dt=6.400000, rms=0.567 (0.131%), neg=0, invalid=766 0282: dt=6.400000, rms=0.566 (0.226%), neg=0, invalid=766 0283: dt=6.400000, rms=0.564 (0.308%), neg=0, invalid=766 0284: dt=6.400000, rms=0.562 (0.367%), neg=0, invalid=766 0285: dt=6.400000, rms=0.561 (0.103%), neg=0, invalid=766 0286: dt=6.400000, rms=0.560 (0.175%), neg=0, invalid=766 0287: dt=6.400000, rms=0.559 (0.235%), neg=0, invalid=766 0288: dt=6.400000, rms=0.557 (0.275%), neg=0, invalid=766 0289: dt=6.400000, rms=0.556 (0.317%), neg=0, invalid=766 0290: dt=6.400000, rms=0.554 (0.343%), neg=0, invalid=766 0291: dt=6.400000, rms=0.552 (0.361%), neg=0, invalid=766 0292: dt=6.400000, rms=0.550 (0.346%), neg=0, invalid=766 0293: dt=6.400000, rms=0.548 (0.329%), neg=0, invalid=766 0294: dt=6.400000, rms=0.546 (0.319%), neg=0, invalid=766 0295: dt=6.400000, rms=0.545 (0.297%), neg=0, invalid=766 0296: dt=6.400000, rms=0.543 (0.266%), neg=0, invalid=766 0297: dt=6.400000, rms=0.542 (0.244%), neg=0, invalid=766 0298: dt=6.400000, rms=0.541 (0.217%), neg=0, invalid=766 0299: dt=6.400000, rms=0.540 (0.202%), neg=0, invalid=766 0300: dt=6.400000, rms=0.539 (0.194%), neg=0, invalid=766 0301: dt=6.400000, rms=0.538 (0.183%), neg=0, invalid=766 0302: dt=6.400000, rms=0.537 (0.172%), neg=0, invalid=766 0303: dt=6.400000, rms=0.536 (0.151%), neg=0, invalid=766 0304: dt=6.400000, rms=0.535 (0.143%), neg=0, invalid=766 0305: dt=6.400000, rms=0.534 (0.139%), neg=0, invalid=766 0306: dt=6.400000, rms=0.534 (0.135%), neg=0, invalid=766 0307: dt=6.400000, rms=0.533 (0.130%), neg=0, invalid=766 0308: dt=6.400000, rms=0.532 (0.130%), neg=0, invalid=766 0309: dt=6.400000, rms=0.532 (0.122%), neg=0, invalid=766 0310: dt=6.400000, rms=0.531 (0.103%), neg=0, invalid=766 0311: dt=6.400000, rms=0.531 (0.082%), neg=0, invalid=766 0312: dt=6.400000, rms=0.530 (0.080%), neg=0, invalid=766 0313: dt=6.400000, rms=0.530 (0.079%), neg=0, invalid=766 0314: dt=6.400000, rms=0.529 (0.084%), neg=0, invalid=766 0315: dt=6.400000, rms=0.529 (0.078%), neg=0, invalid=766 0316: dt=6.400000, rms=0.529 (0.073%), neg=0, invalid=766 0317: dt=6.400000, rms=0.529 (0.011%), neg=0, invalid=766 0318: dt=6.400000, rms=0.528 (0.021%), neg=0, invalid=766 0319: dt=6.400000, rms=0.528 (0.024%), neg=0, invalid=766 0320: dt=6.400000, rms=0.528 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20148.229 ms 0321: dt=32.000000, rms=0.528 (0.018%), neg=0, invalid=766 0322: dt=32.000000, rms=0.528 (0.053%), neg=0, invalid=766 0323: dt=16.000000, rms=0.528 (-0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31710.318 ms 0324: dt=0.000004, rms=0.528 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.528, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18688.191 ms 0325: dt=11.200000, rms=0.526 (0.322%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19748.926 ms 0326: dt=38.400000, rms=0.525 (0.284%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18917.816 ms 0327: dt=8.000000, rms=0.524 (0.082%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21517.365 ms 0328: dt=44.800000, rms=0.523 (0.160%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20197.381 ms 0329: dt=2.800000, rms=0.523 (0.013%), neg=0, invalid=766 0330: dt=2.800000, rms=0.523 (0.012%), neg=0, invalid=766 0331: dt=2.800000, rms=0.523 (0.004%), neg=0, invalid=766 0332: dt=2.800000, rms=0.523 (-0.010%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.554, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18956.359 ms 0333: dt=0.000000, rms=0.554 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.554, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18220.230 ms 0334: dt=0.000000, rms=0.554 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.615, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20625.711 ms 0335: dt=1.280000, rms=0.607 (1.240%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18579.486 ms 0336: dt=0.906250, rms=0.605 (0.309%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20417.699 ms 0337: dt=0.888889, rms=0.605 (0.099%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19974.539 ms 0338: dt=0.384000, rms=0.605 (0.012%), neg=0, invalid=766 0339: dt=0.384000, rms=0.605 (-0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.605, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19870.268 ms 0340: dt=1.792000, rms=0.603 (0.272%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19890.512 ms 0341: dt=1.024000, rms=0.603 (0.046%), neg=0, invalid=766 0342: dt=1.024000, rms=0.603 (0.008%), neg=0, invalid=766 0343: dt=1.024000, rms=0.603 (-0.115%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.556, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18827.316 ms 0344: dt=0.096000, rms=0.552 (0.874%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 16305.321 ms 0345: dt=0.007000, rms=0.551 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19715.057 ms 0346: dt=0.112000, rms=0.547 (0.832%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17803.764 ms 0347: dt=0.028000, rms=0.546 (0.171%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18690.188 ms 0348: dt=0.080000, rms=0.543 (0.456%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17132.068 ms 0349: dt=0.028000, rms=0.543 (0.139%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 16885.461 ms 0350: dt=0.028000, rms=0.542 (0.133%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19240.957 ms 0351: dt=0.130040, rms=0.539 (0.588%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18749.084 ms 0352: dt=0.028000, rms=0.538 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18807.527 ms 0353: dt=0.028000, rms=0.538 (0.097%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18779.447 ms 0354: dt=0.020000, rms=0.537 (0.066%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19441.395 ms 0355: dt=0.028000, rms=0.537 (0.091%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20930.150 ms 0356: dt=0.080000, rms=0.535 (0.248%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17782.924 ms 0357: dt=0.007000, rms=0.535 (0.019%), neg=0, invalid=766 0358: dt=0.007000, rms=0.535 (0.019%), neg=0, invalid=766 0359: dt=0.007000, rms=0.535 (0.036%), neg=0, invalid=766 0360: dt=0.007000, rms=0.535 (0.051%), neg=0, invalid=766 0361: dt=0.007000, rms=0.534 (0.065%), neg=0, invalid=766 0362: dt=0.007000, rms=0.534 (0.075%), neg=0, invalid=766 0363: dt=0.007000, rms=0.533 (0.084%), neg=0, invalid=766 0364: dt=0.007000, rms=0.533 (0.091%), neg=0, invalid=766 0365: dt=0.007000, rms=0.532 (0.098%), neg=0, invalid=766 0366: dt=0.007000, rms=0.532 (0.103%), neg=0, invalid=766 0367: dt=0.007000, rms=0.531 (0.106%), neg=0, invalid=766 0368: dt=0.007000, rms=0.531 (0.108%), neg=0, invalid=766 0369: dt=0.007000, rms=0.530 (0.108%), neg=0, invalid=766 0370: dt=0.007000, rms=0.530 (0.108%), neg=0, invalid=766 0371: dt=0.007000, rms=0.529 (0.107%), neg=0, invalid=766 0372: dt=0.007000, rms=0.529 (0.104%), neg=0, invalid=766 0373: dt=0.007000, rms=0.528 (0.102%), neg=0, invalid=766 0374: dt=0.007000, rms=0.527 (0.099%), neg=0, invalid=766 0375: dt=0.007000, rms=0.527 (0.096%), neg=0, invalid=766 0376: dt=0.007000, rms=0.526 (0.092%), neg=0, invalid=766 0377: dt=0.007000, rms=0.526 (0.087%), neg=0, invalid=766 0378: dt=0.007000, rms=0.526 (0.083%), neg=0, invalid=766 0379: dt=0.007000, rms=0.525 (0.078%), neg=0, invalid=766 0380: dt=0.007000, rms=0.525 (0.073%), neg=0, invalid=766 0381: dt=0.007000, rms=0.524 (0.069%), neg=0, invalid=766 0382: dt=0.007000, rms=0.524 (0.065%), neg=0, invalid=766 0383: dt=0.007000, rms=0.524 (0.061%), neg=0, invalid=766 0384: dt=0.007000, rms=0.523 (0.057%), neg=0, invalid=766 0385: dt=0.007000, rms=0.523 (0.052%), neg=0, invalid=766 0386: dt=0.007000, rms=0.523 (0.051%), neg=0, invalid=766 0387: dt=0.007000, rms=0.523 (0.045%), neg=0, invalid=766 0388: dt=0.007000, rms=0.522 (0.042%), neg=0, invalid=766 0389: dt=0.007000, rms=0.522 (0.038%), neg=0, invalid=766 0390: dt=0.007000, rms=0.522 (0.036%), neg=0, invalid=766 0391: dt=0.007000, rms=0.522 (0.034%), neg=0, invalid=766 0392: dt=0.007000, rms=0.522 (0.031%), neg=0, invalid=766 0393: dt=0.007000, rms=0.522 (0.028%), neg=0, invalid=766 0394: dt=0.007000, rms=0.521 (0.029%), neg=0, invalid=766 0395: dt=0.007000, rms=0.521 (0.027%), neg=0, invalid=766 0396: dt=0.007000, rms=0.521 (0.023%), neg=0, invalid=766 0397: dt=0.007000, rms=0.521 (0.023%), neg=0, invalid=766 0398: dt=0.007000, rms=0.521 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20194.064 ms 0399: dt=0.082627, rms=0.521 (0.017%), neg=0, invalid=766 0400: dt=0.020657, rms=0.521 (0.004%), neg=0, invalid=766 0401: dt=0.010328, rms=0.521 (0.004%), neg=0, invalid=766 0402: dt=0.010328, rms=0.521 (0.001%), neg=0, invalid=766 0403: dt=0.010328, rms=0.521 (0.003%), neg=0, invalid=766 0404: dt=0.010328, rms=0.521 (0.004%), neg=0, invalid=766 0405: dt=0.010328, rms=0.521 (0.006%), neg=0, invalid=766 0406: dt=0.010328, rms=0.521 (0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.521, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18580.984 ms 0407: dt=0.028000, rms=0.520 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17673.041 ms 0408: dt=0.028000, rms=0.520 (0.080%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18646.613 ms 0409: dt=0.020000, rms=0.520 (0.056%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19735.477 ms 0410: dt=0.028000, rms=0.519 (0.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21680.957 ms 0411: dt=0.107143, rms=0.518 (0.261%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18135.547 ms 0412: dt=0.007000, rms=0.518 (0.013%), neg=0, invalid=766 0413: dt=0.007000, rms=0.518 (0.013%), neg=0, invalid=766 0414: dt=0.007000, rms=0.518 (0.025%), neg=0, invalid=766 0415: dt=0.007000, rms=0.517 (0.034%), neg=0, invalid=766 0416: dt=0.007000, rms=0.517 (0.043%), neg=0, invalid=766 0417: dt=0.007000, rms=0.517 (0.050%), neg=0, invalid=766 0418: dt=0.007000, rms=0.517 (0.055%), neg=0, invalid=766 0419: dt=0.007000, rms=0.516 (0.059%), neg=0, invalid=766 0420: dt=0.007000, rms=0.516 (0.062%), neg=0, invalid=766 0421: dt=0.007000, rms=0.516 (0.063%), neg=0, invalid=766 0422: dt=0.007000, rms=0.515 (0.064%), neg=0, invalid=766 0423: dt=0.007000, rms=0.515 (0.064%), neg=0, invalid=766 0424: dt=0.007000, rms=0.515 (0.062%), neg=0, invalid=766 0425: dt=0.007000, rms=0.514 (0.059%), neg=0, invalid=766 0426: dt=0.007000, rms=0.514 (0.058%), neg=0, invalid=766 0427: dt=0.007000, rms=0.514 (0.051%), neg=0, invalid=766 0428: dt=0.007000, rms=0.514 (0.053%), neg=0, invalid=766 0429: dt=0.007000, rms=0.513 (0.047%), neg=0, invalid=766 0430: dt=0.007000, rms=0.513 (0.043%), neg=0, invalid=766 0431: dt=0.007000, rms=0.513 (0.040%), neg=0, invalid=766 0432: dt=0.007000, rms=0.513 (0.034%), neg=0, invalid=766 0433: dt=0.007000, rms=0.513 (0.029%), neg=0, invalid=766 0434: dt=0.007000, rms=0.512 (0.029%), neg=0, invalid=766 0435: dt=0.007000, rms=0.512 (0.022%), neg=0, invalid=766 0436: dt=0.007000, rms=0.512 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19730.688 ms 0437: dt=0.000000, rms=0.512 (-0.001%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27456.428 ms iter 0, gcam->neg = 198 after 77 iterations, nbhd size=4, neg = 0 0438: dt=33.488372, rms=0.496 (2.826%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27681.822 ms iter 0, gcam->neg = 94 after 41 iterations, nbhd size=3, neg = 0 0439: dt=22.277898, rms=0.490 (1.161%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26538.102 ms iter 0, gcam->neg = 54 after 17 iterations, nbhd size=1, neg = 0 0440: dt=6.825688, rms=0.489 (0.194%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 19 iterations, nbhd size=2, neg = 0 0441: dt=6.825688, rms=0.488 (0.120%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 23 iterations, nbhd size=3, neg = 0 0442: dt=6.825688, rms=0.487 (0.188%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 33 iterations, nbhd size=4, neg = 0 0443: dt=6.825688, rms=0.486 (0.207%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 34 iterations, nbhd size=4, neg = 0 0444: dt=6.825688, rms=0.485 (0.339%), neg=0, invalid=766 iter 0, gcam->neg = 22 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.006, neg=5, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 12674.786 ms iter 1, dt=0.000625: new neg 4, old_neg 5, delta 1, rms=0.005 (9.853%) gcamFindOptimalTimeStep: Complete in 12540.134 ms iter 2, dt=0.000410: new neg 0, old_neg 4, delta 4, rms=0.005 (5.246%) 0445: dt=6.825688, rms=0.483 (0.328%), neg=0, invalid=766 0446: dt=6.825688, rms=0.482 (0.172%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0447: dt=6.825688, rms=0.481 (0.205%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 0448: dt=6.825688, rms=0.480 (0.191%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 6 iterations, nbhd size=0, neg = 0 0449: dt=6.825688, rms=0.480 (0.157%), neg=0, invalid=766 iter 0, gcam->neg = 48 after 46 iterations, nbhd size=4, neg = 0 0450: dt=6.825688, rms=0.479 (0.131%), neg=0, invalid=766 iter 0, gcam->neg = 96 after 40 iterations, nbhd size=4, neg = 0 0451: dt=6.825688, rms=0.479 (-0.038%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23457.043 ms 0452: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23247.309 ms iter 0, gcam->neg = 103 after 77 iterations, nbhd size=2, neg = 0 0453: dt=25.600000, rms=0.477 (0.493%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22210.992 ms 0454: dt=11.200000, rms=0.475 (0.332%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21459.504 ms iter 0, gcam->neg = 40 after 200 iterations, nbhd size=4, neg = 10 starting rms=0.005, neg=10, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11689.906 ms iter 1, dt=0.000500: new neg 4, old_neg 10, delta 6, rms=0.003 (25.703%) gcamFindOptimalTimeStep: Complete in 11623.525 ms iter 2, dt=0.000408: new neg 1, old_neg 4, delta 3, rms=0.003 (9.603%) gcamFindOptimalTimeStep: Complete in 11457.224 ms iter 3, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.003 (5.024%) 0455: dt=44.800000, rms=0.472 (0.539%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23373.367 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0456: dt=8.034188, rms=0.471 (0.296%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21953.527 ms iter 0, gcam->neg = 1 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11650.894 ms iter 1, dt=0.000750: new neg 0, old_neg 1, delta 1, rms=0.002 (14.103%) 0457: dt=11.200000, rms=0.471 (0.114%), neg=0, invalid=766 0458: dt=11.200000, rms=0.470 (0.164%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0459: dt=11.200000, rms=0.469 (0.195%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 10718.702 ms iter 1, dt=0.000875: new neg 0, old_neg 1, delta 1, rms=0.003 (15.567%) 0460: dt=11.200000, rms=0.468 (0.191%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0461: dt=11.200000, rms=0.467 (0.090%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0462: dt=11.200000, rms=0.467 (0.099%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11061.767 ms iter 1, dt=0.000875: new neg 0, old_neg 1, delta 1, rms=0.002 (12.109%) 0463: dt=11.200000, rms=0.466 (0.121%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0464: dt=11.200000, rms=0.466 (0.058%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23191.785 ms iter 0, gcam->neg = 80 after 200 iterations, nbhd size=3, neg = 10 starting rms=0.005, neg=10, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11839.198 ms iter 1, dt=0.000625: new neg 7, old_neg 10, delta 3, rms=0.004 (22.080%) gcamFindOptimalTimeStep: Complete in 11581.217 ms iter 2, dt=0.000328: new neg 0, old_neg 7, delta 7, rms=0.004 (9.807%) 0465: dt=102.400000, rms=0.465 (0.176%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22540.518 ms iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0466: dt=9.600000, rms=0.465 (0.133%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 19 iterations, nbhd size=3, neg = 0 0467: dt=9.600000, rms=0.465 (-0.009%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23835.598 ms iter 0, gcam->neg = 10 after 11 iterations, nbhd size=1, neg = 0 0468: dt=2.029851, rms=0.470 (0.041%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23841.852 ms iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0469: dt=2.880000, rms=0.470 (0.028%), neg=0, invalid=766 0470: dt=2.880000, rms=0.470 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11695.825 ms iter 1, dt=0.000875: new neg 1, old_neg 1, delta 0, rms=0.002 (14.471%) gcamFindOptimalTimeStep: Complete in 11584.129 ms iter 2, dt=0.000573: new neg 0, old_neg 1, delta 1, rms=0.002 (6.066%) 0471: dt=2.880000, rms=0.470 (-0.054%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23021.021 ms iter 0, gcam->neg = 34 after 12 iterations, nbhd size=1, neg = 0 0472: dt=6.888889, rms=0.469 (0.212%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24136.840 ms iter 0, gcam->neg = 27 after 10 iterations, nbhd size=1, neg = 0 0473: dt=3.456000, rms=0.468 (0.079%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 1 iterations, nbhd size=0, neg = 0 0474: dt=3.456000, rms=0.468 (0.082%), neg=0, invalid=766 iter 0, gcam->neg = 87 after 39 iterations, nbhd size=3, neg = 0 0475: dt=3.456000, rms=0.467 (0.127%), neg=0, invalid=766 iter 0, gcam->neg = 112 after 19 iterations, nbhd size=1, neg = 0 0476: dt=3.456000, rms=0.467 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 38 after 12 iterations, nbhd size=1, neg = 0 0477: dt=3.456000, rms=0.467 (0.067%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22179.590 ms iter 0, gcam->neg = 68 after 9 iterations, nbhd size=1, neg = 0 0478: dt=5.250000, rms=0.466 (0.237%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22132.830 ms iter 0, gcam->neg = 20 after 7 iterations, nbhd size=1, neg = 0 0479: dt=2.880000, rms=0.465 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0480: dt=2.880000, rms=0.465 (0.115%), neg=0, invalid=766 iter 0, gcam->neg = 58 after 14 iterations, nbhd size=1, neg = 0 0481: dt=2.880000, rms=0.464 (0.162%), neg=0, invalid=766 iter 0, gcam->neg = 47 after 11 iterations, nbhd size=1, neg = 0 0482: dt=2.880000, rms=0.463 (0.152%), neg=0, invalid=766 iter 0, gcam->neg = 81 after 4 iterations, nbhd size=0, neg = 0 0483: dt=2.880000, rms=0.463 (0.139%), neg=0, invalid=766 iter 0, gcam->neg = 63 after 15 iterations, nbhd size=1, neg = 0 0484: dt=2.880000, rms=0.462 (0.108%), neg=0, invalid=766 iter 0, gcam->neg = 54 after 14 iterations, nbhd size=1, neg = 0 0485: dt=2.880000, rms=0.462 (0.122%), neg=0, invalid=766 iter 0, gcam->neg = 84 after 18 iterations, nbhd size=2, neg = 0 0486: dt=2.880000, rms=0.461 (0.118%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21806.076 ms iter 0, gcam->neg = 18 after 2 iterations, nbhd size=0, neg = 0 0487: dt=1.500000, rms=0.461 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 6 iterations, nbhd size=0, neg = 0 0488: dt=1.500000, rms=0.461 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 5 iterations, nbhd size=0, neg = 0 0489: dt=1.500000, rms=0.461 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 5 iterations, nbhd size=0, neg = 0 0490: dt=1.500000, rms=0.461 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 46 after 11 iterations, nbhd size=1, neg = 0 0491: dt=1.500000, rms=0.460 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 35 after 9 iterations, nbhd size=1, neg = 0 0492: dt=1.500000, rms=0.460 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 8 iterations, nbhd size=1, neg = 0 0493: dt=1.500000, rms=0.460 (0.043%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0494: dt=1.500000, rms=0.460 (0.037%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23259.844 ms 0495: dt=0.000000, rms=0.466 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23346.395 ms 0496: dt=0.000000, rms=0.466 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.466, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24160.873 ms 0497: dt=0.000000, rms=0.466 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.455, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24657.350 ms iter 0, gcam->neg = 953 after 34 iterations, nbhd size=3, neg = 0 0498: dt=1.601513, rms=0.418 (8.262%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23859.246 ms 0499: dt=0.000312, rms=0.418 (0.004%), neg=0, invalid=766 0500: dt=0.000312, rms=0.418 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.418, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25252.348 ms 0501: dt=0.000109, rms=0.418 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25048.695 ms 0502: dt=0.000047, rms=0.418 (0.000%), neg=0, invalid=766 0503: dt=0.000047, rms=0.418 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23495.477 ms iter 0, gcam->neg = 276 after 18 iterations, nbhd size=2, neg = 0 0504: dt=0.384000, rms=0.400 (1.640%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23616.402 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0505: dt=0.001000, rms=0.400 (0.003%), neg=0, invalid=766 0506: dt=0.001000, rms=0.400 (0.001%), neg=0, invalid=766 0507: dt=0.001000, rms=0.400 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0508: dt=0.001000, rms=0.400 (0.002%), neg=0, invalid=766 0509: dt=0.001000, rms=0.400 (0.003%), neg=0, invalid=766 0510: dt=0.001000, rms=0.400 (0.004%), neg=0, invalid=766 0511: dt=0.001000, rms=0.400 (0.003%), neg=0, invalid=766 0512: dt=0.001000, rms=0.400 (0.006%), neg=0, invalid=766 0513: dt=0.001000, rms=0.400 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24864.000 ms iter 0, gcam->neg = 9 after 13 iterations, nbhd size=2, neg = 0 0514: dt=0.064000, rms=0.400 (0.063%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24667.070 ms 0515: dt=0.000438, rms=0.400 (0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.400, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24501.369 ms iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0516: dt=0.003000, rms=0.400 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24567.299 ms iter 0, gcam->neg = 222 after 30 iterations, nbhd size=3, neg = 0 0517: dt=0.384000, rms=0.395 (1.176%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24624.090 ms 0518: dt=0.000750, rms=0.395 (-0.001%), neg=0, invalid=766 0519: dt=0.000750, rms=0.395 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 34 iterations, nbhd size=4, neg = 0 0520: dt=0.000750, rms=0.395 (-0.007%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25668.426 ms iter 0, gcam->neg = 54 after 9 iterations, nbhd size=1, neg = 0 0521: dt=0.077206, rms=0.393 (0.326%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25393.014 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0522: dt=0.000250, rms=0.393 (0.004%), neg=0, invalid=766 0523: dt=0.000250, rms=0.393 (0.001%), neg=0, invalid=766 0524: dt=0.000250, rms=0.393 (0.002%), neg=0, invalid=766 0525: dt=0.000250, rms=0.393 (0.002%), neg=0, invalid=766 0526: dt=0.000250, rms=0.393 (0.003%), neg=0, invalid=766 0527: dt=0.000250, rms=0.393 (0.004%), neg=0, invalid=766 0528: dt=0.000250, rms=0.393 (0.004%), neg=0, invalid=766 0529: dt=0.000250, rms=0.393 (0.005%), neg=0, invalid=766 0530: dt=0.000250, rms=0.393 (0.005%), neg=0, invalid=766 0531: dt=0.000250, rms=0.393 (0.006%), neg=0, invalid=766 0532: dt=0.000250, rms=0.393 (0.006%), neg=0, invalid=766 0533: dt=0.000250, rms=0.393 (0.006%), neg=0, invalid=766 0534: dt=0.000250, rms=0.393 (0.006%), neg=0, invalid=766 0535: dt=0.000250, rms=0.393 (0.007%), neg=0, invalid=766 0536: dt=0.000250, rms=0.393 (0.007%), neg=0, invalid=766 0537: dt=0.000250, rms=0.393 (0.007%), neg=0, invalid=766 0538: dt=0.000250, rms=0.393 (0.007%), neg=0, invalid=766 0539: dt=0.000250, rms=0.393 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25687.318 ms iter 0, gcam->neg = 52 after 21 iterations, nbhd size=2, neg = 0 0540: dt=0.112000, rms=0.392 (0.362%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25064.762 ms 0541: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0542: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0543: dt=0.000438, rms=0.392 (0.002%), neg=0, invalid=766 0544: dt=0.000438, rms=0.392 (0.001%), neg=0, invalid=766 0545: dt=0.000438, rms=0.391 (0.003%), neg=0, invalid=766 0546: dt=0.000438, rms=0.391 (0.004%), neg=0, invalid=766 0547: dt=0.000438, rms=0.391 (0.005%), neg=0, invalid=766 0548: dt=0.000438, rms=0.391 (0.005%), neg=0, invalid=766 0549: dt=0.000438, rms=0.391 (0.006%), neg=0, invalid=766 0550: dt=0.000438, rms=0.391 (0.007%), neg=0, invalid=766 0551: dt=0.000438, rms=0.391 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23657.178 ms iter 0, gcam->neg = 46 after 31 iterations, nbhd size=3, neg = 0 0552: dt=0.080000, rms=0.391 (0.180%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23533.801 ms iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0553: dt=0.001000, rms=0.391 (0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.391, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23689.852 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0554: dt=0.004990, rms=0.391 (0.020%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23755.219 ms iter 0, gcam->neg = 84 after 28 iterations, nbhd size=3, neg = 0 0555: dt=0.096000, rms=0.389 (0.397%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24936.820 ms 0556: dt=0.000250, rms=0.389 (-0.001%), neg=0, invalid=766 0557: dt=0.000250, rms=0.389 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0558: dt=0.000250, rms=0.389 (0.002%), neg=0, invalid=766 0559: dt=0.000250, rms=0.389 (0.002%), neg=0, invalid=766 0560: dt=0.000250, rms=0.389 (0.002%), neg=0, invalid=766 0561: dt=0.000250, rms=0.389 (0.003%), neg=0, invalid=766 0562: dt=0.000250, rms=0.389 (0.004%), neg=0, invalid=766 0563: dt=0.000250, rms=0.389 (0.005%), neg=0, invalid=766 0564: dt=0.000250, rms=0.389 (0.005%), neg=0, invalid=766 0565: dt=0.000250, rms=0.389 (0.006%), neg=0, invalid=766 0566: dt=0.000250, rms=0.389 (0.004%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22848.029 ms iter 0, gcam->neg = 14 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11247.344 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0567: dt=2.000000, rms=0.390 (-0.246%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23834.752 ms iter 0, gcam->neg = 64 after 200 iterations, nbhd size=2, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 10473.987 ms iter 1, dt=0.000000: new neg 4, old_neg 4, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0568: dt=6.000000, rms=0.390 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.390, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21421.262 ms iter 0, gcam->neg = 35 after 31 iterations, nbhd size=3, neg = 0 0569: dt=0.565217, rms=0.389 (0.085%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24523.398 ms iter 0, gcam->neg = 32 after 49 iterations, nbhd size=4, neg = 0 0570: dt=0.252000, rms=0.389 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 34 after 49 iterations, nbhd size=4, neg = 0 0571: dt=0.252000, rms=0.389 (0.033%), neg=0, invalid=766 iter 0, gcam->neg = 67 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11145.460 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0572: dt=0.252000, rms=0.389 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25580.363 ms iter 0, gcam->neg = 62 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11183.404 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0573: dt=0.720000, rms=0.389 (0.000%), neg=0, invalid=766 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=766 gcamFindOptimalTimeStep: Complete in 24091.986 ms iter 0, gcam->neg = 20 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11103.102 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0574: dt=0.112000, rms=0.389 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23480.729 ms iter 0, gcam->neg = 19 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11396.341 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0575: dt=0.112000, rms=0.389 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24379.742 ms iter 0, gcam->neg = 2 after 25 iterations, nbhd size=3, neg = 0 0576: dt=0.000094, rms=0.389 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24911.770 ms iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.000, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11355.313 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.000 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0577: dt=0.001250, rms=0.389 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23669.963 ms iter 0, gcam->neg = 5 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.000, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 10338.918 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.000 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0578: dt=0.004000, rms=0.389 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25398.215 ms iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.000, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 10836.011 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.000 (-4.727%) ---------- unfolding failed - restoring original position -------------------- 0579: dt=0.000078, rms=0.389 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23081.506 ms 0580: dt=0.000000, rms=0.389 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23793.049 ms iter 0, gcam->neg = 4 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.000, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 11531.114 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.000 (-4.727%) ---------- unfolding failed - restoring original position -------------------- 0581: dt=0.000078, rms=0.389 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 23697.799 ms 0582: dt=0.000000, rms=0.389 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 3 hours, 1 minutes and 12 seconds. #-------------------------------------- #@# CA Reg Inv Wed May 28 21:28:27 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed May 28 21:29:12 CDT 2014 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /soft/freesurfer/5.1.0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/soft/freesurfer/5.1.0/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11485252 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 51 seconds. #-------------------------------------- #@# SkullLTA Wed May 28 21:30:03 CDT 2014 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /soft/freesurfer/5.1.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.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.log reading '/soft/freesurfer/5.1.0/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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 = (49, 44, 27) --> (206, 199, 215) using (101, 96, 121) as brain centroid... mean wm in atlas = 126, using box (82,77,98) --> (120, 115,144) to find MRI wm before smoothing, mri peak at 103 after smoothing, mri peak at 103, scaling input intensities by 1.223 scaling channel 0 by 1.2233 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10355.6, old_max_log_p =-10347.6 (thresh=-10337.3) 1.020 0.045 0.035 -12.757; -0.033 0.985 0.042 -9.534; -0.021 -0.102 1.120 -14.901; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10345.7, old_max_log_p =-10355.6 (thresh=-10345.2) 1.035 -0.088 0.019 1.418; 0.102 0.996 0.088 -31.713; -0.021 -0.141 1.138 -14.053; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 2 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10345.6, old_max_log_p =-10345.7 (thresh=-10335.4) 1.035 -0.088 0.019 1.418; 0.102 0.996 0.088 -31.713; -0.021 -0.141 1.135 -13.771; 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 1.03500 -0.08840 0.01927 1.41828; 0.10154 0.99603 0.08820 -31.71310; -0.02087 -0.14067 1.13509 -13.77144; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.03500 -0.08840 0.01927 1.41828; 0.10154 0.99603 0.08820 -31.71310; -0.02087 -0.14067 1.13509 -13.77144; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 003: -log(p) = 10345.6 after pass:transform: ( 1.03, -0.09, 0.02, 1.42) ( 0.10, 1.00, 0.09, -31.71) ( -0.02, -0.14, 1.14, -13.77) 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: 005: -log(p) = 10345.6 tol 0.000010 Resulting transform: 1.035 -0.088 0.019 1.418; 0.102 0.996 0.088 -31.713; -0.021 -0.141 1.135 -13.771; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10345.6 (old=-10347.6) transform before final EM align: 1.035 -0.088 0.019 1.418; 0.102 0.996 0.088 -31.713; -0.021 -0.141 1.135 -13.771; 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 1.03500 -0.08840 0.01927 1.41828; 0.10154 0.99603 0.08820 -31.71310; -0.02087 -0.14067 1.13509 -13.77144; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.03500 -0.08840 0.01927 1.41828; 0.10154 0.99603 0.08820 -31.71310; -0.02087 -0.14067 1.13509 -13.77144; 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) = 1146098.9 tol 0.000000 final transform: 1.035 -0.088 0.019 1.418; 0.102 0.996 0.088 -31.713; -0.021 -0.141 1.135 -13.771; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 13 minutes and 2 seconds. #-------------------------------------- #@# SubCort Seg Wed May 28 21:43:06 CDT 2014 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 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri cmdline mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz sysname Linux hostname node1118 machine x86_64 user kovacv 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 -nobigventricles norm.mgz transforms/talairach.m3z /soft/freesurfer/5.1.0/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 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /soft/freesurfer/5.1.0/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /soft/freesurfer/5.1.0/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 = 0.13889 (10) Left_Lateral_Ventricle (4): linear fit = 0.30 x + 0.0 (2853 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2853 voxels, peak = 8), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.13312 (10) Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (1246 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1246 voxels, peak = 7), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.07200 (90) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (256 voxels, overlap=0.878) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (256 voxels, peak = 87), gca=87.3 gca peak = 0.18160 (96) mri peak = 0.08084 (87) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (282 voxels, overlap=0.593) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (282 voxels, peak = 86), gca=86.4 gca peak = 0.27536 (62) mri peak = 0.08387 (72) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (854 voxels, overlap=0.204) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (854 voxels, peak = 71), gca=71.3 gca peak = 0.32745 (63) mri peak = 0.08121 (68) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (941 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (941 voxels, peak = 66), gca=66.1 gca peak = 0.08597 (105) mri peak = 0.05095 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (18431 voxels, overlap=0.744) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (18431 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.06101 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (21347 voxels, overlap=0.750) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (21347 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.05017 (75) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (37312 voxels, overlap=0.350) Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (37312 voxels, peak = 76), gca=75.6 gca peak = 0.08598 (64) mri peak = 0.04878 (72) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (44158 voxels, overlap=0.405) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (44158 voxels, peak = 74), gca=73.6 gca peak = 0.24164 (71) mri peak = 0.11212 (90) Right_Caudate (50): linear fit = 1.23 x + 0.0 (555 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.23 x + 0.0 (555 voxels, peak = 87), gca=87.0 gca peak = 0.18227 (75) mri peak = 0.09274 (78) Left_Caudate (11): linear fit = 1.00 x + 0.0 (647 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (647 voxels, peak = 75), gca=75.0 gca peak = 0.10629 (62) mri peak = 0.04885 (72) Left_Cerebellum_Cortex (8): linear fit = 1.20 x + 0.0 (25420 voxels, overlap=0.446) Left_Cerebellum_Cortex (8): linear fit = 1.20 x + 0.0 (25420 voxels, peak = 74), gca=74.4 gca peak = 0.11668 (59) mri peak = 0.05877 (70) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (31183 voxels, overlap=0.541) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (31183 voxels, peak = 68), gca=67.8 gca peak = 0.17849 (88) mri peak = 0.10805 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (3952 voxels, overlap=0.814) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (3952 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.10794 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4118 voxels, overlap=0.895) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (4118 voxels, peak = 90), gca=90.3 gca peak = 0.41688 (64) mri peak = 0.12200 (69) Left_Amygdala (18): linear fit = 1.08 x + 0.0 (459 voxels, overlap=0.700) Left_Amygdala (18): linear fit = 1.08 x + 0.0 (459 voxels, peak = 69), gca=68.8 gca peak = 0.42394 (62) mri peak = 0.09193 (68) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (442 voxels, overlap=0.434) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (442 voxels, peak = 67), gca=66.7 gca peak = 0.10041 (96) mri peak = 0.05583 (100) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (4017 voxels, overlap=0.661) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (4017 voxels, peak = 103), gca=103.2 gca peak = 0.13978 (88) mri peak = 0.04183 (92) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3592 voxels, overlap=1.000) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (3592 voxels, peak = 92), gca=92.4 gca peak = 0.08514 (81) mri peak = 0.06956 (91) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1568 voxels, overlap=0.545) Left_Putamen (12): linear fit = 1.10 x + 0.0 (1568 voxels, peak = 89), gca=89.1 gca peak = 0.09624 (82) mri peak = 0.09366 (95) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1385 voxels, overlap=0.259) Right_Putamen (51): linear fit = 1.12 x + 0.0 (1385 voxels, peak = 92), gca=92.2 gca peak = 0.07543 (88) mri peak = 0.05604 (91) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9860 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (9860 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.05495 (97) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (796 voxels, overlap=0.833) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (796 voxels, peak = 100), gca=99.7 gca peak = 0.17004 (92) mri peak = 0.06087 (101) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (776 voxels, overlap=0.933) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (776 voxels, peak = 97), gca=96.6 gca peak = 0.21361 (36) mri peak = 0.12287 (14) Third_Ventricle (14): linear fit = 0.35 x + 0.0 (293 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.35 x + 0.0 (293 voxels, peak = 13), gca=12.6 gca peak = 0.26069 (23) mri peak = 0.23780 ( 9) Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (327 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (327 voxels, peak = 8), gca=8.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.12 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.13889 (10) Left_Lateral_Ventricle (4): linear fit = 0.80 x + 0.0 (2853 voxels, overlap=0.939) Left_Lateral_Ventricle (4): linear fit = 0.80 x + 0.0 (2853 voxels, peak = 9), gca=8.8 gca peak = 0.29325 ( 9) mri peak = 0.13312 (10) Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (1246 voxels, overlap=0.965) Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (1246 voxels, peak = 8), gca=8.3 gca peak = 0.25660 (88) mri peak = 0.07200 (90) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (256 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (256 voxels, peak = 88), gca=88.0 gca peak = 0.19255 (86) mri peak = 0.08084 (87) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (282 voxels, overlap=0.999) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (282 voxels, peak = 86), gca=86.0 gca peak = 0.25232 (71) mri peak = 0.08387 (72) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (854 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (854 voxels, peak = 71), gca=71.0 gca peak = 0.29012 (66) mri peak = 0.08121 (68) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (941 voxels, overlap=0.998) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (941 voxels, peak = 66), gca=66.0 gca peak = 0.08006 (112) mri peak = 0.05095 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (18431 voxels, overlap=0.861) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (18431 voxels, peak = 112), gca=112.0 gca peak = 0.08555 (108) mri peak = 0.06101 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (21347 voxels, overlap=0.796) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (21347 voxels, peak = 108), gca=108.0 gca peak = 0.06461 (76) mri peak = 0.05017 (75) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (37312 voxels, overlap=0.872) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (37312 voxels, peak = 74), gca=74.1 gca peak = 0.07675 (73) mri peak = 0.04878 (72) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (44158 voxels, overlap=0.928) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (44158 voxels, peak = 73), gca=73.0 gca peak = 0.22019 (90) mri peak = 0.11212 (90) Right_Caudate (50): linear fit = 1.00 x + 0.0 (555 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (555 voxels, peak = 90), gca=90.0 gca peak = 0.17893 (75) mri peak = 0.09274 (78) Left_Caudate (11): linear fit = 1.00 x + 0.0 (647 voxels, overlap=0.992) Left_Caudate (11): linear fit = 1.00 x + 0.0 (647 voxels, peak = 75), gca=75.0 gca peak = 0.08763 (73) mri peak = 0.04885 (72) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (25420 voxels, overlap=0.983) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (25420 voxels, peak = 71), gca=71.2 gca peak = 0.10751 (68) mri peak = 0.05877 (70) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (31183 voxels, overlap=0.993) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (31183 voxels, peak = 68), gca=68.0 gca peak = 0.16848 (92) mri peak = 0.10805 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3952 voxels, overlap=0.978) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (3952 voxels, peak = 92), gca=92.0 gca peak = 0.15998 (91) mri peak = 0.10794 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4118 voxels, overlap=0.996) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4118 voxels, peak = 91), gca=91.0 gca peak = 0.35959 (68) mri peak = 0.12200 (69) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (459 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (459 voxels, peak = 68), gca=68.0 gca peak = 0.35233 (66) mri peak = 0.09193 (68) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (442 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (442 voxels, peak = 66), gca=66.0 gca peak = 0.10456 (103) mri peak = 0.05583 (100) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4017 voxels, overlap=0.952) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4017 voxels, peak = 103), gca=103.0 gca peak = 0.11301 (92) mri peak = 0.04183 (92) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3592 voxels, overlap=0.992) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3592 voxels, peak = 92), gca=92.0 gca peak = 0.08618 (91) mri peak = 0.06956 (91) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1568 voxels, overlap=0.941) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1568 voxels, peak = 91), gca=91.0 gca peak = 0.08481 (85) mri peak = 0.09366 (95) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1385 voxels, overlap=0.755) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1385 voxels, peak = 85), gca=85.0 gca peak = 0.07243 (90) mri peak = 0.05604 (91) Brain_Stem (16): linear fit = 1.02 x + 0.0 (9860 voxels, overlap=0.860) Brain_Stem (16): linear fit = 1.02 x + 0.0 (9860 voxels, peak = 92), gca=92.2 gca peak = 0.10774 (99) mri peak = 0.05495 (97) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (796 voxels, overlap=0.870) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (796 voxels, peak = 101), gca=101.5 gca peak = 0.14655 (97) mri peak = 0.06087 (101) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (776 voxels, overlap=0.975) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (776 voxels, peak = 99), gca=99.4 gca peak = 0.35640 (14) mri peak = 0.12287 (14) Third_Ventricle (14): linear fit = 0.85 x + 0.0 (293 voxels, overlap=0.980) Third_Ventricle (14): linear fit = 0.85 x + 0.0 (293 voxels, peak = 12), gca=11.9 gca peak = 0.33827 ( 9) mri peak = 0.23780 ( 9) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (327 voxels, overlap=0.923) Fourth_Ventricle (15): linear fit = 0.93 x + 0.0 (327 voxels, peak = 8), gca=8.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.24897 (37) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.51324 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.19452 (37) gca peak Right_Accumbens_area = 0.30179 (88) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.14916 (85) gca peak non_WM_hypointensities = 0.10331 (55) gca peak Optic_Chiasm = 0.34842 (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 0.88 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 26150 gm and wm labels changed (%30 to gray, %70 to white out of all changed labels) 300 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 79784 changed. image ll: -2.176, PF=1.000 pass 2: 13464 changed. image ll: -2.173, PF=1.000 pass 3: 4606 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 15 minutes and 36 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/transforms/cc_up.lta MPS3007-1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/transforms/cc_up.lta reading aseg from /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aseg.auto_noCCseg.mgz reading norm from /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/norm.mgz 29282 voxels in left wm, 30473 in right wm, xrange [123, 133] searching rotation angles z=[-7 7], y=[-3 11] 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 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 global minimum found at slice 127.3, rotations (3.58, -0.08) final transformation (x=127.3, yr=3.580, zr=-0.085): 0.998 0.001 0.062 -7.013; -0.001 1.000 -0.000 14.200; -0.062 -0.000 0.998 11.191; 0.000 0.000 0.000 1.000; updating x range to be [125, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 141 153 eigenvectors: -0.005 0.005 1.000; 0.361 -0.932 0.006; 0.932 0.361 0.003; writing aseg with callosum to /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Wed May 28 21:59:23 CDT 2014 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed May 28 21:59:23 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri mri_normalize -f /lustre/kovacv/FS/post-analysis/MPS3007-1/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using control points from file /lustre/kovacv/FS/post-analysis/MPS3007-1/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 314 control points... only using 314 control points from file, mean 93.6, scaling by 1.18... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 6251 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 3 minutes and 31 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 91 gm peak at 69 (69), valley at 52 (52) csf peak at 35, setting threshold to 57 white matter peak found at 111 white matter peak found at 91 gm peak at 69 (69), valley at 49 (49) csf peak at 35, setting threshold to 57 #-------------------------------------------- #@# Mask BFS Wed May 28 22:02:56 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1430412 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed May 28 22:02:58 CDT 2014 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 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname node1118 machine x86_64 user kovacv 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 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname node1118 machine x86_64 user kovacv 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 (104.0): 105.0 +- 7.7 [80.0 --> 125.0] GM (75.0) : 72.9 +- 12.5 [30.0 --> 96.0] setting bottom of white matter range to 85.4 setting top of gray matter range to 97.9 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... 22867 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4408 filled 378 bright non-wm voxels segmented. 12372 diagonally connected voxels added... white matter segmentation took 1.8 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.46 minutes reading wm segmentation from wm.seg.mgz... 852 voxels added to wm to prevent paths from MTL structures to cortex 5134 additional wm voxels added 0 additional wm voxels added SEG EDIT: 66761 voxels turned on, 50073 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 101 new 101 115,126,128 old 101 new 101 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 82 found - 82 modified | TOTAL: 82 pass 2 (xy+): 0 found - 82 modified | TOTAL: 82 pass 1 (xy-): 62 found - 62 modified | TOTAL: 144 pass 2 (xy-): 0 found - 62 modified | TOTAL: 144 pass 1 (yz+): 85 found - 85 modified | TOTAL: 229 pass 2 (yz+): 0 found - 85 modified | TOTAL: 229 pass 1 (yz-): 100 found - 100 modified | TOTAL: 329 pass 2 (yz-): 0 found - 100 modified | TOTAL: 329 pass 1 (xz+): 79 found - 79 modified | TOTAL: 408 pass 2 (xz+): 0 found - 79 modified | TOTAL: 408 pass 1 (xz-): 63 found - 63 modified | TOTAL: 471 pass 2 (xz-): 0 found - 63 modified | TOTAL: 471 Iteration Number : 1 pass 1 (+++): 128 found - 128 modified | TOTAL: 128 pass 2 (+++): 0 found - 128 modified | TOTAL: 128 pass 1 (+++): 135 found - 135 modified | TOTAL: 263 pass 2 (+++): 0 found - 135 modified | TOTAL: 263 pass 1 (+++): 105 found - 105 modified | TOTAL: 368 pass 2 (+++): 0 found - 105 modified | TOTAL: 368 pass 1 (+++): 143 found - 143 modified | TOTAL: 511 pass 2 (+++): 0 found - 143 modified | TOTAL: 511 Iteration Number : 1 pass 1 (++): 342 found - 342 modified | TOTAL: 342 pass 2 (++): 0 found - 342 modified | TOTAL: 342 pass 1 (+-): 389 found - 389 modified | TOTAL: 731 pass 2 (+-): 1 found - 390 modified | TOTAL: 732 pass 3 (+-): 0 found - 390 modified | TOTAL: 732 pass 1 (--): 311 found - 311 modified | TOTAL: 1043 pass 2 (--): 0 found - 311 modified | TOTAL: 1043 pass 1 (-+): 457 found - 457 modified | TOTAL: 1500 pass 2 (-+): 0 found - 457 modified | TOTAL: 1500 Iteration Number : 2 pass 1 (xy+): 59 found - 59 modified | TOTAL: 59 pass 2 (xy+): 0 found - 59 modified | TOTAL: 59 pass 1 (xy-): 53 found - 53 modified | TOTAL: 112 pass 2 (xy-): 0 found - 53 modified | TOTAL: 112 pass 1 (yz+): 51 found - 51 modified | TOTAL: 163 pass 2 (yz+): 0 found - 51 modified | TOTAL: 163 pass 1 (yz-): 52 found - 52 modified | TOTAL: 215 pass 2 (yz-): 0 found - 52 modified | TOTAL: 215 pass 1 (xz+): 48 found - 48 modified | TOTAL: 263 pass 2 (xz+): 0 found - 48 modified | TOTAL: 263 pass 1 (xz-): 55 found - 55 modified | TOTAL: 318 pass 2 (xz-): 0 found - 55 modified | TOTAL: 318 Iteration Number : 2 pass 1 (+++): 7 found - 7 modified | TOTAL: 7 pass 2 (+++): 0 found - 7 modified | TOTAL: 7 pass 1 (+++): 19 found - 19 modified | TOTAL: 26 pass 2 (+++): 0 found - 19 modified | TOTAL: 26 pass 1 (+++): 8 found - 8 modified | TOTAL: 34 pass 2 (+++): 0 found - 8 modified | TOTAL: 34 pass 1 (+++): 20 found - 20 modified | TOTAL: 54 pass 2 (+++): 0 found - 20 modified | TOTAL: 54 Iteration Number : 2 pass 1 (++): 38 found - 38 modified | TOTAL: 38 pass 2 (++): 0 found - 38 modified | TOTAL: 38 pass 1 (+-): 32 found - 32 modified | TOTAL: 70 pass 2 (+-): 1 found - 33 modified | TOTAL: 71 pass 3 (+-): 0 found - 33 modified | TOTAL: 71 pass 1 (--): 22 found - 22 modified | TOTAL: 93 pass 2 (--): 0 found - 22 modified | TOTAL: 93 pass 1 (-+): 26 found - 26 modified | TOTAL: 119 pass 2 (-+): 0 found - 26 modified | TOTAL: 119 Iteration Number : 3 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 6 found - 6 modified | TOTAL: 9 pass 2 (xy-): 0 found - 6 modified | TOTAL: 9 pass 1 (yz+): 1 found - 1 modified | TOTAL: 10 pass 2 (yz+): 0 found - 1 modified | TOTAL: 10 pass 1 (yz-): 5 found - 5 modified | TOTAL: 15 pass 2 (yz-): 0 found - 5 modified | TOTAL: 15 pass 1 (xz+): 3 found - 3 modified | TOTAL: 18 pass 2 (xz+): 0 found - 3 modified | TOTAL: 18 pass 1 (xz-): 4 found - 4 modified | TOTAL: 22 pass 2 (xz-): 0 found - 4 modified | TOTAL: 22 Iteration Number : 3 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 2 found - 2 modified | TOTAL: 6 pass 2 (+-): 0 found - 2 modified | TOTAL: 6 pass 1 (--): 4 found - 4 modified | TOTAL: 10 pass 2 (--): 0 found - 4 modified | TOTAL: 10 pass 1 (-+): 2 found - 2 modified | TOTAL: 12 pass 2 (-+): 0 found - 2 modified | TOTAL: 12 Iteration Number : 4 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-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 3013 (out of 412040: 0.731240) 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 May 28 22:05:29 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 1.020 0.045 0.035 -12.757; -0.032 1.145 -0.225 17.568; -0.029 0.207 1.030 -33.204; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.020 0.045 0.035 -12.757; -0.032 1.145 -0.225 17.568; -0.029 0.207 1.030 -33.204; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 89 (min = 350, max = 1400), aspect = 0.61 (min = 0.10, max = 0.75) need search nearby using seed (125, 109, 99), TAL = (3.0, -29.0, 19.0) talairach voxel to voxel transform 0.978 -0.031 -0.041 11.682; 0.031 0.839 0.182 -8.286; 0.022 -0.170 0.933 34.246; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 109, 99) --> (3.0, -29.0, 19.0) done. writing output to filled.mgz... filling took 0.6 minutes talairach cc position changed to (3.00, -29.00, 19.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -29.00, 19.00) SRC: (108.88, 104.63, 110.43) search lh wm seed point around talairach space (-15.00, -29.00, 19.00), SRC: (144.08, 105.76, 111.21) 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 May 28 22:06:07 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 5 found - 5 modified | TOTAL: 12 pass 2 (xz-): 0 found - 5 modified | TOTAL: 12 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 210038: 0.007142) 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 40: 634 vertices, 721 faces slice 50: 5824 vertices, 6082 faces slice 60: 13278 vertices, 13630 faces slice 70: 22500 vertices, 22887 faces slice 80: 32168 vertices, 32745 faces slice 90: 46293 vertices, 46994 faces slice 100: 60010 vertices, 60864 faces slice 110: 75456 vertices, 76389 faces slice 120: 89199 vertices, 90118 faces slice 130: 102631 vertices, 103569 faces slice 140: 113392 vertices, 114312 faces slice 150: 122679 vertices, 123553 faces slice 160: 130353 vertices, 131248 faces slice 170: 138059 vertices, 138942 faces slice 180: 143714 vertices, 144543 faces slice 190: 147285 vertices, 148003 faces slice 200: 147756 vertices, 148406 faces slice 210: 147756 vertices, 148406 faces slice 220: 147756 vertices, 148406 faces slice 230: 147756 vertices, 148406 faces slice 240: 147756 vertices, 148406 faces slice 250: 147756 vertices, 148406 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... 147756 voxel in cpt #1: X=-650 [v=147756,e=445218,f=296812] located at (-30.112219, -18.158972, 18.443710) For the whole surface: X=-650 [v=147756,e=445218,f=296812] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed May 28 22:06:13 CDT 2014 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /lustre/kovacv/FS/post-analysis/MPS3007-1/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 May 28 22:06:17 CDT 2014 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts avg radius = 44.2 mm, total surface area = 72297 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.141 (target=0.015) step 005: RMS=0.112 (target=0.015) step 010: RMS=0.101 (target=0.015) step 015: RMS=0.094 (target=0.015) step 020: RMS=0.090 (target=0.015) step 025: RMS=0.088 (target=0.015) step 030: RMS=0.086 (target=0.015) step 035: RMS=0.086 (target=0.015) step 040: RMS=0.085 (target=0.015) step 045: RMS=0.085 (target=0.015) step 050: RMS=0.084 (target=0.015) step 055: RMS=0.084 (target=0.015) step 060: RMS=0.085 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed May 28 22:06:44 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.70 (0.00-->10.20) (max @ vno 57745 --> 59301) face area 0.02 +- 0.04 (-0.40-->1.60) scaling brain by 0.319... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.319, avgs=0 005/300: dt: 0.9000, rms radial error=177.059, avgs=0 010/300: dt: 0.9000, rms radial error=176.502, avgs=0 015/300: dt: 0.9000, rms radial error=175.771, avgs=0 020/300: dt: 0.9000, rms radial error=174.938, avgs=0 025/300: dt: 0.9000, rms radial error=174.048, avgs=0 030/300: dt: 0.9000, rms radial error=173.125, avgs=0 035/300: dt: 0.9000, rms radial error=172.185, avgs=0 040/300: dt: 0.9000, rms radial error=171.236, avgs=0 045/300: dt: 0.9000, rms radial error=170.285, avgs=0 050/300: dt: 0.9000, rms radial error=169.334, avgs=0 055/300: dt: 0.9000, rms radial error=168.387, avgs=0 060/300: dt: 0.9000, rms radial error=167.443, avgs=0 065/300: dt: 0.9000, rms radial error=166.503, avgs=0 070/300: dt: 0.9000, rms radial error=165.568, avgs=0 075/300: dt: 0.9000, rms radial error=164.637, avgs=0 080/300: dt: 0.9000, rms radial error=163.710, avgs=0 085/300: dt: 0.9000, rms radial error=162.789, avgs=0 090/300: dt: 0.9000, rms radial error=161.873, avgs=0 095/300: dt: 0.9000, rms radial error=160.961, avgs=0 100/300: dt: 0.9000, rms radial error=160.054, avgs=0 105/300: dt: 0.9000, rms radial error=159.152, avgs=0 110/300: dt: 0.9000, rms radial error=158.255, avgs=0 115/300: dt: 0.9000, rms radial error=157.363, avgs=0 120/300: dt: 0.9000, rms radial error=156.475, avgs=0 125/300: dt: 0.9000, rms radial error=155.592, avgs=0 130/300: dt: 0.9000, rms radial error=154.714, avgs=0 135/300: dt: 0.9000, rms radial error=153.842, avgs=0 140/300: dt: 0.9000, rms radial error=152.974, avgs=0 145/300: dt: 0.9000, rms radial error=152.111, avgs=0 150/300: dt: 0.9000, rms radial error=151.253, avgs=0 155/300: dt: 0.9000, rms radial error=150.400, avgs=0 160/300: dt: 0.9000, rms radial error=149.552, avgs=0 165/300: dt: 0.9000, rms radial error=148.708, avgs=0 170/300: dt: 0.9000, rms radial error=147.869, avgs=0 175/300: dt: 0.9000, rms radial error=147.034, avgs=0 180/300: dt: 0.9000, rms radial error=146.204, avgs=0 185/300: dt: 0.9000, rms radial error=145.379, avgs=0 190/300: dt: 0.9000, rms radial error=144.558, avgs=0 195/300: dt: 0.9000, rms radial error=143.742, avgs=0 200/300: dt: 0.9000, rms radial error=142.930, avgs=0 205/300: dt: 0.9000, rms radial error=142.123, avgs=0 210/300: dt: 0.9000, rms radial error=141.320, avgs=0 215/300: dt: 0.9000, rms radial error=140.522, avgs=0 220/300: dt: 0.9000, rms radial error=139.728, avgs=0 225/300: dt: 0.9000, rms radial error=138.939, avgs=0 230/300: dt: 0.9000, rms radial error=138.153, avgs=0 235/300: dt: 0.9000, rms radial error=137.372, avgs=0 240/300: dt: 0.9000, rms radial error=136.595, avgs=0 245/300: dt: 0.9000, rms radial error=135.823, avgs=0 250/300: dt: 0.9000, rms radial error=135.055, avgs=0 255/300: dt: 0.9000, rms radial error=134.291, avgs=0 260/300: dt: 0.9000, rms radial error=133.532, avgs=0 265/300: dt: 0.9000, rms radial error=132.777, avgs=0 270/300: dt: 0.9000, rms radial error=132.026, avgs=0 275/300: dt: 0.9000, rms radial error=131.280, avgs=0 280/300: dt: 0.9000, rms radial error=130.537, avgs=0 285/300: dt: 0.9000, rms radial error=129.799, avgs=0 290/300: dt: 0.9000, rms radial error=129.064, avgs=0 295/300: dt: 0.9000, rms radial error=128.334, avgs=0 300/300: dt: 0.9000, rms radial error=127.608, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17599.08 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3206.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 3 (K=160.0), pass 1, starting sse = 481.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00165 epoch 4 (K=640.0), pass 1, starting sse = 87.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00386 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Wed May 28 22:09:59 CDT 2014 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS3007-1 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-650 (nv=147756, nf=296812, ne=445218, g=326) 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... 55836 ambiguous faces found in tessellation segmenting defects... 169 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 0 -merging segment 17 into 8 -merging segment 14 into 20 -merging segment 27 into 23 -merging segment 30 into 26 -merging segment 43 into 33 -merging segment 48 into 33 -merging segment 58 into 37 -merging segment 73 into 50 -merging segment 115 into 52 -merging segment 129 into 52 -merging segment 132 into 130 -merging segment 140 into 135 -merging segment 146 into 142 155 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4030 (-4.7015) -vertex loglikelihood: -6.6962 (-3.3481) -normal dot loglikelihood: -3.5218 (-3.5218) -quad curv loglikelihood: -6.0887 (-3.0444) Total Loglikelihood : -25.7097 CORRECTING DEFECT 0 (vertices=3981, convex hull=1256) After retessellation of defect 0, euler #=-139 (116805,342322,225378) : difference with theory (-152) = -13 CORRECTING DEFECT 1 (vertices=45, convex hull=80) After retessellation of defect 1, euler #=-138 (116818,342397,225441) : difference with theory (-151) = -13 CORRECTING DEFECT 2 (vertices=62, convex hull=63) After retessellation of defect 2, euler #=-137 (116834,342472,225501) : difference with theory (-150) = -13 CORRECTING DEFECT 3 (vertices=52, convex hull=33) After retessellation of defect 3, euler #=-136 (116838,342491,225517) : difference with theory (-149) = -13 CORRECTING DEFECT 4 (vertices=203, convex hull=168) After retessellation of defect 4, euler #=-135 (116912,342795,225748) : difference with theory (-148) = -13 CORRECTING DEFECT 5 (vertices=237, convex hull=211) After retessellation of defect 5, euler #=-134 (117014,343201,226053) : difference with theory (-147) = -13 CORRECTING DEFECT 6 (vertices=17, convex hull=20) After retessellation of defect 6, euler #=-133 (117014,343205,226058) : difference with theory (-146) = -13 CORRECTING DEFECT 7 (vertices=3073, convex hull=961) After retessellation of defect 7, euler #=-136 (117848,346254,228270) : difference with theory (-145) = -9 CORRECTING DEFECT 8 (vertices=61, convex hull=37) After retessellation of defect 8, euler #=-135 (117857,346293,228301) : difference with theory (-144) = -9 CORRECTING DEFECT 9 (vertices=314, convex hull=246) After retessellation of defect 9, euler #=-134 (117981,346794,228679) : difference with theory (-143) = -9 CORRECTING DEFECT 10 (vertices=33, convex hull=67) After retessellation of defect 10, euler #=-133 (117998,346870,228739) : difference with theory (-142) = -9 CORRECTING DEFECT 11 (vertices=40, convex hull=85) After retessellation of defect 11, euler #=-132 (118014,346953,228807) : difference with theory (-141) = -9 CORRECTING DEFECT 12 (vertices=244, convex hull=113) After retessellation of defect 12, euler #=-131 (118071,347172,228970) : difference with theory (-140) = -9 CORRECTING DEFECT 13 (vertices=35, convex hull=33) After retessellation of defect 13, euler #=-130 (118076,347200,228994) : difference with theory (-139) = -9 CORRECTING DEFECT 14 (vertices=45, convex hull=58) After retessellation of defect 14, euler #=-129 (118104,347309,229076) : difference with theory (-138) = -9 CORRECTING DEFECT 15 (vertices=72, convex hull=100) After retessellation of defect 15, euler #=-128 (118143,347464,229193) : difference with theory (-137) = -9 CORRECTING DEFECT 16 (vertices=64, convex hull=106) After retessellation of defect 16, euler #=-127 (118160,347555,229268) : difference with theory (-136) = -9 CORRECTING DEFECT 17 (vertices=68, convex hull=72) After retessellation of defect 17, euler #=-125 (118174,347624,229325) : difference with theory (-135) = -10 CORRECTING DEFECT 18 (vertices=60, convex hull=95) After retessellation of defect 18, euler #=-124 (118186,347700,229390) : difference with theory (-134) = -10 CORRECTING DEFECT 19 (vertices=10, convex hull=28) After retessellation of defect 19, euler #=-123 (118187,347713,229403) : difference with theory (-133) = -10 CORRECTING DEFECT 20 (vertices=83, convex hull=126) After retessellation of defect 20, euler #=-121 (118221,347880,229538) : difference with theory (-132) = -11 CORRECTING DEFECT 21 (vertices=36, convex hull=73) After retessellation of defect 21, euler #=-120 (118247,347984,229617) : difference with theory (-131) = -11 CORRECTING DEFECT 22 (vertices=409, convex hull=326) After retessellation of defect 22, euler #=-119 (118448,348762,230195) : difference with theory (-130) = -11 CORRECTING DEFECT 23 (vertices=2010, convex hull=1159) After retessellation of defect 23, euler #=-122 (119425,352366,232819) : difference with theory (-129) = -7 CORRECTING DEFECT 24 (vertices=33, convex hull=38) After retessellation of defect 24, euler #=-121 (119430,352396,232845) : difference with theory (-128) = -7 CORRECTING DEFECT 25 (vertices=58, convex hull=35) After retessellation of defect 25, euler #=-120 (119438,352430,232872) : difference with theory (-127) = -7 CORRECTING DEFECT 26 (vertices=15, convex hull=20) After retessellation of defect 26, euler #=-119 (119440,352439,232880) : difference with theory (-126) = -7 CORRECTING DEFECT 27 (vertices=66, convex hull=140) After retessellation of defect 27, euler #=-118 (119473,352597,233006) : difference with theory (-125) = -7 CORRECTING DEFECT 28 (vertices=614, convex hull=348) After retessellation of defect 28, euler #=-115 (119605,353175,233455) : difference with theory (-124) = -9 CORRECTING DEFECT 29 (vertices=49, convex hull=36) After retessellation of defect 29, euler #=-114 (119610,353209,233485) : difference with theory (-123) = -9 CORRECTING DEFECT 30 (vertices=42, convex hull=31) After retessellation of defect 30, euler #=-113 (119614,353230,233503) : difference with theory (-122) = -9 CORRECTING DEFECT 31 (vertices=21, convex hull=35) After retessellation of defect 31, euler #=-112 (119617,353252,233523) : difference with theory (-121) = -9 CORRECTING DEFECT 32 (vertices=236, convex hull=96) After retessellation of defect 32, euler #=-110 (119631,353342,233601) : difference with theory (-120) = -10 CORRECTING DEFECT 33 (vertices=9, convex hull=19) After retessellation of defect 33, euler #=-109 (119632,353350,233609) : difference with theory (-119) = -10 CORRECTING DEFECT 34 (vertices=84, convex hull=77) After retessellation of defect 34, euler #=-108 (119661,353473,233704) : difference with theory (-118) = -10 CORRECTING DEFECT 35 (vertices=26, convex hull=64) After retessellation of defect 35, euler #=-107 (119669,353520,233744) : difference with theory (-117) = -10 CORRECTING DEFECT 36 (vertices=463, convex hull=144) After retessellation of defect 36, euler #=-106 (119743,353811,233962) : difference with theory (-116) = -10 CORRECTING DEFECT 37 (vertices=20, convex hull=27) After retessellation of defect 37, euler #=-105 (119745,353827,233977) : difference with theory (-115) = -10 CORRECTING DEFECT 38 (vertices=58, convex hull=73) After retessellation of defect 38, euler #=-104 (119771,353933,234058) : difference with theory (-114) = -10 CORRECTING DEFECT 39 (vertices=39, convex hull=49) After retessellation of defect 39, euler #=-103 (119780,353979,234096) : difference with theory (-113) = -10 CORRECTING DEFECT 40 (vertices=15, convex hull=33) After retessellation of defect 40, euler #=-102 (119781,353992,234109) : difference with theory (-112) = -10 CORRECTING DEFECT 41 (vertices=85, convex hull=101) After retessellation of defect 41, euler #=-101 (119835,354201,234265) : difference with theory (-111) = -10 CORRECTING DEFECT 42 (vertices=60, convex hull=131) After retessellation of defect 42, euler #=-100 (119874,354382,234408) : difference with theory (-110) = -10 CORRECTING DEFECT 43 (vertices=2308, convex hull=1049) After retessellation of defect 43, euler #=-101 (120740,357583,236742) : difference with theory (-109) = -8 CORRECTING DEFECT 44 (vertices=105, convex hull=50) After retessellation of defect 44, euler #=-100 (120756,357648,236792) : difference with theory (-108) = -8 CORRECTING DEFECT 45 (vertices=4744, convex hull=2084) After retessellation of defect 45, euler #=-101 (122286,363407,241020) : difference with theory (-107) = -6 CORRECTING DEFECT 46 (vertices=529, convex hull=276) After retessellation of defect 46, euler #=-100 (122362,363767,241305) : difference with theory (-106) = -6 CORRECTING DEFECT 47 (vertices=5, convex hull=16) After retessellation of defect 47, euler #=-99 (122362,363770,241309) : difference with theory (-105) = -6 CORRECTING DEFECT 48 (vertices=78, convex hull=115) After retessellation of defect 48, euler #=-98 (122415,363984,241471) : difference with theory (-104) = -6 CORRECTING DEFECT 49 (vertices=36, convex hull=28) After retessellation of defect 49, euler #=-97 (122418,364003,241488) : difference with theory (-103) = -6 CORRECTING DEFECT 50 (vertices=31, convex hull=26) After retessellation of defect 50, euler #=-96 (122422,364019,241501) : difference with theory (-102) = -6 CORRECTING DEFECT 51 (vertices=39, convex hull=25) After retessellation of defect 51, euler #=-95 (122423,364028,241510) : difference with theory (-101) = -6 CORRECTING DEFECT 52 (vertices=40, convex hull=87) After retessellation of defect 52, euler #=-94 (122439,364115,241582) : difference with theory (-100) = -6 CORRECTING DEFECT 53 (vertices=40, convex hull=27) After retessellation of defect 53, euler #=-93 (122446,364143,241604) : difference with theory (-99) = -6 CORRECTING DEFECT 54 (vertices=657, convex hull=283) After retessellation of defect 54, euler #=-93 (122652,364918,242173) : difference with theory (-98) = -5 CORRECTING DEFECT 55 (vertices=27, convex hull=27) After retessellation of defect 55, euler #=-92 (122655,364935,242188) : difference with theory (-97) = -5 CORRECTING DEFECT 56 (vertices=8, convex hull=19) After retessellation of defect 56, euler #=-91 (122655,364944,242198) : difference with theory (-96) = -5 CORRECTING DEFECT 57 (vertices=257, convex hull=251) After retessellation of defect 57, euler #=-90 (122744,365330,242496) : difference with theory (-95) = -5 CORRECTING DEFECT 58 (vertices=45, convex hull=74) After retessellation of defect 58, euler #=-90 (122761,365421,242570) : difference with theory (-94) = -4 CORRECTING DEFECT 59 (vertices=322, convex hull=240) After retessellation of defect 59, euler #=-90 (122895,365955,242970) : difference with theory (-93) = -3 CORRECTING DEFECT 60 (vertices=591, convex hull=130) After retessellation of defect 60, euler #=-89 (122988,366301,243224) : difference with theory (-92) = -3 CORRECTING DEFECT 61 (vertices=6, convex hull=14) After retessellation of defect 61, euler #=-88 (122988,366305,243229) : difference with theory (-91) = -3 CORRECTING DEFECT 62 (vertices=261, convex hull=177) After retessellation of defect 62, euler #=-89 (123066,366641,243486) : difference with theory (-90) = -1 CORRECTING DEFECT 63 (vertices=128, convex hull=40) After retessellation of defect 63, euler #=-88 (123079,366698,243531) : difference with theory (-89) = -1 CORRECTING DEFECT 64 (vertices=38, convex hull=62) After retessellation of defect 64, euler #=-87 (123088,366749,243574) : difference with theory (-88) = -1 CORRECTING DEFECT 65 (vertices=21, convex hull=46) After retessellation of defect 65, euler #=-87 (123096,366794,243611) : difference with theory (-87) = 0 CORRECTING DEFECT 66 (vertices=220, convex hull=51) After retessellation of defect 66, euler #=-87 (123115,366879,243677) : difference with theory (-86) = 1 CORRECTING DEFECT 67 (vertices=6, convex hull=11) After retessellation of defect 67, euler #=-86 (123116,366887,243685) : difference with theory (-85) = 1 CORRECTING DEFECT 68 (vertices=278, convex hull=91) After retessellation of defect 68, euler #=-85 (123143,367002,243774) : difference with theory (-84) = 1 CORRECTING DEFECT 69 (vertices=79, convex hull=139) After retessellation of defect 69, euler #=-84 (123186,367191,243921) : difference with theory (-83) = 1 CORRECTING DEFECT 70 (vertices=26, convex hull=24) Warning - incorrect dp selected!!!!(-69.889821 >= -69.889830 ) After retessellation of defect 70, euler #=-83 (123191,367212,243938) : difference with theory (-82) = 1 CORRECTING DEFECT 71 (vertices=183, convex hull=204) After retessellation of defect 71, euler #=-82 (123295,367613,244236) : difference with theory (-81) = 1 CORRECTING DEFECT 72 (vertices=211, convex hull=100) After retessellation of defect 72, euler #=-81 (123331,367763,244351) : difference with theory (-80) = 1 CORRECTING DEFECT 73 (vertices=94, convex hull=78) After retessellation of defect 73, euler #=-81 (123372,367923,244470) : difference with theory (-79) = 2 CORRECTING DEFECT 74 (vertices=24, convex hull=86) After retessellation of defect 74, euler #=-80 (123388,368005,244537) : difference with theory (-78) = 2 CORRECTING DEFECT 75 (vertices=347, convex hull=375) After retessellation of defect 75, euler #=-79 (123488,368499,244932) : difference with theory (-77) = 2 CORRECTING DEFECT 76 (vertices=19, convex hull=36) After retessellation of defect 76, euler #=-78 (123491,368524,244955) : difference with theory (-76) = 2 CORRECTING DEFECT 77 (vertices=48, convex hull=30) After retessellation of defect 77, euler #=-77 (123500,368559,244982) : difference with theory (-75) = 2 CORRECTING DEFECT 78 (vertices=19, convex hull=23) After retessellation of defect 78, euler #=-76 (123505,368580,244999) : difference with theory (-74) = 2 CORRECTING DEFECT 79 (vertices=11, convex hull=30) After retessellation of defect 79, euler #=-75 (123509,368601,245017) : difference with theory (-73) = 2 CORRECTING DEFECT 80 (vertices=61, convex hull=60) After retessellation of defect 80, euler #=-74 (123520,368659,245065) : difference with theory (-72) = 2 CORRECTING DEFECT 81 (vertices=28, convex hull=28) After retessellation of defect 81, euler #=-73 (123521,368674,245080) : difference with theory (-71) = 2 CORRECTING DEFECT 82 (vertices=102, convex hull=97) After retessellation of defect 82, euler #=-72 (123546,368792,245174) : difference with theory (-70) = 2 CORRECTING DEFECT 83 (vertices=17, convex hull=51) After retessellation of defect 83, euler #=-71 (123556,368839,245212) : difference with theory (-69) = 2 CORRECTING DEFECT 84 (vertices=23, convex hull=29) After retessellation of defect 84, euler #=-70 (123559,368856,245227) : difference with theory (-68) = 2 CORRECTING DEFECT 85 (vertices=82, convex hull=93) After retessellation of defect 85, euler #=-69 (123604,369028,245355) : difference with theory (-67) = 2 CORRECTING DEFECT 86 (vertices=26, convex hull=47) After retessellation of defect 86, euler #=-68 (123615,369080,245397) : difference with theory (-66) = 2 CORRECTING DEFECT 87 (vertices=31, convex hull=13) After retessellation of defect 87, euler #=-67 (123617,369092,245408) : difference with theory (-65) = 2 CORRECTING DEFECT 88 (vertices=24, convex hull=27) After retessellation of defect 88, euler #=-66 (123620,369108,245422) : difference with theory (-64) = 2 CORRECTING DEFECT 89 (vertices=22, convex hull=16) After retessellation of defect 89, euler #=-65 (123623,369120,245432) : difference with theory (-63) = 2 CORRECTING DEFECT 90 (vertices=23, convex hull=26) After retessellation of defect 90, euler #=-64 (123640,369178,245474) : difference with theory (-62) = 2 CORRECTING DEFECT 91 (vertices=31, convex hull=69) After retessellation of defect 91, euler #=-63 (123651,369237,245523) : difference with theory (-61) = 2 CORRECTING DEFECT 92 (vertices=34, convex hull=63) After retessellation of defect 92, euler #=-62 (123670,369314,245582) : difference with theory (-60) = 2 CORRECTING DEFECT 93 (vertices=19, convex hull=26) After retessellation of defect 93, euler #=-61 (123675,369337,245601) : difference with theory (-59) = 2 CORRECTING DEFECT 94 (vertices=40, convex hull=41) After retessellation of defect 94, euler #=-60 (123684,369379,245635) : difference with theory (-58) = 2 CORRECTING DEFECT 95 (vertices=626, convex hull=79) After retessellation of defect 95, euler #=-59 (123701,369462,245702) : difference with theory (-57) = 2 CORRECTING DEFECT 96 (vertices=69, convex hull=112) After retessellation of defect 96, euler #=-58 (123711,369535,245766) : difference with theory (-56) = 2 CORRECTING DEFECT 97 (vertices=21, convex hull=10) After retessellation of defect 97, euler #=-57 (123711,369536,245768) : difference with theory (-55) = 2 CORRECTING DEFECT 98 (vertices=38, convex hull=71) After retessellation of defect 98, euler #=-56 (123736,369637,245845) : difference with theory (-54) = 2 CORRECTING DEFECT 99 (vertices=74, convex hull=83) After retessellation of defect 99, euler #=-55 (123759,369737,245923) : difference with theory (-53) = 2 CORRECTING DEFECT 100 (vertices=28, convex hull=29) After retessellation of defect 100, euler #=-54 (123762,369759,245943) : difference with theory (-52) = 2 CORRECTING DEFECT 101 (vertices=168, convex hull=56) After retessellation of defect 101, euler #=-53 (123781,369839,246005) : difference with theory (-51) = 2 CORRECTING DEFECT 102 (vertices=299, convex hull=96) After retessellation of defect 102, euler #=-52 (123799,369935,246084) : difference with theory (-50) = 2 CORRECTING DEFECT 103 (vertices=45, convex hull=95) After retessellation of defect 103, euler #=-51 (123813,370019,246155) : difference with theory (-49) = 2 CORRECTING DEFECT 104 (vertices=18, convex hull=25) After retessellation of defect 104, euler #=-50 (123817,370041,246174) : difference with theory (-48) = 2 CORRECTING DEFECT 105 (vertices=20, convex hull=44) After retessellation of defect 105, euler #=-49 (123827,370087,246211) : difference with theory (-47) = 2 CORRECTING DEFECT 106 (vertices=395, convex hull=307) After retessellation of defect 106, euler #=-48 (123925,370519,246546) : difference with theory (-46) = 2 CORRECTING DEFECT 107 (vertices=53, convex hull=78) After retessellation of defect 107, euler #=-47 (123938,370591,246606) : difference with theory (-45) = 2 CORRECTING DEFECT 108 (vertices=44, convex hull=72) After retessellation of defect 108, euler #=-46 (123959,370680,246675) : difference with theory (-44) = 2 CORRECTING DEFECT 109 (vertices=5, convex hull=23) After retessellation of defect 109, euler #=-45 (123960,370688,246683) : difference with theory (-43) = 2 CORRECTING DEFECT 110 (vertices=24, convex hull=60) After retessellation of defect 110, euler #=-44 (123974,370752,246734) : difference with theory (-42) = 2 CORRECTING DEFECT 111 (vertices=23, convex hull=14) After retessellation of defect 111, euler #=-43 (123976,370760,246741) : difference with theory (-41) = 2 CORRECTING DEFECT 112 (vertices=5, convex hull=18) After retessellation of defect 112, euler #=-42 (123976,370763,246745) : difference with theory (-40) = 2 CORRECTING DEFECT 113 (vertices=10, convex hull=30) After retessellation of defect 113, euler #=-41 (123978,370777,246758) : difference with theory (-39) = 2 CORRECTING DEFECT 114 (vertices=139, convex hull=109) After retessellation of defect 114, euler #=-40 (124027,370980,246913) : difference with theory (-38) = 2 CORRECTING DEFECT 115 (vertices=11, convex hull=24) After retessellation of defect 115, euler #=-39 (124028,370991,246924) : difference with theory (-37) = 2 CORRECTING DEFECT 116 (vertices=37, convex hull=24) After retessellation of defect 116, euler #=-38 (124032,371013,246943) : difference with theory (-36) = 2 CORRECTING DEFECT 117 (vertices=5, convex hull=19) After retessellation of defect 117, euler #=-37 (124033,371020,246950) : difference with theory (-35) = 2 CORRECTING DEFECT 118 (vertices=104, convex hull=45) After retessellation of defect 118, euler #=-36 (124045,371076,246995) : difference with theory (-34) = 2 CORRECTING DEFECT 119 (vertices=129, convex hull=121) After retessellation of defect 119, euler #=-34 (124069,371207,247104) : difference with theory (-33) = 1 CORRECTING DEFECT 120 (vertices=31, convex hull=80) After retessellation of defect 120, euler #=-33 (124087,371292,247172) : difference with theory (-32) = 1 CORRECTING DEFECT 121 (vertices=45, convex hull=22) After retessellation of defect 121, euler #=-32 (124091,371315,247192) : difference with theory (-31) = 1 CORRECTING DEFECT 122 (vertices=13, convex hull=30) After retessellation of defect 122, euler #=-31 (124092,371326,247203) : difference with theory (-30) = 1 CORRECTING DEFECT 123 (vertices=83, convex hull=163) After retessellation of defect 123, euler #=-29 (124140,371545,247376) : difference with theory (-29) = 0 CORRECTING DEFECT 124 (vertices=448, convex hull=148) After retessellation of defect 124, euler #=-28 (124204,371811,247579) : difference with theory (-28) = 0 CORRECTING DEFECT 125 (vertices=20, convex hull=16) After retessellation of defect 125, euler #=-27 (124207,371824,247590) : difference with theory (-27) = 0 CORRECTING DEFECT 126 (vertices=18, convex hull=25) After retessellation of defect 126, euler #=-26 (124209,371838,247603) : difference with theory (-26) = 0 CORRECTING DEFECT 127 (vertices=34, convex hull=62) After retessellation of defect 127, euler #=-25 (124224,371912,247663) : difference with theory (-25) = 0 CORRECTING DEFECT 128 (vertices=569, convex hull=169) After retessellation of defect 128, euler #=-24 (124271,372133,247838) : difference with theory (-24) = 0 CORRECTING DEFECT 129 (vertices=751, convex hull=156) After retessellation of defect 129, euler #=-23 (124330,372399,248046) : difference with theory (-23) = 0 CORRECTING DEFECT 130 (vertices=91, convex hull=90) After retessellation of defect 130, euler #=-22 (124339,372467,248106) : difference with theory (-22) = 0 CORRECTING DEFECT 131 (vertices=85, convex hull=48) After retessellation of defect 131, euler #=-21 (124360,372547,248166) : difference with theory (-21) = 0 CORRECTING DEFECT 132 (vertices=27, convex hull=29) After retessellation of defect 132, euler #=-20 (124366,372576,248190) : difference with theory (-20) = 0 CORRECTING DEFECT 133 (vertices=5, convex hull=14) After retessellation of defect 133, euler #=-19 (124367,372582,248196) : difference with theory (-19) = 0 CORRECTING DEFECT 134 (vertices=251, convex hull=85) After retessellation of defect 134, euler #=-18 (124387,372681,248276) : difference with theory (-18) = 0 CORRECTING DEFECT 135 (vertices=45, convex hull=25) After retessellation of defect 135, euler #=-17 (124388,372694,248289) : difference with theory (-17) = 0 CORRECTING DEFECT 136 (vertices=36, convex hull=55) After retessellation of defect 136, euler #=-16 (124401,372752,248335) : difference with theory (-16) = 0 CORRECTING DEFECT 137 (vertices=68, convex hull=59) After retessellation of defect 137, euler #=-15 (124409,372801,248377) : difference with theory (-15) = 0 CORRECTING DEFECT 138 (vertices=84, convex hull=113) After retessellation of defect 138, euler #=-14 (124431,372913,248468) : difference with theory (-14) = 0 CORRECTING DEFECT 139 (vertices=29, convex hull=66) After retessellation of defect 139, euler #=-13 (124440,372968,248515) : difference with theory (-13) = 0 CORRECTING DEFECT 140 (vertices=241, convex hull=81) After retessellation of defect 140, euler #=-12 (124472,373097,248613) : difference with theory (-12) = 0 CORRECTING DEFECT 141 (vertices=209, convex hull=55) After retessellation of defect 141, euler #=-11 (124484,373157,248662) : difference with theory (-11) = 0 CORRECTING DEFECT 142 (vertices=77, convex hull=83) After retessellation of defect 142, euler #=-10 (124504,373258,248744) : difference with theory (-10) = 0 CORRECTING DEFECT 143 (vertices=122, convex hull=41) After retessellation of defect 143, euler #=-9 (124513,373301,248779) : difference with theory (-9) = 0 CORRECTING DEFECT 144 (vertices=276, convex hull=53) After retessellation of defect 144, euler #=-8 (124530,373374,248836) : difference with theory (-8) = 0 CORRECTING DEFECT 145 (vertices=34, convex hull=82) After retessellation of defect 145, euler #=-7 (124548,373458,248903) : difference with theory (-7) = 0 CORRECTING DEFECT 146 (vertices=20, convex hull=57) After retessellation of defect 146, euler #=-6 (124557,373507,248944) : difference with theory (-6) = 0 CORRECTING DEFECT 147 (vertices=24, convex hull=60) After retessellation of defect 147, euler #=-5 (124568,373561,248988) : difference with theory (-5) = 0 CORRECTING DEFECT 148 (vertices=15, convex hull=20) After retessellation of defect 148, euler #=-4 (124568,373569,248997) : difference with theory (-4) = 0 CORRECTING DEFECT 149 (vertices=20, convex hull=26) After retessellation of defect 149, euler #=-3 (124568,373580,249009) : difference with theory (-3) = 0 CORRECTING DEFECT 150 (vertices=9, convex hull=20) After retessellation of defect 150, euler #=-2 (124571,373595,249022) : difference with theory (-2) = 0 CORRECTING DEFECT 151 (vertices=45, convex hull=67) After retessellation of defect 151, euler #=-1 (124594,373692,249097) : difference with theory (-1) = 0 CORRECTING DEFECT 152 (vertices=41, convex hull=75) After retessellation of defect 152, euler #=0 (124605,373760,249155) : difference with theory (0) = 0 CORRECTING DEFECT 153 (vertices=23, convex hull=51) After retessellation of defect 153, euler #=1 (124614,373805,249192) : difference with theory (1) = 0 CORRECTING DEFECT 154 (vertices=26, convex hull=75) After retessellation of defect 154, euler #=2 (124631,373887,249258) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.34 (0.01-->10.94) (max @ vno 37986 --> 40028) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.34 (0.01-->10.94) (max @ vno 37986 --> 40028) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 511 mutations (35.3%), 935 crossovers (64.7%), 1002 vertices were eliminated building final representation... 23125 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=124631, nf=249258, ne=373887, g=0) writing corrected surface to /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.orig... defective orientation at vertex 85498(85499) with faces 163435 and 247926 defective orientation at vertex 85498(86319) with faces 163435 and 248017 defective orientation at vertex 85499(85498) with faces 163435 and 247926 defective orientation at vertex 85499(85500) with faces 163437 and 247923 defective orientation at vertex 85500(85499) with faces 163437 and 247923 defective orientation at vertex 85500(85507) with faces 163439 and 247898 defective orientation at vertex 85507(85500) with faces 163439 and 247898 defective orientation at vertex 85507(86327) with faces 163439 and 247865 defective orientation at vertex 86309(86319) with faces 165007 and 248017 defective orientation at vertex 86309(86310) with faces 165007 and 247875 defective orientation at vertex 86310(86309) with faces 165007 and 247875 defective orientation at vertex 86310(86319) with faces 165007 and 247849 defective orientation at vertex 86319(85498) with faces 163435 and 248017 defective orientation at vertex 86319(86320) with faces 163436 and 247841 defective orientation at vertex 86319(86310) with faces 165007 and 247849 defective orientation at vertex 86319(86309) with faces 248017 and 165007 defective orientation at vertex 86320(86319) with faces 163436 and 247841 defective orientation at vertex 86320(86327) with faces 163438 and 247866 defective orientation at vertex 86327(86320) with faces 163438 and 247866 defective orientation at vertex 86327(85507) with faces 163439 and 247865 0.016 % of the vertices (20 vertices) exhibit an orientation change topology fixing took 96.3 minutes 0 defective edges removing intersecting faces 000: 3153 intersecting 001: 293 intersecting 002: 157 intersecting 003: 67 intersecting 004: 47 intersecting 005: 40 intersecting expanding nbhd size to 2 006: 40 intersecting 007: 34 intersecting 008: 33 intersecting 009: 32 intersecting 010: 33 intersecting 011: 11 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 124631 - 373887 + 249258 = 2 --> 0 holes F =2V-4: 249258 = 249262-4 (0) 2E=3F: 747774 = 747774 (0) total defect index = 0 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 1359 intersecting 001: 264 intersecting 002: 142 intersecting 003: 66 intersecting 004: 46 intersecting 005: 38 intersecting 006: 37 intersecting 007: 33 intersecting 008: 28 intersecting 009: 23 intersecting 010: 5 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu May 29 00:03:57 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS3007-1 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... 22326 bright wm thresholded. 602 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.orig... computing class statistics... border white: 272146 voxels (1.62%) border gray 320381 voxels (1.91%) WM (95.0): 96.2 +- 8.5 [70.0 --> 110.0] GM (84.0) : 82.4 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.8 (was 70) setting MAX_BORDER_WHITE to 115.5 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 55.6 (was 40) setting MAX_GRAY to 98.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.4 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.27 (0.01-->5.35) (max @ vno 15713 --> 118094) face area 0.27 +- 0.15 (0.00-->6.25) mean absolute distance = 0.92 +- 1.17 4710 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=107, GM=80 using class modes intead of means.... mean inside = 96.4, mean outside = 81.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=88.0, 1348 (1348) missing vertices, mean dist 0.2 [1.1 (%35.9)->0.8 (%64.1))] %50 local maxima, %44 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.87 +- 0.31 (0.02-->5.34) (max @ vno 81277 --> 81295) face area 0.27 +- 0.17 (0.00-->4.16) mean absolute distance = 0.52 +- 0.75 4261 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4685239.5, rms=9.04 001: dt: 0.5000, sse=6122246.0, rms=6.99 002: dt: 0.5000, sse=6545728.0, rms=5.95 003: dt: 0.5000, sse=6966783.0, rms=5.34 004: dt: 0.5000, sse=7043067.5, rms=4.89 005: dt: 0.5000, sse=7143925.5, rms=4.49 006: dt: 0.5000, sse=7101875.5, rms=4.16 007: dt: 0.5000, sse=7133125.0, rms=3.90 008: dt: 0.5000, sse=7115813.0, rms=3.73 009: dt: 0.5000, sse=7123830.5, rms=3.64 010: dt: 0.5000, sse=7109085.0, rms=3.56 rms = 3.53, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=7148708.0, rms=3.53 012: dt: 0.2500, sse=5307082.0, rms=3.08 013: dt: 0.2500, sse=5095877.0, rms=2.97 rms = 2.92, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4973374.5, rms=2.92 rms = 2.88, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=4913730.5, rms=2.88 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=90.7, 972 (419) missing vertices, mean dist -0.3 [0.6 (%70.3)->0.4 (%29.7))] %73 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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 0.87 +- 0.31 (0.04-->6.06) (max @ vno 81277 --> 81295) face area 0.32 +- 0.19 (0.00-->4.81) mean absolute distance = 0.35 +- 0.51 3499 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5300793.0, rms=4.67 016: dt: 0.5000, sse=5633114.5, rms=3.40 017: dt: 0.5000, sse=6229001.0, rms=3.20 018: dt: 0.5000, sse=6460429.5, rms=3.12 rms = 3.17, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5565692.5, rms=2.72 020: dt: 0.2500, sse=5303773.5, rms=2.53 021: dt: 0.2500, sse=5166139.5, rms=2.46 rms = 2.44, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5103244.0, rms=2.44 rms = 2.41, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=5055890.5, rms=2.41 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=92.2, 950 (273) missing vertices, mean dist -0.1 [0.4 (%66.5)->0.3 (%33.5))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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 0.87 +- 0.31 (0.03-->6.28) (max @ vno 81277 --> 81295) face area 0.31 +- 0.19 (0.00-->4.85) mean absolute distance = 0.28 +- 0.43 3605 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5174282.5, rms=3.35 024: dt: 0.5000, sse=5594492.5, rms=2.78 rms = 2.86, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5325358.5, rms=2.45 026: dt: 0.2500, sse=5348371.5, rms=2.32 rms = 2.27, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=5311570.5, rms=2.27 rms = 2.22, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5208791.5, rms=2.22 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=92.7, 1145 (232) missing vertices, mean dist -0.1 [0.3 (%55.3)->0.3 (%44.7))] %86 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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 /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5219698.5, rms=2.34 029: dt: 0.5000, sse=6930510.0, rms=2.17 rms = 2.51, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=6307734.0, rms=1.96 rms = 1.95, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=6043523.0, rms=1.95 032: dt: 0.1250, sse=6040633.5, rms=1.89 rms = 1.85, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=6013272.0, rms=1.85 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group generating cortex label... 28 non-cortical segments detected only using segment with 2037 vertices erasing segment 1 (vno[0] = 41943) erasing segment 2 (vno[0] = 43912) erasing segment 3 (vno[0] = 44843) erasing segment 4 (vno[0] = 48218) erasing segment 5 (vno[0] = 53961) erasing segment 6 (vno[0] = 57192) erasing segment 7 (vno[0] = 57211) erasing segment 8 (vno[0] = 58400) erasing segment 9 (vno[0] = 59557) erasing segment 10 (vno[0] = 60805) erasing segment 11 (vno[0] = 62014) erasing segment 12 (vno[0] = 63225) erasing segment 13 (vno[0] = 64428) erasing segment 14 (vno[0] = 65557) erasing segment 15 (vno[0] = 67563) erasing segment 16 (vno[0] = 70139) erasing segment 17 (vno[0] = 72066) erasing segment 18 (vno[0] = 79408) erasing segment 19 (vno[0] = 79412) erasing segment 20 (vno[0] = 80328) erasing segment 21 (vno[0] = 82989) erasing segment 22 (vno[0] = 86238) erasing segment 23 (vno[0] = 86990) erasing segment 24 (vno[0] = 88588) erasing segment 25 (vno[0] = 89248) erasing segment 26 (vno[0] = 89850) erasing segment 27 (vno[0] = 91043) writing cortex label to /lustre/kovacv/FS/post-analysis/MPS3007-1/label/lh.cortex.label... LabelWrite: saving to /lustre/kovacv/FS/post-analysis/MPS3007-1/label/lh.cortex.label writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.area vertex spacing 0.86 +- 0.30 (0.02-->6.52) (max @ vno 81277 --> 81295) face area 0.31 +- 0.19 (0.00-->5.08) refinement took 4.0 minutes #-------------------------------------------- #@# Smooth2 lh Thu May 29 00:07:56 CDT 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu May 29 00:07:59 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 44.0 mm, total surface area = 69132 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.131 (target=0.015) step 005: RMS=0.094 (target=0.015) step 010: RMS=0.076 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.057 (target=0.015) step 025: RMS=0.050 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.024 (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 295 vertices thresholded to be in k1 ~ [-0.38 0.34], k2 ~ [-0.13 0.08] total integrated curvature = 0.039*4pi (0.491) --> 1 handles ICI = 1.5, FI = 11.4, variation=194.140 155 vertices thresholded to be in [-0.02 0.04] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 145 vertices thresholded to be in [-0.21 0.13] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.020, std = 0.029 done. #-------------------------------------------- #@# Sphere lh Thu May 29 00:09:28 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.61 hours scaling brain by 0.311... pass 1: epoch 1 of 3 starting distance error %20.84 pass 1: epoch 2 of 3 starting distance error %20.76 unfolding complete - removing small folds... starting distance error %20.29 removing remaining folds... final distance error %20.34 expanding nbhd size to 1 1354: 6 negative triangles #-------------------------------------------- #@# Surf Reg lh Thu May 29 01:46:06 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_register -curv ../surf/lh.sphere /soft/freesurfer/5.1.0/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /soft/freesurfer/5.1.0/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.582 curvature mean = 0.048, std = 0.931 curvature mean = 0.028, std = 0.877 curvature mean = -0.002, std = 0.973 curvature mean = 0.012, std = 0.947 curvature mean = -0.003, std = 0.986 curvature mean = 0.005, std = 0.975 curvature mean = -0.005, std = 0.990 curvature mean = 0.001, std = 0.988 curvature mean = -0.047, std = 0.464 curvature mean = 0.002, std = 0.067 curvature mean = 0.064, std = 0.223 curvature mean = 0.001, std = 0.080 curvature mean = 0.038, std = 0.333 curvature mean = 0.001, std = 0.086 curvature mean = 0.023, std = 0.446 curvature mean = 0.000, std = 0.090 curvature mean = 0.010, std = 0.554 expanding nbhd size to 1 1110: 6 negative triangles #-------------------------------------------- #@# Jacobian white lh Thu May 29 02:18:42 CDT 2014 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu May 29 02:18:43 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mrisp_paint -a 5 /soft/freesurfer/5.1.0/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 /soft/freesurfer/5.1.0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu May 29 02:18:45 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.1.0/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /soft/freesurfer/5.1.0/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... 948 labels changed using aseg relabeling using gibbs priors... 000: 2774 changed, 124631 examined... 001: 641 changed, 12030 examined... 002: 150 changed, 3626 examined... 003: 61 changed, 845 examined... 004: 23 changed, 385 examined... 005: 16 changed, 141 examined... 006: 9 changed, 106 examined... 007: 1 changed, 54 examined... 008: 0 changed, 6 examined... 236 labels changed using aseg 000: 111 total segments, 62 labels (382 vertices) changed 001: 46 total segments, 5 labels (10 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 62 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2081 vertices marked for relabeling... 2081 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 34 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu May 29 02:19:19 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS3007-1 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... 22326 bright wm thresholded. 602 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.orig... computing class statistics... border white: 272146 voxels (1.62%) border gray 320381 voxels (1.91%) WM (95.0): 96.2 +- 8.5 [70.0 --> 110.0] GM (84.0) : 82.4 +- 12.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.8 (was 70) setting MAX_BORDER_WHITE to 115.5 (was 105) setting MIN_BORDER_WHITE to 80.0 (was 85) setting MAX_CSF to 55.6 (was 40) setting MAX_GRAY to 98.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.4 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=107, GM=80 using class modes intead of means.... mean inside = 96.4, mean outside = 81.3 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.27 (0.01-->5.35) (max @ vno 15713 --> 118094) face area 0.27 +- 0.15 (0.00-->6.25) mean absolute distance = 0.92 +- 1.17 4392 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 77 points - only 0.00% unknown deleting segment 1 with 52 points - only 0.00% unknown deleting segment 2 with 20 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown deleting segment 8 with 407 points - only 0.00% unknown deleting segment 9 with 12 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown deleting segment 11 with 16 points - only 0.00% unknown mean border=88.0, 1375 (1352) missing vertices, mean dist 0.2 [1.1 (%35.9)->0.8 (%64.1))] %50 local maxima, %44 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.87 +- 0.31 (0.02-->5.34) (max @ vno 81277 --> 81295) face area 0.27 +- 0.16 (0.00-->4.16) mean absolute distance = 0.52 +- 0.75 4314 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4696275.5, rms=9.03 001: dt: 0.5000, sse=6142390.5, rms=6.98 002: dt: 0.5000, sse=6563536.0, rms=5.94 003: dt: 0.5000, sse=6989824.0, rms=5.33 004: dt: 0.5000, sse=7065450.0, rms=4.88 005: dt: 0.5000, sse=7171469.5, rms=4.49 006: dt: 0.5000, sse=7129190.0, rms=4.15 007: dt: 0.5000, sse=7161787.5, rms=3.90 008: dt: 0.5000, sse=7146134.5, rms=3.73 009: dt: 0.5000, sse=7150905.5, rms=3.63 010: dt: 0.5000, sse=7140588.0, rms=3.55 rms = 3.52, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=7181726.5, rms=3.52 012: dt: 0.2500, sse=5323692.0, rms=3.08 013: dt: 0.2500, sse=5109666.5, rms=2.96 rms = 2.92, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4988671.5, rms=2.92 rms = 2.88, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=4929538.0, rms=2.88 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 88 points - only 0.00% unknown deleting segment 1 with 150 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 5 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 281 points - only 0.00% unknown deleting segment 9 with 20 points - only 0.00% unknown deleting segment 10 with 14 points - only 7.14% unknown deleting segment 11 with 17 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 75 points - only 1.33% unknown deleting segment 15 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 16 with 4 points - only 0.00% unknown deleting segment 17 with 18 points - only 33.33% unknown mean border=90.7, 998 (419) missing vertices, mean dist -0.3 [0.6 (%70.3)->0.4 (%29.7))] %73 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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 0.87 +- 0.31 (0.04-->6.06) (max @ vno 81277 --> 81295) face area 0.32 +- 0.19 (0.00-->4.81) mean absolute distance = 0.35 +- 0.51 3525 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5328394.0, rms=4.67 016: dt: 0.5000, sse=5663118.5, rms=3.41 017: dt: 0.5000, sse=6269678.0, rms=3.21 018: dt: 0.5000, sse=6498093.5, rms=3.13 rms = 3.19, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=5598326.0, rms=2.73 020: dt: 0.2500, sse=5338832.5, rms=2.55 021: dt: 0.2500, sse=5198121.5, rms=2.48 rms = 2.46, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5139180.5, rms=2.46 rms = 2.43, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=5086511.5, rms=2.43 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 91 points - only 0.00% unknown deleting segment 1 with 136 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 341 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 75 points - only 1.33% unknown deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 25 points - only 0.00% unknown deleting segment 11 with 19 points - only 36.84% unknown mean border=92.2, 965 (274) missing vertices, mean dist -0.1 [0.4 (%66.5)->0.3 (%33.5))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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 0.87 +- 0.30 (0.03-->6.28) (max @ vno 81277 --> 81295) face area 0.31 +- 0.19 (0.00-->4.85) mean absolute distance = 0.28 +- 0.43 3604 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5204638.0, rms=3.35 024: dt: 0.5000, sse=5631973.0, rms=2.80 rms = 2.87, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5359278.0, rms=2.47 026: dt: 0.2500, sse=5381290.5, rms=2.33 rms = 2.28, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=5343432.5, rms=2.28 rms = 2.24, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5242978.0, rms=2.24 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 98 points - only 0.00% unknown deleting segment 1 with 147 points - only 0.00% unknown deleting segment 2 with 7 points - only 0.00% unknown deleting segment 3 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 390 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown deleting segment 8 with 75 points - only 1.33% unknown deleting segment 9 with 9 points - only 0.00% unknown deleting segment 10 with 8 points - only 0.00% unknown deleting segment 11 with 36 points - only 0.00% unknown deleting segment 12 with 19 points - only 36.84% unknown mean border=92.7, 1172 (235) missing vertices, mean dist -0.1 [0.3 (%55.3)->0.3 (%44.7))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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=5254747.0, rms=2.35 029: dt: 0.5000, sse=6988012.0, rms=2.19 rms = 2.53, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=6356379.5, rms=1.98 rms = 1.97, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=6087231.0, rms=1.97 032: dt: 0.1250, sse=6085294.5, rms=1.89 rms = 1.86, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=6054897.0, rms=1.86 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=67.0, 1336 (1336) missing vertices, mean dist 2.4 [1.3 (%0.2)->3.1 (%99.8))] %37 local maxima, %36 large gradients and %21 min vals, 642 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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=18678788.0, rms=26.25 001: dt: 0.5000, sse=15581964.0, rms=23.50 002: dt: 0.5000, sse=13334736.0, rms=21.25 003: dt: 0.5000, sse=11730065.0, rms=19.43 004: dt: 0.5000, sse=10729603.0, rms=17.94 005: dt: 0.5000, sse=10066205.0, rms=16.68 006: dt: 0.5000, sse=9640257.0, rms=15.59 007: dt: 0.5000, sse=9260154.0, rms=14.57 008: dt: 0.5000, sse=9003823.0, rms=13.62 009: dt: 0.5000, sse=8756803.0, rms=12.75 010: dt: 0.5000, sse=8670164.0, rms=12.05 011: dt: 0.5000, sse=8564645.0, rms=11.46 012: dt: 0.5000, sse=8531146.0, rms=10.96 013: dt: 0.5000, sse=8490039.0, rms=10.49 014: dt: 0.5000, sse=8502516.0, rms=10.05 015: dt: 0.5000, sse=8423695.0, rms=9.60 016: dt: 0.5000, sse=8368462.0, rms=9.13 017: dt: 0.5000, sse=8272223.5, rms=8.66 018: dt: 0.5000, sse=8261387.0, rms=8.25 019: dt: 0.5000, sse=8179197.5, rms=7.89 020: dt: 0.5000, sse=8178221.0, rms=7.60 021: dt: 0.5000, sse=8124141.5, rms=7.33 022: dt: 0.5000, sse=8136697.5, rms=7.16 023: dt: 0.5000, sse=8138413.0, rms=7.00 024: dt: 0.5000, sse=8116984.0, rms=6.91 025: dt: 0.5000, sse=8067840.5, rms=6.82 026: dt: 0.5000, sse=8031511.0, rms=6.76 027: dt: 0.5000, sse=7998755.0, rms=6.68 rms = 6.64, time step reduction 1 of 3 to 0.250... 028: dt: 0.5000, sse=8020282.5, rms=6.64 029: dt: 0.2500, sse=5818929.5, rms=5.55 030: dt: 0.2500, sse=5640838.5, rms=5.27 positioning took 2.2 minutes mean border=62.7, 1672 (147) missing vertices, mean dist 0.3 [0.2 (%29.8)->0.5 (%70.2))] %54 local maxima, %26 large gradients and %15 min vals, 346 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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=6938633.0, rms=8.25 031: dt: 0.5000, sse=7435641.0, rms=7.37 032: dt: 0.5000, sse=8153022.5, rms=7.02 rms = 7.23, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=6537569.0, rms=5.75 034: dt: 0.2500, sse=6129785.0, rms=5.54 rms = 5.70, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=5836983.5, rms=5.26 036: dt: 0.1250, sse=5474824.0, rms=4.87 037: dt: 0.1250, sse=5398774.5, rms=4.73 038: dt: 0.1250, sse=5370631.5, rms=4.67 rms = 4.64, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5362115.0, rms=4.64 positioning took 0.8 minutes mean border=60.8, 2202 (116) missing vertices, mean dist 0.1 [0.2 (%33.6)->0.3 (%66.4))] %61 local maxima, %18 large gradients and %15 min vals, 332 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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=5526925.5, rms=5.32 rms = 6.91, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5341451.5, rms=4.75 rms = 4.74, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=5480792.5, rms=4.74 042: dt: 0.1250, sse=5265063.5, rms=4.47 043: dt: 0.1250, sse=5271226.5, rms=4.36 rms = 4.32, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=5283133.0, rms=4.32 positioning took 0.4 minutes mean border=60.1, 3709 (107) missing vertices, mean dist 0.1 [0.2 (%43.3)->0.2 (%56.7))] %61 local maxima, %17 large gradients and %15 min vals, 340 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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 /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5299534.0, rms=4.41 rms = 5.85, time step reduction 1 of 3 to 0.250... 045: dt: 0.2500, sse=5269690.0, rms=4.22 rms = 4.22, time step reduction 2 of 3 to 0.125... 046: dt: 0.2500, sse=5605315.5, rms=4.22 047: dt: 0.1250, sse=5428971.0, rms=4.06 048: dt: 0.1250, sse=5436924.5, rms=3.97 rms = 3.93, time step reduction 3 of 3 to 0.062... 049: dt: 0.1250, sse=5452791.0, rms=3.93 positioning took 0.4 minutes writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.area.pial vertex spacing 1.03 +- 0.52 (0.02-->9.91) (max @ vno 116711 --> 116744) face area 0.42 +- 0.39 (0.00-->9.70) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 124631 vertices processed 25000 of 124631 vertices processed 50000 of 124631 vertices processed 75000 of 124631 vertices processed 100000 of 124631 vertices processed 0 of 124631 vertices processed 25000 of 124631 vertices processed 50000 of 124631 vertices processed 75000 of 124631 vertices processed 100000 of 124631 vertices processed thickness calculation complete, 6164:9565 truncations. 41123 vertices at 0 distance 57608 vertices at 1 distance 59104 vertices at 2 distance 40688 vertices at 3 distance 21467 vertices at 4 distance 9883 vertices at 5 distance 4274 vertices at 6 distance 1939 vertices at 7 distance 1010 vertices at 8 distance 566 vertices at 9 distance 385 vertices at 10 distance 273 vertices at 11 distance 214 vertices at 12 distance 174 vertices at 13 distance 125 vertices at 14 distance 113 vertices at 15 distance 80 vertices at 16 distance 70 vertices at 17 distance 59 vertices at 18 distance 38 vertices at 19 distance 87 vertices at 20 distance writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.thickness positioning took 8.5 minutes #-------------------------------------------- #@# Surf Volume lh Thu May 29 02:27:48 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 ] #----------------------------------------- #@# Parcellation Stats lh Thu May 29 02:27:48 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 MPS3007-1 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/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 923 579 1589 2.724 0.829 0.171 0.127 41 5.2 bankssts 758 488 1993 3.648 0.920 0.113 0.035 6 1.1 caudalanteriorcingulate 3318 2201 8192 3.018 0.863 0.150 0.079 67 11.5 caudalmiddlefrontal 2610 1562 3778 2.135 0.708 0.193 0.215 184 23.9 cuneus 407 267 2096 4.419 0.530 0.206 0.141 12 2.2 entorhinal 3543 2385 8975 3.085 0.867 0.241 0.356 876 37.8 fusiform 4767 3031 12805 3.147 1.001 0.220 0.310 585 74.8 inferiorparietal 4038 2480 11128 3.357 1.061 0.221 0.213 1005 38.2 inferiortemporal 1494 919 3425 3.295 1.361 0.239 1.045 2749 106.7 isthmuscingulate 8628 5273 14834 2.346 0.927 0.221 0.269 808 64.9 lateraloccipital 3419 2118 8595 3.188 0.901 0.164 0.118 117 15.8 lateralorbitofrontal 5180 3015 7128 2.214 0.815 0.191 0.153 273 35.6 lingual 2540 1633 6795 3.262 1.007 0.175 0.135 135 12.5 medialorbitofrontal 3410 2058 9909 3.358 0.935 0.189 0.192 193 26.9 middletemporal 1054 672 2753 3.295 0.972 0.187 0.243 79 14.5 parahippocampal 2534 1403 4333 2.729 0.717 0.154 0.160 126 19.5 paracentral 1856 1217 5203 3.227 0.825 0.142 0.069 30 6.0 parsopercularis 951 624 2943 3.223 0.803 0.211 0.140 51 5.1 parsorbitalis 1394 954 4018 3.078 0.913 0.175 0.097 42 5.8 parstriangularis 1530 1070 1443 1.580 0.612 0.333 0.431 288 21.7 pericalcarine 6999 3931 11481 2.432 0.866 0.211 0.541 4503 102.8 postcentral 1484 990 3621 3.324 0.743 0.158 0.083 41 5.0 posteriorcingulate 7284 4480 16903 3.052 0.930 0.175 0.166 435 51.2 precentral 4851 3108 11225 2.923 1.002 0.170 0.148 327 26.8 precuneus 1048 717 2521 3.097 1.185 0.177 0.095 30 3.5 rostralanteriorcingulate 6032 3930 15264 2.968 0.829 0.161 0.095 150 21.0 rostralmiddlefrontal 8653 5837 27836 3.541 0.879 0.167 0.103 264 37.7 superiorfrontal 7608 4736 15803 2.689 0.893 0.193 0.186 766 47.6 superiorparietal 7024 3945 12851 2.819 0.942 0.222 0.437 1391 119.2 superiortemporal 7147 4260 14229 2.853 0.969 0.248 0.420 1265 112.0 supramarginal 290 190 1226 3.714 0.698 0.249 0.261 20 2.6 frontalpole 614 380 2659 4.143 0.635 0.212 8.381 398 4.9 temporalpole 1035 544 1915 2.924 0.725 0.248 0.376 111 18.7 transversetemporal 2922 1984 8376 3.867 1.040 0.148 0.154 314 16.9 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu May 29 02:27:58 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.1.0/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /soft/freesurfer/5.1.0/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... 1 labels changed using aseg relabeling using gibbs priors... 000: 8508 changed, 124631 examined... 001: 2010 changed, 32581 examined... 002: 622 changed, 10354 examined... 003: 255 changed, 3545 examined... 004: 119 changed, 1440 examined... 005: 51 changed, 665 examined... 006: 18 changed, 285 examined... 007: 11 changed, 101 examined... 008: 9 changed, 62 examined... 009: 4 changed, 39 examined... 010: 2 changed, 21 examined... 011: 0 changed, 10 examined... 3 labels changed using aseg 000: 296 total segments, 220 labels (2866 vertices) changed 001: 105 total segments, 30 labels (163 vertices) changed 002: 77 total segments, 2 labels (19 vertices) changed 003: 76 total segments, 1 labels (1 vertices) changed 004: 75 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 102 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1525 vertices marked for relabeling... 1525 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 38 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu May 29 02:28:36 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 MPS3007-1 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/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 974 633 2549 3.165 0.872 0.176 0.095 32 3.3 G_and_S_frontomargin 2510 1472 5196 2.781 0.926 0.268 0.504 513 31.6 G_and_S_occipital_inf 1712 952 3362 2.677 0.892 0.211 0.406 1807 42.3 G_and_S_paracentral 1545 904 4054 3.299 1.033 0.213 0.499 785 18.0 G_and_S_subcentral 401 289 1641 3.532 0.673 0.197 0.165 19 1.8 G_and_S_transv_frontopol 1995 1348 4981 3.207 0.979 0.162 0.100 52 7.4 G_and_S_cingul-Ant 1163 793 2888 3.311 0.812 0.123 0.050 14 2.4 G_and_S_cingul-Mid-Ant 1145 767 2408 3.061 0.641 0.114 0.048 16 2.2 G_and_S_cingul-Mid-Post 445 271 1532 3.892 1.042 0.216 0.147 19 2.5 G_cingul-Post-dorsal 464 271 723 2.256 1.448 0.190 0.241 20 2.6 G_cingul-Post-ventral 2343 1407 3306 2.053 0.720 0.221 0.265 196 26.1 G_cuneus 1317 810 4496 3.644 0.694 0.182 0.237 101 15.5 G_front_inf-Opercular 418 273 1533 3.459 0.642 0.222 0.157 30 2.6 G_front_inf-Orbital 738 497 2701 3.445 0.765 0.203 0.131 32 4.1 G_front_inf-Triangul 3425 2247 11300 3.283 0.876 0.179 0.117 108 17.0 G_front_middle 6558 4257 22891 3.647 0.881 0.191 0.144 315 43.8 G_front_sup 464 338 1937 4.361 0.761 0.164 0.223 31 2.2 G_Ins_lg_and_S_cent_ins 403 268 1951 4.754 0.361 0.130 0.051 4 0.9 G_insular_short 2097 1299 5864 3.084 1.017 0.236 0.470 343 16.8 G_occipital_middle 1934 1269 5306 2.944 1.012 0.206 0.177 86 10.3 G_occipital_sup 1266 811 3877 3.267 0.884 0.275 0.344 581 20.7 G_oc-temp_lat-fusifor 3181 1785 3930 1.981 0.730 0.193 0.123 115 17.1 G_oc-temp_med-Lingual 1159 755 3961 3.730 0.968 0.212 0.249 92 15.9 G_oc-temp_med-Parahip 2547 1544 7947 3.384 0.903 0.201 0.167 135 16.5 G_orbital 2096 1323 7607 3.487 1.099 0.265 0.283 232 25.6 G_pariet_inf-Angular 4175 2299 7842 2.742 1.005 0.302 0.596 1112 87.3 G_pariet_inf-Supramar 2663 1520 5485 2.718 0.963 0.228 0.274 551 26.2 G_parietal_sup 2963 1384 4565 2.481 0.732 0.255 0.786 1802 43.9 G_postcentral 2812 1680 8768 3.396 0.895 0.205 0.214 245 23.5 G_precentral 2246 1373 6426 3.124 0.978 0.223 0.258 304 21.1 G_precuneus 782 540 2957 3.511 0.840 0.204 0.130 30 3.9 G_rectus 343 190 512 2.907 1.032 0.196 0.324 64 3.0 G_subcallosal 1014 505 1934 2.958 0.761 0.249 0.473 125 28.3 G_temp_sup-G_T_transv 2647 1342 5407 2.719 1.100 0.311 0.752 867 67.7 G_temp_sup-Lateral 514 321 1506 3.739 0.867 0.154 0.112 10 2.2 G_temp_sup-Plan_polar 1579 912 2490 2.632 0.880 0.175 0.314 418 24.8 G_temp_sup-Plan_tempo 2406 1454 7885 3.592 1.166 0.243 0.235 446 24.6 G_temporal_inf 2106 1201 7200 3.618 0.973 0.220 0.270 171 22.9 G_temporal_middle 326 209 742 3.015 0.950 0.158 0.065 7 0.9 Lat_Fis-ant-Horizont 163 109 282 2.492 0.507 0.111 0.040 1 0.2 Lat_Fis-ant-Vertical 1615 1014 2657 2.839 0.818 0.164 0.251 68 18.6 Lat_Fis-post 3070 1908 3246 1.691 0.547 0.230 0.204 182 21.8 Pole_occipital 1364 875 5359 3.771 0.901 0.218 3.865 435 10.8 Pole_temporal 1801 1191 2262 2.204 1.186 0.245 0.342 296 20.1 S_calcarine 3510 2230 4349 2.205 0.715 0.151 0.139 253 18.9 S_central 1177 798 1956 2.592 0.575 0.100 0.030 7 1.4 S_cingul-Marginalis 433 280 816 3.326 0.682 0.110 0.040 3 0.8 S_circular_insula_ant 1522 972 2876 3.415 1.104 0.144 0.163 58 10.6 S_circular_insula_inf 1473 990 2755 2.959 0.805 0.119 0.082 158 3.0 S_circular_insula_sup 611 422 1148 2.772 0.641 0.158 0.061 9 1.8 S_collat_transv_ant 521 341 797 2.647 0.707 0.137 0.073 11 1.8 S_collat_transv_post 1902 1260 3403 2.627 0.698 0.136 0.091 27 4.3 S_front_inf 897 588 1763 2.580 0.638 0.122 0.041 11 1.5 S_front_middle 2133 1426 3860 2.845 0.704 0.122 0.045 23 4.3 S_front_sup 251 174 619 3.105 0.778 0.264 0.307 26 2.7 S_interm_prim-Jensen 3080 1999 5808 2.650 0.774 0.153 0.127 110 13.7 S_intrapariet_and_P_trans 719 455 1112 2.292 0.520 0.200 0.181 48 3.9 S_oc_middle_and_Lunatus 1150 756 1717 2.395 0.692 0.167 0.119 65 4.0 S_oc_sup_and_transversal 426 303 1053 3.162 1.011 0.193 0.131 11 2.4 S_occipital_ant 552 347 1070 3.052 0.720 0.229 0.199 158 5.6 S_oc-temp_lat 2512 1635 4491 2.699 0.779 0.178 0.131 101 16.3 S_oc-temp_med_and_Lingual 262 181 544 2.672 0.724 0.150 0.041 3 0.5 S_orbital_lateral 1007 632 1939 3.335 0.997 0.182 0.171 119 9.2 S_orbital_med-olfact 1130 750 2413 2.971 0.954 0.133 0.054 13 2.5 S_orbital-H_Shaped 2401 1580 4305 2.621 0.962 0.140 0.066 37 6.4 S_parieto_occipital 983 610 2259 3.783 1.032 0.257 1.443 2722 102.7 S_pericallosal 2424 1655 4037 2.556 0.733 0.153 0.095 61 9.3 S_postcentral 1402 910 2833 3.031 0.878 0.130 0.057 19 3.7 S_precentral-inf-part 1202 801 1996 2.659 0.757 0.122 0.043 10 2.2 S_precentral-sup-part 542 361 1156 2.900 1.174 0.161 0.070 11 1.8 S_suborbital 779 471 1716 3.039 0.780 0.165 0.111 27 4.0 S_subparietal 1162 744 1970 2.886 0.564 0.159 0.138 392 6.6 S_temporal_inf 3861 2434 7053 2.901 0.743 0.166 0.231 363 51.5 S_temporal_sup 432 263 564 2.277 0.645 0.157 0.104 16 1.3 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Thu May 29 02:28:46 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 2 found - 2 modified | TOTAL: 8 pass 2 (xz+): 0 found - 2 modified | TOTAL: 8 pass 1 (xz-): 3 found - 3 modified | TOTAL: 11 pass 2 (xz-): 0 found - 3 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 2 found - 2 modified | TOTAL: 4 pass 2 (--): 0 found - 2 modified | TOTAL: 4 pass 1 (-+): 1 found - 1 modified | TOTAL: 5 pass 2 (-+): 0 found - 1 modified | TOTAL: 5 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 18 (out of 190693: 0.009439) 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 40: 109 vertices, 141 faces slice 50: 3368 vertices, 3547 faces slice 60: 9592 vertices, 9894 faces slice 70: 17383 vertices, 17788 faces slice 80: 28952 vertices, 29561 faces slice 90: 42794 vertices, 43489 faces slice 100: 56069 vertices, 56880 faces slice 110: 71953 vertices, 72915 faces slice 120: 86060 vertices, 87042 faces slice 130: 100223 vertices, 101352 faces slice 140: 111768 vertices, 112869 faces slice 150: 121211 vertices, 122321 faces slice 160: 129493 vertices, 130634 faces slice 170: 137722 vertices, 138850 faces slice 180: 143211 vertices, 144298 faces slice 190: 147475 vertices, 148438 faces slice 200: 148332 vertices, 149224 faces slice 210: 148332 vertices, 149224 faces slice 220: 148332 vertices, 149224 faces slice 230: 148332 vertices, 149224 faces slice 240: 148332 vertices, 149224 faces slice 250: 148332 vertices, 149224 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... 148332 voxel in cpt #1: X=-892 [v=148332,e=447672,f=298448] located at (29.609909, -15.377269, 17.329134) For the whole surface: X=-892 [v=148332,e=447672,f=298448] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu May 29 02:28:51 CDT 2014 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Thu May 29 02:28:55 CDT 2014 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts avg radius = 44.0 mm, total surface area = 70809 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.150 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.110 (target=0.015) step 015: RMS=0.104 (target=0.015) step 020: RMS=0.101 (target=0.015) step 025: RMS=0.099 (target=0.015) step 030: RMS=0.098 (target=0.015) step 035: RMS=0.098 (target=0.015) step 040: RMS=0.097 (target=0.015) step 045: RMS=0.096 (target=0.015) step 050: RMS=0.096 (target=0.015) step 055: RMS=0.096 (target=0.015) step 060: RMS=0.097 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu May 29 02:29:20 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.92 +- 0.74 (0.00-->10.98) (max @ vno 105989 --> 105990) face area 0.02 +- 0.04 (-0.24-->0.95) scaling brain by 0.322... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.226, avgs=0 005/300: dt: 0.9000, rms radial error=176.967, avgs=0 010/300: dt: 0.9000, rms radial error=176.409, avgs=0 015/300: dt: 0.9000, rms radial error=175.677, avgs=0 020/300: dt: 0.9000, rms radial error=174.844, avgs=0 025/300: dt: 0.9000, rms radial error=173.953, avgs=0 030/300: dt: 0.9000, rms radial error=173.030, avgs=0 035/300: dt: 0.9000, rms radial error=172.090, avgs=0 040/300: dt: 0.9000, rms radial error=171.143, avgs=0 045/300: dt: 0.9000, rms radial error=170.193, avgs=0 050/300: dt: 0.9000, rms radial error=169.243, avgs=0 055/300: dt: 0.9000, rms radial error=168.297, avgs=0 060/300: dt: 0.9000, rms radial error=167.353, avgs=0 065/300: dt: 0.9000, rms radial error=166.414, avgs=0 070/300: dt: 0.9000, rms radial error=165.479, avgs=0 075/300: dt: 0.9000, rms radial error=164.549, avgs=0 080/300: dt: 0.9000, rms radial error=163.624, avgs=0 085/300: dt: 0.9000, rms radial error=162.703, avgs=0 090/300: dt: 0.9000, rms radial error=161.788, avgs=0 095/300: dt: 0.9000, rms radial error=160.877, avgs=0 100/300: dt: 0.9000, rms radial error=159.970, avgs=0 105/300: dt: 0.9000, rms radial error=159.069, avgs=0 110/300: dt: 0.9000, rms radial error=158.172, avgs=0 115/300: dt: 0.9000, rms radial error=157.280, avgs=0 120/300: dt: 0.9000, rms radial error=156.393, avgs=0 125/300: dt: 0.9000, rms radial error=155.510, avgs=0 130/300: dt: 0.9000, rms radial error=154.633, avgs=0 135/300: dt: 0.9000, rms radial error=153.760, avgs=0 140/300: dt: 0.9000, rms radial error=152.892, avgs=0 145/300: dt: 0.9000, rms radial error=152.028, avgs=0 150/300: dt: 0.9000, rms radial error=151.169, avgs=0 155/300: dt: 0.9000, rms radial error=150.315, avgs=0 160/300: dt: 0.9000, rms radial error=149.466, avgs=0 165/300: dt: 0.9000, rms radial error=148.621, avgs=0 170/300: dt: 0.9000, rms radial error=147.780, avgs=0 175/300: dt: 0.9000, rms radial error=146.944, avgs=0 180/300: dt: 0.9000, rms radial error=146.115, avgs=0 185/300: dt: 0.9000, rms radial error=145.290, avgs=0 190/300: dt: 0.9000, rms radial error=144.471, avgs=0 195/300: dt: 0.9000, rms radial error=143.656, avgs=0 200/300: dt: 0.9000, rms radial error=142.845, avgs=0 205/300: dt: 0.9000, rms radial error=142.040, avgs=0 210/300: dt: 0.9000, rms radial error=141.240, avgs=0 215/300: dt: 0.9000, rms radial error=140.441, avgs=0 220/300: dt: 0.9000, rms radial error=139.653, avgs=0 225/300: dt: 0.9000, rms radial error=138.862, avgs=0 230/300: dt: 0.9000, rms radial error=138.080, avgs=0 235/300: dt: 0.9000, rms radial error=137.301, avgs=0 240/300: dt: 0.9000, rms radial error=136.521, avgs=0 245/300: dt: 0.9000, rms radial error=135.753, avgs=0 250/300: dt: 0.9000, rms radial error=134.985, avgs=0 255/300: dt: 0.9000, rms radial error=134.221, avgs=0 260/300: dt: 0.9000, rms radial error=133.466, avgs=0 265/300: dt: 0.9000, rms radial error=132.711, avgs=0 270/300: dt: 0.9000, rms radial error=131.961, avgs=0 275/300: dt: 0.9000, rms radial error=131.219, avgs=0 280/300: dt: 0.9000, rms radial error=130.473, avgs=0 285/300: dt: 0.9000, rms radial error=129.737, avgs=0 290/300: dt: 0.9000, rms radial error=129.016, avgs=0 295/300: dt: 0.9000, rms radial error=128.275, avgs=0 300/300: dt: 0.9000, rms radial error=127.562, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 17767.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 3360.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 3 (K=160.0), pass 1, starting sse = 563.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/10 = 0.00238 epoch 4 (K=640.0), pass 1, starting sse = 114.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00614 finalwriting spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu May 29 02:33:09 CDT 2014 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS3007-1 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-892 (nv=148332, nf=298448, ne=447672, g=447) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 73154 ambiguous faces found in tessellation segmenting defects... 196 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 8 -merging segment 11 into 10 -merging segment 31 into 21 -merging segment 49 into 27 -merging segment 41 into 33 -merging segment 37 into 34 -merging segment 57 into 42 -merging segment 73 into 42 -merging segment 53 into 52 -merging segment 66 into 65 -merging segment 88 into 71 -merging segment 79 into 87 -merging segment 117 into 94 -merging segment 111 into 100 -merging segment 114 into 102 -merging segment 106 into 102 -merging segment 115 into 108 -merging segment 132 into 110 -merging segment 165 into 110 -merging segment 120 into 118 -merging segment 139 into 122 -merging segment 147 into 124 -merging segment 142 into 129 -merging segment 135 into 129 -merging segment 138 into 133 -merging segment 131 into 133 -merging segment 158 into 155 169 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4368 (-4.7184) -vertex loglikelihood: -6.5742 (-3.2871) -normal dot loglikelihood: -3.4830 (-3.4830) -quad curv loglikelihood: -6.1642 (-3.0821) Total Loglikelihood : -25.6582 CORRECTING DEFECT 0 (vertices=7, convex hull=18) After retessellation of defect 0, euler #=-144 (107283,312060,204633) : difference with theory (-166) = -22 CORRECTING DEFECT 1 (vertices=23, convex hull=53) After retessellation of defect 1, euler #=-143 (107295,312114,204676) : difference with theory (-165) = -22 CORRECTING DEFECT 2 (vertices=4842, convex hull=1886) After retessellation of defect 2, euler #=-149 (108825,317762,208788) : difference with theory (-164) = -15 CORRECTING DEFECT 3 (vertices=38, convex hull=64) After retessellation of defect 3, euler #=-148 (108833,317807,208826) : difference with theory (-163) = -15 CORRECTING DEFECT 4 (vertices=26, convex hull=57) After retessellation of defect 4, euler #=-147 (108842,317855,208866) : difference with theory (-162) = -15 CORRECTING DEFECT 5 (vertices=18, convex hull=43) After retessellation of defect 5, euler #=-146 (108850,317893,208897) : difference with theory (-161) = -15 CORRECTING DEFECT 6 (vertices=192, convex hull=109) After retessellation of defect 6, euler #=-145 (108894,318080,209041) : difference with theory (-160) = -15 CORRECTING DEFECT 7 (vertices=25, convex hull=24) After retessellation of defect 7, euler #=-144 (108897,318099,209058) : difference with theory (-159) = -15 CORRECTING DEFECT 8 (vertices=18, convex hull=35) After retessellation of defect 8, euler #=-142 (108901,318126,209083) : difference with theory (-158) = -16 CORRECTING DEFECT 9 (vertices=77, convex hull=35) After retessellation of defect 9, euler #=-141 (108904,318147,209102) : difference with theory (-157) = -16 CORRECTING DEFECT 10 (vertices=97, convex hull=145) After retessellation of defect 10, euler #=-139 (108949,318349,209261) : difference with theory (-156) = -17 CORRECTING DEFECT 11 (vertices=217, convex hull=295) After retessellation of defect 11, euler #=-138 (109079,318881,209664) : difference with theory (-155) = -17 CORRECTING DEFECT 12 (vertices=189, convex hull=49) After retessellation of defect 12, euler #=-137 (109092,318937,209708) : difference with theory (-154) = -17 CORRECTING DEFECT 13 (vertices=24, convex hull=28) After retessellation of defect 13, euler #=-136 (109094,318953,209723) : difference with theory (-153) = -17 CORRECTING DEFECT 14 (vertices=23, convex hull=32) After retessellation of defect 14, euler #=-135 (109096,318970,209739) : difference with theory (-152) = -17 CORRECTING DEFECT 15 (vertices=22, convex hull=16) After retessellation of defect 15, euler #=-134 (109097,318980,209749) : difference with theory (-151) = -17 CORRECTING DEFECT 16 (vertices=43, convex hull=34) After retessellation of defect 16, euler #=-133 (109102,319008,209773) : difference with theory (-150) = -17 CORRECTING DEFECT 17 (vertices=82, convex hull=69) After retessellation of defect 17, euler #=-132 (109119,319088,209837) : difference with theory (-149) = -17 CORRECTING DEFECT 18 (vertices=48, convex hull=94) After retessellation of defect 18, euler #=-131 (109137,319180,209912) : difference with theory (-148) = -17 CORRECTING DEFECT 19 (vertices=633, convex hull=334) After retessellation of defect 19, euler #=-129 (109271,319765,210365) : difference with theory (-147) = -18 CORRECTING DEFECT 20 (vertices=95, convex hull=73) After retessellation of defect 20, euler #=-128 (109289,319852,210435) : difference with theory (-146) = -18 CORRECTING DEFECT 21 (vertices=39, convex hull=70) After retessellation of defect 21, euler #=-127 (109298,319903,210478) : difference with theory (-145) = -18 CORRECTING DEFECT 22 (vertices=31, convex hull=77) After retessellation of defect 22, euler #=-126 (109309,319965,210530) : difference with theory (-144) = -18 CORRECTING DEFECT 23 (vertices=123, convex hull=64) After retessellation of defect 23, euler #=-125 (109348,320107,210634) : difference with theory (-143) = -18 CORRECTING DEFECT 24 (vertices=19, convex hull=33) After retessellation of defect 24, euler #=-124 (109348,320120,210648) : difference with theory (-142) = -18 CORRECTING DEFECT 25 (vertices=527, convex hull=302) After retessellation of defect 25, euler #=-122 (109491,320723,211110) : difference with theory (-141) = -19 CORRECTING DEFECT 26 (vertices=142, convex hull=127) After retessellation of defect 26, euler #=-121 (109547,320943,211275) : difference with theory (-140) = -19 CORRECTING DEFECT 27 (vertices=562, convex hull=192) After retessellation of defect 27, euler #=-122 (109675,321429,211632) : difference with theory (-139) = -17 CORRECTING DEFECT 28 (vertices=38, convex hull=56) After retessellation of defect 28, euler #=-121 (109685,321479,211673) : difference with theory (-138) = -17 CORRECTING DEFECT 29 (vertices=98, convex hull=60) After retessellation of defect 29, euler #=-120 (109697,321542,211725) : difference with theory (-137) = -17 CORRECTING DEFECT 30 (vertices=276, convex hull=221) After retessellation of defect 30, euler #=-118 (109771,321877,211988) : difference with theory (-136) = -18 CORRECTING DEFECT 31 (vertices=94, convex hull=128) After retessellation of defect 31, euler #=-116 (109795,322011,212100) : difference with theory (-135) = -19 CORRECTING DEFECT 32 (vertices=19, convex hull=23) After retessellation of defect 32, euler #=-115 (109796,322019,212108) : difference with theory (-134) = -19 CORRECTING DEFECT 33 (vertices=35, convex hull=81) After retessellation of defect 33, euler #=-114 (109818,322117,212185) : difference with theory (-133) = -19 CORRECTING DEFECT 34 (vertices=45, convex hull=22) After retessellation of defect 34, euler #=-113 (109821,322131,212197) : difference with theory (-132) = -19 CORRECTING DEFECT 35 (vertices=20, convex hull=23) After retessellation of defect 35, euler #=-112 (109823,322144,212209) : difference with theory (-131) = -19 CORRECTING DEFECT 36 (vertices=808, convex hull=285) After retessellation of defect 36, euler #=-113 (109920,322587,212554) : difference with theory (-130) = -17 CORRECTING DEFECT 37 (vertices=2556, convex hull=938) After retessellation of defect 37, euler #=-117 (110829,325867,214921) : difference with theory (-129) = -12 CORRECTING DEFECT 38 (vertices=282, convex hull=109) After retessellation of defect 38, euler #=-116 (110889,326100,215095) : difference with theory (-128) = -12 CORRECTING DEFECT 39 (vertices=64, convex hull=64) After retessellation of defect 39, euler #=-115 (110901,326165,215149) : difference with theory (-127) = -12 CORRECTING DEFECT 40 (vertices=58, convex hull=40) After retessellation of defect 40, euler #=-114 (110905,326190,215171) : difference with theory (-126) = -12 CORRECTING DEFECT 41 (vertices=10, convex hull=18) After retessellation of defect 41, euler #=-113 (110906,326199,215180) : difference with theory (-125) = -12 CORRECTING DEFECT 42 (vertices=46, convex hull=39) After retessellation of defect 42, euler #=-112 (110910,326228,215206) : difference with theory (-124) = -12 CORRECTING DEFECT 43 (vertices=43, convex hull=54) After retessellation of defect 43, euler #=-111 (110919,326276,215246) : difference with theory (-123) = -12 CORRECTING DEFECT 44 (vertices=47, convex hull=62) After retessellation of defect 44, euler #=-110 (110932,326337,215295) : difference with theory (-122) = -12 CORRECTING DEFECT 45 (vertices=461, convex hull=366) After retessellation of defect 45, euler #=-109 (111052,326881,215720) : difference with theory (-121) = -12 CORRECTING DEFECT 46 (vertices=1031, convex hull=621) After retessellation of defect 46, euler #=-109 (111447,328389,216833) : difference with theory (-120) = -11 CORRECTING DEFECT 47 (vertices=766, convex hull=241) After retessellation of defect 47, euler #=-109 (111493,328649,217047) : difference with theory (-119) = -10 CORRECTING DEFECT 48 (vertices=18, convex hull=55) After retessellation of defect 48, euler #=-108 (111501,328694,217085) : difference with theory (-118) = -10 CORRECTING DEFECT 49 (vertices=236, convex hull=89) After retessellation of defect 49, euler #=-107 (111523,328807,217177) : difference with theory (-117) = -10 CORRECTING DEFECT 50 (vertices=52, convex hull=114) After retessellation of defect 50, euler #=-106 (111557,328954,217291) : difference with theory (-116) = -10 CORRECTING DEFECT 51 (vertices=36, convex hull=19) After retessellation of defect 51, euler #=-105 (111562,328975,217308) : difference with theory (-115) = -10 CORRECTING DEFECT 52 (vertices=42, convex hull=21) After retessellation of defect 52, euler #=-104 (111566,328995,217325) : difference with theory (-114) = -10 CORRECTING DEFECT 53 (vertices=131, convex hull=45) After retessellation of defect 53, euler #=-103 (111575,329040,217362) : difference with theory (-113) = -10 CORRECTING DEFECT 54 (vertices=57, convex hull=85) After retessellation of defect 54, euler #=-102 (111604,329167,217461) : difference with theory (-112) = -10 CORRECTING DEFECT 55 (vertices=55, convex hull=56) After retessellation of defect 55, euler #=-101 (111630,329267,217536) : difference with theory (-111) = -10 CORRECTING DEFECT 56 (vertices=77, convex hull=110) After retessellation of defect 56, euler #=-100 (111687,329489,217702) : difference with theory (-110) = -10 CORRECTING DEFECT 57 (vertices=71, convex hull=48) After retessellation of defect 57, euler #=-98 (111698,329544,217748) : difference with theory (-109) = -11 CORRECTING DEFECT 58 (vertices=23, convex hull=44) After retessellation of defect 58, euler #=-97 (111701,329570,217772) : difference with theory (-108) = -11 CORRECTING DEFECT 59 (vertices=879, convex hull=465) After retessellation of defect 59, euler #=-99 (112026,330805,218680) : difference with theory (-107) = -8 CORRECTING DEFECT 60 (vertices=957, convex hull=423) After retessellation of defect 60, euler #=-99 (112330,331947,219518) : difference with theory (-106) = -7 CORRECTING DEFECT 61 (vertices=73, convex hull=92) After retessellation of defect 61, euler #=-98 (112353,332053,219602) : difference with theory (-105) = -7 CORRECTING DEFECT 62 (vertices=325, convex hull=257) After retessellation of defect 62, euler #=-96 (112487,332587,220004) : difference with theory (-104) = -8 CORRECTING DEFECT 63 (vertices=22, convex hull=32) After retessellation of defect 63, euler #=-95 (112488,332599,220016) : difference with theory (-103) = -8 CORRECTING DEFECT 64 (vertices=15, convex hull=22) After retessellation of defect 64, euler #=-94 (112490,332614,220030) : difference with theory (-102) = -8 CORRECTING DEFECT 65 (vertices=29, convex hull=26) After retessellation of defect 65, euler #=-93 (112493,332629,220043) : difference with theory (-101) = -8 CORRECTING DEFECT 66 (vertices=34, convex hull=22) After retessellation of defect 66, euler #=-92 (112497,332646,220057) : difference with theory (-100) = -8 CORRECTING DEFECT 67 (vertices=100, convex hull=116) After retessellation of defect 67, euler #=-92 (112521,332771,220158) : difference with theory (-99) = -7 CORRECTING DEFECT 68 (vertices=61, convex hull=102) After retessellation of defect 68, euler #=-92 (112556,332924,220276) : difference with theory (-98) = -6 CORRECTING DEFECT 69 (vertices=29, convex hull=52) After retessellation of defect 69, euler #=-91 (112565,332970,220314) : difference with theory (-97) = -6 CORRECTING DEFECT 70 (vertices=7, convex hull=23) After retessellation of defect 70, euler #=-90 (112566,332983,220327) : difference with theory (-96) = -6 CORRECTING DEFECT 71 (vertices=36, convex hull=55) After retessellation of defect 71, euler #=-89 (112586,333063,220388) : difference with theory (-95) = -6 CORRECTING DEFECT 72 (vertices=225, convex hull=53) After retessellation of defect 72, euler #=-88 (112601,333129,220440) : difference with theory (-94) = -6 CORRECTING DEFECT 73 (vertices=14, convex hull=25) After retessellation of defect 73, euler #=-87 (112603,333143,220453) : difference with theory (-93) = -6 CORRECTING DEFECT 74 (vertices=21, convex hull=45) After retessellation of defect 74, euler #=-86 (112615,333199,220498) : difference with theory (-92) = -6 CORRECTING DEFECT 75 (vertices=32, convex hull=50) After retessellation of defect 75, euler #=-85 (112627,333252,220540) : difference with theory (-91) = -6 CORRECTING DEFECT 76 (vertices=234, convex hull=112) After retessellation of defect 76, euler #=-83 (112644,333357,220630) : difference with theory (-90) = -7 CORRECTING DEFECT 77 (vertices=8, convex hull=17) After retessellation of defect 77, euler #=-82 (112645,333364,220637) : difference with theory (-89) = -7 CORRECTING DEFECT 78 (vertices=136, convex hull=107) After retessellation of defect 78, euler #=-81 (112674,333496,220741) : difference with theory (-88) = -7 CORRECTING DEFECT 79 (vertices=514, convex hull=145) After retessellation of defect 79, euler #=-81 (112839,334061,221141) : difference with theory (-87) = -6 CORRECTING DEFECT 80 (vertices=36, convex hull=25) After retessellation of defect 80, euler #=-80 (112843,334078,221155) : difference with theory (-86) = -6 CORRECTING DEFECT 81 (vertices=28, convex hull=16) After retessellation of defect 81, euler #=-79 (112847,334093,221167) : difference with theory (-85) = -6 CORRECTING DEFECT 82 (vertices=1043, convex hull=615) After retessellation of defect 82, euler #=-78 (113272,335710,222360) : difference with theory (-84) = -6 CORRECTING DEFECT 83 (vertices=41, convex hull=77) After retessellation of defect 83, euler #=-77 (113296,335818,222445) : difference with theory (-83) = -6 CORRECTING DEFECT 84 (vertices=48, convex hull=84) After retessellation of defect 84, euler #=-76 (113314,335914,222524) : difference with theory (-82) = -6 CORRECTING DEFECT 85 (vertices=59, convex hull=61) After retessellation of defect 85, euler #=-75 (113325,335975,222575) : difference with theory (-81) = -6 CORRECTING DEFECT 86 (vertices=43, convex hull=34) After retessellation of defect 86, euler #=-74 (113331,336003,222598) : difference with theory (-80) = -6 CORRECTING DEFECT 87 (vertices=38, convex hull=92) After retessellation of defect 87, euler #=-73 (113346,336085,222666) : difference with theory (-79) = -6 CORRECTING DEFECT 88 (vertices=149, convex hull=92) After retessellation of defect 88, euler #=-71 (113357,336157,222729) : difference with theory (-78) = -7 CORRECTING DEFECT 89 (vertices=48, convex hull=48) After retessellation of defect 89, euler #=-70 (113369,336215,222776) : difference with theory (-77) = -7 CORRECTING DEFECT 90 (vertices=1489, convex hull=817) After retessellation of defect 90, euler #=-67 (113871,338137,224199) : difference with theory (-76) = -9 CORRECTING DEFECT 91 (vertices=30, convex hull=32) After retessellation of defect 91, euler #=-66 (113878,338167,224223) : difference with theory (-75) = -9 CORRECTING DEFECT 92 (vertices=10, convex hull=38) After retessellation of defect 92, euler #=-65 (113881,338191,224245) : difference with theory (-74) = -9 CORRECTING DEFECT 93 (vertices=17, convex hull=15) After retessellation of defect 93, euler #=-64 (113883,338200,224253) : difference with theory (-73) = -9 CORRECTING DEFECT 94 (vertices=33, convex hull=28) After retessellation of defect 94, euler #=-63 (113888,338226,224275) : difference with theory (-72) = -9 CORRECTING DEFECT 95 (vertices=3647, convex hull=686) After retessellation of defect 95, euler #=-64 (114775,341273,226434) : difference with theory (-71) = -7 CORRECTING DEFECT 96 (vertices=9, convex hull=15) After retessellation of defect 96, euler #=-63 (114777,341283,226443) : difference with theory (-70) = -7 CORRECTING DEFECT 97 (vertices=3609, convex hull=637) After retessellation of defect 97, euler #=-63 (115695,344418,228660) : difference with theory (-69) = -6 CORRECTING DEFECT 98 (vertices=6, convex hull=26) After retessellation of defect 98, euler #=-62 (115697,344431,228672) : difference with theory (-68) = -6 CORRECTING DEFECT 99 (vertices=11, convex hull=14) After retessellation of defect 99, euler #=-61 (115698,344437,228678) : difference with theory (-67) = -6 CORRECTING DEFECT 100 (vertices=32, convex hull=28) After retessellation of defect 100, euler #=-60 (115703,344458,228695) : difference with theory (-66) = -6 CORRECTING DEFECT 101 (vertices=184, convex hull=100) After retessellation of defect 101, euler #=-58 (115729,344587,228800) : difference with theory (-65) = -7 CORRECTING DEFECT 102 (vertices=20, convex hull=27) After retessellation of defect 102, euler #=-57 (115732,344606,228817) : difference with theory (-64) = -7 CORRECTING DEFECT 103 (vertices=78, convex hull=33) After retessellation of defect 103, euler #=-56 (115741,344643,228846) : difference with theory (-63) = -7 CORRECTING DEFECT 104 (vertices=384, convex hull=263) After retessellation of defect 104, euler #=-54 (115896,345243,229293) : difference with theory (-62) = -8 CORRECTING DEFECT 105 (vertices=34, convex hull=86) After retessellation of defect 105, euler #=-53 (115911,345322,229358) : difference with theory (-61) = -8 CORRECTING DEFECT 106 (vertices=1484, convex hull=197) After retessellation of defect 106, euler #=-51 (116007,345707,229649) : difference with theory (-60) = -9 CORRECTING DEFECT 107 (vertices=38, convex hull=32) After retessellation of defect 107, euler #=-50 (116011,345728,229667) : difference with theory (-59) = -9 CORRECTING DEFECT 108 (vertices=37, convex hull=69) After retessellation of defect 108, euler #=-49 (116020,345781,229712) : difference with theory (-58) = -9 CORRECTING DEFECT 109 (vertices=222, convex hull=67) After retessellation of defect 109, euler #=-48 (116030,345837,229759) : difference with theory (-57) = -9 CORRECTING DEFECT 110 (vertices=67, convex hull=61) After retessellation of defect 110, euler #=-47 (116041,345892,229804) : difference with theory (-56) = -9 CORRECTING DEFECT 111 (vertices=77, convex hull=99) After retessellation of defect 111, euler #=-44 (116052,345974,229878) : difference with theory (-55) = -11 CORRECTING DEFECT 112 (vertices=9, convex hull=15) After retessellation of defect 112, euler #=-43 (116053,345982,229886) : difference with theory (-54) = -11 CORRECTING DEFECT 113 (vertices=2067, convex hull=690) After retessellation of defect 113, euler #=-47 (116674,348244,231523) : difference with theory (-53) = -6 CORRECTING DEFECT 114 (vertices=20, convex hull=19) After retessellation of defect 114, euler #=-46 (116676,348254,231532) : difference with theory (-52) = -6 CORRECTING DEFECT 115 (vertices=76, convex hull=87) After retessellation of defect 115, euler #=-45 (116703,348376,231628) : difference with theory (-51) = -6 CORRECTING DEFECT 116 (vertices=76, convex hull=35) After retessellation of defect 116, euler #=-44 (116721,348442,231677) : difference with theory (-50) = -6 CORRECTING DEFECT 117 (vertices=34, convex hull=65) After retessellation of defect 117, euler #=-43 (116735,348510,231732) : difference with theory (-49) = -6 CORRECTING DEFECT 118 (vertices=113, convex hull=94) After retessellation of defect 118, euler #=-43 (116784,348705,231878) : difference with theory (-48) = -5 CORRECTING DEFECT 119 (vertices=21, convex hull=17) After retessellation of defect 119, euler #=-42 (116786,348715,231887) : difference with theory (-47) = -5 CORRECTING DEFECT 120 (vertices=46, convex hull=68) After retessellation of defect 120, euler #=-41 (116798,348780,231941) : difference with theory (-46) = -5 CORRECTING DEFECT 121 (vertices=85, convex hull=88) After retessellation of defect 121, euler #=-40 (116815,348870,232015) : difference with theory (-45) = -5 CORRECTING DEFECT 122 (vertices=94, convex hull=52) After retessellation of defect 122, euler #=-39 (116824,348919,232056) : difference with theory (-44) = -5 CORRECTING DEFECT 123 (vertices=32, convex hull=30) After retessellation of defect 123, euler #=-38 (116832,348951,232081) : difference with theory (-43) = -5 CORRECTING DEFECT 124 (vertices=55, convex hull=86) After retessellation of defect 124, euler #=-37 (116861,349077,232179) : difference with theory (-42) = -5 CORRECTING DEFECT 125 (vertices=6, convex hull=26) After retessellation of defect 125, euler #=-36 (116864,349093,232193) : difference with theory (-41) = -5 CORRECTING DEFECT 126 (vertices=44, convex hull=77) After retessellation of defect 126, euler #=-35 (116891,349204,232278) : difference with theory (-40) = -5 CORRECTING DEFECT 127 (vertices=33, convex hull=73) After retessellation of defect 127, euler #=-34 (116910,349291,232347) : difference with theory (-39) = -5 CORRECTING DEFECT 128 (vertices=260, convex hull=212) After retessellation of defect 128, euler #=-33 (117000,349665,232632) : difference with theory (-38) = -5 CORRECTING DEFECT 129 (vertices=7, convex hull=35) After retessellation of defect 129, euler #=-32 (117002,349683,232649) : difference with theory (-37) = -5 CORRECTING DEFECT 130 (vertices=157, convex hull=96) After retessellation of defect 130, euler #=-30 (117020,349781,232731) : difference with theory (-36) = -6 CORRECTING DEFECT 131 (vertices=29, convex hull=23) After retessellation of defect 131, euler #=-30 (117022,349799,232747) : difference with theory (-35) = -5 CORRECTING DEFECT 132 (vertices=23, convex hull=22) After retessellation of defect 132, euler #=-29 (117026,349815,232760) : difference with theory (-34) = -5 CORRECTING DEFECT 133 (vertices=40, convex hull=44) After retessellation of defect 133, euler #=-28 (117037,349862,232797) : difference with theory (-33) = -5 CORRECTING DEFECT 134 (vertices=44, convex hull=80) After retessellation of defect 134, euler #=-27 (117066,349983,232890) : difference with theory (-32) = -5 CORRECTING DEFECT 135 (vertices=35, convex hull=33) After retessellation of defect 135, euler #=-26 (117072,350011,232913) : difference with theory (-31) = -5 CORRECTING DEFECT 136 (vertices=1058, convex hull=462) After retessellation of defect 136, euler #=-28 (117333,351047,233686) : difference with theory (-30) = -2 CORRECTING DEFECT 137 (vertices=99, convex hull=72) After retessellation of defect 137, euler #=-27 (117344,351109,233738) : difference with theory (-29) = -2 CORRECTING DEFECT 138 (vertices=373, convex hull=144) After retessellation of defect 138, euler #=-26 (117426,351425,233973) : difference with theory (-28) = -2 CORRECTING DEFECT 139 (vertices=45, convex hull=85) After retessellation of defect 139, euler #=-25 (117451,351533,234057) : difference with theory (-27) = -2 CORRECTING DEFECT 140 (vertices=1306, convex hull=344) After retessellation of defect 140, euler #=-25 (117629,352251,234597) : difference with theory (-26) = -1 CORRECTING DEFECT 141 (vertices=587, convex hull=139) After retessellation of defect 141, euler #=-24 (117673,352455,234758) : difference with theory (-25) = -1 CORRECTING DEFECT 142 (vertices=26, convex hull=71) After retessellation of defect 142, euler #=-23 (117690,352531,234818) : difference with theory (-24) = -1 CORRECTING DEFECT 143 (vertices=33, convex hull=67) After retessellation of defect 143, euler #=-22 (117712,352625,234891) : difference with theory (-23) = -1 CORRECTING DEFECT 144 (vertices=22, convex hull=18) After retessellation of defect 144, euler #=-21 (117713,352632,234898) : difference with theory (-22) = -1 CORRECTING DEFECT 145 (vertices=28, convex hull=56) After retessellation of defect 145, euler #=-20 (117726,352695,234949) : difference with theory (-21) = -1 CORRECTING DEFECT 146 (vertices=43, convex hull=28) After retessellation of defect 146, euler #=-19 (117731,352719,234969) : difference with theory (-20) = -1 CORRECTING DEFECT 147 (vertices=18, convex hull=44) After retessellation of defect 147, euler #=-18 (117742,352769,235009) : difference with theory (-19) = -1 CORRECTING DEFECT 148 (vertices=48, convex hull=90) After retessellation of defect 148, euler #=-17 (117764,352873,235092) : difference with theory (-18) = -1 CORRECTING DEFECT 149 (vertices=203, convex hull=65) After retessellation of defect 149, euler #=-16 (117782,352953,235155) : difference with theory (-17) = -1 CORRECTING DEFECT 150 (vertices=6, convex hull=12) After retessellation of defect 150, euler #=-15 (117783,352959,235161) : difference with theory (-16) = -1 CORRECTING DEFECT 151 (vertices=241, convex hull=147) After retessellation of defect 151, euler #=-14 (117863,353260,235383) : difference with theory (-15) = -1 CORRECTING DEFECT 152 (vertices=14, convex hull=24) After retessellation of defect 152, euler #=-13 (117864,353270,235393) : difference with theory (-14) = -1 CORRECTING DEFECT 153 (vertices=27, convex hull=55) After retessellation of defect 153, euler #=-12 (117878,353333,235443) : difference with theory (-13) = -1 CORRECTING DEFECT 154 (vertices=19, convex hull=27) After retessellation of defect 154, euler #=-11 (117880,353349,235458) : difference with theory (-12) = -1 CORRECTING DEFECT 155 (vertices=29, convex hull=23) After retessellation of defect 155, euler #=-10 (117883,353365,235472) : difference with theory (-11) = -1 CORRECTING DEFECT 156 (vertices=161, convex hull=40) After retessellation of defect 156, euler #=-9 (117891,353402,235502) : difference with theory (-10) = -1 CORRECTING DEFECT 157 (vertices=29, convex hull=22) After retessellation of defect 157, euler #=-8 (117893,353415,235514) : difference with theory (-9) = -1 CORRECTING DEFECT 158 (vertices=124, convex hull=56) After retessellation of defect 158, euler #=-8 (117906,353482,235568) : difference with theory (-8) = 0 CORRECTING DEFECT 159 (vertices=23, convex hull=56) After retessellation of defect 159, euler #=-7 (117919,353540,235614) : difference with theory (-7) = 0 CORRECTING DEFECT 160 (vertices=135, convex hull=52) After retessellation of defect 160, euler #=-6 (117935,353613,235672) : difference with theory (-6) = 0 CORRECTING DEFECT 161 (vertices=81, convex hull=25) After retessellation of defect 161, euler #=-5 (117940,353636,235691) : difference with theory (-5) = 0 CORRECTING DEFECT 162 (vertices=72, convex hull=87) After retessellation of defect 162, euler #=-4 (117975,353781,235802) : difference with theory (-4) = 0 CORRECTING DEFECT 163 (vertices=8, convex hull=27) After retessellation of defect 163, euler #=-3 (117976,353794,235815) : difference with theory (-3) = 0 CORRECTING DEFECT 164 (vertices=24, convex hull=63) After retessellation of defect 164, euler #=-2 (117990,353860,235868) : difference with theory (-2) = 0 CORRECTING DEFECT 165 (vertices=25, convex hull=48) After retessellation of defect 165, euler #=-1 (117999,353905,235905) : difference with theory (-1) = 0 CORRECTING DEFECT 166 (vertices=35, convex hull=63) After retessellation of defect 166, euler #=0 (118012,353972,235960) : difference with theory (0) = 0 CORRECTING DEFECT 167 (vertices=25, convex hull=79) After retessellation of defect 167, euler #=1 (118026,354042,236017) : difference with theory (1) = 0 CORRECTING DEFECT 168 (vertices=50, convex hull=69) After retessellation of defect 168, euler #=2 (118050,354144,236096) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.91 +- 0.38 (0.03-->13.07) (max @ vno 16521 --> 109525) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.91 +- 0.38 (0.03-->13.07) (max @ vno 16521 --> 109525) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 550 mutations (36.7%), 947 crossovers (63.3%), 894 vertices were eliminated building final representation... 30282 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=118050, nf=236096, ne=354144, g=0) writing corrected surface to /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.orig... defective orientation at vertex 50530(50545) with faces 96344 and 226604 defective orientation at vertex 50530(51809) with faces 96345 and 226487 defective orientation at vertex 50531(50545) with faces 96344 and 228633 defective orientation at vertex 50531(51809) with faces 96345 and 228634 defective orientation at vertex 50545(50530) with faces 96344 and 226604 defective orientation at vertex 50545(50531) with faces 96344 and 228633 defective orientation at vertex 51809(50531) with faces 96345 and 228634 defective orientation at vertex 51809(50530) with faces 96345 and 226487 defective orientation at vertex 84636(85225) with faces 160458 and 234402 defective orientation at vertex 84636(84643) with faces 234581 and 160458 defective orientation at vertex 84643(84636) with faces 160458 and 234581 defective orientation at vertex 84643(85238) with faces 160459 and 234582 defective orientation at vertex 85225(84636) with faces 160458 and 234402 defective orientation at vertex 85225(85238) with faces 160459 and 234374 defective orientation at vertex 85238(85225) with faces 160459 and 234374 defective orientation at vertex 85238(84643) with faces 160459 and 234582 0.014 % of the vertices (16 vertices) exhibit an orientation change topology fixing took 98.6 minutes 0 defective edges removing intersecting faces 000: 3804 intersecting 001: 268 intersecting 002: 87 intersecting 003: 48 intersecting 004: 29 intersecting 005: 6 intersecting 006: 9 intersecting 007: 3 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 118050 - 354144 + 236096 = 2 --> 0 holes F =2V-4: 236096 = 236100-4 (0) 2E=3F: 708288 = 708288 (0) total defect index = 0 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 1850 intersecting 001: 207 intersecting 002: 76 intersecting 003: 50 intersecting 004: 26 intersecting 005: 9 intersecting 006: 6 intersecting 007: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu May 29 04:11:56 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS3007-1 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... 15270 bright wm thresholded. 542 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.orig... computing class statistics... border white: 272146 voxels (1.62%) border gray 320381 voxels (1.91%) WM (96.0): 95.8 +- 8.2 [70.0 --> 110.0] GM (85.0) : 82.6 +- 12.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 108.2 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 59.1 (was 40) setting MAX_GRAY to 91.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.29 (0.01-->7.70) (max @ vno 113921 --> 114711) face area 0.27 +- 0.16 (0.00-->6.48) mean absolute distance = 0.88 +- 1.23 4711 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=100, GM=84 using class modes intead of means.... mean inside = 95.4, mean outside = 81.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.5, 1057 (1057) missing vertices, mean dist -0.1 [1.1 (%42.8)->0.7 (%57.2))] %42 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.86 +- 0.32 (0.03-->7.52) (max @ vno 108336 --> 108395) face area 0.27 +- 0.17 (0.00-->6.51) mean absolute distance = 0.48 +- 0.77 4119 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3891537.5, rms=7.42 001: dt: 0.5000, sse=5665967.5, rms=5.30 002: dt: 0.5000, sse=6023666.5, rms=4.29 003: dt: 0.5000, sse=6360286.0, rms=3.85 004: dt: 0.5000, sse=6495568.5, rms=3.63 005: dt: 0.5000, sse=6533684.0, rms=3.50 006: dt: 0.5000, sse=6585948.5, rms=3.40 007: dt: 0.5000, sse=6595062.5, rms=3.33 008: dt: 0.5000, sse=6602714.5, rms=3.28 rms = 3.24, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6585768.0, rms=3.24 010: dt: 0.2500, sse=4939895.5, rms=2.75 011: dt: 0.2500, sse=4728109.5, rms=2.64 rms = 2.62, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4616361.0, rms=2.62 rms = 2.58, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4562636.5, rms=2.58 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=91.1, 988 (431) missing vertices, mean dist -0.2 [0.6 (%59.8)->0.3 (%40.2))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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 0.86 +- 0.32 (0.04-->7.49) (max @ vno 108336 --> 108395) face area 0.31 +- 0.19 (0.00-->7.45) mean absolute distance = 0.35 +- 0.53 3483 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4743079.5, rms=3.59 014: dt: 0.5000, sse=5112796.0, rms=2.90 015: dt: 0.5000, sse=5752224.0, rms=2.83 rms = 2.83, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=5143902.5, rms=2.53 017: dt: 0.2500, sse=4911414.5, rms=2.36 rms = 2.33, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=4881412.5, rms=2.33 rms = 2.28, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=4794625.5, rms=2.28 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.3, 1080 (323) missing vertices, mean dist -0.1 [0.4 (%61.5)->0.3 (%38.5))] %74 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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 0.86 +- 0.32 (0.05-->7.55) (max @ vno 108336 --> 108395) face area 0.31 +- 0.19 (0.00-->7.90) mean absolute distance = 0.29 +- 0.44 3014 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4862332.0, rms=2.91 020: dt: 0.5000, sse=5240744.0, rms=2.52 rms = 2.56, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=5027281.5, rms=2.24 022: dt: 0.2500, sse=5064917.5, rms=2.12 rms = 2.08, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5034055.5, rms=2.08 rms = 2.04, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4980366.5, rms=2.04 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=92.8, 1177 (260) missing vertices, mean dist -0.1 [0.3 (%52.9)->0.2 (%47.1))] %78 local maxima, %15 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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 /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4991298.0, rms=2.17 025: dt: 0.5000, sse=6577355.0, rms=1.89 rms = 2.25, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=6034272.5, rms=1.72 rms = 1.75, time step reduction 2 of 3 to 0.125... rms = 1.69, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=5968782.0, rms=1.69 positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group generating cortex label... 23 non-cortical segments detected only using segment with 1833 vertices erasing segment 1 (vno[0] = 39724) erasing segment 2 (vno[0] = 39726) erasing segment 3 (vno[0] = 41857) erasing segment 4 (vno[0] = 43005) erasing segment 5 (vno[0] = 44193) erasing segment 6 (vno[0] = 44207) erasing segment 7 (vno[0] = 49251) erasing segment 8 (vno[0] = 53099) erasing segment 9 (vno[0] = 61515) erasing segment 10 (vno[0] = 66069) erasing segment 11 (vno[0] = 70092) erasing segment 12 (vno[0] = 70894) erasing segment 13 (vno[0] = 73285) erasing segment 14 (vno[0] = 74854) erasing segment 15 (vno[0] = 75601) erasing segment 16 (vno[0] = 76210) erasing segment 17 (vno[0] = 76237) erasing segment 18 (vno[0] = 76239) erasing segment 19 (vno[0] = 78243) erasing segment 20 (vno[0] = 81773) erasing segment 21 (vno[0] = 116793) erasing segment 22 (vno[0] = 117132) writing cortex label to /lustre/kovacv/FS/post-analysis/MPS3007-1/label/rh.cortex.label... LabelWrite: saving to /lustre/kovacv/FS/post-analysis/MPS3007-1/label/rh.cortex.label writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.curv writing smoothed area to rh.area writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.area vertex spacing 0.87 +- 0.32 (0.04-->7.51) (max @ vno 108336 --> 108395) face area 0.31 +- 0.19 (0.00-->7.98) refinement took 3.3 minutes #-------------------------------------------- #@# Smooth2 rh Thu May 29 04:15:12 CDT 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Thu May 29 04:15:14 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 44.1 mm, total surface area = 64754 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.136 (target=0.015) step 005: RMS=0.099 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.069 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.042 (target=0.015) step 040: RMS=0.038 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.030 (target=0.015) step 060: RMS=0.028 (target=0.015) inflation complete. inflation took 0.3 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 283 vertices thresholded to be in k1 ~ [-0.64 0.44], k2 ~ [-0.23 0.18] total integrated curvature = -0.199*4pi (-2.503) --> 1 handles ICI = 1.5, FI = 11.4, variation=200.606 154 vertices thresholded to be in [-0.07 0.08] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.004 126 vertices thresholded to be in [-0.32 0.20] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.024, std = 0.033 done. #-------------------------------------------- #@# Sphere rh Thu May 29 04:16:39 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.29 hours scaling brain by 0.315... pass 1: epoch 1 of 3 starting distance error %23.97 pass 1: epoch 2 of 3 starting distance error %23.79 unfolding complete - removing small folds... starting distance error %23.46 removing remaining folds... final distance error %23.50 expanding nbhd size to 1 1317: 4 negative triangles #-------------------------------------------- #@# Surf Reg rh Thu May 29 05:33:59 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_register -curv ../surf/rh.sphere /soft/freesurfer/5.1.0/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /soft/freesurfer/5.1.0/average/rh.average.curvature.filled.buckner40.tif... singular matrix in quadratic form writing registered surface to ../surf/rh.sphere.reg... curvature mean = 0.000, std = 0.565 curvature mean = 0.024, std = 0.928 curvature mean = 0.029, std = 0.887 curvature mean = -0.060, std = 0.940 curvature mean = 0.015, std = 0.943 curvature mean = -0.067, std = 0.947 curvature mean = 0.006, std = 0.971 curvature mean = -0.068, std = 0.949 curvature mean = 0.002, std = 0.985 curvature mean = -0.055, std = 0.494 curvature mean = 0.001, std = 0.070 curvature mean = 0.073, std = 0.216 curvature mean = 0.000, std = 0.085 curvature mean = 0.046, std = 0.325 curvature mean = 0.000, std = 0.091 curvature mean = 0.028, std = 0.435 curvature mean = 0.000, std = 0.093 curvature mean = 0.011, std = 0.560 expanding nbhd size to 1 1123: 4 negative triangles #-------------------------------------------- #@# Jacobian white rh Thu May 29 06:05:14 CDT 2014 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu May 29 06:05:15 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mrisp_paint -a 5 /soft/freesurfer/5.1.0/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 /soft/freesurfer/5.1.0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu May 29 06:05:17 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.1.0/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /soft/freesurfer/5.1.0/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... 1449 labels changed using aseg relabeling using gibbs priors... 000: 2733 changed, 118050 examined... 001: 657 changed, 11771 examined... 002: 170 changed, 3615 examined... 003: 60 changed, 1032 examined... 004: 33 changed, 360 examined... 005: 18 changed, 196 examined... 006: 13 changed, 101 examined... 007: 5 changed, 68 examined... 008: 0 changed, 36 examined... 121 labels changed using aseg 000: 108 total segments, 68 labels (440 vertices) changed 001: 42 total segments, 2 labels (2 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 45 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2182 vertices marked for relabeling... 2182 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 33 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu May 29 06:05:49 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS3007-1 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... 15270 bright wm thresholded. 542 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.orig... computing class statistics... border white: 272146 voxels (1.62%) border gray 320381 voxels (1.91%) WM (96.0): 95.8 +- 8.2 [70.0 --> 110.0] GM (85.0) : 82.6 +- 12.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 108.2 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 59.1 (was 40) setting MAX_GRAY to 91.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.6 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=100, GM=84 using class modes intead of means.... mean inside = 95.4, mean outside = 81.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.80 +- 0.29 (0.01-->7.70) (max @ vno 113921 --> 114711) face area 0.27 +- 0.16 (0.00-->6.48) mean absolute distance = 0.88 +- 1.23 4796 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 104 points - only 0.00% unknown deleting segment 2 with 392 points - only 0.51% unknown removing 4 vertex label from ripped group deleting segment 5 with 24 points - only 0.00% unknown deleting segment 6 with 87 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown deleting segment 9 with 11 points - only 0.00% unknown deleting segment 10 with 20 points - only 0.00% unknown mean border=89.5, 1098 (1076) missing vertices, mean dist -0.1 [1.1 (%42.8)->0.7 (%57.2))] %42 local maxima, %52 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.86 +- 0.32 (0.03-->7.52) (max @ vno 108336 --> 108395) face area 0.27 +- 0.17 (0.00-->6.51) mean absolute distance = 0.48 +- 0.78 4205 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3905968.8, rms=7.41 001: dt: 0.5000, sse=5697205.0, rms=5.30 002: dt: 0.5000, sse=6053361.0, rms=4.28 003: dt: 0.5000, sse=6389327.5, rms=3.84 004: dt: 0.5000, sse=6521759.5, rms=3.62 005: dt: 0.5000, sse=6564011.0, rms=3.49 006: dt: 0.5000, sse=6613435.0, rms=3.40 007: dt: 0.5000, sse=6625904.5, rms=3.33 008: dt: 0.5000, sse=6632646.0, rms=3.28 rms = 3.24, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6621343.5, rms=3.24 010: dt: 0.2500, sse=4959810.0, rms=2.74 011: dt: 0.2500, sse=4747741.5, rms=2.64 rms = 2.61, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=4637887.0, rms=2.61 rms = 2.58, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=4587357.0, rms=2.58 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 8 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 63 points - only 0.00% unknown deleting segment 6 with 378 points - only 0.00% unknown deleting segment 9 with 27 points - only 0.00% unknown deleting segment 11 with 48 points - only 0.00% unknown deleting segment 12 with 179 points - only 27.37% unknown removing 4 vertex label from ripped group deleting segment 13 with 4 points - only 0.00% unknown deleting segment 14 with 22 points - only 0.00% unknown deleting segment 15 with 20 points - only 0.00% unknown deleting segment 16 with 10 points - only 0.00% unknown deleting segment 17 with 17 points - only 0.00% unknown deleting segment 18 with 5 points - only 0.00% unknown mean border=91.1, 1072 (452) missing vertices, mean dist -0.2 [0.6 (%59.9)->0.3 (%40.1))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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 0.86 +- 0.32 (0.04-->7.49) (max @ vno 108336 --> 108395) face area 0.31 +- 0.19 (0.00-->7.45) mean absolute distance = 0.35 +- 0.53 3495 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4787393.5, rms=3.58 014: dt: 0.5000, sse=5151497.5, rms=2.90 015: dt: 0.5000, sse=5804578.0, rms=2.83 rms = 2.83, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=5191859.5, rms=2.53 017: dt: 0.2500, sse=4954142.5, rms=2.37 rms = 2.33, time step reduction 2 of 3 to 0.125... 018: dt: 0.2500, sse=4916848.0, rms=2.33 rms = 2.29, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=4828674.0, rms=2.29 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 10 points - only 0.00% unknown deleting segment 4 with 15 points - only 0.00% unknown deleting segment 5 with 32 points - only 0.00% unknown deleting segment 6 with 378 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 27 points - only 0.00% unknown deleting segment 10 with 73 points - only 0.00% unknown deleting segment 11 with 171 points - only 24.56% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown deleting segment 13 with 5 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown deleting segment 15 with 21 points - only 0.00% unknown deleting segment 16 with 20 points - only 0.00% unknown deleting segment 17 with 17 points - only 0.00% unknown mean border=92.3, 1173 (338) missing vertices, mean dist -0.1 [0.4 (%61.5)->0.3 (%38.5))] %75 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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 0.86 +- 0.32 (0.04-->7.55) (max @ vno 108336 --> 108395) face area 0.31 +- 0.19 (0.00-->7.90) mean absolute distance = 0.29 +- 0.44 3033 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4895903.5, rms=2.91 020: dt: 0.5000, sse=5279745.0, rms=2.52 rms = 2.55, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=5063606.0, rms=2.24 022: dt: 0.2500, sse=5103359.5, rms=2.12 rms = 2.08, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5076821.5, rms=2.08 rms = 2.04, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5019272.0, rms=2.04 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 14 points - only 0.00% unknown deleting segment 1 with 15 points - only 0.00% unknown deleting segment 2 with 16 points - only 0.00% unknown deleting segment 3 with 405 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 6 with 27 points - only 0.00% unknown deleting segment 8 with 84 points - only 0.00% unknown deleting segment 9 with 180 points - only 27.22% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 5 points - only 0.00% unknown deleting segment 13 with 22 points - only 0.00% unknown deleting segment 14 with 5 points - only 0.00% unknown deleting segment 15 with 20 points - only 0.00% unknown deleting segment 16 with 17 points - only 0.00% unknown mean border=92.8, 1286 (276) missing vertices, mean dist -0.1 [0.3 (%52.9)->0.2 (%47.1))] %78 local maxima, %15 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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=5030531.0, rms=2.16 025: dt: 0.5000, sse=6629650.5, rms=1.88 rms = 2.24, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=6091421.0, rms=1.71 rms = 1.73, time step reduction 2 of 3 to 0.125... rms = 1.68, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=6022922.0, rms=1.68 positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 25.00% unknown smoothing surface for 5 iterations... mean border=70.1, 1339 (1339) missing vertices, mean dist 2.4 [0.9 (%0.3)->3.1 (%99.7))] %42 local maxima, %32 large gradients and %20 min vals, 1404 gradients ignored tol=1.0e-04, sigma=2.0, host=node1, 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=14424950.0, rms=23.28 001: dt: 0.5000, sse=12105960.0, rms=20.74 002: dt: 0.5000, sse=10448678.0, rms=18.66 003: dt: 0.5000, sse=9377386.0, rms=16.98 004: dt: 0.5000, sse=8731136.0, rms=15.61 005: dt: 0.5000, sse=8293752.5, rms=14.44 006: dt: 0.5000, sse=7983686.0, rms=13.47 007: dt: 0.5000, sse=7786759.5, rms=12.62 008: dt: 0.5000, sse=7613353.5, rms=11.88 009: dt: 0.5000, sse=7559050.5, rms=11.21 010: dt: 0.5000, sse=7506210.5, rms=10.64 011: dt: 0.5000, sse=7524430.0, rms=10.15 012: dt: 0.5000, sse=7510937.0, rms=9.72 013: dt: 0.5000, sse=7581625.0, rms=9.33 014: dt: 0.5000, sse=7597868.5, rms=9.00 015: dt: 0.5000, sse=7640783.0, rms=8.69 016: dt: 0.5000, sse=7644982.5, rms=8.39 017: dt: 0.5000, sse=7689227.5, rms=8.11 018: dt: 0.5000, sse=7651047.0, rms=7.83 019: dt: 0.5000, sse=7660799.5, rms=7.55 020: dt: 0.5000, sse=7643471.0, rms=7.28 021: dt: 0.5000, sse=7665111.0, rms=7.06 022: dt: 0.5000, sse=7634214.5, rms=6.85 023: dt: 0.5000, sse=7668571.5, rms=6.69 024: dt: 0.5000, sse=7645442.5, rms=6.54 025: dt: 0.5000, sse=7611747.5, rms=6.43 026: dt: 0.5000, sse=7592732.5, rms=6.31 027: dt: 0.5000, sse=7624905.5, rms=6.23 028: dt: 0.5000, sse=7570868.5, rms=6.14 029: dt: 0.5000, sse=7546690.5, rms=6.06 030: dt: 0.5000, sse=7534950.5, rms=5.99 positioning took 2.1 minutes mean border=65.5, 1715 (266) missing vertices, mean dist 0.4 [0.3 (%28.7)->0.8 (%71.3))] %58 local maxima, %22 large gradients and %14 min vals, 798 gradients ignored tol=1.0e-04, sigma=1.0, host=node1, 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=8941862.0, rms=9.02 031: dt: 0.5000, sse=7910735.0, rms=7.31 032: dt: 0.5000, sse=8585553.0, rms=7.05 033: dt: 0.5000, sse=8650901.0, rms=6.83 034: dt: 0.5000, sse=9030952.0, rms=6.73 035: dt: 0.5000, sse=8965075.0, rms=6.56 036: dt: 0.5000, sse=9142050.0, rms=6.50 037: dt: 0.5000, sse=9003602.0, rms=6.36 rms = 6.36, time step reduction 1 of 3 to 0.250... 038: dt: 0.5000, sse=9143149.0, rms=6.36 039: dt: 0.2500, sse=7043087.0, rms=5.43 040: dt: 0.2500, sse=6934245.0, rms=5.15 rms = 5.16, time step reduction 2 of 3 to 0.125... 041: dt: 0.1250, sse=6687147.0, rms=4.95 042: dt: 0.1250, sse=6314396.5, rms=4.66 043: dt: 0.1250, sse=6212997.0, rms=4.58 rms = 4.57, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=6173588.5, rms=4.57 positioning took 1.1 minutes mean border=63.5, 2268 (169) missing vertices, mean dist 0.2 [0.2 (%31.5)->0.4 (%68.5))] %64 local maxima, %15 large gradients and %14 min vals, 771 gradients ignored tol=1.0e-04, sigma=0.5, host=node1, 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=6348546.0, rms=5.31 rms = 6.28, time step reduction 1 of 3 to 0.250... 045: dt: 0.2500, sse=6141623.0, rms=4.85 046: dt: 0.2500, sse=6132851.5, rms=4.78 rms = 4.87, time step reduction 2 of 3 to 0.125... 047: dt: 0.1250, sse=6041860.5, rms=4.68 048: dt: 0.1250, sse=5950375.5, rms=4.56 049: dt: 0.1250, sse=5933503.5, rms=4.50 rms = 4.48, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=5973502.0, rms=4.48 positioning took 0.5 minutes mean border=62.9, 3871 (145) missing vertices, mean dist 0.1 [0.2 (%40.6)->0.3 (%59.4))] %65 local maxima, %13 large gradients and %14 min vals, 669 gradients ignored tol=1.0e-04, sigma=0.2, host=node1, 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 /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5970009.0, rms=4.50 rms = 5.46, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=5943113.5, rms=4.32 rms = 4.30, time step reduction 2 of 3 to 0.125... 052: dt: 0.2500, sse=6248616.5, rms=4.30 053: dt: 0.1250, sse=6100365.5, rms=4.19 054: dt: 0.1250, sse=6134825.0, rms=4.11 rms = 4.08, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=6183403.0, rms=4.08 positioning took 0.4 minutes writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.area.pial vertex spacing 1.07 +- 0.56 (0.03-->8.38) (max @ vno 113921 --> 114711) face area 0.45 +- 0.43 (0.00-->11.90) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 118050 vertices processed 25000 of 118050 vertices processed 50000 of 118050 vertices processed 75000 of 118050 vertices processed 100000 of 118050 vertices processed 0 of 118050 vertices processed 25000 of 118050 vertices processed 50000 of 118050 vertices processed 75000 of 118050 vertices processed 100000 of 118050 vertices processed thickness calculation complete, 8023:14532 truncations. 35125 vertices at 0 distance 47873 vertices at 1 distance 53262 vertices at 2 distance 40655 vertices at 3 distance 24126 vertices at 4 distance 11910 vertices at 5 distance 5482 vertices at 6 distance 2631 vertices at 7 distance 1518 vertices at 8 distance 884 vertices at 9 distance 582 vertices at 10 distance 428 vertices at 11 distance 293 vertices at 12 distance 208 vertices at 13 distance 148 vertices at 14 distance 139 vertices at 15 distance 101 vertices at 16 distance 92 vertices at 17 distance 93 vertices at 18 distance 82 vertices at 19 distance 142 vertices at 20 distance writing curvature file /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.thickness positioning took 8.1 minutes #-------------------------------------------- #@# Surf Volume rh Thu May 29 06:13:53 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 rh Thu May 29 06:13:54 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 MPS3007-1 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/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 1262 803 2344 2.796 0.798 0.154 0.220 107 5.4 bankssts 1231 800 3435 2.837 1.479 0.158 0.073 26 3.9 caudalanteriorcingulate 2536 1623 7876 3.338 1.045 0.159 0.092 63 10.3 caudalmiddlefrontal 1529 987 1743 1.639 0.566 0.283 0.255 175 17.5 cuneus 659 335 1627 3.204 1.058 0.240 0.342 88 7.2 entorhinal 3662 2272 8839 3.291 0.850 0.202 0.461 258 26.8 fusiform 6606 4160 15549 2.976 1.103 0.224 0.290 478 64.7 inferiorparietal 4069 2445 9985 3.167 1.039 0.232 0.318 465 51.2 inferiortemporal 1971 1255 3611 2.553 1.031 0.172 0.112 53 10.7 isthmuscingulate 4907 2859 10752 2.941 1.010 0.214 0.301 948 47.2 lateraloccipital 3297 1946 8187 3.321 1.024 0.172 0.178 149 18.6 lateralorbitofrontal 1763 1267 3038 2.553 0.684 0.207 0.135 102 9.0 lingual 2492 1534 6104 3.076 0.797 0.198 0.236 188 20.4 medialorbitofrontal 5079 2941 12090 3.198 1.002 0.249 0.363 602 65.8 middletemporal 983 595 2131 2.859 0.907 0.135 0.113 41 4.8 parahippocampal 2866 1707 6617 2.809 0.901 0.187 0.196 261 28.3 paracentral 1614 1056 4525 3.218 0.918 0.146 0.084 32 5.6 parsopercularis 1071 688 3558 3.601 0.802 0.195 0.136 57 6.1 parsorbitalis 1801 1182 5972 3.512 0.920 0.167 0.094 54 7.7 parstriangularis 1119 747 1772 2.146 0.638 0.257 0.222 81 10.6 pericalcarine 3422 2136 9614 3.318 0.988 0.187 0.203 247 25.1 postcentral 1697 1096 3206 2.358 1.244 0.226 0.305 244 16.9 posteriorcingulate 7593 4759 20866 3.074 1.041 0.194 0.222 734 57.5 precentral 7670 4940 15666 2.534 1.040 0.227 0.210 644 65.4 precuneus 1361 853 3711 3.480 0.735 0.176 0.128 70 6.9 rostralanteriorcingulate 6174 3924 16713 3.028 0.930 0.179 0.277 711 29.5 rostralmiddlefrontal 9532 6293 30352 3.409 1.027 0.190 0.230 1118 68.9 superiorfrontal 7577 4461 13945 2.596 0.883 0.207 0.265 946 82.6 superiorparietal 4495 2624 12638 3.499 1.037 0.203 0.332 521 52.0 superiortemporal 5540 3212 10163 2.719 0.950 0.233 0.291 775 72.6 supramarginal 412 260 1815 3.996 0.606 0.243 0.460 31 4.9 frontalpole 692 408 2311 3.835 1.211 0.251 0.257 54 8.2 temporalpole 540 291 1109 3.090 0.781 0.227 0.289 57 8.2 transversetemporal 3404 2115 8916 3.861 1.028 0.168 0.257 377 23.4 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu May 29 06:14:03 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS3007-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.1.0/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /soft/freesurfer/5.1.0/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... 2 labels changed using aseg relabeling using gibbs priors... 000: 8809 changed, 118050 examined... 001: 2162 changed, 33874 examined... 002: 667 changed, 11008 examined... 003: 275 changed, 3634 examined... 004: 146 changed, 1545 examined... 005: 61 changed, 795 examined... 006: 34 changed, 337 examined... 007: 23 changed, 200 examined... 008: 11 changed, 119 examined... 009: 5 changed, 64 examined... 010: 2 changed, 30 examined... 011: 0 changed, 18 examined... 0 labels changed using aseg 000: 306 total segments, 224 labels (2528 vertices) changed 001: 102 total segments, 20 labels (68 vertices) changed 002: 83 total segments, 1 labels (2 vertices) changed 003: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 118 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1533 vertices marked for relabeling... 1533 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 36 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu May 29 06:14:39 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 MPS3007-1 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/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 751 489 2022 2.932 1.061 0.169 0.087 28 2.7 G_and_S_frontomargin 819 507 2138 3.429 1.030 0.208 0.143 30 5.5 G_and_S_occipital_inf 1796 1117 4686 2.968 0.939 0.190 0.149 94 11.9 G_and_S_paracentral 1228 753 4843 3.945 0.945 0.203 0.335 81 13.0 G_and_S_subcentral 978 650 3275 3.202 0.798 0.203 1.259 472 6.8 G_and_S_transv_frontopol 2737 1817 6942 3.210 0.840 0.155 0.082 79 9.6 G_and_S_cingul-Ant 1515 990 4562 3.347 1.051 0.173 0.424 521 7.4 G_and_S_cingul-Mid-Ant 1459 936 4573 3.135 1.201 0.210 0.192 105 10.6 G_and_S_cingul-Mid-Post 583 359 1440 2.978 1.122 0.200 0.184 27 3.9 G_cingul-Post-dorsal 532 315 1053 2.335 1.009 0.177 0.108 17 2.7 G_cingul-Post-ventral 1394 905 1681 1.677 0.612 0.272 0.237 103 15.7 G_cuneus 1386 861 5052 3.678 0.797 0.173 0.146 68 8.3 G_front_inf-Opercular 491 299 1783 3.796 0.679 0.200 0.154 31 3.4 G_front_inf-Orbital 900 585 3896 3.904 0.713 0.192 0.112 30 4.4 G_front_inf-Triangul 2997 1778 11037 3.617 0.905 0.206 0.158 201 20.1 G_front_middle 6818 4358 23596 3.480 1.058 0.206 0.235 697 68.0 G_front_sup 429 283 1483 4.504 0.774 0.201 0.216 28 3.2 G_Ins_lg_and_S_cent_ins 575 301 2183 4.597 0.532 0.187 0.210 164 3.8 G_insular_short 2013 1139 5446 3.281 1.079 0.221 0.370 448 20.7 G_occipital_middle 1700 927 2398 2.264 0.716 0.244 0.332 378 28.7 G_occipital_sup 1424 843 4059 3.441 0.803 0.187 0.726 91 7.7 G_oc-temp_lat-fusifor 652 432 1241 2.589 0.551 0.247 0.269 88 4.5 G_oc-temp_med-Lingual 1790 966 4452 3.391 1.018 0.214 0.390 167 18.7 G_oc-temp_med-Parahip 2415 1383 8526 3.751 0.964 0.200 0.238 158 17.1 G_orbital 2525 1532 5892 2.896 1.241 0.307 0.539 332 40.1 G_pariet_inf-Angular 2955 1608 5431 2.584 0.993 0.263 0.356 574 47.8 G_pariet_inf-Supramar 2732 1556 5844 2.815 0.877 0.214 0.292 315 32.0 G_parietal_sup 1106 691 3225 3.300 0.922 0.186 0.134 43 6.7 G_postcentral 3724 2239 11270 3.163 1.055 0.199 0.235 306 34.5 G_precentral 4656 2804 10808 2.725 1.014 0.225 0.206 449 41.1 G_precuneus 750 431 2044 3.002 0.676 0.234 0.424 92 8.4 G_rectus 435 238 621 2.457 0.975 0.290 0.482 80 9.2 G_subcallosal 405 217 857 2.998 0.879 0.219 0.299 51 5.9 G_temp_sup-G_T_transv 2141 1104 6436 3.459 1.123 0.267 0.598 485 35.6 G_temp_sup-Lateral 790 464 2726 4.372 0.737 0.193 0.294 78 12.8 G_temp_sup-Plan_polar 649 407 1411 2.749 0.864 0.138 0.130 16 2.9 G_temp_sup-Plan_tempo 2069 1200 6546 3.581 0.989 0.245 0.437 334 35.2 G_temporal_inf 3403 1812 8900 3.299 1.048 0.262 0.409 429 46.3 G_temporal_middle 284 201 533 2.722 0.708 0.121 0.038 2 0.5 Lat_Fis-ant-Horizont 189 126 720 3.929 0.783 0.142 0.057 2 0.4 Lat_Fis-ant-Vertical 1532 990 2645 2.980 0.953 0.172 0.159 64 12.4 Lat_Fis-post 2563 1562 4870 2.693 0.817 0.214 0.235 448 26.5 Pole_occipital 1690 1016 4346 3.042 1.376 0.321 0.410 207 29.3 Pole_temporal 1161 714 1667 2.119 0.697 0.252 0.219 75 12.5 S_calcarine 1409 924 2486 2.672 0.888 0.221 0.217 318 11.0 S_central 1133 745 2076 2.477 0.747 0.197 0.305 122 11.5 S_cingul-Marginalis 622 412 1205 3.298 0.759 0.132 0.060 16 1.7 S_circular_insula_ant 949 626 2250 3.897 0.740 0.164 0.399 82 4.9 S_circular_insula_inf 1310 899 2413 2.953 0.795 0.136 0.105 62 6.4 S_circular_insula_sup 720 498 1389 2.969 0.706 0.227 0.180 32 5.4 S_collat_transv_ant 242 154 607 3.559 0.767 0.148 0.070 6 0.7 S_collat_transv_post 1295 855 2125 2.406 0.743 0.130 0.056 22 3.2 S_front_inf 1515 997 2973 2.653 0.699 0.152 0.082 38 4.9 S_front_middle 1870 1268 3976 2.975 0.827 0.158 0.102 67 8.8 S_front_sup 820 524 1112 2.498 0.676 0.140 0.072 15 3.0 S_interm_prim-Jensen 2294 1464 4014 2.545 0.848 0.166 0.192 129 11.0 S_intrapariet_and_P_trans 594 381 1296 2.627 1.205 0.238 0.392 93 3.8 S_oc_middle_and_Lunatus 1179 741 2807 3.079 1.253 0.196 0.191 117 10.1 S_oc_sup_and_transversal 450 291 716 2.521 0.618 0.188 0.124 18 2.5 S_occipital_ant 710 462 1678 3.795 0.734 0.201 0.222 87 5.4 S_oc-temp_lat 1608 1103 2690 2.692 0.600 0.129 0.058 16 4.2 S_oc-temp_med_and_Lingual 331 223 612 2.678 0.553 0.142 0.080 6 1.0 S_orbital_lateral 691 465 1198 2.785 0.945 0.134 0.050 8 1.4 S_orbital_med-olfact 1058 659 2341 3.229 0.983 0.151 0.092 27 4.4 S_orbital-H_Shaped 1212 975 1331 1.489 0.432 0.366 0.367 194 16.2 S_parieto_occipital 2245 1467 3358 2.409 1.284 0.161 0.084 104 8.0 S_pericallosal 1330 864 2233 2.565 0.680 0.162 0.099 32 6.1 S_postcentral 1527 1056 3857 2.998 0.897 0.140 0.058 23 3.8 S_precentral-inf-part 1348 806 2939 3.033 1.139 0.197 0.331 158 9.8 S_precentral-sup-part 151 98 405 3.608 0.671 0.143 0.061 2 0.4 S_suborbital 2303 1498 4434 2.729 0.995 0.165 0.153 149 14.1 S_subparietal 1474 966 2522 2.866 0.625 0.181 0.135 61 8.4 S_temporal_inf 4954 3156 10042 2.933 0.791 0.164 0.153 258 32.4 S_temporal_sup 141 95 538 3.973 0.867 0.181 0.084 3 0.6 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Thu May 29 06:14:48 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon MPS3007-1 SUBJECTS_DIR is /lustre/kovacv/FS/post-analysis 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 = 3 writing volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu May 29 06:21:55 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /soft/freesurfer/5.1.0/ASegStatsLUT.txt --subject MPS3007-1 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /soft/freesurfer/5.1.0/ASegStatsLUT.txt --subject MPS3007-1 sysname Linux hostname node1118 machine x86_64 user kovacv atlas_icv (eTIV) = 1454913 mm^3 (det: 1.338984 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 170297 rh white matter volume 148455 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 193655.358053, pTot = 455830.297050 c = 262174.938997 rh surface-based volumes (mm3): wTot = 167057.129261, pTot = 433990.298580 c = 266933.169320 Computing SupraTentVolCor SupraTentVolCor = 54617.000 SupraTentVol = 944437.596 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 11517 11517 4 5 Left-Inf-Lat-Vent 1236 1236 5 7 Left-Cerebellum-White-Matter 14305 14305 6 8 Left-Cerebellum-Cortex 61494 61494 7 10 Left-Thalamus-Proper 6556 6556 8 11 Left-Caudate 3333 3333 9 12 Left-Putamen 4669 4669 10 13 Left-Pallidum 1219 1219 11 14 3rd-Ventricle 1986 1986 12 15 4th-Ventricle 1666 1666 13 16 Brain-Stem 17195 17195 14 17 Left-Hippocampus 3511 3511 15 18 Left-Amygdala 1599 1599 16 24 CSF 1933 1933 17 26 Left-Accumbens-area 481 481 18 28 Left-VentralDC 2835 2835 19 30 Left-vessel 10 10 20 31 Left-choroid-plexus 1615 1615 23 43 Right-Lateral-Ventricle 5316 5316 24 44 Right-Inf-Lat-Vent 397 397 25 46 Right-Cerebellum-White-Matter 11553 11553 26 47 Right-Cerebellum-Cortex 67277 67277 27 49 Right-Thalamus-Proper 6598 6598 28 50 Right-Caudate 3030 3030 29 51 Right-Putamen 4892 4892 30 52 Right-Pallidum 1085 1085 31 53 Right-Hippocampus 4151 4151 32 54 Right-Amygdala 1595 1595 33 58 Right-Accumbens-area 562 562 34 60 Right-VentralDC 2751 2751 35 62 Right-vessel 37 37 36 63 Right-choroid-plexus 2010 2010 37 72 5th-Ventricle 0 38 77 WM-hypointensities 5029 5029 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 32 32 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 230 230 45 251 CC_Posterior 374 374 46 252 CC_Mid_Posterior 133 133 47 253 CC_Central 217 217 48 254 CC_Mid_Anterior 222 222 49 255 CC_Anterior 423 423 Reporting on 45 segmentations SubCortGrayVol = 194833 #----------------------------------------- #@# AParc-to-ASeg Thu May 29 06:26:20 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1 mri_aparc2aseg --s MPS3007-1 --volmask SUBJECTS_DIR /lustre/kovacv/FS/post-analysis subject MPS3007-1 outvol /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post-analysis/MPS3007-1/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 /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post-analysis/MPS3007-1/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 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 = 521532 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aparc+aseg.mgz /lustre/kovacv/FS/post-analysis/MPS3007-1 mri_aparc2aseg --s MPS3007-1 --volmask --a2009s SUBJECTS_DIR /lustre/kovacv/FS/post-analysis subject MPS3007-1 outvol /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post-analysis/MPS3007-1/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 /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post-analysis/MPS3007-1/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 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 /lustre/kovacv/FS/post-analysis/MPS3007-1/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 = 521532 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu May 29 06:28:28 CDT 2014 /lustre/kovacv/FS/post-analysis/MPS3007-1 mri_aparc2aseg --s MPS3007-1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /lustre/kovacv/FS/post-analysis subject MPS3007-1 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aparc+aseg.mgz Reading lh white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post-analysis/MPS3007-1/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 /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post-analysis/MPS3007-1/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 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/ribbon.mgz Loading filled from /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7286 vertices from left hemi Ripped 7424 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 /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/aseg.mgz Loading Ctx Seg File /lustre/kovacv/FS/post-analysis/MPS3007-1/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 = 822372 Used brute-force search on 3 voxels Fixing Parahip LH WM Found 22 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 832.000000 7 k 2.000000 8 k 3.000000 9 k 1.000000 10 k 1.000000 11 k 2.000000 12 k 2.000000 13 k 4.000000 14 k 21.000000 15 k 4.000000 16 k 2.000000 17 k 6.000000 18 k 1.000000 19 k 3.000000 20 k 2.000000 21 k 1.000000 Fixing Parahip RH WM Found 18 clusters 0 k 4.000000 1 k 1.000000 2 k 4.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 2.000000 7 k 1.000000 8 k 1.000000 9 k 734.000000 10 k 4.000000 11 k 1.000000 12 k 1.000000 13 k 15.000000 14 k 1.000000 15 k 1.000000 16 k 1.000000 17 k 1.000000 Writing output aseg to mri/wmparc.mgz /lustre/kovacv/FS/post-analysis/MPS3007-1 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject MPS3007-1 --surf-wm-vol --ctab /soft/freesurfer/5.1.0/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject MPS3007-1 --surf-wm-vol --ctab /soft/freesurfer/5.1.0/WMParcStatsLUT.txt --etiv sysname Linux hostname node1118 machine x86_64 user kovacv atlas_icv (eTIV) = 1454913 mm^3 (det: 1.338984 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 170297 rh white matter volume 148455 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1441589 # brainmaskvolume 1441589.0 # nbrainsegvoxels 247388 # brainsegvolume 247388.0 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 1 3001 wm-lh-bankssts 1286 1286 2 3002 wm-lh-caudalanteriorcingulate 2118 2118 3 3003 wm-lh-caudalmiddlefrontal 5358 5358 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 3223 3223 6 3006 wm-lh-entorhinal 371 371 7 3007 wm-lh-fusiform 4403 4403 8 3008 wm-lh-inferiorparietal 5888 5888 9 3009 wm-lh-inferiortemporal 3979 3979 10 3010 wm-lh-isthmuscingulate 2649 2649 11 3011 wm-lh-lateraloccipital 9863 9863 12 3012 wm-lh-lateralorbitofrontal 4457 4457 13 3013 wm-lh-lingual 5310 5310 14 3014 wm-lh-medialorbitofrontal 2415 2415 15 3015 wm-lh-middletemporal 3128 3128 16 3016 wm-lh-parahippocampal 996 996 17 3017 wm-lh-paracentral 3165 3165 18 3018 wm-lh-parsopercularis 2231 2231 19 3019 wm-lh-parsorbitalis 797 797 20 3020 wm-lh-parstriangularis 2024 2024 21 3021 wm-lh-pericalcarine 2638 2638 22 3022 wm-lh-postcentral 5709 5709 23 3023 wm-lh-posteriorcingulate 2973 2973 24 3024 wm-lh-precentral 10124 10124 25 3025 wm-lh-precuneus 5750 5750 26 3026 wm-lh-rostralanteriorcingulate 2122 2122 27 3027 wm-lh-rostralmiddlefrontal 8214 8214 28 3028 wm-lh-superiorfrontal 12534 12534 29 3029 wm-lh-superiorparietal 8306 8306 30 3030 wm-lh-superiortemporal 7185 7185 31 3031 wm-lh-supramarginal 7546 7546 32 3032 wm-lh-frontalpole 207 207 33 3033 wm-lh-temporalpole 514 514 34 3034 wm-lh-transversetemporal 888 888 35 3035 wm-lh-insula 7568 7568 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2220 2220 120 4002 wm-rh-caudalanteriorcingulate 2418 2418 121 4003 wm-rh-caudalmiddlefrontal 4084 4084 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1162 1162 124 4006 wm-rh-entorhinal 406 406 125 4007 wm-rh-fusiform 3815 3815 126 4008 wm-rh-inferiorparietal 8170 8170 127 4009 wm-rh-inferiortemporal 3688 3688 128 4010 wm-rh-isthmuscingulate 2502 2502 129 4011 wm-rh-lateraloccipital 4152 4152 130 4012 wm-rh-lateralorbitofrontal 4243 4243 131 4013 wm-rh-lingual 2793 2793 132 4014 wm-rh-medialorbitofrontal 2599 2599 133 4015 wm-rh-middletemporal 3456 3456 134 4016 wm-rh-parahippocampal 924 924 135 4017 wm-rh-paracentral 2523 2523 136 4018 wm-rh-parsopercularis 2317 2317 137 4019 wm-rh-parsorbitalis 936 936 138 4020 wm-rh-parstriangularis 2357 2357 139 4021 wm-rh-pericalcarine 1147 1147 140 4022 wm-rh-postcentral 4725 4725 141 4023 wm-rh-posteriorcingulate 2275 2275 142 4024 wm-rh-precentral 9124 9124 143 4025 wm-rh-precuneus 8363 8363 144 4026 wm-rh-rostralanteriorcingulate 1878 1878 145 4027 wm-rh-rostralmiddlefrontal 7332 7332 146 4028 wm-rh-superiorfrontal 14326 14326 147 4029 wm-rh-superiorparietal 7488 7488 148 4030 wm-rh-superiortemporal 4549 4549 149 4031 wm-rh-supramarginal 5144 5144 150 4032 wm-rh-frontalpole 274 274 151 4033 wm-rh-temporalpole 651 651 152 4034 wm-rh-transversetemporal 770 770 153 4035 wm-rh-insula 7615 7615 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 14821 14821 237 5002 Right-UnsegmentedWhiteMatter 13069 13069 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /lustre/kovacv/FS/post-analysis/MPS3007-1/label #-------------------------------------------- #@# BA Labels lh Thu May 29 06:38:00 CDT 2014 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA1.label --trgsubject MPS3007-1 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 711 Checking for and removing duplicates Writing label file ./lh.BA1.label 4840 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA2.label --trgsubject MPS3007-1 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 998 Checking for and removing duplicates Writing label file ./lh.BA2.label 8907 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA3a.label --trgsubject MPS3007-1 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 370 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4447 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA3b.label --trgsubject MPS3007-1 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 992 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6975 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA4a.label --trgsubject MPS3007-1 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 681 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6465 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA4p.label --trgsubject MPS3007-1 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 338 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4408 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA6.label --trgsubject MPS3007-1 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 1332 Checking for and removing duplicates Writing label file ./lh.BA6.label 14921 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA44.label --trgsubject MPS3007-1 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 313 Checking for and removing duplicates Writing label file ./lh.BA44.label 4494 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA45.label --trgsubject MPS3007-1 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 278 Checking for and removing duplicates Writing label file ./lh.BA45.label 3700 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.V1.label --trgsubject MPS3007-1 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 1281 Checking for and removing duplicates Writing label file ./lh.V1.label 5922 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.V2.label --trgsubject MPS3007-1 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 4703 Checking for and removing duplicates Writing label file ./lh.V2.label 12817 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.MT.label --trgsubject MPS3007-1 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 476 Checking for and removing duplicates Writing label file ./lh.MT.label 2494 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s MPS3007-1 --hemi lh --ctab /soft/freesurfer/5.1.0/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 --a BA --maxstatwinner --noverbose Reading ctab /soft/freesurfer/5.1.0/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /lustre/kovacv/FS/post-analysis/MPS3007-1/label cmdline mris_label2annot --s MPS3007-1 --hemi lh --ctab /soft/freesurfer/5.1.0/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 --a BA --maxstatwinner --noverbose sysname Linux hostname node1118 machine x86_64 user kovacv subject MPS3007-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/post-analysis ColorTable /soft/freesurfer/5.1.0/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post-analysis/MPS3007-1/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 84979 unhit vertices Writing annot to /lustre/kovacv/FS/post-analysis/MPS3007-1/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab MPS3007-1 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /soft/freesurfer/5.1.0/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 1317 579 2086 2.472 0.664 0.288 0.492 312 24.4 BA1 3860 2354 6480 2.614 0.815 0.202 0.566 1651 41.8 BA2 1120 736 1136 1.929 0.452 0.156 0.389 352 5.6 BA3a 2928 1667 4341 2.176 0.836 0.208 0.286 1036 39.5 BA3b 1716 943 3689 3.062 0.803 0.199 0.214 170 17.2 BA4a 1358 837 2203 2.830 0.726 0.166 0.148 52 7.1 BA4p 8242 5272 25575 3.466 0.976 0.177 0.129 322 46.4 BA6 2018 1257 5502 3.423 0.871 0.165 0.173 112 17.0 BA44 2255 1535 6379 3.002 0.873 0.170 0.121 63 8.7 BA45 2812 1941 2824 1.571 0.585 0.296 0.337 402 35.0 V1 10352 6004 14430 2.168 0.824 0.197 0.191 626 70.8 V2 1674 1120 4394 3.002 0.966 0.281 0.766 467 20.9 MT #-------------------------------------------- #@# BA Labels rh Thu May 29 06:39:23 CDT 2014 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA1.label --trgsubject MPS3007-1 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 106 Checking for and removing duplicates Writing label file ./rh.BA1.label 4068 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA2.label --trgsubject MPS3007-1 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./rh.BA2.label 6848 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA3a.label --trgsubject MPS3007-1 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4063 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA3b.label --trgsubject MPS3007-1 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 144 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4666 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA4a.label --trgsubject MPS3007-1 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 943 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6690 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA4p.label --trgsubject MPS3007-1 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 312 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4785 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA6.label --trgsubject MPS3007-1 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 2852 Checking for and removing duplicates Writing label file ./rh.BA6.label 15108 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA44.label --trgsubject MPS3007-1 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 959 Checking for and removing duplicates Writing label file ./rh.BA44.label 7871 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA45.label --trgsubject MPS3007-1 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 650 Checking for and removing duplicates Writing label file ./rh.BA45.label 6005 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.V1.label --trgsubject MPS3007-1 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 543 Checking for and removing duplicates Writing label file ./rh.V1.label 5270 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.V2.label --trgsubject MPS3007-1 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 841 Checking for and removing duplicates Writing label file ./rh.V2.label 8857 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.MT.label --trgsubject MPS3007-1 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post-analysis/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = MPS3007-1 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 /lustre/kovacv/FS/post-analysis FREESURFER_HOME /soft/freesurfer/5.1.0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /lustre/kovacv/FS/post-analysis/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post-analysis/MPS3007-1/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 Number of reverse mapping hits = 344 Checking for and removing duplicates Writing label file ./rh.MT.label 2276 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s MPS3007-1 --hemi rh --ctab /soft/freesurfer/5.1.0/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 --a BA --maxstatwinner --noverbose Reading ctab /soft/freesurfer/5.1.0/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /lustre/kovacv/FS/post-analysis/MPS3007-1/label cmdline mris_label2annot --s MPS3007-1 --hemi rh --ctab /soft/freesurfer/5.1.0/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 --a BA --maxstatwinner --noverbose sysname Linux hostname node1118 machine x86_64 user kovacv subject MPS3007-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/post-analysis ColorTable /soft/freesurfer/5.1.0/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post-analysis/MPS3007-1/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 87356 unhit vertices Writing annot to /lustre/kovacv/FS/post-analysis/MPS3007-1/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab MPS3007-1 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /soft/freesurfer/5.1.0/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 462 277 1485 3.518 0.932 0.203 0.150 26 3.2 BA1 1779 1165 3702 2.721 0.823 0.165 0.118 50 8.0 BA2 566 364 1148 2.964 0.933 0.229 0.256 267 3.9 BA3a 1151 717 3402 3.428 0.956 0.196 0.169 66 8.7 BA3b 1413 876 3474 2.781 0.865 0.201 0.288 214 19.7 BA4a 787 521 1801 2.733 1.056 0.211 0.169 34 5.7 BA4p 9475 5975 26862 3.139 1.089 0.203 0.254 950 88.8 BA6 3461 2261 10482 3.332 0.985 0.154 0.086 76 12.9 BA44 3394 2186 10570 3.349 0.960 0.174 0.112 159 15.8 BA45 2167 1335 3711 2.353 0.668 0.270 0.321 529 31.8 V1 4491 2899 7494 2.329 0.963 0.225 0.180 232 32.2 V2 1548 908 3114 2.815 1.013 0.219 0.446 262 14.2 MT /lustre/kovacv/FS/post-analysis/MPS3007-1/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Thu May 29 06:40:43 CDT 2014 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS3007-1 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject MPS3007-1. processing subject lh.EC_average... reading output surface /lustre/kovacv/FS/post-analysis/MPS3007-1/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 846 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label MPS3007-1 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/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 324 188 1310 3.859 0.664 0.230 0.219 277 4.1 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Thu May 29 06:40:53 CDT 2014 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS3007-1 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject MPS3007-1. processing subject rh.EC_average... reading output surface /lustre/kovacv/FS/post-analysis/MPS3007-1/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 958 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label MPS3007-1 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/post-analysis/MPS3007-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post-analysis/MPS3007-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post-analysis/MPS3007-1/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 466 204 911 2.997 1.000 0.251 0.410 92 6.9 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s MPS3007-1 finished without error at Thu May 29 06:41:03 CDT 2014