Tue Dec 31 12:16:18 CST 2013 /lustre/kovacv/FS/post_analysis/MPS1036-1 /soft/freesurfer/5.3.0_1/bin/recon-all -all -subjid MPS1036-1 -bigventricles subjid MPS1036-1 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Actual FREESURFER_HOME /panfs/roc/itascasoft/freesurfer/5.3.0_1 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux node1108 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 2646956 63285288 0 14272 985400 -/+ buffers/cache: 1647284 64284960 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: 2013/12/31-18:16:18-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: $ TimeStamp: 2013/12/31-18:16:19-GMT BuildTimeStamp: Nov 16 2013 21:04:35 CVS: $Id: mri_ca_register.c,v 1.87 2013/11/14 16:15:12 fischl Exp $ User: kovacv Machine: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:19-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-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: node1108 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: 2013/12/31-18:16:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: kovacv Machine: node1108 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: 2013/12/31-18:16:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: kovacv Machine: node1108 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: 2013/12/31-18:16:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: kovacv Machine: node1108 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: 2013/12/31-18:16:21-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: node1108 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: 2013/12/31-18:16:21-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: node1108 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: 2013/12/31-18:16:21-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: node1108 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: 2013/12/31-18:16:21-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: node1108 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: 2013/12/31-18:16:21-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: node1108 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: 2013/12/31-18:16:21-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: node1108 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: 2013/12/31-18:16:21-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: node1108 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /soft/freesurfer/5.3.0_1/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_1/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Tue Dec 31 12:16:21 CST 2013 Found 1 runs /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig/001.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_convert /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/orig.mgz --conform mri_convert /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/rawavg.mgz... TR=2530.00, TE=3.65, TI=1100.00, flip angle=7.00 i_ras = (-0, -1, 0) j_ras = (-0.0975829, -0, -0.995227) k_ras = (-0.995227, -0, 0.0975829) Original Data has (1, 1, 1) mm size and (256, 256, 240) 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/post_analysis/MPS1036-1/mri/orig.mgz... mri_add_xform_to_header -c /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/transforms/talairach.xfm /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/orig.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Dec 31 12:16:36 CST 2013 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Tue Dec 31 12:18:40 CST 2013 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4781, pval=0.1531 >= threshold=0.0050) awk -f /soft/freesurfer/5.3.0_1/bin/extract_talairach_avi_QA.awk /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/transforms/talairach_avi.log tal_QC_AZS /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/transforms/talairach_avi.log TalAviQA: 0.93619 z-score: -9 #-------------------------------------------- #@# Nu Intensity Correction Tue Dec 31 12:18:40 CST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri /soft/freesurfer/5.3.0_1/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 node1108 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 Tue Dec 31 12:18:41 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.27671 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27671/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27671/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, 0, 2.23517e-08) j_ras = (-7.45058e-09, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.27671/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Dec 31 12:18:42 CST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.27671/nu0.mnc ./tmp.mri_nu_correct.mni.27671/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27671/0/ [kovacv@node1108:/lustre/kovacv/FS/post_analysis/MPS1036-1/mri/] [2013-12-31 12:18:42] running: /soft/freesurfer/5.3.0_1/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.27671/0/ ./tmp.mri_nu_correct.mni.27671/nu0.mnc ./tmp.mri_nu_correct.mni.27671/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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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00210118 [kovacv@node1108:/lustre/kovacv/FS/post_analysis/MPS1036-1/mri/] [2013-12-31 12:19:31] running: /soft/freesurfer/5.3.0_1/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.27671/nu0.mnc ./tmp.mri_nu_correct.mni.27671/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Tue Dec 31 12:19:41 CST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.27671/nu1.mnc ./tmp.mri_nu_correct.mni.27671/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27671/1/ [kovacv@node1108:/lustre/kovacv/FS/post_analysis/MPS1036-1/mri/] [2013-12-31 12:19:41] running: /soft/freesurfer/5.3.0_1/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.27671/1/ ./tmp.mri_nu_correct.mni.27671/nu1.mnc ./tmp.mri_nu_correct.mni.27671/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.27671/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27671/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /lustre/kovacv/FS/post_analysis/MPS1036-1/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.27671/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27671/ones.mgz sysname Linux hostname node1108 machine x86_64 user kovacv input ./tmp.mri_nu_correct.mni.27671/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27671/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.27671/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27671/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27671/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.27671/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27671/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27671/input.mean.dat sysname Linux hostname node1108 machine x86_64 user kovacv UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27671/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.27671/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27671/ones.mgz --i ./tmp.mri_nu_correct.mni.27671/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27671/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27671/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.27671/ones.mgz --i ./tmp.mri_nu_correct.mni.27671/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27671/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27671/output.mean.dat sysname Linux hostname node1108 machine x86_64 user kovacv UseRobust 0 Loading ./tmp.mri_nu_correct.mni.27671/ones.mgz Loading ./tmp.mri_nu_correct.mni.27671/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.27671/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.27671/nu2.mnc ./tmp.mri_nu_correct.mni.27671/nu2.mnc mul .95202984617911133716 Saving result to './tmp.mri_nu_correct.mni.27671/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27671/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.27671/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.27671/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 2.23517e-08) j_ras = (-7.45058e-09, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping (20, 140) to ( 3, 110) Tue Dec 31 12:20:50 CST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Dec 31 12:20:51 CST 2013 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.975 0.055 -0.135 3.206; -0.020 0.927 0.009 -53.922; 0.126 0.054 0.991 -31.390; 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 = 9 Starting OpenSpline(): npoints = 9 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 95 gm peak at 66 (66), valley at 8 (8) csf peak at 9, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 57 (57) csf peak at 18, setting threshold to 62 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 1 seconds. #-------------------------------------------- #@# Skull Stripping Tue Dec 31 12:22:52 CST 2013 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_em_register -skull nu.mgz /soft/freesurfer/5.3.0_1/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_1/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=7.0 skull bounding box = (48, 13, 42) --> (202, 255, 238) using (99, 94, 140) as brain centroid... mean wm in atlas = 126, using box (80,64,116) --> (117, 123,164) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 103, scaling input intensities by 1.223 scaling channel 0 by 1.2233 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.740718 @ (9.091, 27.273, -27.273) max log p = -4.709023 @ (-13.636, -4.545, -4.545) max log p = -4.680501 @ (6.818, 2.273, 2.273) max log p = -4.666212 @ (-1.136, 5.682, -1.136) max log p = -4.654366 @ (2.841, -0.568, -1.705) max log p = -4.654366 @ (0.000, 0.000, 0.000) Found translation: (4.0, 30.1, -32.4): log p = -4.654 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.6, old_max_log_p =-4.7 (thresh=-4.6) 0.966 -0.250 -0.067 40.149; 0.259 0.933 0.250 -29.916; 0.000 -0.239 0.893 4.144; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.890 -0.186 -0.164 57.064; 0.257 0.894 0.364 -41.924; 0.100 -0.418 0.900 7.365; 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=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.872 -0.190 -0.235 67.394; 0.277 0.884 0.321 -37.512; 0.166 -0.400 0.899 -0.312; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.857 -0.260 -0.228 72.971; 0.345 0.872 0.343 -47.698; 0.128 -0.422 0.895 6.899; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.857 -0.260 -0.228 72.971; 0.345 0.872 0.343 -47.698; 0.128 -0.422 0.895 6.899; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.847 -0.270 -0.240 76.725; 0.357 0.870 0.331 -47.509; 0.138 -0.417 0.897 4.979; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.847 -0.270 -0.240 76.725; 0.357 0.870 0.331 -47.509; 0.138 -0.417 0.897 4.979; 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 0.84672 -0.27005 -0.23981 76.72513; 0.35746 0.86975 0.33093 -47.50924; 0.13804 -0.41747 0.89682 4.97892; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.84672 -0.27005 -0.23981 76.72513; 0.35746 0.86975 0.33093 -47.50924; 0.13804 -0.41747 0.89682 4.97892; 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: 0.847 -0.270 -0.240 76.725; 0.357 0.870 0.331 -47.509; 0.138 -0.417 0.897 4.979; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.6 (old=-4.8) transform before final EM align: 0.847 -0.270 -0.240 76.725; 0.357 0.870 0.331 -47.509; 0.138 -0.417 0.897 4.979; 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 0.84672 -0.27005 -0.23981 76.72513; 0.35746 0.86975 0.33093 -47.50924; 0.13804 -0.41747 0.89682 4.97892; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.84672 -0.27005 -0.23981 76.72513; 0.35746 0.86975 0.33093 -47.50924; 0.13804 -0.41747 0.89682 4.97892; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.9 tol 0.000000 final transform: 0.847 -0.270 -0.240 76.725; 0.357 0.870 0.331 -47.509; 0.138 -0.417 0.897 4.979; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 23 minutes and 38 seconds. mri_watershed -T1 -brain_atlas /soft/freesurfer/5.3.0_1/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=88 z=139 r=96 first estimation of the main basin volume: 3790404 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=134, y=44, z=114, Imax=255 CSF=15, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=23815177358 voxels, voxel volume =1.000 = 23815177358 mmm3 = 23815178.240 cm3 done. PostAnalyze...Basin Prior 761 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=125,y=91, z=136, r=9954 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 41896 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = -1035613415 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1108685951 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1077980926 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1076754778 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=82 , nb = 1079026352 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 8, 58, 79 after analyzing : 4, 41, 58, 50 RIGHT_CER before analyzing : 5, 7, 41, 92 after analyzing : 5, 29, 41, 44 LEFT_CER before analyzing : 4, 7, 57, 88 after analyzing : 4, 40, 57, 52 RIGHT_BRAIN before analyzing : 4, 8, 58, 79 after analyzing : 4, 41, 58, 50 LEFT_BRAIN before analyzing : 4, 8, 57, 81 after analyzing : 4, 40, 57, 50 OTHER before analyzing : 82, 66, 65, 71 after analyzing : 37, 66, 66, 67 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.008 curvature mean = 78.684, std = 6.285 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 7.29, sigma = 11.80 after rotation: sse = 7.29, sigma = 11.80 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 8.81, its var is 12.44 before Erosion-Dilatation 7.75% of inacurate vertices after Erosion-Dilatation 11.51% 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...44 iterations mri_strip_skull: done peeling brain Brain Size = 2208476 voxels, voxel volume = 1.000 mm3 = 2208476 mmm3 = 2208.476 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Dec 31 12:46:51 CST 2013 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /soft/freesurfer/5.3.0_1/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_1/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=11.0 skull bounding box = (48, 26, 46) --> (201, 177, 234) using (99, 76, 140) as brain centroid... mean wm in atlas = 107, using box (80,57,117) --> (117, 94,163) to find MRI wm before smoothing, mri peak at 98 after smoothing, mri peak at 99, scaling input intensities by 1.081 scaling channel 0 by 1.08081 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.525606 @ (9.091, 27.273, -27.273) max log p = -4.449532 @ (-13.636, 4.545, -4.545) max log p = -4.449532 @ (0.000, 0.000, 0.000) max log p = -4.437634 @ (3.409, 1.136, 1.136) max log p = -4.430987 @ (-0.568, -0.568, -1.705) max log p = -4.425931 @ (-1.420, 0.284, -1.989) Found translation: (-3.1, 32.7, -34.4): log p = -4.426 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.4 (thresh=-4.4) 0.775 -0.196 -0.295 84.169; 0.141 1.041 -0.208 39.880; 0.323 0.076 0.785 -52.994; 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) 0.874 -0.179 -0.209 57.892; 0.090 0.945 -0.285 65.544; 0.235 0.235 0.784 -54.952; 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) 0.902 -0.028 -0.132 30.507; -0.012 0.934 -0.210 65.488; 0.108 0.188 0.790 -35.309; 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) 0.902 -0.028 -0.132 30.507; -0.012 0.934 -0.210 65.488; 0.108 0.188 0.790 -35.309; 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) 0.902 -0.022 -0.141 31.580; -0.019 0.933 -0.209 66.331; 0.116 0.187 0.788 -35.929; 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) 0.898 -0.024 -0.147 33.072; -0.019 0.932 -0.208 66.393; 0.123 0.187 0.788 -36.868; 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) 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 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) 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 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 0.89795 -0.02352 -0.14655 33.07225; -0.01947 0.93331 -0.20851 66.33132; 0.12342 0.18758 0.78973 -37.20156; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.89795 -0.02352 -0.14655 33.07225; -0.01947 0.93331 -0.20851 66.33132; 0.12342 0.18758 0.78973 -37.20156; 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: 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.8) transform before final EM align: 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 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 0.89795 -0.02352 -0.14655 33.07225; -0.01947 0.93331 -0.20851 66.33132; 0.12342 0.18758 0.78973 -37.20156; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.89795 -0.02352 -0.14655 33.07225; -0.01947 0.93331 -0.20851 66.33132; 0.12342 0.18758 0.78973 -37.20156; 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: 012: -log(p) = 643.8 tol 0.000000 final transform: 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 21 minutes and 10 seconds. #-------------------------------------- #@# CA Normalize Tue Dec 31 13:08:02 CST 2013 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /soft/freesurfer/5.3.0_1/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_1/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=11.0 skull bounding box = (48, 26, 46) --> (201, 177, 234) using (99, 76, 140) as brain centroid... mean wm in atlas = 107, using box (80,57,117) --> (117, 94,163) to find MRI wm before smoothing, mri peak at 98 after smoothing, mri peak at 99, scaling input intensities by 1.081 scaling channel 0 by 1.08081 using 244171 sample points... INFO: compute sample coordinates transform 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 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 (112, 17, 39) --> (199, 148, 242) Left_Cerebral_White_Matter: limiting intensities to 108.0 --> 229.0 0 of 1 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (55, 17, 47) --> (139, 150, 245) Right_Cerebral_White_Matter: limiting intensities to 142.0 --> 229.0 1 of 3 (33.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (121, 97, 57) --> (176, 146, 124) Left_Cerebellum_White_Matter: limiting intensities to 128.0 --> 229.0 6 of 9 (66.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (71, 97, 60) --> (124, 146, 129) Right_Cerebellum_White_Matter: limiting intensities to 117.0 --> 229.0 0 of 8 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 99, 93) --> (145, 167, 142) Brain_Stem: limiting intensities to 123.0 --> 229.0 9 of 10 (90.0%) samples deleted using 31 total control points for intensity normalization... bias field = 0.733 +- 0.071 0 of 15 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (112, 17, 39) --> (199, 148, 242) Left_Cerebral_White_Matter: limiting intensities to 112.0 --> 178.0 31 of 59 (52.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (55, 17, 47) --> (139, 150, 245) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 178.0 32 of 65 (49.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (121, 97, 57) --> (176, 146, 124) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 178.0 7 of 21 (33.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (71, 97, 60) --> (124, 146, 129) Right_Cerebellum_White_Matter: limiting intensities to 76.0 --> 178.0 0 of 36 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 99, 93) --> (145, 167, 142) Brain_Stem: limiting intensities to 76.0 --> 178.0 0 of 79 (0.0%) samples deleted using 260 total control points for intensity normalization... bias field = 0.982 +- 0.057 0 of 190 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (112, 17, 39) --> (199, 148, 242) Left_Cerebral_White_Matter: limiting intensities to 108.0 --> 169.0 74 of 84 (88.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (55, 17, 47) --> (139, 150, 245) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 169.0 73 of 108 (67.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (121, 97, 57) --> (176, 146, 124) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 169.0 12 of 35 (34.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (71, 97, 60) --> (124, 146, 129) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 169.0 0 of 54 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 99, 93) --> (145, 167, 142) Brain_Stem: limiting intensities to 74.0 --> 169.0 0 of 107 (0.0%) samples deleted using 388 total control points for intensity normalization... bias field = 1.012 +- 0.056 0 of 229 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 25 seconds. #-------------------------------------- #@# CA Reg Tue Dec 31 13:09:27 CST 2013 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_ca_register -bigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /soft/freesurfer/5.3.0_1/average/RB_all_2008-03-26.gca transforms/talairach.m3z 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_1/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.71 (predicted orig area = 11.2) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 registering ventricular system... rms increased (dt=3.2500) - undoing step... rms increased (dt=1.6500) - undoing step... rms increased (dt=0.8500) - undoing step... iter 0, gcam->neg = 1412 after 18 iterations, nbhd size=0, neg = 0 starting rms=0.02597, compressed=6188, removing compressions in lattice.... iter 1, O dt=0.122935: new compressed 6337, old_compressed 6188, delta -149, rms=0.02408 iter 2, O dt=0.094780: new compressed 6422, old_compressed 6337, delta -85, rms=0.02267 iter 3, O dt=0.092789: new compressed 6485, old_compressed 6422, delta -63, rms=0.02155 iter 4, O dt=0.084099: new compressed 6525, old_compressed 6485, delta -40, rms=0.02058 iter 5, O dt=0.080398: new compressed 6561, old_compressed 6525, delta -36, rms=0.01973 iter 6, O dt=0.079985: new compressed 6573, old_compressed 6561, delta -12, rms=0.01895 iter 7, O dt=0.074667: new compressed 6593, old_compressed 6573, delta -20, rms=0.01825 iter 8, O dt=0.072456: new compressed 6570, old_compressed 6593, delta 23, rms=0.01763 iter 9, O dt=0.071658: new compressed 6577, old_compressed 6570, delta -7, rms=0.01705 iter 10, O dt=0.068743: new compressed 6577, old_compressed 6577, delta 0, rms=0.01653 iter 11, O dt=0.068311: new compressed 6553, old_compressed 6577, delta 24, rms=0.01604 iter 12, O dt=0.064000: new compressed 6521, old_compressed 6553, delta 32, rms=0.01561 iter 13, O dt=0.063896: new compressed 6511, old_compressed 6521, delta 10, rms=0.01521 iter 14, O dt=0.063057: new compressed 6505, old_compressed 6511, delta 6, rms=0.01483 iter 15, O dt=0.061556: new compressed 6484, old_compressed 6505, delta 21, rms=0.01448 iter 16, O dt=0.060868: new compressed 6468, old_compressed 6484, delta 16, rms=0.01415 iter 17, O dt=0.059651: new compressed 6441, old_compressed 6468, delta 27, rms=0.01384 iter 18, O dt=0.058740: new compressed 6413, old_compressed 6441, delta 28, rms=0.01356 iter 19, O dt=0.056181: new compressed 6390, old_compressed 6413, delta 23, rms=0.01330 iter 20, O dt=0.056741: new compressed 6365, old_compressed 6390, delta 25, rms=0.01306 iter 21, O dt=0.054632: new compressed 6335, old_compressed 6365, delta 30, rms=0.01283 iter 22, O dt=0.053333: new compressed 6314, old_compressed 6335, delta 21, rms=0.01262 iter 23, O dt=0.053333: new compressed 6274, old_compressed 6314, delta 40, rms=0.01241 iter 24, O dt=0.052498: new compressed 6253, old_compressed 6274, delta 21, rms=0.01223 iter 25, O dt=0.051978: new compressed 6218, old_compressed 6253, delta 35, rms=0.01205 iter 26, O dt=0.052214: new compressed 6182, old_compressed 6218, delta 36, rms=0.01188 iter 27, O dt=0.051630: new compressed 6156, old_compressed 6182, delta 26, rms=0.01171 iter 28, O dt=0.050992: new compressed 6118, old_compressed 6156, delta 38, rms=0.01156 iter 29, O dt=0.050769: new compressed 6086, old_compressed 6118, delta 32, rms=0.01141 iter 30, O dt=0.050383: new compressed 6047, old_compressed 6086, delta 39, rms=0.01127 iter 31, O dt=0.049690: new compressed 6020, old_compressed 6047, delta 27, rms=0.01114 iter 32, O dt=0.049823: new compressed 5982, old_compressed 6020, delta 38, rms=0.01101 iter 33, O dt=0.048968: new compressed 5950, old_compressed 5982, delta 32, rms=0.01089 iter 34, O dt=0.049305: new compressed 5908, old_compressed 5950, delta 42, rms=0.01078 iter 35, O dt=0.048780: new compressed 5871, old_compressed 5908, delta 37, rms=0.01066 iter 36, O dt=0.048815: new compressed 5835, old_compressed 5871, delta 36, rms=0.01056 iter 37, O dt=0.048669: new compressed 5793, old_compressed 5835, delta 42, rms=0.01045 iter 38, O dt=0.048413: new compressed 5758, old_compressed 5793, delta 35, rms=0.01036 iter 39, O dt=0.048683: new compressed 5718, old_compressed 5758, delta 40, rms=0.01026 iter 40, O dt=0.048019: new compressed 5681, old_compressed 5718, delta 37, rms=0.01017 iter 41, O dt=0.048978: new compressed 5639, old_compressed 5681, delta 42, rms=0.01008 iter 42, O dt=0.047690: new compressed 5589, old_compressed 5639, delta 50, rms=0.00999 iter 43, O dt=0.049246: new compressed 5549, old_compressed 5589, delta 40, rms=0.00991 iter 44, O dt=0.047342: new compressed 5501, old_compressed 5549, delta 48, rms=0.00983 iter 45, O dt=0.049906: new compressed 5448, old_compressed 5501, delta 53, rms=0.00975 iter 46, O dt=0.047280: new compressed 5403, old_compressed 5448, delta 45, rms=0.00967 iter 47, O dt=0.050050: new compressed 5351, old_compressed 5403, delta 52, rms=0.00960 iter 48, O dt=0.047924: new compressed 5309, old_compressed 5351, delta 42, rms=0.00953 iter 49, O dt=0.049947: new compressed 5270, old_compressed 5309, delta 39, rms=0.00946 iter 50, O dt=0.048780: new compressed 5240, old_compressed 5270, delta 30, rms=0.00939 iter 51, O dt=0.049697: new compressed 5197, old_compressed 5240, delta 43, rms=0.00932 iter 52, O dt=0.050168: new compressed 5157, old_compressed 5197, delta 40, rms=0.00925 iter 53, O dt=0.049520: new compressed 5118, old_compressed 5157, delta 39, rms=0.00919 iter 54, O dt=0.051247: new compressed 5075, old_compressed 5118, delta 43, rms=0.00913 iter 55, O dt=0.050904: new compressed 5025, old_compressed 5075, delta 50, rms=0.00907 iter 56, O dt=0.050684: new compressed 4996, old_compressed 5025, delta 29, rms=0.00901 iter 57, O dt=0.051638: new compressed 4959, old_compressed 4996, delta 37, rms=0.00895 iter 58, O dt=0.051999: new compressed 4921, old_compressed 4959, delta 38, rms=0.00889 iter 59, O dt=0.051511: new compressed 4887, old_compressed 4921, delta 34, rms=0.00883 iter 60, O dt=0.053333: new compressed 4848, old_compressed 4887, delta 39, rms=0.00878 iter 61, O dt=0.052083: new compressed 4806, old_compressed 4848, delta 42, rms=0.00872 iter 62, O dt=0.053333: new compressed 4774, old_compressed 4806, delta 32, rms=0.00867 iter 63, O dt=0.053333: new compressed 4738, old_compressed 4774, delta 36, rms=0.00862 iter 64, O dt=0.053333: new compressed 4696, old_compressed 4738, delta 42, rms=0.00856 iter 65, O dt=0.053333: new compressed 4652, old_compressed 4696, delta 44, rms=0.00851 iter 66, O dt=0.057471: new compressed 4619, old_compressed 4652, delta 33, rms=0.00846 iter 67, O dt=0.053333: new compressed 4584, old_compressed 4619, delta 35, rms=0.00841 iter 68, O dt=0.053333: new compressed 4545, old_compressed 4584, delta 39, rms=0.00836 iter 69, O dt=0.061060: new compressed 4506, old_compressed 4545, delta 39, rms=0.00832 iter 70, O dt=0.053333: new compressed 4474, old_compressed 4506, delta 32, rms=0.00827 iter 71, O dt=0.064000: new compressed 4418, old_compressed 4474, delta 56, rms=0.00822 iter 72, O dt=0.053333: new compressed 4377, old_compressed 4418, delta 41, rms=0.00817 iter 73, O dt=0.064000: new compressed 4346, old_compressed 4377, delta 31, rms=0.00813 iter 74, O dt=0.057229: new compressed 4322, old_compressed 4346, delta 24, rms=0.00808 iter 75, O dt=0.053333: new compressed 4289, old_compressed 4322, delta 33, rms=0.00804 iter 76, O dt=0.064000: new compressed 4245, old_compressed 4289, delta 44, rms=0.00800 iter 77, O dt=0.062342: new compressed 4206, old_compressed 4245, delta 39, rms=0.00795 iter 78, O dt=0.061108: new compressed 4159, old_compressed 4206, delta 47, rms=0.00791 iter 79, O dt=0.064000: new compressed 4118, old_compressed 4159, delta 41, rms=0.00787 iter 80, O dt=0.060922: new compressed 4079, old_compressed 4118, delta 39, rms=0.00783 iter 81, O dt=0.064000: new compressed 4035, old_compressed 4079, delta 44, rms=0.00778 iter 82, O dt=0.064000: new compressed 3997, old_compressed 4035, delta 38, rms=0.00774 iter 83, O dt=0.064000: new compressed 3972, old_compressed 3997, delta 25, rms=0.00770 iter 84, O dt=0.064000: new compressed 3937, old_compressed 3972, delta 35, rms=0.00766 iter 85, O dt=0.064000: new compressed 3901, old_compressed 3937, delta 36, rms=0.00762 iter 86, O dt=0.064000: new compressed 3863, old_compressed 3901, delta 38, rms=0.00759 iter 87, O dt=0.074441: new compressed 3823, old_compressed 3863, delta 40, rms=0.00755 iter 88, O dt=0.064000: new compressed 3788, old_compressed 3823, delta 35, rms=0.00751 iter 89, O dt=0.074667: new compressed 3757, old_compressed 3788, delta 31, rms=0.00747 iter 90, O dt=0.064000: new compressed 3731, old_compressed 3757, delta 26, rms=0.00743 iter 91, O dt=0.074667: new compressed 3678, old_compressed 3731, delta 53, rms=0.00739 iter 92, O dt=0.064000: new compressed 3650, old_compressed 3678, delta 28, rms=0.00736 iter 93, O dt=0.074667: new compressed 3607, old_compressed 3650, delta 43, rms=0.00732 iter 94, O dt=0.074667: new compressed 3570, old_compressed 3607, delta 37, rms=0.00729 iter 95, O dt=0.072409: new compressed 3526, old_compressed 3570, delta 44, rms=0.00725 iter 96, O dt=0.074667: new compressed 3484, old_compressed 3526, delta 42, rms=0.00721 iter 97, O dt=0.074667: new compressed 3446, old_compressed 3484, delta 38, rms=0.00718 iter 98, O dt=0.074667: new compressed 3418, old_compressed 3446, delta 28, rms=0.00714 iter 99, O dt=0.074667: new compressed 3382, old_compressed 3418, delta 36, rms=0.00711 iter 100, O dt=0.074667: new compressed 3349, old_compressed 3382, delta 33, rms=0.00708 iter 101, O dt=0.074667: new compressed 3312, old_compressed 3349, delta 37, rms=0.00704 iter 102, O dt=0.085648: new compressed 3268, old_compressed 3312, delta 44, rms=0.00701 iter 103, O dt=0.074667: new compressed 3233, old_compressed 3268, delta 35, rms=0.00697 iter 104, O dt=0.074667: new compressed 3192, old_compressed 3233, delta 41, rms=0.00694 iter 105, O dt=0.074667: new compressed 3165, old_compressed 3192, delta 27, rms=0.00691 iter 106, O dt=0.074667: new compressed 3131, old_compressed 3165, delta 34, rms=0.00688 iter 107, O dt=0.074667: new compressed 3105, old_compressed 3131, delta 26, rms=0.00685 iter 108, O dt=0.074667: new compressed 3078, old_compressed 3105, delta 27, rms=0.00682 iter 109, O dt=0.128000: new compressed 3031, old_compressed 3078, delta 47, rms=0.00678 iter 110, O dt=0.074667: new compressed 2993, old_compressed 3031, delta 38, rms=0.00674 iter 111, O dt=0.113176: new compressed 2958, old_compressed 2993, delta 35, rms=0.00671 iter 112, O dt=0.074667: new compressed 2933, old_compressed 2958, delta 25, rms=0.00668 iter 113, O dt=0.081466: new compressed 2913, old_compressed 2933, delta 20, rms=0.00665 iter 114, O dt=0.102083: new compressed 2874, old_compressed 2913, delta 39, rms=0.00662 iter 115, O dt=0.074667: new compressed 2846, old_compressed 2874, delta 28, rms=0.00659 iter 116, O dt=0.125000: new compressed 2795, old_compressed 2846, delta 51, rms=0.00655 iter 117, O dt=0.089227: new compressed 2770, old_compressed 2795, delta 25, rms=0.00652 iter 118, O dt=0.074667: new compressed 2754, old_compressed 2770, delta 16, rms=0.00649 iter 119, O dt=0.082364: new compressed 2725, old_compressed 2754, delta 29, rms=0.00647 iter 120, O dt=0.196118: new compressed 2654, old_compressed 2725, delta 71, rms=0.00643 iter 121, O dt=0.074667: new compressed 2628, old_compressed 2654, delta 26, rms=0.00638 iter 122, O dt=0.256250: new compressed 2548, old_compressed 2628, delta 80, rms=0.00634 iter 123, O dt=0.082212: new compressed 2532, old_compressed 2548, delta 16, rms=0.00629 iter 124, O dt=0.137620: new compressed 2501, old_compressed 2532, delta 31, rms=0.00626 iter 125, O dt=0.081897: new compressed 2490, old_compressed 2501, delta 11, rms=0.00623 iter 126, O dt=0.206967: new compressed 2433, old_compressed 2490, delta 57, rms=0.00620 iter 127, O dt=0.074667: new compressed 2417, old_compressed 2433, delta 16, rms=0.00615 iter 128, O dt=0.216146: new compressed 2353, old_compressed 2417, delta 64, rms=0.00611 iter 129, O dt=0.074667: new compressed 2343, old_compressed 2353, delta 10, rms=0.00608 iter 130, O dt=0.148570: new compressed 2312, old_compressed 2343, delta 31, rms=0.00605 iter 131, O dt=0.151042: new compressed 2260, old_compressed 2312, delta 52, rms=0.00602 iter 132, O dt=0.087340: new compressed 2248, old_compressed 2260, delta 12, rms=0.00599 iter 133, O dt=0.130147: new compressed 2217, old_compressed 2248, delta 31, rms=0.00596 iter 134, O dt=0.150463: new compressed 2168, old_compressed 2217, delta 49, rms=0.00594 iter 135, O dt=0.074667: new compressed 2165, old_compressed 2168, delta 3, rms=0.00591 iter 136, O dt=0.416769: new compressed 2030, old_compressed 2165, delta 135, rms=0.00585 iter 137, O dt=0.088682: new compressed 2056, old_compressed 2030, delta -26, rms=0.00580 iter 138, O dt=0.170455: new compressed 2012, old_compressed 2056, delta 44, rms=0.00577 iter 139, O dt=0.097711: new compressed 1990, old_compressed 2012, delta 22, rms=0.00575 iter 140, O dt=0.162371: new compressed 1948, old_compressed 1990, delta 42, rms=0.00572 iter 141, O dt=0.090948: new compressed 1935, old_compressed 1948, delta 13, rms=0.00570 iter 142, O dt=0.465999: new compressed 1774, old_compressed 1935, delta 161, rms=0.00564 iter 143, O dt=0.099112: new compressed 1797, old_compressed 1774, delta -23, rms=0.00559 iter 144, O dt=0.187842: new compressed 1724, old_compressed 1797, delta 73, rms=0.00557 iter 145, O dt=0.074667: new compressed 1743, old_compressed 1724, delta -19, rms=0.00555 iter 146, O dt=2.871186: new compressed 933, old_compressed 1743, delta 810, rms=0.00525 iter 147, O dt=0.154492: new compressed 914, old_compressed 933, delta 19, rms=0.00510 iter 148, O dt=0.148043: new compressed 931, old_compressed 914, delta -17, rms=0.00506 iter 149, O dt=0.232464: new compressed 889, old_compressed 931, delta 42, rms=0.00504 iter 150, O dt=0.165461: new compressed 866, old_compressed 889, delta 23, rms=0.00501 starting rms=0.00501, compressed=860, removing compressions in lattice.... iter 1, O dt=0.216692: new compressed 800, old_compressed 860, delta 60, rms=0.00499 iter 2, O dt=0.167500: new compressed 785, old_compressed 800, delta 15, rms=0.00497 iter 3, O dt=0.217125: new compressed 723, old_compressed 785, delta 62, rms=0.00495 iter 4, O dt=0.180459: new compressed 697, old_compressed 723, delta 26, rms=0.00493 iter 5, O dt=0.186191: new compressed 663, old_compressed 697, delta 34, rms=0.00491 iter 6, O dt=0.225847: new compressed 612, old_compressed 663, delta 51, rms=0.00489 iter 7, O dt=0.170968: new compressed 591, old_compressed 612, delta 21, rms=0.00486 iter 8, O dt=0.242029: new compressed 524, old_compressed 591, delta 67, rms=0.00484 iter 9, O dt=0.095559: new compressed 566, old_compressed 524, delta -42, rms=0.00483 iter 10, O dt=8.069185: new compressed 208, old_compressed 566, delta 358, rms=0.00433 iter 11, O dt=0.203603: new compressed 80, old_compressed 208, delta 128, rms=0.00415 iter 12, O dt=0.192786: new compressed 20, old_compressed 80, delta 60, rms=0.00412 iter 13, O dt=0.400656: new compressed 27, old_compressed 20, delta -7, rms=0.00410 iter 14, O dt=0.213333: new compressed 12, old_compressed 27, delta 15, rms=0.00408 iter 15, O dt=0.437118: new compressed 21, old_compressed 12, delta -9, rms=0.00407 iter 16, O dt=0.213333: new compressed 7, old_compressed 21, delta 14, rms=0.00405 iter 17, O dt=0.487952: new compressed 17, old_compressed 7, delta -10, rms=0.00403 iter 18, O dt=0.256000: new compressed 12, old_compressed 17, delta 5, rms=0.00402 iter 19, O dt=0.381260: new compressed 18, old_compressed 12, delta -6, rms=0.00400 iter 20, O dt=0.272638: new compressed 12, old_compressed 18, delta 6, rms=0.00399 iter 21, O dt=0.408297: new compressed 17, old_compressed 12, delta -5, rms=0.00397 iter 22, O dt=0.299788: new compressed 11, old_compressed 17, delta 6, rms=0.00395 iter 23, O dt=0.380556: new compressed 14, old_compressed 11, delta -3, rms=0.00394 iter 24, O dt=0.315025: new compressed 4, old_compressed 14, delta 10, rms=0.00392 iter 25, O dt=0.495238: new compressed 22, old_compressed 4, delta -18, rms=0.00391 iter 26, O dt=0.255263: new compressed 0, old_compressed 22, delta 22, rms=0.00389 rms increased (dt=0.4500) - undoing step... starting rms=0.00545, compressed=859, removing compressions in lattice.... iter 1, O dt=0.243131: new compressed 737, old_compressed 859, delta 122, rms=0.00468 iter 2, O dt=0.120161: new compressed 627, old_compressed 737, delta 110, rms=0.00433 iter 3, O dt=0.080988: new compressed 563, old_compressed 627, delta 64, rms=0.00424 iter 4, O dt=0.094562: new compressed 498, old_compressed 563, delta 65, rms=0.00417 iter 5, O dt=0.074667: new compressed 465, old_compressed 498, delta 33, rms=0.00411 iter 6, O dt=0.090625: new compressed 403, old_compressed 465, delta 62, rms=0.00407 iter 7, O dt=0.064000: new compressed 389, old_compressed 403, delta 14, rms=0.00403 iter 8, O dt=0.139101: new compressed 318, old_compressed 389, delta 71, rms=0.00399 iter 9, O dt=0.074667: new compressed 307, old_compressed 318, delta 11, rms=0.00394 iter 10, O dt=0.074667: new compressed 282, old_compressed 307, delta 25, rms=0.00392 iter 11, O dt=0.074667: new compressed 268, old_compressed 282, delta 14, rms=0.00390 iter 12, O dt=0.074667: new compressed 240, old_compressed 268, delta 28, rms=0.00388 iter 13, O dt=0.074667: new compressed 224, old_compressed 240, delta 16, rms=0.00386 iter 14, O dt=0.074667: new compressed 215, old_compressed 224, delta 9, rms=0.00384 iter 15, O dt=0.074667: new compressed 201, old_compressed 215, delta 14, rms=0.00382 iter 16, O dt=0.074667: new compressed 186, old_compressed 201, delta 15, rms=0.00381 iter 17, O dt=0.074667: new compressed 172, old_compressed 186, delta 14, rms=0.00379 iter 18, O dt=0.152669: new compressed 132, old_compressed 172, delta 40, rms=0.00377 iter 19, O dt=0.113870: new compressed 115, old_compressed 132, delta 17, rms=0.00375 iter 20, O dt=0.074667: new compressed 121, old_compressed 115, delta -6, rms=0.00373 iter 21, O dt=0.074667: new compressed 112, old_compressed 121, delta 9, rms=0.00372 iter 22, O dt=0.256000: new compressed 67, old_compressed 112, delta 45, rms=0.00370 iter 23, O dt=0.130307: new compressed 57, old_compressed 67, delta 10, rms=0.00368 iter 24, O dt=0.074667: new compressed 66, old_compressed 57, delta -9, rms=0.00366 iter 25, O dt=0.304952: new compressed 44, old_compressed 66, delta 22, rms=0.00364 iter 26, O dt=0.144737: new compressed 46, old_compressed 44, delta -2, rms=0.00362 iter 27, O dt=0.074667: new compressed 40, old_compressed 46, delta 6, rms=0.00360 iter 28, O dt=0.782118: new compressed 19, old_compressed 40, delta 21, rms=0.00356 iter 29, O dt=0.169265: new compressed 23, old_compressed 19, delta -4, rms=0.00353 iter 30, O dt=0.170667: new compressed 28, old_compressed 23, delta -5, rms=0.00351 iter 31, O dt=0.170667: new compressed 17, old_compressed 28, delta 11, rms=0.00350 iter 32, O dt=0.197938: new compressed 25, old_compressed 17, delta -8, rms=0.00349 iter 33, O dt=0.206880: new compressed 19, old_compressed 25, delta 6, rms=0.00348 iter 34, O dt=0.191540: new compressed 15, old_compressed 19, delta 4, rms=0.00346 iter 35, O dt=0.238095: new compressed 19, old_compressed 15, delta -4, rms=0.00345 iter 36, O dt=0.205798: new compressed 13, old_compressed 19, delta 6, rms=0.00344 iter 37, O dt=0.235127: new compressed 12, old_compressed 13, delta 1, rms=0.00343 iter 38, O dt=0.238462: new compressed 10, old_compressed 12, delta 2, rms=0.00341 iter 39, O dt=0.256637: new compressed 11, old_compressed 10, delta -1, rms=0.00340 iter 40, O dt=0.260511: new compressed 10, old_compressed 11, delta 1, rms=0.00339 iter 41, O dt=0.251553: new compressed 4, old_compressed 10, delta 6, rms=0.00338 iter 42, O dt=0.325124: new compressed 11, old_compressed 4, delta -7, rms=0.00337 iter 43, O dt=0.235808: new compressed 0, old_compressed 11, delta 11, rms=0.00335 starting rms=0.00336, compressed=1, removing compressions in lattice.... iter 1, O dt=0.340686: new compressed 12, old_compressed 1, delta -11, rms=0.00335 iter 2, O dt=0.228033: new compressed 0, old_compressed 12, delta 12, rms=0.00334 rms increased (dt=0.2500) - undoing step... iter 0, gcam->neg = 633 after 11 iterations, nbhd size=0, neg = 0 starting rms=0.00893, compressed=1091, removing compressions in lattice.... iter 1, O dt=0.128000: new compressed 1073, old_compressed 1091, delta 18, rms=0.00723 iter 2, O dt=0.100898: new compressed 1054, old_compressed 1073, delta 19, rms=0.00638 iter 3, O dt=0.087511: new compressed 1063, old_compressed 1054, delta -9, rms=0.00584 iter 4, O dt=0.079861: new compressed 1060, old_compressed 1063, delta 3, rms=0.00547 iter 5, O dt=0.074764: new compressed 1050, old_compressed 1060, delta 10, rms=0.00518 iter 6, O dt=0.072299: new compressed 1047, old_compressed 1050, delta 3, rms=0.00496 iter 7, O dt=0.058303: new compressed 1040, old_compressed 1047, delta 7, rms=0.00480 iter 8, O dt=0.061636: new compressed 1028, old_compressed 1040, delta 12, rms=0.00467 iter 9, O dt=0.052289: new compressed 1013, old_compressed 1028, delta 15, rms=0.00457 iter 10, O dt=0.050703: new compressed 1013, old_compressed 1013, delta 0, rms=0.00449 iter 11, O dt=0.048307: new compressed 1005, old_compressed 1013, delta 8, rms=0.00442 iter 12, O dt=0.042667: new compressed 997, old_compressed 1005, delta 8, rms=0.00436 iter 13, O dt=0.055697: new compressed 991, old_compressed 997, delta 6, rms=0.00431 iter 14, O dt=0.041536: new compressed 980, old_compressed 991, delta 11, rms=0.00426 iter 15, O dt=0.053333: new compressed 968, old_compressed 980, delta 12, rms=0.00421 iter 16, O dt=0.042477: new compressed 954, old_compressed 968, delta 14, rms=0.00417 iter 17, O dt=0.053333: new compressed 945, old_compressed 954, delta 9, rms=0.00413 iter 18, O dt=0.042667: new compressed 937, old_compressed 945, delta 8, rms=0.00410 iter 19, O dt=0.053333: new compressed 925, old_compressed 937, delta 12, rms=0.00407 iter 20, O dt=0.048271: new compressed 904, old_compressed 925, delta 21, rms=0.00403 iter 21, O dt=0.051945: new compressed 886, old_compressed 904, delta 18, rms=0.00401 iter 22, O dt=0.050316: new compressed 865, old_compressed 886, delta 21, rms=0.00398 iter 23, O dt=0.053333: new compressed 853, old_compressed 865, delta 12, rms=0.00395 iter 24, O dt=0.053333: new compressed 839, old_compressed 853, delta 14, rms=0.00393 iter 25, O dt=0.053030: new compressed 824, old_compressed 839, delta 15, rms=0.00390 iter 26, O dt=0.053333: new compressed 808, old_compressed 824, delta 16, rms=0.00388 iter 27, O dt=0.053333: new compressed 803, old_compressed 808, delta 5, rms=0.00386 iter 28, O dt=0.053333: new compressed 783, old_compressed 803, delta 20, rms=0.00384 iter 29, O dt=0.064000: new compressed 761, old_compressed 783, delta 22, rms=0.00382 iter 30, O dt=0.053333: new compressed 745, old_compressed 761, delta 16, rms=0.00380 iter 31, O dt=0.064000: new compressed 734, old_compressed 745, delta 11, rms=0.00378 iter 32, O dt=0.053333: new compressed 718, old_compressed 734, delta 16, rms=0.00376 iter 33, O dt=0.074667: new compressed 689, old_compressed 718, delta 29, rms=0.00374 iter 34, O dt=0.064000: new compressed 673, old_compressed 689, delta 16, rms=0.00372 iter 35, O dt=0.064000: new compressed 663, old_compressed 673, delta 10, rms=0.00371 iter 36, O dt=0.064000: new compressed 649, old_compressed 663, delta 14, rms=0.00369 iter 37, O dt=0.064000: new compressed 624, old_compressed 649, delta 25, rms=0.00367 iter 38, O dt=0.074667: new compressed 606, old_compressed 624, delta 18, rms=0.00366 iter 39, O dt=0.064000: new compressed 578, old_compressed 606, delta 28, rms=0.00364 iter 40, O dt=0.074667: new compressed 567, old_compressed 578, delta 11, rms=0.00363 iter 41, O dt=0.074667: new compressed 535, old_compressed 567, delta 32, rms=0.00361 iter 42, O dt=0.074667: new compressed 520, old_compressed 535, delta 15, rms=0.00360 iter 43, O dt=0.074667: new compressed 499, old_compressed 520, delta 21, rms=0.00358 iter 44, O dt=0.074667: new compressed 488, old_compressed 499, delta 11, rms=0.00357 iter 45, O dt=0.074667: new compressed 478, old_compressed 488, delta 10, rms=0.00356 iter 46, O dt=0.074667: new compressed 474, old_compressed 478, delta 4, rms=0.00354 iter 47, O dt=0.077933: new compressed 451, old_compressed 474, delta 23, rms=0.00353 iter 48, O dt=0.172596: new compressed 387, old_compressed 451, delta 64, rms=0.00352 iter 49, O dt=0.074667: new compressed 371, old_compressed 387, delta 16, rms=0.00350 iter 50, O dt=0.117063: new compressed 333, old_compressed 371, delta 38, rms=0.00348 iter 51, O dt=0.074701: new compressed 325, old_compressed 333, delta 8, rms=0.00347 iter 52, O dt=0.116898: new compressed 295, old_compressed 325, delta 30, rms=0.00346 iter 53, O dt=0.074667: new compressed 288, old_compressed 295, delta 7, rms=0.00345 iter 54, O dt=0.104371: new compressed 253, old_compressed 288, delta 35, rms=0.00344 iter 55, O dt=0.146429: new compressed 226, old_compressed 253, delta 27, rms=0.00342 iter 56, O dt=0.074667: new compressed 207, old_compressed 226, delta 19, rms=0.00341 iter 57, O dt=0.273438: new compressed 156, old_compressed 207, delta 51, rms=0.00340 iter 58, O dt=0.074667: new compressed 157, old_compressed 156, delta -1, rms=0.00338 iter 59, O dt=0.216418: new compressed 118, old_compressed 157, delta 39, rms=0.00336 iter 60, O dt=0.102022: new compressed 108, old_compressed 118, delta 10, rms=0.00335 iter 61, O dt=0.182181: new compressed 92, old_compressed 108, delta 16, rms=0.00334 iter 62, O dt=0.083333: new compressed 74, old_compressed 92, delta 18, rms=0.00333 iter 63, O dt=0.238426: new compressed 72, old_compressed 74, delta 2, rms=0.00331 iter 64, O dt=0.074667: new compressed 36, old_compressed 72, delta 36, rms=0.00330 iter 65, O dt=0.768000: new compressed 56, old_compressed 36, delta -20, rms=0.00327 iter 66, O dt=0.108728: new compressed 33, old_compressed 56, delta 23, rms=0.00324 iter 67, O dt=0.127532: new compressed 17, old_compressed 33, delta 16, rms=0.00323 iter 68, O dt=0.334677: new compressed 50, old_compressed 17, delta -33, rms=0.00322 iter 69, O dt=0.074667: new compressed 0, old_compressed 50, delta 50, rms=0.00321 iter 0, gcam->neg = 549 after 10 iterations, nbhd size=0, neg = 0 starting rms=0.00983, compressed=1647, removing compressions in lattice.... iter 1, O dt=0.174620: new compressed 1704, old_compressed 1647, delta -57, rms=0.00736 iter 2, O dt=0.097547: new compressed 1710, old_compressed 1704, delta -6, rms=0.00650 iter 3, O dt=0.078026: new compressed 1721, old_compressed 1710, delta -11, rms=0.00606 iter 4, O dt=0.073547: new compressed 1716, old_compressed 1721, delta 5, rms=0.00574 iter 5, O dt=0.065255: new compressed 1701, old_compressed 1716, delta 15, rms=0.00550 iter 6, O dt=0.055779: new compressed 1709, old_compressed 1701, delta -8, rms=0.00534 iter 7, O dt=0.058245: new compressed 1702, old_compressed 1709, delta 7, rms=0.00519 iter 8, O dt=0.052128: new compressed 1683, old_compressed 1702, delta 19, rms=0.00508 iter 9, O dt=0.052092: new compressed 1669, old_compressed 1683, delta 14, rms=0.00498 iter 10, O dt=0.050507: new compressed 1642, old_compressed 1669, delta 27, rms=0.00490 iter 11, O dt=0.048529: new compressed 1618, old_compressed 1642, delta 24, rms=0.00482 iter 12, O dt=0.048910: new compressed 1592, old_compressed 1618, delta 26, rms=0.00476 iter 13, O dt=0.045516: new compressed 1571, old_compressed 1592, delta 21, rms=0.00470 iter 14, O dt=0.049217: new compressed 1541, old_compressed 1571, delta 30, rms=0.00465 iter 15, O dt=0.042667: new compressed 1519, old_compressed 1541, delta 22, rms=0.00460 iter 16, O dt=0.053333: new compressed 1481, old_compressed 1519, delta 38, rms=0.00455 iter 17, O dt=0.042667: new compressed 1463, old_compressed 1481, delta 18, rms=0.00451 iter 18, O dt=0.053333: new compressed 1436, old_compressed 1463, delta 27, rms=0.00447 iter 19, O dt=0.045757: new compressed 1421, old_compressed 1436, delta 15, rms=0.00443 iter 20, O dt=0.051479: new compressed 1385, old_compressed 1421, delta 36, rms=0.00440 iter 21, O dt=0.049494: new compressed 1359, old_compressed 1385, delta 26, rms=0.00436 iter 22, O dt=0.048758: new compressed 1336, old_compressed 1359, delta 23, rms=0.00433 iter 23, O dt=0.053327: new compressed 1304, old_compressed 1336, delta 32, rms=0.00430 iter 24, O dt=0.049858: new compressed 1276, old_compressed 1304, delta 28, rms=0.00427 iter 25, O dt=0.053333: new compressed 1259, old_compressed 1276, delta 17, rms=0.00424 iter 26, O dt=0.053333: new compressed 1232, old_compressed 1259, delta 27, rms=0.00421 iter 27, O dt=0.052204: new compressed 1200, old_compressed 1232, delta 32, rms=0.00418 iter 28, O dt=0.056027: new compressed 1168, old_compressed 1200, delta 32, rms=0.00416 iter 29, O dt=0.053333: new compressed 1139, old_compressed 1168, delta 29, rms=0.00413 iter 30, O dt=0.053333: new compressed 1116, old_compressed 1139, delta 23, rms=0.00411 iter 31, O dt=0.064000: new compressed 1073, old_compressed 1116, delta 43, rms=0.00408 iter 32, O dt=0.053333: new compressed 1056, old_compressed 1073, delta 17, rms=0.00406 iter 33, O dt=0.064000: new compressed 1022, old_compressed 1056, delta 34, rms=0.00404 iter 34, O dt=0.064000: new compressed 988, old_compressed 1022, delta 34, rms=0.00401 iter 35, O dt=0.053333: new compressed 967, old_compressed 988, delta 21, rms=0.00399 iter 36, O dt=0.074667: new compressed 935, old_compressed 967, delta 32, rms=0.00397 iter 37, O dt=0.064000: new compressed 902, old_compressed 935, delta 33, rms=0.00395 iter 38, O dt=0.064000: new compressed 889, old_compressed 902, delta 13, rms=0.00393 iter 39, O dt=0.064000: new compressed 843, old_compressed 889, delta 46, rms=0.00391 iter 40, O dt=0.074667: new compressed 812, old_compressed 843, delta 31, rms=0.00389 iter 41, O dt=0.064000: new compressed 790, old_compressed 812, delta 22, rms=0.00387 iter 42, O dt=0.074667: new compressed 755, old_compressed 790, delta 35, rms=0.00385 iter 43, O dt=0.074667: new compressed 729, old_compressed 755, delta 26, rms=0.00383 iter 44, O dt=0.074667: new compressed 694, old_compressed 729, delta 35, rms=0.00381 iter 45, O dt=0.074667: new compressed 668, old_compressed 694, delta 26, rms=0.00380 iter 46, O dt=0.074667: new compressed 631, old_compressed 668, delta 37, rms=0.00378 iter 47, O dt=0.074667: new compressed 621, old_compressed 631, delta 10, rms=0.00376 iter 48, O dt=0.074667: new compressed 596, old_compressed 621, delta 25, rms=0.00375 iter 49, O dt=0.074667: new compressed 586, old_compressed 596, delta 10, rms=0.00373 iter 50, O dt=0.074667: new compressed 558, old_compressed 586, delta 28, rms=0.00371 iter 51, O dt=0.165328: new compressed 505, old_compressed 558, delta 53, rms=0.00369 iter 52, O dt=0.074667: new compressed 501, old_compressed 505, delta 4, rms=0.00367 iter 53, O dt=0.103709: new compressed 460, old_compressed 501, delta 41, rms=0.00365 iter 54, O dt=0.081069: new compressed 446, old_compressed 460, delta 14, rms=0.00364 iter 55, O dt=0.122359: new compressed 404, old_compressed 446, delta 42, rms=0.00362 iter 56, O dt=0.074667: new compressed 394, old_compressed 404, delta 10, rms=0.00361 iter 57, O dt=0.113475: new compressed 362, old_compressed 394, delta 32, rms=0.00359 iter 58, O dt=0.074667: new compressed 354, old_compressed 362, delta 8, rms=0.00358 iter 59, O dt=0.156627: new compressed 317, old_compressed 354, delta 37, rms=0.00356 iter 60, O dt=0.074667: new compressed 306, old_compressed 317, delta 11, rms=0.00355 iter 61, O dt=0.190476: new compressed 257, old_compressed 306, delta 49, rms=0.00353 iter 62, O dt=0.074667: new compressed 245, old_compressed 257, delta 12, rms=0.00351 iter 63, O dt=0.154265: new compressed 205, old_compressed 245, delta 40, rms=0.00350 iter 64, O dt=0.107253: new compressed 184, old_compressed 205, delta 21, rms=0.00348 iter 65, O dt=0.074667: new compressed 166, old_compressed 184, delta 18, rms=0.00347 iter 66, O dt=0.436298: new compressed 105, old_compressed 166, delta 61, rms=0.00344 iter 67, O dt=0.074667: new compressed 76, old_compressed 105, delta 29, rms=0.00342 iter 68, O dt=0.431897: new compressed 94, old_compressed 76, delta -18, rms=0.00339 iter 69, O dt=0.074667: new compressed 14, old_compressed 94, delta 80, rms=0.00337 iter 70, O dt=0.494361: new compressed 57, old_compressed 14, delta -43, rms=0.00334 iter 71, O dt=0.148649: new compressed 48, old_compressed 57, delta 9, rms=0.00332 iter 72, O dt=0.074667: new compressed 3, old_compressed 48, delta 45, rms=0.00331 iter 73, O dt=0.863542: new compressed 29, old_compressed 3, delta -26, rms=0.00325 iter 74, O dt=0.128000: new compressed 10, old_compressed 29, delta 19, rms=0.00324 iter 75, O dt=0.223724: new compressed 23, old_compressed 10, delta -13, rms=0.00323 iter 76, O dt=0.074667: new compressed 0, old_compressed 23, delta 23, rms=0.00322 starting rms=0.00786, compressed=1639, removing compressions in lattice.... iter 1, O dt=0.269078: new compressed 1677, old_compressed 1639, delta -38, rms=0.00669 iter 2, O dt=0.100161: new compressed 1760, old_compressed 1677, delta -83, rms=0.00584 iter 3, O dt=0.059868: new compressed 1766, old_compressed 1760, delta -6, rms=0.00561 iter 4, O dt=0.045372: new compressed 1754, old_compressed 1766, delta 12, rms=0.00549 iter 5, O dt=0.039944: new compressed 1740, old_compressed 1754, delta 14, rms=0.00540 iter 6, O dt=0.037974: new compressed 1726, old_compressed 1740, delta 14, rms=0.00532 iter 7, O dt=0.039854: new compressed 1718, old_compressed 1726, delta 8, rms=0.00525 iter 8, O dt=0.036301: new compressed 1709, old_compressed 1718, delta 9, rms=0.00518 iter 9, O dt=0.038041: new compressed 1695, old_compressed 1709, delta 14, rms=0.00512 iter 10, O dt=0.035548: new compressed 1682, old_compressed 1695, delta 13, rms=0.00507 iter 11, O dt=0.039663: new compressed 1673, old_compressed 1682, delta 9, rms=0.00503 iter 12, O dt=0.032683: new compressed 1663, old_compressed 1673, delta 10, rms=0.00497 iter 13, O dt=0.037749: new compressed 1657, old_compressed 1663, delta 6, rms=0.00493 iter 14, O dt=0.033088: new compressed 1639, old_compressed 1657, delta 18, rms=0.00489 iter 15, O dt=0.033741: new compressed 1622, old_compressed 1639, delta 17, rms=0.00486 iter 16, O dt=0.034162: new compressed 1609, old_compressed 1622, delta 13, rms=0.00482 iter 17, O dt=0.033173: new compressed 1597, old_compressed 1609, delta 12, rms=0.00479 iter 18, O dt=0.035513: new compressed 1579, old_compressed 1597, delta 18, rms=0.00476 iter 19, O dt=0.018667: new compressed 1576, old_compressed 1579, delta 3, rms=0.00473 iter 20, O dt=0.326531: new compressed 1433, old_compressed 1576, delta 143, rms=0.00460 iter 21, O dt=0.057392: new compressed 1422, old_compressed 1433, delta 11, rms=0.00450 iter 22, O dt=0.049438: new compressed 1391, old_compressed 1422, delta 31, rms=0.00444 iter 23, O dt=0.040575: new compressed 1383, old_compressed 1391, delta 8, rms=0.00441 iter 24, O dt=0.052703: new compressed 1375, old_compressed 1383, delta 8, rms=0.00438 iter 25, O dt=0.038775: new compressed 1358, old_compressed 1375, delta 17, rms=0.00436 iter 26, O dt=0.042667: new compressed 1347, old_compressed 1358, delta 11, rms=0.00434 iter 27, O dt=0.042614: new compressed 1321, old_compressed 1347, delta 26, rms=0.00432 iter 28, O dt=0.042667: new compressed 1305, old_compressed 1321, delta 16, rms=0.00430 iter 29, O dt=0.042667: new compressed 1280, old_compressed 1305, delta 25, rms=0.00428 iter 30, O dt=0.042667: new compressed 1251, old_compressed 1280, delta 29, rms=0.00426 iter 31, O dt=0.042667: new compressed 1234, old_compressed 1251, delta 17, rms=0.00425 iter 32, O dt=0.042667: new compressed 1216, old_compressed 1234, delta 18, rms=0.00423 iter 33, O dt=0.042667: new compressed 1201, old_compressed 1216, delta 15, rms=0.00421 iter 34, O dt=0.053333: new compressed 1167, old_compressed 1201, delta 34, rms=0.00420 iter 35, O dt=0.042667: new compressed 1151, old_compressed 1167, delta 16, rms=0.00418 iter 36, O dt=0.053333: new compressed 1132, old_compressed 1151, delta 19, rms=0.00416 iter 37, O dt=0.042667: new compressed 1118, old_compressed 1132, delta 14, rms=0.00415 iter 38, O dt=0.053333: new compressed 1104, old_compressed 1118, delta 14, rms=0.00413 iter 39, O dt=0.042667: new compressed 1095, old_compressed 1104, delta 9, rms=0.00411 iter 40, O dt=0.064000: new compressed 1059, old_compressed 1095, delta 36, rms=0.00410 iter 41, O dt=0.042667: new compressed 1052, old_compressed 1059, delta 7, rms=0.00408 iter 42, O dt=0.072199: new compressed 1018, old_compressed 1052, delta 34, rms=0.00406 iter 43, O dt=0.042667: new compressed 1008, old_compressed 1018, delta 10, rms=0.00405 iter 44, O dt=0.083726: new compressed 954, old_compressed 1008, delta 54, rms=0.00403 iter 45, O dt=0.042667: new compressed 958, old_compressed 954, delta -4, rms=0.00401 iter 46, O dt=0.106078: new compressed 898, old_compressed 958, delta 60, rms=0.00399 iter 47, O dt=0.042667: new compressed 905, old_compressed 898, delta -7, rms=0.00397 iter 48, O dt=0.085579: new compressed 873, old_compressed 905, delta 32, rms=0.00396 iter 49, O dt=0.053333: new compressed 869, old_compressed 873, delta 4, rms=0.00394 iter 50, O dt=0.064000: new compressed 844, old_compressed 869, delta 25, rms=0.00393 iter 51, O dt=0.053333: new compressed 825, old_compressed 844, delta 19, rms=0.00391 iter 52, O dt=0.074667: new compressed 796, old_compressed 825, delta 29, rms=0.00390 iter 53, O dt=0.053333: new compressed 790, old_compressed 796, delta 6, rms=0.00389 iter 54, O dt=0.092160: new compressed 750, old_compressed 790, delta 40, rms=0.00387 iter 55, O dt=0.053333: new compressed 748, old_compressed 750, delta 2, rms=0.00386 iter 56, O dt=0.090517: new compressed 709, old_compressed 748, delta 39, rms=0.00384 iter 57, O dt=0.053333: new compressed 699, old_compressed 709, delta 10, rms=0.00383 iter 58, O dt=0.088684: new compressed 667, old_compressed 699, delta 32, rms=0.00381 iter 59, O dt=0.064000: new compressed 658, old_compressed 667, delta 9, rms=0.00380 iter 60, O dt=0.074667: new compressed 635, old_compressed 658, delta 23, rms=0.00379 iter 61, O dt=0.064000: new compressed 621, old_compressed 635, delta 14, rms=0.00377 iter 62, O dt=0.074667: new compressed 604, old_compressed 621, delta 17, rms=0.00376 iter 63, O dt=0.074667: new compressed 587, old_compressed 604, delta 17, rms=0.00375 iter 64, O dt=0.074667: new compressed 562, old_compressed 587, delta 25, rms=0.00374 iter 65, O dt=0.074667: new compressed 553, old_compressed 562, delta 9, rms=0.00372 iter 66, O dt=0.082021: new compressed 533, old_compressed 553, delta 20, rms=0.00371 iter 67, O dt=0.074667: new compressed 513, old_compressed 533, delta 20, rms=0.00370 iter 68, O dt=0.101151: new compressed 486, old_compressed 513, delta 27, rms=0.00369 iter 69, O dt=0.074667: new compressed 462, old_compressed 486, delta 24, rms=0.00367 iter 70, O dt=0.079673: new compressed 451, old_compressed 462, delta 11, rms=0.00366 iter 71, O dt=0.080454: new compressed 427, old_compressed 451, delta 24, rms=0.00365 iter 72, O dt=0.099270: new compressed 412, old_compressed 427, delta 15, rms=0.00364 iter 73, O dt=0.076415: new compressed 390, old_compressed 412, delta 22, rms=0.00363 iter 74, O dt=0.108263: new compressed 370, old_compressed 390, delta 20, rms=0.00362 iter 75, O dt=0.091875: new compressed 352, old_compressed 370, delta 18, rms=0.00360 iter 76, O dt=0.078072: new compressed 346, old_compressed 352, delta 6, rms=0.00359 iter 77, O dt=0.105943: new compressed 317, old_compressed 346, delta 29, rms=0.00358 iter 78, O dt=0.100507: new compressed 299, old_compressed 317, delta 18, rms=0.00357 iter 79, O dt=0.084906: new compressed 284, old_compressed 299, delta 15, rms=0.00356 iter 80, O dt=0.110723: new compressed 263, old_compressed 284, delta 21, rms=0.00355 iter 81, O dt=0.087620: new compressed 242, old_compressed 263, delta 21, rms=0.00354 iter 82, O dt=0.130155: new compressed 224, old_compressed 242, delta 18, rms=0.00352 iter 83, O dt=0.087623: new compressed 205, old_compressed 224, delta 19, rms=0.00351 iter 84, O dt=0.108381: new compressed 186, old_compressed 205, delta 19, rms=0.00350 iter 85, O dt=0.106151: new compressed 165, old_compressed 186, delta 21, rms=0.00349 iter 86, O dt=0.108430: new compressed 151, old_compressed 165, delta 14, rms=0.00348 iter 87, O dt=0.104476: new compressed 129, old_compressed 151, delta 22, rms=0.00347 iter 88, O dt=0.122111: new compressed 121, old_compressed 129, delta 8, rms=0.00346 iter 89, O dt=0.099311: new compressed 101, old_compressed 121, delta 20, rms=0.00345 iter 90, O dt=0.135456: new compressed 87, old_compressed 101, delta 14, rms=0.00344 iter 91, O dt=0.097147: new compressed 65, old_compressed 87, delta 22, rms=0.00343 iter 92, O dt=0.158696: new compressed 71, old_compressed 65, delta -6, rms=0.00342 iter 93, O dt=0.084731: new compressed 31, old_compressed 71, delta 40, rms=0.00341 iter 94, O dt=0.191108: new compressed 51, old_compressed 31, delta -20, rms=0.00339 iter 95, O dt=0.091185: new compressed 15, old_compressed 51, delta 36, rms=0.00338 iter 96, O dt=0.187049: new compressed 39, old_compressed 15, delta -24, rms=0.00337 iter 97, O dt=0.094766: new compressed 6, old_compressed 39, delta 33, rms=0.00336 iter 98, O dt=0.191522: new compressed 31, old_compressed 6, delta -25, rms=0.00335 iter 99, O dt=0.098149: new compressed 2, old_compressed 31, delta 29, rms=0.00334 iter 100, O dt=0.222917: new compressed 34, old_compressed 2, delta -32, rms=0.00333 iter 101, O dt=0.084877: new compressed 0, old_compressed 34, delta 34, rms=0.00332 starting rms=0.00428, compressed=994, removing compressions in lattice.... iter 1, O dt=0.074667: new compressed 1011, old_compressed 994, delta -17, rms=0.00422 iter 2, O dt=0.048064: new compressed 1021, old_compressed 1011, delta -10, rms=0.00417 iter 3, O dt=0.039425: new compressed 1021, old_compressed 1021, delta 0, rms=0.00414 iter 4, O dt=0.039875: new compressed 1007, old_compressed 1021, delta 14, rms=0.00412 iter 5, O dt=0.039289: new compressed 1005, old_compressed 1007, delta 2, rms=0.00410 iter 6, O dt=0.037704: new compressed 999, old_compressed 1005, delta 6, rms=0.00408 iter 7, O dt=0.039402: new compressed 992, old_compressed 999, delta 7, rms=0.00406 iter 8, O dt=0.041722: new compressed 971, old_compressed 992, delta 21, rms=0.00405 iter 9, O dt=0.040213: new compressed 974, old_compressed 971, delta -3, rms=0.00403 iter 10, O dt=0.042667: new compressed 959, old_compressed 974, delta 15, rms=0.00401 iter 11, O dt=0.042667: new compressed 945, old_compressed 959, delta 14, rms=0.00400 iter 12, O dt=0.042667: new compressed 924, old_compressed 945, delta 21, rms=0.00398 iter 13, O dt=0.042667: new compressed 906, old_compressed 924, delta 18, rms=0.00397 iter 14, O dt=0.053333: new compressed 882, old_compressed 906, delta 24, rms=0.00395 iter 15, O dt=0.042063: new compressed 880, old_compressed 882, delta 2, rms=0.00394 iter 16, O dt=0.053333: new compressed 859, old_compressed 880, delta 21, rms=0.00392 iter 17, O dt=0.042667: new compressed 849, old_compressed 859, delta 10, rms=0.00391 iter 18, O dt=0.053333: new compressed 840, old_compressed 849, delta 9, rms=0.00390 iter 19, O dt=0.053333: new compressed 823, old_compressed 840, delta 17, rms=0.00388 iter 20, O dt=0.042667: new compressed 822, old_compressed 823, delta 1, rms=0.00387 iter 21, O dt=0.078042: new compressed 793, old_compressed 822, delta 29, rms=0.00386 iter 22, O dt=0.042667: new compressed 787, old_compressed 793, delta 6, rms=0.00384 iter 23, O dt=0.089840: new compressed 745, old_compressed 787, delta 42, rms=0.00383 iter 24, O dt=0.042667: new compressed 749, old_compressed 745, delta -4, rms=0.00381 iter 25, O dt=0.087744: new compressed 705, old_compressed 749, delta 44, rms=0.00380 iter 26, O dt=0.042667: new compressed 711, old_compressed 705, delta -6, rms=0.00379 iter 27, O dt=0.129295: new compressed 651, old_compressed 711, delta 60, rms=0.00377 iter 28, O dt=0.042667: new compressed 657, old_compressed 651, delta -6, rms=0.00375 iter 29, O dt=0.131303: new compressed 602, old_compressed 657, delta 55, rms=0.00374 iter 30, O dt=0.042667: new compressed 606, old_compressed 602, delta -4, rms=0.00372 iter 31, O dt=0.163580: new compressed 551, old_compressed 606, delta 55, rms=0.00371 iter 32, O dt=0.053333: new compressed 541, old_compressed 551, delta 10, rms=0.00369 iter 33, O dt=0.084868: new compressed 518, old_compressed 541, delta 23, rms=0.00368 iter 34, O dt=0.067425: new compressed 504, old_compressed 518, delta 14, rms=0.00367 iter 35, O dt=0.064000: new compressed 491, old_compressed 504, delta 13, rms=0.00366 iter 36, O dt=0.084213: new compressed 463, old_compressed 491, delta 28, rms=0.00365 iter 37, O dt=0.064000: new compressed 452, old_compressed 463, delta 11, rms=0.00364 iter 38, O dt=0.090182: new compressed 430, old_compressed 452, delta 22, rms=0.00363 iter 39, O dt=0.074667: new compressed 409, old_compressed 430, delta 21, rms=0.00361 iter 40, O dt=0.074667: new compressed 399, old_compressed 409, delta 10, rms=0.00360 iter 41, O dt=0.088599: new compressed 369, old_compressed 399, delta 30, rms=0.00359 iter 42, O dt=0.074667: new compressed 356, old_compressed 369, delta 13, rms=0.00358 iter 43, O dt=0.085050: new compressed 343, old_compressed 356, delta 13, rms=0.00357 iter 44, O dt=0.082795: new compressed 317, old_compressed 343, delta 26, rms=0.00356 iter 45, O dt=0.088335: new compressed 300, old_compressed 317, delta 17, rms=0.00355 iter 46, O dt=0.087944: new compressed 287, old_compressed 300, delta 13, rms=0.00354 iter 47, O dt=0.086551: new compressed 272, old_compressed 287, delta 15, rms=0.00353 iter 48, O dt=0.095739: new compressed 254, old_compressed 272, delta 18, rms=0.00352 iter 49, O dt=0.085090: new compressed 226, old_compressed 254, delta 28, rms=0.00351 iter 50, O dt=0.103677: new compressed 214, old_compressed 226, delta 12, rms=0.00351 iter 51, O dt=0.084865: new compressed 197, old_compressed 214, delta 17, rms=0.00350 iter 52, O dt=0.110982: new compressed 176, old_compressed 197, delta 21, rms=0.00349 iter 53, O dt=0.085480: new compressed 155, old_compressed 176, delta 21, rms=0.00348 iter 54, O dt=0.117679: new compressed 143, old_compressed 155, delta 12, rms=0.00347 iter 55, O dt=0.086863: new compressed 114, old_compressed 143, delta 29, rms=0.00346 iter 56, O dt=0.123461: new compressed 108, old_compressed 114, delta 6, rms=0.00345 iter 57, O dt=0.089076: new compressed 86, old_compressed 108, delta 22, rms=0.00344 iter 58, O dt=0.119462: new compressed 69, old_compressed 86, delta 17, rms=0.00343 iter 59, O dt=0.104727: new compressed 62, old_compressed 69, delta 7, rms=0.00342 iter 60, O dt=0.104762: new compressed 50, old_compressed 62, delta 12, rms=0.00341 iter 61, O dt=0.125884: new compressed 53, old_compressed 50, delta -3, rms=0.00340 iter 62, O dt=0.093066: new compressed 22, old_compressed 53, delta 31, rms=0.00339 iter 63, O dt=0.156250: new compressed 45, old_compressed 22, delta -23, rms=0.00338 iter 64, O dt=0.090625: new compressed 12, old_compressed 45, delta 33, rms=0.00337 iter 65, O dt=0.158082: new compressed 32, old_compressed 12, delta -20, rms=0.00336 iter 66, O dt=0.104036: new compressed 14, old_compressed 32, delta 18, rms=0.00335 iter 67, O dt=0.134137: new compressed 21, old_compressed 14, delta -7, rms=0.00334 iter 68, O dt=0.119768: new compressed 14, old_compressed 21, delta 7, rms=0.00333 iter 69, O dt=0.126967: new compressed 10, old_compressed 14, delta 4, rms=0.00332 iter 70, O dt=0.129401: new compressed 11, old_compressed 10, delta -1, rms=0.00332 iter 71, O dt=0.126826: new compressed 8, old_compressed 11, delta 3, rms=0.00331 iter 72, O dt=0.135475: new compressed 7, old_compressed 8, delta 1, rms=0.00330 iter 73, O dt=0.129319: new compressed 4, old_compressed 7, delta 3, rms=0.00329 iter 74, O dt=0.139654: new compressed 4, old_compressed 4, delta 0, rms=0.00328 iter 75, O dt=0.133658: new compressed 1, old_compressed 4, delta 3, rms=0.00327 iter 76, O dt=0.142425: new compressed 2, old_compressed 1, delta -1, rms=0.00326 iter 77, O dt=0.139105: new compressed 0, old_compressed 2, delta 2, rms=0.00326 starting rms=0.00305, compressed=42, removing compressions in lattice.... iter 1, O dt=0.298667: new compressed 3, old_compressed 42, delta 39, rms=0.00299 iter 2, O dt=0.298667: new compressed 8, old_compressed 3, delta -5, rms=0.00296 iter 3, O dt=0.177419: new compressed 1, old_compressed 8, delta 7, rms=0.00294 iter 4, O dt=0.253631: new compressed 5, old_compressed 1, delta -4, rms=0.00292 iter 5, O dt=0.197273: new compressed 1, old_compressed 5, delta 4, rms=0.00290 iter 6, O dt=0.366577: new compressed 3, old_compressed 1, delta -2, rms=0.00287 iter 7, O dt=0.239822: new compressed 1, old_compressed 3, delta 2, rms=0.00285 iter 8, O dt=0.312005: new compressed 0, old_compressed 1, delta 1, rms=0.00283 iter 0, gcam->neg = 339 after 9 iterations, nbhd size=0, neg = 0 starting rms=0.00977, compressed=1651, removing compressions in lattice.... iter 1, O dt=0.168531: new compressed 1584, old_compressed 1651, delta 67, rms=0.00686 iter 2, O dt=0.110937: new compressed 1531, old_compressed 1584, delta 53, rms=0.00578 iter 3, O dt=0.104673: new compressed 1501, old_compressed 1531, delta 30, rms=0.00517 iter 4, O dt=0.084246: new compressed 1476, old_compressed 1501, delta 25, rms=0.00483 iter 5, O dt=0.082336: new compressed 1421, old_compressed 1476, delta 55, rms=0.00460 iter 6, O dt=0.070783: new compressed 1389, old_compressed 1421, delta 32, rms=0.00445 iter 7, O dt=0.070856: new compressed 1323, old_compressed 1389, delta 66, rms=0.00433 iter 8, O dt=0.063712: new compressed 1290, old_compressed 1323, delta 33, rms=0.00424 iter 9, O dt=0.066364: new compressed 1235, old_compressed 1290, delta 55, rms=0.00417 iter 10, O dt=0.064000: new compressed 1167, old_compressed 1235, delta 68, rms=0.00411 iter 11, O dt=0.064000: new compressed 1103, old_compressed 1167, delta 64, rms=0.00405 iter 12, O dt=0.074667: new compressed 1036, old_compressed 1103, delta 67, rms=0.00400 iter 13, O dt=0.064000: new compressed 987, old_compressed 1036, delta 49, rms=0.00395 iter 14, O dt=0.074667: new compressed 930, old_compressed 987, delta 57, rms=0.00391 iter 15, O dt=0.074667: new compressed 875, old_compressed 930, delta 55, rms=0.00387 iter 16, O dt=0.074667: new compressed 822, old_compressed 875, delta 53, rms=0.00384 iter 17, O dt=0.074667: new compressed 759, old_compressed 822, delta 63, rms=0.00380 iter 18, O dt=0.091383: new compressed 694, old_compressed 759, delta 65, rms=0.00377 iter 19, O dt=0.074667: new compressed 645, old_compressed 694, delta 49, rms=0.00374 iter 20, O dt=0.074667: new compressed 610, old_compressed 645, delta 35, rms=0.00371 iter 21, O dt=0.074667: new compressed 566, old_compressed 610, delta 44, rms=0.00369 iter 22, O dt=0.170667: new compressed 462, old_compressed 566, delta 104, rms=0.00365 iter 23, O dt=0.074667: new compressed 421, old_compressed 462, delta 41, rms=0.00362 iter 24, O dt=0.194222: new compressed 352, old_compressed 421, delta 69, rms=0.00359 iter 25, O dt=0.074667: new compressed 308, old_compressed 352, delta 44, rms=0.00355 iter 26, O dt=0.201582: new compressed 269, old_compressed 308, delta 39, rms=0.00353 iter 27, O dt=0.074667: new compressed 213, old_compressed 269, delta 56, rms=0.00350 iter 28, O dt=0.223180: new compressed 203, old_compressed 213, delta 10, rms=0.00347 iter 29, O dt=0.074667: new compressed 146, old_compressed 203, delta 57, rms=0.00345 iter 30, O dt=0.305952: new compressed 154, old_compressed 146, delta -8, rms=0.00342 iter 31, O dt=0.074667: new compressed 79, old_compressed 154, delta 75, rms=0.00339 iter 32, O dt=0.613946: new compressed 101, old_compressed 79, delta -22, rms=0.00334 iter 33, O dt=0.107833: new compressed 50, old_compressed 101, delta 51, rms=0.00331 iter 34, O dt=0.161585: new compressed 35, old_compressed 50, delta 15, rms=0.00329 iter 35, O dt=0.169643: new compressed 34, old_compressed 35, delta 1, rms=0.00328 iter 36, O dt=0.157812: new compressed 25, old_compressed 34, delabel assignment complete, 0 changed (0.00%) lta 9, rms=0.00326 iter 37, O dt=0.183712: new compressed 25, old_compressed 25, delta 0, rms=0.00325 iter 38, O dt=0.125000: new compressed 1, old_compressed 25, delta 24, rms=0.00323 iter 39, O dt=0.270455: new compressed 20, old_compressed 1, delta -19, rms=0.00321 iter 40, O dt=0.138480: new compressed 1, old_compressed 20, delta 19, rms=0.00320 iter 41, O dt=0.253106: new compressed 18, old_compressed 1, delta -17, rms=0.00319 iter 42, O dt=0.102431: new compressed 0, old_compressed 18, delta 18, rms=0.00317 starting rms=0.00322, compressed=5, removing compressions in lattice.... iter 1, O dt=1.359259: new compressed 42, old_compressed 5, delta -37, rms=0.00316 iter 2, O dt=0.119344: new compressed 3, old_compressed 42, delta 39, rms=0.00311 iter 3, O dt=0.298667: new compressed 4, old_compressed 3, delta -1, rms=0.00310 iter 4, O dt=0.213333: new compressed 2, old_compressed 4, delta 2, rms=0.00308 iter 5, O dt=0.298667: new compressed 5, old_compressed 2, delta -3, rms=0.00307 iter 6, O dt=0.188264: new compressed 1, old_compressed 5, delta 4, rms=0.00306 iter 7, O dt=0.425000: new compressed 17, old_compressed 1, delta -16, rms=0.00305 iter 8, O dt=0.074667: new compressed 0, old_compressed 17, delta 17, rms=0.00303 rms increased (dt=0.1000) - undoing step... starting rms=0.00320, compressed=9, removing compressions in lattice.... iter 1, O dt=0.640000: new compressed 47, old_compressed 9, delta -38, rms=0.00317 iter 2, O dt=0.152256: new compressed 3, old_compressed 47, delta 44, rms=0.00315 iter 3, O dt=0.218975: new compressed 8, old_compressed 3, delta -5, rms=0.00313 iter 4, O dt=0.215909: new compressed 8, old_compressed 8, delta 0, rms=0.00312 iter 5, O dt=0.183468: new compressed 2, old_compressed 8, delta 6, rms=0.00311 iter 6, O dt=0.197917: new compressed 0, old_compressed 2, delta 2, rms=0.00309 rms increased (dt=0.0500) - undoing step... **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.282, neg=0, invalid=96777 0012: dt=129.472000, rms=1.173 (8.524%), neg=0, invalid=96777 0013: dt=129.472000, rms=1.106 (5.687%), neg=0, invalid=96777 0014: dt=129.472000, rms=1.060 (4.179%), neg=0, invalid=96777 0015: dt=129.472000, rms=1.025 (3.261%), neg=0, invalid=96777 0016: dt=2.023000, rms=1.025 (0.041%), neg=0, invalid=96777 0017: dt=1.011500, rms=1.025 (0.022%), neg=0, invalid=96777 0018: dt=0.252875, rms=1.025 (0.006%), neg=0, invalid=96777 0019: dt=0.063219, rms=1.025 (0.001%), neg=0, invalid=96777 0020: dt=0.031609, rms=1.025 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.026, neg=0, invalid=96777 0021: dt=0.031609, rms=1.025 (0.092%), neg=0, invalid=96777 0022: dt=0.000000, rms=1.025 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.034, neg=0, invalid=96777 0023: dt=9.072000, rms=1.024 (0.970%), neg=0, invalid=96777 0024: dt=1.944000, rms=1.022 (0.187%), neg=0, invalid=96777 0025: dt=0.060750, rms=1.022 (0.007%), neg=0, invalid=96777 0026: dt=0.003797, rms=1.022 (0.000%), neg=0, invalid=96777 0027: dt=0.000949, rms=1.022 (0.000%), neg=0, invalid=96777 0028: dt=0.000000, rms=1.022 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.023, neg=0, invalid=96777 0029: dt=0.000000, rms=1.022 (0.091%), neg=0, invalid=96777 0030: dt=0.000000, rms=1.022 (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=1.053, neg=0, invalid=96777 0031: dt=2.800000, rms=1.044 (0.892%), neg=0, invalid=96777 0032: dt=0.700000, rms=1.041 (0.198%), neg=0, invalid=96777 0033: dt=0.350000, rms=1.040 (0.099%), neg=0, invalid=96777 0034: dt=0.021875, rms=1.040 (0.006%), neg=0, invalid=96777 0035: dt=0.010937, rms=1.040 (0.003%), neg=0, invalid=96777 0036: dt=0.002734, rms=1.040 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.041, neg=0, invalid=96777 0037: dt=0.002734, rms=1.040 (0.083%), neg=0, invalid=96777 0038: dt=0.002734, rms=1.040 (0.000%), neg=0, invalid=96777 0039: dt=0.000684, rms=1.040 (0.000%), neg=0, invalid=96777 0040: dt=0.000342, rms=1.040 (0.000%), neg=0, invalid=96777 0041: dt=0.000085, rms=1.040 (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=1.133, neg=0, invalid=96777 0042: dt=0.000000, rms=1.132 (0.070%), neg=0, invalid=96777 0043: dt=0.000000, rms=1.132 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.133, neg=0, invalid=96777 0044: dt=0.000000, rms=1.132 (0.070%), neg=0, invalid=96777 0045: dt=0.000000, rms=1.132 (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=1.307, neg=0, invalid=96777 0046: dt=1.792000, rms=1.273 (2.570%), neg=0, invalid=96777 0047: dt=2.560000, rms=1.261 (0.962%), neg=0, invalid=96777 0048: dt=2.507692, rms=1.234 (2.133%), neg=0, invalid=96777 0049: dt=1.068182, rms=1.227 (0.620%), neg=0, invalid=96777 0050: dt=1.792000, rms=1.222 (0.348%), neg=0, invalid=96777 0051: dt=2.277778, rms=1.211 (0.951%), neg=0, invalid=96777 0052: dt=0.768000, rms=1.208 (0.254%), neg=0, invalid=96777 0053: dt=1.792000, rms=1.205 (0.208%), neg=0, invalid=96777 0054: dt=1.792000, rms=1.199 (0.518%), neg=0, invalid=96777 0055: dt=1.792000, rms=1.194 (0.397%), neg=0, invalid=96777 0056: dt=1.792000, rms=1.194 (0.026%), neg=0, invalid=96777 0057: dt=1.792000, rms=1.194 (0.021%), neg=0, invalid=96777 0058: dt=1.792000, rms=1.192 (0.158%), neg=0, invalid=96777 0059: dt=1.024000, rms=1.190 (0.113%), neg=0, invalid=96777 0060: dt=1.024000, rms=1.190 (0.057%), neg=0, invalid=96777 0061: dt=1.024000, rms=1.189 (0.083%), neg=0, invalid=96777 0062: dt=1.024000, rms=1.187 (0.125%), neg=0, invalid=96777 0063: dt=1.024000, rms=1.186 (0.090%), neg=0, invalid=96777 0064: dt=1.024000, rms=1.185 (0.075%), neg=0, invalid=96777 0065: dt=1.024000, rms=1.185 (0.005%), neg=0, invalid=96777 0066: dt=1.024000, rms=1.185 (0.006%), neg=0, invalid=96777 0067: dt=1.024000, rms=1.185 (0.011%), neg=0, invalid=96777 0068: dt=1.024000, rms=1.185 (0.019%), neg=0, invalid=96777 0069: dt=1.024000, rms=1.184 (0.027%), neg=0, invalid=96777 0070: dt=1.024000, rms=1.184 (0.020%), neg=0, invalid=96777 0071: dt=1.024000, rms=1.184 (0.014%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.185, neg=0, invalid=96777 0072: dt=0.448000, rms=1.184 (0.105%), neg=0, invalid=96777 0073: dt=0.000000, rms=1.184 (0.000%), neg=0, invalid=96777 0074: dt=0.100000, rms=1.184 (-0.005%), 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=1.138, neg=0, invalid=96777 0075: dt=1.134868, rms=1.114 (2.149%), neg=0, invalid=96777 0076: dt=0.112000, rms=1.111 (0.213%), neg=0, invalid=96777 0077: dt=0.112000, rms=1.110 (0.080%), neg=0, invalid=96777 0078: dt=0.112000, rms=1.110 (-0.123%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.111, neg=0, invalid=96777 0079: dt=0.112000, rms=1.110 (0.163%), neg=0, invalid=96777 0080: dt=0.028000, rms=1.110 (0.003%), neg=0, invalid=96777 0081: dt=0.028000, rms=1.110 (-0.002%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.16103 (18) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (5797 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (5797 voxels, peak = 15), gca=14.8 gca peak = 0.14022 (22) mri peak = 0.16173 (18) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (4911 voxels, overlap=0.089) Right_Lateral_Ventricle (43): linear fit = 0.68 x + 0.0 (4911 voxels, peak = 15), gca=14.9 gca peak = 0.24234 (100) mri peak = 0.07519 (89) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (533 voxels, overlap=0.231) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (533 voxels, peak = 88), gca=88.5 gca peak = 0.19192 (97) mri peak = 0.09649 (77) Left_Pallidum (13): linear fit = 0.81 x + 0.0 (485 voxels, overlap=0.032) Left_Pallidum (13): linear fit = 0.81 x + 0.0 (485 voxels, peak = 78), gca=78.1 gca peak = 0.24007 (63) mri peak = 0.07614 (69) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (1295 voxels, overlap=0.872) Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (1295 voxels, peak = 66), gca=66.5 gca peak = 0.29892 (64) mri peak = 0.06456 (67) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1483 voxels, overlap=0.980) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1483 voxels, peak = 65), gca=65.0 gca peak = 0.12541 (104) mri peak = 0.05401 (90) Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (127027 voxels, overlap=0.991) Right_Cerebral_White_Matter (41): linear fit = 0.98 x + 0.0 (127027 voxels, peak = 101), gca=101.4 gca peak = 0.13686 (104) mri peak = 0.05018 (99) Left_Cerebral_White_Matter (2): linear fit = 0.95 x + 0.0 (122225 voxels, overlap=0.994) Left_Cerebral_White_Matter (2): linear fit = 0.95 x + 0.0 (122225 voxels, peak = 99), gca=99.3 gca peak = 0.11691 (63) mri peak = 0.03801 (79) Left_Cerebral_Cortex (3): linear fit = 1.24 x + 0.0 (32358 voxels, overlap=0.055) Left_Cerebral_Cortex (3): linear fit = 1.24 x + 0.0 (32358 voxels, peak = 78), gca=77.8 gca peak = 0.13270 (63) mri peak = 0.03058 (79) Right_Cerebral_Cortex (42): linear fit = 1.32 x + 0.0 (54284 voxels, overlap=0.014) Right_Cerebral_Cortex (42): linear fit = 1.32 x + 0.0 (54284 voxels, peak = 83), gca=82.8 gca peak = 0.15182 (70) mri peak = 0.10511 (63) Right_Caudate (50): linear fit = 0.86 x + 0.0 (839 voxels, overlap=0.451) Right_Caudate (50): linear fit = 0.86 x + 0.0 (839 voxels, peak = 60), gca=59.9 gca peak = 0.14251 (76) mri peak = 0.07116 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1601 voxels, overlap=0.937) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1601 voxels, peak = 76), gca=76.0 gca peak = 0.12116 (60) mri peak = 0.04154 (75) Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (19453 voxels, overlap=0.063) Left_Cerebellum_Cortex (8): linear fit = 1.22 x + 0.0 (19453 voxels, peak = 73), gca=72.9 gca peak = 0.12723 (61) mri peak = 0.04638 (72) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (34318 voxels, overlap=0.071) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (34318 voxels, peak = 73), gca=72.9 gca peak = 0.22684 (88) mri peak = 0.05009 (75) Left_Cerebellum_White_Matter (7): linear fit = 0.86 x + 0.0 (16120 voxels, overlap=0.228) Left_Cerebellum_White_Matter (7): linear fit = 0.86 x + 0.0 (16120 voxels, peak = 75), gca=75.2 gca peak = 0.21067 (87) mri peak = 0.04782 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (15569 voxels, overlap=0.999) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (15569 voxels, peak = 90), gca=90.0 gca peak = 0.25455 (62) mri peak = 0.07644 (65) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (291 voxels, overlap=0.988) Left_Amygdala (18): linear fit = 1.09 x + 0.0 (291 voxels, peak = 67), gca=67.3 gca peak = 0.39668 (62) mri peak = 0.08400 (63) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (336 voxels, overlap=0.981) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (336 voxels, peak = 64), gca=63.5 gca peak = 0.10129 (93) mri peak = 0.05378 (101) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (7743 voxels, overlap=0.990) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (7743 voxels, peak = 96), gca=96.3 gca peak = 0.12071 (89) mri peak = 0.07132 (80) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (5284 voxels, overlap=0.935) Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (5284 voxels, peak = 83), gca=83.2 gca peak = 0.13716 (82) mri peak = 0.04529 (80) Left_Putamen (12): linear fit = 0.93 x + 0.0 (3654 voxels, overlap=0.671) Left_Putamen (12): linear fit = 0.93 x + 0.0 (3654 voxels, peak = 76), gca=75.8 gca peak = 0.15214 (84) mri peak = 0.05595 (69) Right_Putamen (51): linear fit = 0.86 x + 0.0 (4413 voxels, overlap=0.381) Right_Putamen (51): linear fit = 0.86 x + 0.0 (4413 voxels, peak = 72), gca=71.8 gca peak = 0.08983 (85) mri peak = 0.07782 (87) Brain_Stem (16): linear fit = 1.03 x + 0.0 (16760 voxels, overlap=0.777) Brain_Stem (16): linear fit = 1.03 x + 0.0 (16760 voxels, peak = 88), gca=88.0 gca peak = 0.11809 (92) mri peak = 0.08242 (88) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1687 voxels, overlap=0.781) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1687 voxels, peak = 92), gca=91.5 gca peak = 0.12914 (94) mri peak = 0.08919 (94) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1822 voxels, overlap=0.782) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1822 voxels, peak = 94), gca=94.5 gca peak = 0.21100 (36) mri peak = 0.14816 (22) Third_Ventricle (14): linear fit = 0.61 x + 0.0 (180 voxels, overlap=0.042) Third_Ventricle (14): linear fit = 0.61 x + 0.0 (180 voxels, peak = 22), gca=21.8 gca peak = 0.13542 (27) mri peak = 0.11684 (19) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (1283 voxels, overlap=0.584) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (1283 voxels, peak = 22), gca=22.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.12 x + 0.0 estimating mean wm scale to be 0.97 x + 0.0 estimating mean csf scale to be 0.70 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.160, neg=0, invalid=96777 0082: dt=129.472000, rms=1.092 (5.837%), neg=0, invalid=96777 0083: dt=129.472000, rms=1.051 (3.772%), neg=0, invalid=96777 0084: dt=32.368000, rms=1.043 (0.779%), neg=0, invalid=96777 0085: dt=2.023000, rms=1.042 (0.048%), neg=0, invalid=96777 0086: dt=2.023000, rms=1.042 (0.047%), neg=0, invalid=96777 0087: dt=0.505750, rms=1.041 (0.011%), neg=0, invalid=96777 0088: dt=0.252875, rms=1.041 (0.006%), neg=0, invalid=96777 0089: dt=0.126438, rms=1.041 (0.000%), neg=0, invalid=96777 0090: dt=0.031609, rms=1.041 (0.001%), neg=0, invalid=96777 0091: dt=0.007902, rms=1.041 (0.000%), neg=0, invalid=96777 0092: dt=0.003951, rms=1.041 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.042, neg=0, invalid=96777 0093: dt=0.000000, rms=1.041 (0.093%), neg=0, invalid=96777 0094: dt=0.000000, rms=1.041 (0.000%), neg=0, invalid=96777 0095: dt=0.001660, rms=1.041 (0.000%), neg=0, invalid=96777 0096: dt=0.000208, rms=1.041 (0.000%), neg=0, invalid=96777 0097: dt=0.000104, rms=1.041 (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=1.042, neg=0, invalid=96777 0098: dt=0.000000, rms=1.041 (0.093%), neg=0, invalid=96777 0099: dt=0.000000, rms=1.041 (0.000%), neg=0, invalid=96777 0100: dt=0.000003, rms=1.041 (0.000%), neg=0, invalid=96777 0101: dt=0.000002, rms=1.041 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.042, neg=0, invalid=96777 0102: dt=0.000000, rms=1.041 (0.093%), neg=0, invalid=96777 0103: dt=0.000000, rms=1.041 (0.000%), neg=0, invalid=96777 0104: dt=0.000002, rms=1.041 (0.000%), neg=0, invalid=96777 0105: dt=0.000001, rms=1.041 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.043, neg=0, invalid=96777 0106: dt=0.000000, rms=1.042 (0.093%), neg=0, invalid=96777 0107: dt=0.000000, rms=1.042 (0.000%), neg=0, invalid=96777 0108: dt=0.000000, rms=1.042 (0.000%), neg=0, invalid=96777 0109: dt=0.000000, rms=1.042 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.043, neg=0, invalid=96777 0110: dt=0.000000, rms=1.042 (0.093%), neg=0, invalid=96777 0111: dt=0.000000, rms=1.042 (0.000%), neg=0, invalid=96777 0112: dt=0.000000, rms=1.042 (-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=1.044, neg=0, invalid=96777 0113: dt=0.000000, rms=1.043 (0.092%), neg=0, invalid=96777 0114: dt=0.000000, rms=1.043 (0.000%), neg=0, invalid=96777 0115: dt=0.000000, rms=1.043 (0.000%), neg=0, invalid=96777 0116: dt=0.000000, rms=1.043 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.044, neg=0, invalid=96777 0117: dt=0.000000, rms=1.043 (0.092%), neg=0, invalid=96777 0118: dt=0.000000, rms=1.043 (0.000%), neg=0, invalid=96777 0119: dt=0.000000, rms=1.043 (-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=1.048, neg=0, invalid=96777 0120: dt=0.000000, rms=1.047 (0.092%), neg=0, invalid=96777 0121: dt=0.000000, rms=1.047 (0.000%), neg=0, invalid=96777 0122: dt=0.000000, rms=1.047 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.048, neg=0, invalid=96777 0123: dt=0.000000, rms=1.047 (0.092%), neg=0, invalid=96777 0124: dt=0.000000, rms=1.047 (0.000%), neg=0, invalid=96777 0125: dt=0.000000, rms=1.047 (-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=1.042, neg=0, invalid=96777 0126: dt=0.448000, rms=1.024 (1.766%), neg=0, invalid=96777 0127: dt=0.448000, rms=1.012 (1.170%), neg=0, invalid=96777 0128: dt=0.320000, rms=1.005 (0.666%), neg=0, invalid=96777 0129: dt=0.001750, rms=1.005 (0.004%), neg=0, invalid=96777 0130: dt=0.000219, rms=1.005 (0.000%), neg=0, invalid=96777 0131: dt=0.000109, rms=1.005 (0.000%), neg=0, invalid=96777 0132: dt=0.000055, rms=1.005 (0.000%), neg=0, invalid=96777 0133: dt=0.000027, rms=1.005 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.006, neg=0, invalid=96777 0134: dt=0.000000, rms=1.005 (0.095%), neg=0, invalid=96777 0135: dt=0.000000, rms=1.005 (0.000%), neg=0, invalid=96777 0136: dt=0.000002, rms=1.005 (0.000%), neg=0, invalid=96777 0137: dt=0.000001, rms=1.005 (0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.004, neg=0, invalid=96777 iter 0, gcam->neg = 23 after 200 iterations, nbhd size=4, neg = 17 starting rms=0.013, neg=17, removing folds in lattice.... iter 1, dt=0.384000: new neg 1, old_neg 17, delta 16, rms=0.000 (96.491%) iter 2, dt=0.014393: new neg 1, old_neg 1, delta 0, rms=0.000 (9.251%) iter 3, dt=0.118164: new neg 1, old_neg 1, delta 0, rms=0.000 (16.515%) iter 4, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.020%) iter 5, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.019%) iter 6, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.019%) iter 7, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.018%) iter 8, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.017%) iter 9, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.017%) iter 10, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 11, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 12, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 13, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 14, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 15, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 16, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 17, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 18, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 19, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 20, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 21, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 22, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 23, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 24, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 25, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 26, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 27, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 28, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 29, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 30, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 31, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 32, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 33, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 34, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 35, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) ---------- unfolding failed - restoring original position -------------------- 0138: dt=517.888000, rms=1.003 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 23 after 200 iterations, nbhd size=4, neg = 17 starting rms=0.013, neg=17, removing folds in lattice.... iter 1, dt=0.384000: new neg 1, old_neg 17, delta 16, rms=0.000 (96.491%) iter 2, dt=0.014393: new neg 1, old_neg 1, delta 0, rms=0.000 (9.251%) iter 3, dt=0.118164: new neg 1, old_neg 1, delta 0, rms=0.000 (16.515%) iter 4, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.020%) iter 5, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.019%) iter 6, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.019%) iter 7, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.018%) iter 8, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.017%) iter 9, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.017%) iter 10, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 11, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 12, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 13, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 14, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 15, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 16, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 17, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 18, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 19, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 20, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 21, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 22, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 23, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 24, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 25, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 26, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 27, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 28, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 29, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 30, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 31, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 32, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 33, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 34, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 35, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) ---------- unfolding failed - restoring original position -------------------- 0139: dt=517.888000, rms=1.003 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.004, neg=0, invalid=96777 iter 0, gcam->neg = 23 after 200 iterations, nbhd size=3, neg = 16 starting rms=0.012, neg=16, removing folds in lattice.... iter 1, dt=0.384000: new neg 1, old_neg 16, delta 15, rms=0.001 (95.874%) iter 2, dt=0.066797: new neg 1, old_neg 1, delta 0, rms=0.000 (14.970%) iter 3, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.191%) iter 4, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.180%) iter 5, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.169%) iter 6, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.159%) iter 7, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.150%) iter 8, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.141%) iter 9, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.133%) iter 10, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.125%) iter 11, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.117%) iter 12, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.109%) iter 13, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.100%) iter 14, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.092%) iter 15, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.085%) iter 16, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.079%) iter 17, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.074%) iter 18, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.069%) iter 19, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.064%) iter 20, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.060%) iter 21, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.057%) iter 22, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.054%) iter 23, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.051%) iter 24, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.048%) iter 25, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.044%) iter 26, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.041%) iter 27, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.038%) iter 28, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.036%) iter 29, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.034%) iter 30, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.032%) iter 31, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.030%) iter 32, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.028%) iter 33, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.027%) iter 34, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.026%) iter 35, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.025%) iter 36, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.024%) iter 37, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.023%) iter 38, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.022%) iter 39, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.021%) iter 40, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.020%) iter 41, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.019%) iter 42, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.019%) iter 43, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.018%) iter 44, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.018%) iter 45, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.017%) iter 46, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.017%) iter 47, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 48, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 49, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 50, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 51, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 52, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 53, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 54, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 55, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 56, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 57, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 58, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 59, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 60, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 61, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 62, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 63, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 64, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 65, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 66, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 67, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 68, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 69, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 70, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 71, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 72, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 73, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 74, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 75, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) ---------- unfolding failed - restoring original position -------------------- 0140: dt=887.808000, rms=1.003 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 23 after 200 iterations, nbhd size=3, neg = 16 starting rms=0.012, neg=16, removing folds in lattice.... iter 1, dt=0.384000: new neg 1, old_neg 16, delta 15, rms=0.001 (95.874%) iter 2, dt=0.066797: new neg 1, old_neg 1, delta 0, rms=0.000 (14.970%) iter 3, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.191%) iter 4, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.180%) iter 5, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.169%) iter 6, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.159%) iter 7, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.150%) iter 8, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.141%) iter 9, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.133%) iter 10, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.125%) iter 11, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.117%) iter 12, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.109%) iter 13, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.100%) iter 14, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.092%) iter 15, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.085%) iter 16, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.079%) iter 17, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.074%) iter 18, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.069%) iter 19, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.064%) iter 20, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.060%) iter 21, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.057%) iter 22, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.054%) iter 23, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.051%) iter 24, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.048%) iter 25, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.044%) iter 26, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.041%) iter 27, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.038%) iter 28, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.036%) iter 29, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.034%) iter 30, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.032%) iter 31, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.030%) iter 32, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.028%) iter 33, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.027%) iter 34, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.026%) iter 35, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.025%) iter 36, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.024%) iter 37, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.023%) iter 38, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.022%) iter 39, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.021%) iter 40, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.020%) iter 41, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.019%) iter 42, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.019%) iter 43, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.018%) iter 44, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.018%) iter 45, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.017%) iter 46, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.017%) iter 47, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 48, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.016%) iter 49, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 50, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 51, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.015%) iter 52, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 53, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 54, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.014%) iter 55, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 56, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 57, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 58, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.013%) iter 59, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 60, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 61, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 62, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 63, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.012%) iter 64, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 65, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 66, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 67, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 68, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 69, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 70, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.011%) iter 71, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 72, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 73, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 74, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) iter 75, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.000 (0.010%) ---------- unfolding failed - restoring original position -------------------- 0141: dt=887.808000, rms=1.003 (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=1.004, neg=0, invalid=96777 iter 0, gcam->neg = 309 after 200 iterations, nbhd size=4, neg = 42 starting rms=0.022, neg=42, removing folds in lattice.... iter 1, dt=0.384000: new neg 65, old_neg 42, delta -23, rms=0.014 (39.589%) iter 2, dt=0.002294: new neg 64, old_neg 65, delta 1, rms=0.013 (0.856%) iter 3, dt=0.002294: new neg 62, old_neg 64, delta 2, rms=0.013 (0.857%) iter 4, dt=0.002294: new neg 60, old_neg 62, delta 2, rms=0.013 (0.859%) iter 5, dt=0.002294: new neg 58, old_neg 60, delta 2, rms=0.013 (0.861%) iter 6, dt=0.002294: new neg 57, old_neg 58, delta 1, rms=0.013 (0.863%) iter 7, dt=0.002294: new neg 53, old_neg 57, delta 4, rms=0.013 (0.865%) iter 8, dt=0.002294: new neg 52, old_neg 53, delta 1, rms=0.013 (0.868%) iter 9, dt=0.002294: new neg 51, old_neg 52, delta 1, rms=0.013 (0.870%) iter 10, dt=0.002294: new neg 51, old_neg 51, delta 0, rms=0.013 (0.873%) iter 11, dt=0.002294: new neg 49, old_neg 51, delta 2, rms=0.012 (0.876%) iter 12, dt=0.002294: new neg 48, old_neg 49, delta 1, rms=0.012 (0.879%) iter 13, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.012 (0.882%) iter 14, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.012 (0.885%) iter 15, dt=0.002294: new neg 47, old_neg 48, delta 1, rms=0.012 (0.889%) iter 16, dt=0.002294: new neg 46, old_neg 47, delta 1, rms=0.012 (0.892%) iter 17, dt=0.002294: new neg 46, old_neg 46, delta 0, rms=0.012 (0.896%) iter 18, dt=0.002294: new neg 45, old_neg 46, delta 1, rms=0.012 (0.899%) iter 19, dt=0.002294: new neg 45, old_neg 45, delta 0, rms=0.012 (0.903%) iter 20, dt=0.002294: new neg 45, old_neg 45, delta 0, rms=0.011 (0.906%) iter 21, dt=0.002294: new neg 45, old_neg 45, delta 0, rms=0.011 (0.910%) iter 22, dt=0.002294: new neg 43, old_neg 45, delta 2, rms=0.011 (0.913%) iter 23, dt=0.002294: new neg 40, old_neg 43, delta 3, rms=0.011 (0.916%) iter 24, dt=0.002294: new neg 38, old_neg 40, delta 2, rms=0.011 (0.918%) iter 25, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.011 (0.921%) iter 26, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.011 (0.923%) iter 27, dt=0.002294: new neg 36, old_neg 38, delta 2, rms=0.011 (0.925%) iter 28, dt=0.002294: new neg 35, old_neg 36, delta 1, rms=0.011 (0.927%) iter 29, dt=0.002294: new neg 35, old_neg 35, delta 0, rms=0.011 (0.928%) iter 30, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.010 (0.929%) iter 31, dt=0.002294: new neg 32, old_neg 34, delta 2, rms=0.010 (0.930%) iter 32, dt=0.002294: new neg 29, old_neg 32, delta 3, rms=0.010 (0.931%) iter 33, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (0.931%) iter 34, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (0.932%) iter 35, dt=0.002294: new neg 26, old_neg 29, delta 3, rms=0.010 (0.932%) iter 36, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.010 (0.932%) iter 37, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.010 (0.933%) iter 38, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.010 (0.933%) iter 39, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.010 (0.934%) iter 40, dt=0.002294: new neg 22, old_neg 24, delta 2, rms=0.010 (0.934%) iter 41, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.009 (0.935%) iter 42, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.009 (0.936%) iter 43, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.009 (0.936%) iter 44, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (0.937%) iter 45, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (0.938%) iter 46, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (0.938%) iter 47, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (0.939%) iter 48, dt=0.002294: new neg 18, old_neg 20, delta 2, rms=0.009 (0.940%) iter 49, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.009 (0.940%) iter 50, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.009 (0.942%) iter 51, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.009 (0.943%) iter 52, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.009 (0.944%) iter 53, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (0.947%) iter 54, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (0.949%) iter 55, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.008 (0.952%) iter 56, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.954%) iter 57, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.957%) iter 58, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.960%) iter 59, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.963%) iter 60, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.964%) iter 61, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.964%) iter 62, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.008 (0.963%) iter 63, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.008 (0.960%) iter 64, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.008 (0.956%) iter 65, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.008 (0.951%) iter 66, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (0.945%) iter 67, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (0.938%) iter 68, dt=0.002294: new neg 11, old_neg 13, delta 2, rms=0.007 (0.932%) iter 69, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.927%) iter 70, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.922%) iter 71, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.918%) iter 72, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.915%) iter 73, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.914%) iter 74, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.007 (0.913%) iter 75, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.007 (0.913%) iter 76, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.913%) iter 77, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.913%) iter 78, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.913%) iter 79, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.912%) iter 80, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.911%) iter 81, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (0.909%) iter 82, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (0.907%) iter 83, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (0.905%) iter 84, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (0.902%) iter 85, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (0.899%) iter 86, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (0.897%) iter 87, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (0.896%) iter 88, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (0.896%) iter 89, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (0.898%) iter 90, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.903%) iter 91, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.910%) iter 92, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.918%) iter 93, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.006 (0.926%) iter 94, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.934%) iter 95, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.943%) iter 96, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.951%) iter 97, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.960%) iter 98, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.968%) iter 99, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.975%) iter 100, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.981%) ---------- unfolding failed - restoring original position -------------------- 0142: dt=145.152000, rms=1.003 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 309 after 200 iterations, nbhd size=4, neg = 42 starting rms=0.022, neg=42, removing folds in lattice.... iter 1, dt=0.384000: new neg 65, old_neg 42, delta -23, rms=0.014 (39.589%) iter 2, dt=0.002294: new neg 64, old_neg 65, delta 1, rms=0.013 (0.856%) iter 3, dt=0.002294: new neg 62, old_neg 64, delta 2, rms=0.013 (0.857%) iter 4, dt=0.002294: new neg 60, old_neg 62, delta 2, rms=0.013 (0.859%) iter 5, dt=0.002294: new neg 58, old_neg 60, delta 2, rms=0.013 (0.861%) iter 6, dt=0.002294: new neg 57, old_neg 58, delta 1, rms=0.013 (0.863%) iter 7, dt=0.002294: new neg 53, old_neg 57, delta 4, rms=0.013 (0.865%) iter 8, dt=0.002294: new neg 52, old_neg 53, delta 1, rms=0.013 (0.868%) iter 9, dt=0.002294: new neg 51, old_neg 52, delta 1, rms=0.013 (0.870%) iter 10, dt=0.002294: new neg 51, old_neg 51, delta 0, rms=0.013 (0.873%) iter 11, dt=0.002294: new neg 49, old_neg 51, delta 2, rms=0.012 (0.876%) iter 12, dt=0.002294: new neg 48, old_neg 49, delta 1, rms=0.012 (0.879%) iter 13, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.012 (0.882%) iter 14, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.012 (0.885%) iter 15, dt=0.002294: new neg 47, old_neg 48, delta 1, rms=0.012 (0.889%) iter 16, dt=0.002294: new neg 46, old_neg 47, delta 1, rms=0.012 (0.892%) iter 17, dt=0.002294: new neg 46, old_neg 46, delta 0, rms=0.012 (0.896%) iter 18, dt=0.002294: new neg 45, old_neg 46, delta 1, rms=0.012 (0.899%) iter 19, dt=0.002294: new neg 45, old_neg 45, delta 0, rms=0.012 (0.903%) iter 20, dt=0.002294: new neg 45, old_neg 45, delta 0, rms=0.011 (0.906%) iter 21, dt=0.002294: new neg 45, old_neg 45, delta 0, rms=0.011 (0.910%) iter 22, dt=0.002294: new neg 43, old_neg 45, delta 2, rms=0.011 (0.913%) iter 23, dt=0.002294: new neg 40, old_neg 43, delta 3, rms=0.011 (0.916%) iter 24, dt=0.002294: new neg 38, old_neg 40, delta 2, rms=0.011 (0.918%) iter 25, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.011 (0.921%) iter 26, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.011 (0.923%) iter 27, dt=0.002294: new neg 36, old_neg 38, delta 2, rms=0.011 (0.925%) iter 28, dt=0.002294: new neg 35, old_neg 36, delta 1, rms=0.011 (0.927%) iter 29, dt=0.002294: new neg 35, old_neg 35, delta 0, rms=0.011 (0.928%) iter 30, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.010 (0.929%) iter 31, dt=0.002294: new neg 32, old_neg 34, delta 2, rms=0.010 (0.930%) iter 32, dt=0.002294: new neg 29, old_neg 32, delta 3, rms=0.010 (0.931%) iter 33, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (0.931%) iter 34, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (0.932%) iter 35, dt=0.002294: new neg 26, old_neg 29, delta 3, rms=0.010 (0.932%) iter 36, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.010 (0.932%) iter 37, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.010 (0.933%) iter 38, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.010 (0.933%) iter 39, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.010 (0.934%) iter 40, dt=0.002294: new neg 22, old_neg 24, delta 2, rms=0.010 (0.934%) iter 41, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.009 (0.935%) iter 42, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.009 (0.936%) iter 43, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.009 (0.936%) iter 44, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (0.937%) iter 45, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (0.938%) iter 46, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (0.938%) iter 47, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (0.939%) iter 48, dt=0.002294: new neg 18, old_neg 20, delta 2, rms=0.009 (0.940%) iter 49, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.009 (0.940%) iter 50, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.009 (0.942%) iter 51, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.009 (0.943%) iter 52, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.009 (0.944%) iter 53, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (0.947%) iter 54, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (0.949%) iter 55, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.008 (0.952%) iter 56, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.954%) iter 57, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.957%) iter 58, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.960%) iter 59, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.963%) iter 60, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.964%) iter 61, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (0.964%) iter 62, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.008 (0.963%) iter 63, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.008 (0.960%) iter 64, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.008 (0.956%) iter 65, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.008 (0.951%) iter 66, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (0.945%) iter 67, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (0.938%) iter 68, dt=0.002294: new neg 11, old_neg 13, delta 2, rms=0.007 (0.932%) iter 69, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.927%) iter 70, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.922%) iter 71, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.918%) iter 72, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.915%) iter 73, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (0.914%) iter 74, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.007 (0.913%) iter 75, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.007 (0.913%) iter 76, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.913%) iter 77, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.913%) iter 78, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.913%) iter 79, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.912%) iter 80, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (0.911%) iter 81, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (0.909%) iter 82, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (0.907%) iter 83, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (0.905%) iter 84, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (0.902%) iter 85, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (0.899%) iter 86, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (0.897%) iter 87, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (0.896%) iter 88, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (0.896%) iter 89, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (0.898%) iter 90, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.903%) iter 91, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.910%) iter 92, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.918%) iter 93, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.006 (0.926%) iter 94, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.934%) iter 95, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.943%) iter 96, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.951%) iter 97, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.960%) iter 98, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (0.968%) iter 99, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.975%) iter 100, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.981%) ---------- unfolding failed - restoring original position -------------------- 0143: dt=145.152000, rms=1.003 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.004, neg=0, invalid=96777 iter 0, gcam->neg = 3496 after 205 iterations, nbhd size=3, neg = 135 starting rms=0.040, neg=135, removing folds in lattice.... iter 1, dt=0.128000: new neg 95, old_neg 135, delta 40, rms=0.035 (11.570%) iter 2, dt=0.002294: new neg 94, old_neg 95, delta 1, rms=0.035 (0.319%) iter 3, dt=0.002294: new neg 94, old_neg 94, delta 0, rms=0.035 (0.315%) iter 4, dt=0.002294: new neg 93, old_neg 94, delta 1, rms=0.035 (0.311%) iter 5, dt=0.002294: new neg 90, old_neg 93, delta 3, rms=0.035 (0.307%) iter 6, dt=0.000102: new neg 90, old_neg 90, delta 0, rms=0.035 (0.014%) iter 7, dt=0.000006: new neg 90, old_neg 90, delta 0, rms=0.035 (0.001%) ---------- unfolding failed - restoring original position -------------------- 0144: dt=331.776000, rms=1.003 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 3496 after 205 iterations, nbhd size=3, neg = 135 starting rms=0.040, neg=135, removing folds in lattice.... iter 1, dt=0.128000: new neg 95, old_neg 135, delta 40, rms=0.035 (11.570%) iter 2, dt=0.002294: new neg 94, old_neg 95, delta 1, rms=0.035 (0.319%) iter 3, dt=0.002294: new neg 94, old_neg 94, delta 0, rms=0.035 (0.315%) iter 4, dt=0.002294: new neg 93, old_neg 94, delta 1, rms=0.035 (0.311%) iter 5, dt=0.002294: new neg 90, old_neg 93, delta 3, rms=0.035 (0.307%) iter 6, dt=0.000102: new neg 90, old_neg 90, delta 0, rms=0.035 (0.014%) iter 7, dt=0.000006: new neg 90, old_neg 90, delta 0, rms=0.035 (0.001%) ---------- unfolding failed - restoring original position -------------------- 0145: dt=331.776000, rms=1.003 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.004, neg=0, invalid=96777 iter 0, gcam->neg = 10045 after 200 iterations, nbhd size=3, neg = 105 starting rms=0.042, neg=105, removing folds in lattice.... iter 1, dt=0.227783: new neg 169, old_neg 105, delta -64, rms=0.034 (19.329%) iter 2, dt=0.002294: new neg 165, old_neg 169, delta 4, rms=0.034 (0.460%) iter 3, dt=0.002294: new neg 160, old_neg 165, delta 5, rms=0.033 (0.455%) iter 4, dt=0.002294: new neg 159, old_neg 160, delta 1, rms=0.033 (0.451%) iter 5, dt=0.002294: new neg 150, old_neg 159, delta 9, rms=0.033 (0.446%) iter 6, dt=0.002294: new neg 146, old_neg 150, delta 4, rms=0.033 (0.442%) iter 7, dt=0.002294: new neg 139, old_neg 146, delta 7, rms=0.033 (0.437%) iter 8, dt=0.002294: new neg 135, old_neg 139, delta 4, rms=0.033 (0.433%) iter 9, dt=0.002294: new neg 130, old_neg 135, delta 5, rms=0.033 (0.428%) iter 10, dt=0.002294: new neg 124, old_neg 130, delta 6, rms=0.032 (0.424%) iter 11, dt=0.002294: new neg 121, old_neg 124, delta 3, rms=0.032 (0.420%) iter 12, dt=0.002294: new neg 118, old_neg 121, delta 3, rms=0.032 (0.415%) iter 13, dt=0.002294: new neg 112, old_neg 118, delta 6, rms=0.032 (0.411%) iter 14, dt=0.002294: new neg 110, old_neg 112, delta 2, rms=0.032 (0.407%) iter 15, dt=0.002294: new neg 106, old_neg 110, delta 4, rms=0.032 (0.403%) iter 16, dt=0.002294: new neg 106, old_neg 106, delta 0, rms=0.032 (0.399%) iter 17, dt=0.002294: new neg 103, old_neg 106, delta 3, rms=0.032 (0.395%) iter 18, dt=0.002294: new neg 102, old_neg 103, delta 1, rms=0.031 (0.391%) iter 19, dt=0.002294: new neg 101, old_neg 102, delta 1, rms=0.031 (0.387%) iter 20, dt=0.002294: new neg 95, old_neg 101, delta 6, rms=0.031 (0.383%) iter 21, dt=0.002294: new neg 93, old_neg 95, delta 2, rms=0.031 (0.380%) iter 22, dt=0.002294: new neg 89, old_neg 93, delta 4, rms=0.031 (0.376%) iter 23, dt=0.002294: new neg 85, old_neg 89, delta 4, rms=0.031 (0.372%) iter 24, dt=0.002294: new neg 80, old_neg 85, delta 5, rms=0.031 (0.369%) iter 25, dt=0.002294: new neg 77, old_neg 80, delta 3, rms=0.031 (0.365%) iter 26, dt=0.002294: new neg 74, old_neg 77, delta 3, rms=0.030 (0.362%) iter 27, dt=0.002294: new neg 69, old_neg 74, delta 5, rms=0.030 (0.359%) iter 28, dt=0.002294: new neg 67, old_neg 69, delta 2, rms=0.030 (0.356%) iter 29, dt=0.002294: new neg 65, old_neg 67, delta 2, rms=0.030 (0.352%) iter 30, dt=0.002294: new neg 64, old_neg 65, delta 1, rms=0.030 (0.349%) iter 31, dt=0.002294: new neg 60, old_neg 64, delta 4, rms=0.030 (0.346%) iter 32, dt=0.002294: new neg 56, old_neg 60, delta 4, rms=0.030 (0.343%) iter 33, dt=0.002294: new neg 53, old_neg 56, delta 3, rms=0.030 (0.341%) iter 34, dt=0.002294: new neg 52, old_neg 53, delta 1, rms=0.030 (0.338%) iter 35, dt=0.002294: new neg 50, old_neg 52, delta 2, rms=0.030 (0.335%) iter 36, dt=0.002294: new neg 49, old_neg 50, delta 1, rms=0.029 (0.332%) iter 37, dt=0.002294: new neg 49, old_neg 49, delta 0, rms=0.029 (0.330%) iter 38, dt=0.002294: new neg 48, old_neg 49, delta 1, rms=0.029 (0.327%) iter 39, dt=0.002294: new neg 46, old_neg 48, delta 2, rms=0.029 (0.325%) iter 40, dt=0.002294: new neg 45, old_neg 46, delta 1, rms=0.029 (0.323%) iter 41, dt=0.002294: new neg 41, old_neg 45, delta 4, rms=0.029 (0.320%) iter 42, dt=0.002294: new neg 40, old_neg 41, delta 1, rms=0.029 (0.318%) iter 43, dt=0.002294: new neg 39, old_neg 40, delta 1, rms=0.029 (0.316%) iter 44, dt=0.002294: new neg 39, old_neg 39, delta 0, rms=0.029 (0.314%) iter 45, dt=0.002294: new neg 39, old_neg 39, delta 0, rms=0.029 (0.312%) iter 46, dt=0.002294: new neg 39, old_neg 39, delta 0, rms=0.029 (0.310%) iter 47, dt=0.002294: new neg 38, old_neg 39, delta 1, rms=0.028 (0.308%) iter 48, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.028 (0.306%) iter 49, dt=0.002294: new neg 37, old_neg 38, delta 1, rms=0.028 (0.304%) iter 50, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.028 (0.302%) iter 51, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.028 (0.301%) iter 52, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.028 (0.299%) iter 53, dt=0.002294: new neg 36, old_neg 37, delta 1, rms=0.028 (0.297%) iter 54, dt=0.002294: new neg 36, old_neg 36, delta 0, rms=0.028 (0.295%) iter 55, dt=0.002294: new neg 34, old_neg 36, delta 2, rms=0.028 (0.294%) iter 56, dt=0.002294: new neg 31, old_neg 34, delta 3, rms=0.028 (0.292%) iter 57, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.028 (0.291%) iter 58, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.028 (0.289%) iter 59, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.027 (0.288%) iter 60, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.027 (0.287%) iter 61, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.027 (0.285%) iter 62, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.027 (0.284%) iter 63, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.027 (0.283%) iter 64, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.027 (0.282%) iter 65, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.027 (0.280%) iter 66, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.027 (0.279%) iter 67, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.027 (0.278%) iter 68, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.027 (0.277%) iter 69, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.027 (0.276%) iter 70, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.027 (0.275%) iter 71, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.027 (0.274%) iter 72, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.273%) iter 73, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.273%) iter 74, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.272%) iter 75, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.271%) iter 76, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.270%) iter 77, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.269%) iter 78, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.269%) iter 79, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.026 (0.268%) iter 80, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.267%) iter 81, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.267%) iter 82, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.266%) iter 83, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.265%) iter 84, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.265%) iter 85, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.264%) iter 86, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.025 (0.264%) iter 87, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.025 (0.263%) iter 88, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.025 (0.263%) iter 89, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.262%) iter 90, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.262%) iter 91, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.262%) iter 92, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.261%) iter 93, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.261%) iter 94, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.261%) iter 95, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.025 (0.260%) iter 96, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.260%) iter 97, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.260%) iter 98, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.260%) iter 99, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.260%) iter 100, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.259%) ---------- unfolding failed - restoring original position -------------------- 0146: dt=71.721236, rms=1.003 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 10045 after 200 iterations, nbhd size=3, neg = 105 starting rms=0.042, neg=105, removing folds in lattice.... iter 1, dt=0.227783: new neg 169, old_neg 105, delta -64, rms=0.034 (19.329%) iter 2, dt=0.002294: new neg 165, old_neg 169, delta 4, rms=0.034 (0.460%) iter 3, dt=0.002294: new neg 160, old_neg 165, delta 5, rms=0.033 (0.455%) iter 4, dt=0.002294: new neg 159, old_neg 160, delta 1, rms=0.033 (0.451%) iter 5, dt=0.002294: new neg 150, old_neg 159, delta 9, rms=0.033 (0.446%) iter 6, dt=0.002294: new neg 146, old_neg 150, delta 4, rms=0.033 (0.442%) iter 7, dt=0.002294: new neg 139, old_neg 146, delta 7, rms=0.033 (0.437%) iter 8, dt=0.002294: new neg 135, old_neg 139, delta 4, rms=0.033 (0.433%) iter 9, dt=0.002294: new neg 130, old_neg 135, delta 5, rms=0.033 (0.428%) iter 10, dt=0.002294: new neg 124, old_neg 130, delta 6, rms=0.032 (0.424%) iter 11, dt=0.002294: new neg 121, old_neg 124, delta 3, rms=0.032 (0.420%) iter 12, dt=0.002294: new neg 118, old_neg 121, delta 3, rms=0.032 (0.415%) iter 13, dt=0.002294: new neg 112, old_neg 118, delta 6, rms=0.032 (0.411%) iter 14, dt=0.002294: new neg 110, old_neg 112, delta 2, rms=0.032 (0.407%) iter 15, dt=0.002294: new neg 106, old_neg 110, delta 4, rms=0.032 (0.403%) iter 16, dt=0.002294: new neg 106, old_neg 106, delta 0, rms=0.032 (0.399%) iter 17, dt=0.002294: new neg 103, old_neg 106, delta 3, rms=0.032 (0.395%) iter 18, dt=0.002294: new neg 102, old_neg 103, delta 1, rms=0.031 (0.391%) iter 19, dt=0.002294: new neg 101, old_neg 102, delta 1, rms=0.031 (0.387%) iter 20, dt=0.002294: new neg 95, old_neg 101, delta 6, rms=0.031 (0.383%) iter 21, dt=0.002294: new neg 93, old_neg 95, delta 2, rms=0.031 (0.380%) iter 22, dt=0.002294: new neg 89, old_neg 93, delta 4, rms=0.031 (0.376%) iter 23, dt=0.002294: new neg 85, old_neg 89, delta 4, rms=0.031 (0.372%) iter 24, dt=0.002294: new neg 80, old_neg 85, delta 5, rms=0.031 (0.369%) iter 25, dt=0.002294: new neg 77, old_neg 80, delta 3, rms=0.031 (0.365%) iter 26, dt=0.002294: new neg 74, old_neg 77, delta 3, rms=0.030 (0.362%) iter 27, dt=0.002294: new neg 69, old_neg 74, delta 5, rms=0.030 (0.359%) iter 28, dt=0.002294: new neg 67, old_neg 69, delta 2, rms=0.030 (0.356%) iter 29, dt=0.002294: new neg 65, old_neg 67, delta 2, rms=0.030 (0.352%) iter 30, dt=0.002294: new neg 64, old_neg 65, delta 1, rms=0.030 (0.349%) iter 31, dt=0.002294: new neg 60, old_neg 64, delta 4, rms=0.030 (0.346%) iter 32, dt=0.002294: new neg 56, old_neg 60, delta 4, rms=0.030 (0.343%) iter 33, dt=0.002294: new neg 53, old_neg 56, delta 3, rms=0.030 (0.341%) iter 34, dt=0.002294: new neg 52, old_neg 53, delta 1, rms=0.030 (0.338%) iter 35, dt=0.002294: new neg 50, old_neg 52, delta 2, rms=0.030 (0.335%) iter 36, dt=0.002294: new neg 49, old_neg 50, delta 1, rms=0.029 (0.332%) iter 37, dt=0.002294: new neg 49, old_neg 49, delta 0, rms=0.029 (0.330%) iter 38, dt=0.002294: new neg 48, old_neg 49, delta 1, rms=0.029 (0.327%) iter 39, dt=0.002294: new neg 46, old_neg 48, delta 2, rms=0.029 (0.325%) iter 40, dt=0.002294: new neg 45, old_neg 46, delta 1, rms=0.029 (0.323%) iter 41, dt=0.002294: new neg 41, old_neg 45, delta 4, rms=0.029 (0.320%) iter 42, dt=0.002294: new neg 40, old_neg 41, delta 1, rms=0.029 (0.318%) iter 43, dt=0.002294: new neg 39, old_neg 40, delta 1, rms=0.029 (0.316%) iter 44, dt=0.002294: new neg 39, old_neg 39, delta 0, rms=0.029 (0.314%) iter 45, dt=0.002294: new neg 39, old_neg 39, delta 0, rms=0.029 (0.312%) iter 46, dt=0.002294: new neg 39, old_neg 39, delta 0, rms=0.029 (0.310%) iter 47, dt=0.002294: new neg 38, old_neg 39, delta 1, rms=0.028 (0.308%) iter 48, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.028 (0.306%) iter 49, dt=0.002294: new neg 37, old_neg 38, delta 1, rms=0.028 (0.304%) iter 50, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.028 (0.302%) iter 51, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.028 (0.301%) iter 52, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.028 (0.299%) iter 53, dt=0.002294: new neg 36, old_neg 37, delta 1, rms=0.028 (0.297%) iter 54, dt=0.002294: new neg 36, old_neg 36, delta 0, rms=0.028 (0.295%) iter 55, dt=0.002294: new neg 34, old_neg 36, delta 2, rms=0.028 (0.294%) iter 56, dt=0.002294: new neg 31, old_neg 34, delta 3, rms=0.028 (0.292%) iter 57, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.028 (0.291%) iter 58, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.028 (0.289%) iter 59, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.027 (0.288%) iter 60, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.027 (0.287%) iter 61, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.027 (0.285%) iter 62, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.027 (0.284%) iter 63, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.027 (0.283%) iter 64, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.027 (0.282%) iter 65, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.027 (0.280%) iter 66, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.027 (0.279%) iter 67, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.027 (0.278%) iter 68, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.027 (0.277%) iter 69, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.027 (0.276%) iter 70, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.027 (0.275%) iter 71, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.027 (0.274%) iter 72, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.273%) iter 73, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.273%) iter 74, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.272%) iter 75, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.271%) iter 76, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.270%) iter 77, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.269%) iter 78, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.026 (0.269%) iter 79, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.026 (0.268%) iter 80, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.267%) iter 81, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.267%) iter 82, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.266%) iter 83, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.265%) iter 84, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.265%) iter 85, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.026 (0.264%) iter 86, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.025 (0.264%) iter 87, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.025 (0.263%) iter 88, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.025 (0.263%) iter 89, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.262%) iter 90, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.262%) iter 91, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.262%) iter 92, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.261%) iter 93, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.261%) iter 94, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.025 (0.261%) iter 95, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.025 (0.260%) iter 96, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.260%) iter 97, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.260%) iter 98, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.260%) iter 99, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.260%) iter 100, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.025 (0.259%) ---------- unfolding failed - restoring original position -------------------- 0147: dt=71.721236, rms=1.003 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.004, neg=0, invalid=96777 iter 0, gcam->neg = 3448 after 200 iterations, nbhd size=3, neg = 24 starting rms=0.025, neg=24, removing folds in lattice.... iter 1, dt=0.224000: new neg 75, old_neg 24, delta -51, rms=0.018 (26.519%) iter 2, dt=0.002294: new neg 73, old_neg 75, delta 2, rms=0.018 (0.801%) iter 3, dt=0.002294: new neg 71, old_neg 73, delta 2, rms=0.018 (0.798%) iter 4, dt=0.002294: new neg 69, old_neg 71, delta 2, rms=0.018 (0.795%) iter 5, dt=0.002294: new neg 68, old_neg 69, delta 1, rms=0.018 (0.791%) iter 6, dt=0.002294: new neg 62, old_neg 68, delta 6, rms=0.018 (0.788%) iter 7, dt=0.002294: new neg 60, old_neg 62, delta 2, rms=0.017 (0.785%) iter 8, dt=0.002294: new neg 59, old_neg 60, delta 1, rms=0.017 (0.781%) iter 9, dt=0.002294: new neg 58, old_neg 59, delta 1, rms=0.017 (0.778%) iter 10, dt=0.002294: new neg 57, old_neg 58, delta 1, rms=0.017 (0.775%) iter 11, dt=0.002294: new neg 55, old_neg 57, delta 2, rms=0.017 (0.771%) iter 12, dt=0.002294: new neg 55, old_neg 55, delta 0, rms=0.017 (0.768%) iter 13, dt=0.002294: new neg 54, old_neg 55, delta 1, rms=0.017 (0.765%) iter 14, dt=0.002294: new neg 53, old_neg 54, delta 1, rms=0.017 (0.762%) iter 15, dt=0.002294: new neg 53, old_neg 53, delta 0, rms=0.016 (0.758%) iter 16, dt=0.002294: new neg 53, old_neg 53, delta 0, rms=0.016 (0.755%) iter 17, dt=0.002294: new neg 51, old_neg 53, delta 2, rms=0.016 (0.752%) iter 18, dt=0.002294: new neg 49, old_neg 51, delta 2, rms=0.016 (0.749%) iter 19, dt=0.002294: new neg 47, old_neg 49, delta 2, rms=0.016 (0.746%) iter 20, dt=0.002294: new neg 46, old_neg 47, delta 1, rms=0.016 (0.743%) iter 21, dt=0.002294: new neg 45, old_neg 46, delta 1, rms=0.016 (0.740%) iter 22, dt=0.002294: new neg 43, old_neg 45, delta 2, rms=0.016 (0.737%) iter 23, dt=0.002294: new neg 43, old_neg 43, delta 0, rms=0.015 (0.733%) iter 24, dt=0.002294: new neg 41, old_neg 43, delta 2, rms=0.015 (0.730%) iter 25, dt=0.002294: new neg 35, old_neg 41, delta 6, rms=0.015 (0.727%) iter 26, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.015 (0.724%) iter 27, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.015 (0.720%) iter 28, dt=0.002294: new neg 31, old_neg 33, delta 2, rms=0.015 (0.717%) iter 29, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.015 (0.713%) iter 30, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.015 (0.709%) iter 31, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.015 (0.704%) iter 32, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.015 (0.699%) iter 33, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.014 (0.694%) iter 34, dt=0.002294: new neg 25, old_neg 27, delta 2, rms=0.014 (0.688%) iter 35, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.014 (0.681%) iter 36, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.014 (0.674%) iter 37, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.014 (0.666%) iter 38, dt=0.002294: new neg 20, old_neg 22, delta 2, rms=0.014 (0.657%) iter 39, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.014 (0.648%) iter 40, dt=0.002294: new neg 19, old_neg 19, delta 0, rms=0.014 (0.639%) iter 41, dt=0.002294: new neg 19, old_neg 19, delta 0, rms=0.014 (0.630%) iter 42, dt=0.002294: new neg 18, old_neg 19, delta 1, rms=0.014 (0.621%) iter 43, dt=0.002294: new neg 16, old_neg 18, delta 2, rms=0.013 (0.612%) iter 44, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.013 (0.603%) iter 45, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.013 (0.594%) iter 46, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.013 (0.585%) iter 47, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.013 (0.576%) iter 48, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.013 (0.567%) iter 49, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.013 (0.558%) iter 50, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.013 (0.549%) iter 51, dt=0.002294: new neg 7, old_neg 9, delta 2, rms=0.013 (0.540%) iter 52, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.013 (0.531%) iter 53, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.013 (0.522%) iter 54, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.514%) iter 55, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.505%) iter 56, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.498%) iter 57, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.490%) iter 58, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.012 (0.483%) iter 59, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.012 (0.476%) iter 60, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.012 (0.470%) iter 61, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.012 (0.464%) iter 62, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.012 (0.458%) iter 63, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.453%) iter 64, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.448%) iter 65, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.443%) iter 66, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.439%) iter 67, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.435%) iter 68, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.432%) iter 69, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.429%) iter 70, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.426%) iter 71, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.423%) iter 72, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.421%) iter 73, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.419%) iter 74, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.418%) iter 75, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.012 (0.416%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.415%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.413%) iter 78, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.412%) iter 79, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.411%) iter 80, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.410%) iter 81, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.410%) iter 82, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.409%) iter 83, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.408%) iter 84, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.407%) iter 85, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.406%) iter 86, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.405%) iter 87, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.402%) iter 88, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.399%) iter 89, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.394%) iter 90, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.386%) iter 91, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.375%) iter 92, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.361%) iter 93, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.011 (0.343%) iter 94, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.011 (0.324%) iter 95, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.011 (0.304%) iter 96, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.011 (0.285%) iter 97, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.268%) iter 98, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.254%) iter 99, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.242%) iter 100, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.233%) ---------- unfolding failed - restoring original position -------------------- 0148: dt=81.653170, rms=1.003 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 3448 after 200 iterations, nbhd size=3, neg = 24 starting rms=0.025, neg=24, removing folds in lattice.... iter 1, dt=0.224000: new neg 75, old_neg 24, delta -51, rms=0.018 (26.519%) iter 2, dt=0.002294: new neg 73, old_neg 75, delta 2, rms=0.018 (0.801%) iter 3, dt=0.002294: new neg 71, old_neg 73, delta 2, rms=0.018 (0.798%) iter 4, dt=0.002294: new neg 69, old_neg 71, delta 2, rms=0.018 (0.795%) iter 5, dt=0.002294: new neg 68, old_neg 69, delta 1, rms=0.018 (0.791%) iter 6, dt=0.002294: new neg 62, old_neg 68, delta 6, rms=0.018 (0.788%) iter 7, dt=0.002294: new neg 60, old_neg 62, delta 2, rms=0.017 (0.785%) iter 8, dt=0.002294: new neg 59, old_neg 60, delta 1, rms=0.017 (0.781%) iter 9, dt=0.002294: new neg 58, old_neg 59, delta 1, rms=0.017 (0.778%) iter 10, dt=0.002294: new neg 57, old_neg 58, delta 1, rms=0.017 (0.775%) iter 11, dt=0.002294: new neg 55, old_neg 57, delta 2, rms=0.017 (0.771%) iter 12, dt=0.002294: new neg 55, old_neg 55, delta 0, rms=0.017 (0.768%) iter 13, dt=0.002294: new neg 54, old_neg 55, delta 1, rms=0.017 (0.765%) iter 14, dt=0.002294: new neg 53, old_neg 54, delta 1, rms=0.017 (0.762%) iter 15, dt=0.002294: new neg 53, old_neg 53, delta 0, rms=0.016 (0.758%) iter 16, dt=0.002294: new neg 53, old_neg 53, delta 0, rms=0.016 (0.755%) iter 17, dt=0.002294: new neg 51, old_neg 53, delta 2, rms=0.016 (0.752%) iter 18, dt=0.002294: new neg 49, old_neg 51, delta 2, rms=0.016 (0.749%) iter 19, dt=0.002294: new neg 47, old_neg 49, delta 2, rms=0.016 (0.746%) iter 20, dt=0.002294: new neg 46, old_neg 47, delta 1, rms=0.016 (0.743%) iter 21, dt=0.002294: new neg 45, old_neg 46, delta 1, rms=0.016 (0.740%) iter 22, dt=0.002294: new neg 43, old_neg 45, delta 2, rms=0.016 (0.737%) iter 23, dt=0.002294: new neg 43, old_neg 43, delta 0, rms=0.015 (0.733%) iter 24, dt=0.002294: new neg 41, old_neg 43, delta 2, rms=0.015 (0.730%) iter 25, dt=0.002294: new neg 35, old_neg 41, delta 6, rms=0.015 (0.727%) iter 26, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.015 (0.724%) iter 27, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.015 (0.720%) iter 28, dt=0.002294: new neg 31, old_neg 33, delta 2, rms=0.015 (0.717%) iter 29, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.015 (0.713%) iter 30, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.015 (0.709%) iter 31, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.015 (0.704%) iter 32, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.015 (0.699%) iter 33, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.014 (0.694%) iter 34, dt=0.002294: new neg 25, old_neg 27, delta 2, rms=0.014 (0.688%) iter 35, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.014 (0.681%) iter 36, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.014 (0.674%) iter 37, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.014 (0.666%) iter 38, dt=0.002294: new neg 20, old_neg 22, delta 2, rms=0.014 (0.657%) iter 39, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.014 (0.648%) iter 40, dt=0.002294: new neg 19, old_neg 19, delta 0, rms=0.014 (0.639%) iter 41, dt=0.002294: new neg 19, old_neg 19, delta 0, rms=0.014 (0.630%) iter 42, dt=0.002294: new neg 18, old_neg 19, delta 1, rms=0.014 (0.621%) iter 43, dt=0.002294: new neg 16, old_neg 18, delta 2, rms=0.013 (0.612%) iter 44, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.013 (0.603%) iter 45, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.013 (0.594%) iter 46, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.013 (0.585%) iter 47, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.013 (0.576%) iter 48, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.013 (0.567%) iter 49, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.013 (0.558%) iter 50, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.013 (0.549%) iter 51, dt=0.002294: new neg 7, old_neg 9, delta 2, rms=0.013 (0.540%) iter 52, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.013 (0.531%) iter 53, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.013 (0.522%) iter 54, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.514%) iter 55, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.505%) iter 56, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.498%) iter 57, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.490%) iter 58, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.012 (0.483%) iter 59, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.012 (0.476%) iter 60, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.012 (0.470%) iter 61, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.012 (0.464%) iter 62, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.012 (0.458%) iter 63, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.453%) iter 64, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.448%) iter 65, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.443%) iter 66, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.439%) iter 67, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.435%) iter 68, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.432%) iter 69, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.429%) iter 70, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.426%) iter 71, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.423%) iter 72, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.421%) iter 73, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.419%) iter 74, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.012 (0.418%) iter 75, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.012 (0.416%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.415%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.413%) iter 78, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.412%) iter 79, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.411%) iter 80, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.410%) iter 81, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.410%) iter 82, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.409%) iter 83, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.408%) iter 84, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.407%) iter 85, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.406%) iter 86, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.405%) iter 87, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.402%) iter 88, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.399%) iter 89, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.394%) iter 90, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.386%) iter 91, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.375%) iter 92, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.011 (0.361%) iter 93, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.011 (0.343%) iter 94, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.011 (0.324%) iter 95, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.011 (0.304%) iter 96, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.011 (0.285%) iter 97, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.268%) iter 98, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.254%) iter 99, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.242%) iter 100, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.233%) ---------- unfolding failed - restoring original position -------------------- 0149: dt=81.653170, rms=1.003 (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=1.004, neg=0, invalid=96777 iter 0, gcam->neg = 16513 after 200 iterations, nbhd size=1, neg = 21 starting rms=0.039, neg=21, removing folds in lattice.... iter 1, dt=0.228925: new neg 126, old_neg 21, delta -105, rms=0.028 (28.455%) iter 2, dt=0.002294: new neg 124, old_neg 126, delta 2, rms=0.028 (0.623%) iter 3, dt=0.002294: new neg 119, old_neg 124, delta 5, rms=0.027 (0.618%) iter 4, dt=0.002294: new neg 113, old_neg 119, delta 6, rms=0.027 (0.614%) iter 5, dt=0.002294: new neg 112, old_neg 113, delta 1, rms=0.027 (0.609%) iter 6, dt=0.002294: new neg 107, old_neg 112, delta 5, rms=0.027 (0.604%) iter 7, dt=0.002294: new neg 104, old_neg 107, delta 3, rms=0.027 (0.598%) iter 8, dt=0.002294: new neg 98, old_neg 104, delta 6, rms=0.027 (0.593%) iter 9, dt=0.002294: new neg 95, old_neg 98, delta 3, rms=0.026 (0.588%) iter 10, dt=0.002294: new neg 90, old_neg 95, delta 5, rms=0.026 (0.583%) iter 11, dt=0.002294: new neg 86, old_neg 90, delta 4, rms=0.026 (0.577%) iter 12, dt=0.002294: new neg 80, old_neg 86, delta 6, rms=0.026 (0.572%) iter 13, dt=0.002294: new neg 77, old_neg 80, delta 3, rms=0.026 (0.566%) iter 14, dt=0.002294: new neg 71, old_neg 77, delta 6, rms=0.026 (0.560%) iter 15, dt=0.002294: new neg 69, old_neg 71, delta 2, rms=0.026 (0.555%) iter 16, dt=0.002294: new neg 64, old_neg 69, delta 5, rms=0.025 (0.549%) iter 17, dt=0.002294: new neg 62, old_neg 64, delta 2, rms=0.025 (0.544%) iter 18, dt=0.002294: new neg 62, old_neg 62, delta 0, rms=0.025 (0.539%) iter 19, dt=0.002294: new neg 60, old_neg 62, delta 2, rms=0.025 (0.533%) iter 20, dt=0.002294: new neg 58, old_neg 60, delta 2, rms=0.025 (0.528%) iter 21, dt=0.002294: new neg 57, old_neg 58, delta 1, rms=0.025 (0.523%) iter 22, dt=0.002294: new neg 56, old_neg 57, delta 1, rms=0.025 (0.519%) iter 23, dt=0.002294: new neg 53, old_neg 56, delta 3, rms=0.024 (0.514%) iter 24, dt=0.002294: new neg 51, old_neg 53, delta 2, rms=0.024 (0.509%) iter 25, dt=0.002294: new neg 51, old_neg 51, delta 0, rms=0.024 (0.505%) iter 26, dt=0.002294: new neg 48, old_neg 51, delta 3, rms=0.024 (0.500%) iter 27, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.024 (0.496%) iter 28, dt=0.002294: new neg 43, old_neg 48, delta 5, rms=0.024 (0.491%) iter 29, dt=0.002294: new neg 43, old_neg 43, delta 0, rms=0.024 (0.487%) iter 30, dt=0.002294: new neg 42, old_neg 43, delta 1, rms=0.024 (0.483%) iter 31, dt=0.002294: new neg 42, old_neg 42, delta 0, rms=0.023 (0.478%) iter 32, dt=0.002294: new neg 41, old_neg 42, delta 1, rms=0.023 (0.474%) iter 33, dt=0.002294: new neg 40, old_neg 41, delta 1, rms=0.023 (0.470%) iter 34, dt=0.002294: new neg 38, old_neg 40, delta 2, rms=0.023 (0.466%) iter 35, dt=0.002294: new neg 36, old_neg 38, delta 2, rms=0.023 (0.461%) iter 36, dt=0.002294: new neg 32, old_neg 36, delta 4, rms=0.023 (0.457%) iter 37, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.023 (0.453%) iter 38, dt=0.002294: new neg 29, old_neg 32, delta 3, rms=0.023 (0.449%) iter 39, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.023 (0.444%) iter 40, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.023 (0.440%) iter 41, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.022 (0.436%) iter 42, dt=0.002294: new neg 24, old_neg 28, delta 4, rms=0.022 (0.432%) iter 43, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.022 (0.428%) iter 44, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.022 (0.423%) iter 45, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.022 (0.419%) iter 46, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.022 (0.415%) iter 47, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.022 (0.411%) iter 48, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.022 (0.407%) iter 49, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.022 (0.403%) iter 50, dt=0.002294: new neg 18, old_neg 20, delta 2, rms=0.022 (0.399%) iter 51, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.022 (0.395%) iter 52, dt=0.002294: new neg 16, old_neg 18, delta 2, rms=0.021 (0.392%) iter 53, dt=0.002294: new neg 15, old_neg 16, delta 1, rms=0.021 (0.388%) iter 54, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.021 (0.384%) iter 55, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.021 (0.380%) iter 56, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.021 (0.376%) iter 57, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.021 (0.373%) iter 58, dt=0.002294: new neg 10, old_neg 12, delta 2, rms=0.021 (0.369%) iter 59, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.021 (0.365%) iter 60, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.021 (0.361%) iter 61, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.021 (0.356%) iter 62, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.021 (0.352%) iter 63, dt=0.002294: new neg 5, old_neg 8, delta 3, rms=0.021 (0.347%) iter 64, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.021 (0.341%) iter 65, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.020 (0.335%) iter 66, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.329%) iter 67, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.324%) iter 68, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.318%) iter 69, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.314%) iter 70, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.309%) iter 71, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.306%) iter 72, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.302%) iter 73, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.020 (0.299%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.020 (0.296%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.020 (0.293%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.020 (0.290%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.020 (0.287%) iter 78, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.020 (0.283%) iter 79, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.020 (0.280%) iter 80, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.020 (0.276%) iter 81, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.020 (0.272%) iter 82, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.268%) iter 83, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.264%) iter 84, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.260%) iter 85, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.256%) iter 86, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.253%) iter 87, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.250%) iter 88, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.248%) iter 89, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.245%) iter 90, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.243%) iter 91, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.241%) iter 92, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.239%) iter 93, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.237%) iter 94, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.236%) iter 95, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.234%) iter 96, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.232%) iter 97, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.231%) iter 98, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.230%) iter 99, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.228%) iter 100, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.227%) ---------- unfolding failed - restoring original position -------------------- 0150: dt=30.870588, rms=1.003 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 16513 after 200 iterations, nbhd size=1, neg = 21 starting rms=0.039, neg=21, removing folds in lattice.... iter 1, dt=0.228925: new neg 126, old_neg 21, delta -105, rms=0.028 (28.455%) iter 2, dt=0.002294: new neg 124, old_neg 126, delta 2, rms=0.028 (0.623%) iter 3, dt=0.002294: new neg 119, old_neg 124, delta 5, rms=0.027 (0.618%) iter 4, dt=0.002294: new neg 113, old_neg 119, delta 6, rms=0.027 (0.614%) iter 5, dt=0.002294: new neg 112, old_neg 113, delta 1, rms=0.027 (0.609%) iter 6, dt=0.002294: new neg 107, old_neg 112, delta 5, rms=0.027 (0.604%) iter 7, dt=0.002294: new neg 104, old_neg 107, delta 3, rms=0.027 (0.598%) iter 8, dt=0.002294: new neg 98, old_neg 104, delta 6, rms=0.027 (0.593%) iter 9, dt=0.002294: new neg 95, old_neg 98, delta 3, rms=0.026 (0.588%) iter 10, dt=0.002294: new neg 90, old_neg 95, delta 5, rms=0.026 (0.583%) iter 11, dt=0.002294: new neg 86, old_neg 90, delta 4, rms=0.026 (0.577%) iter 12, dt=0.002294: new neg 80, old_neg 86, delta 6, rms=0.026 (0.572%) iter 13, dt=0.002294: new neg 77, old_neg 80, delta 3, rms=0.026 (0.566%) iter 14, dt=0.002294: new neg 71, old_neg 77, delta 6, rms=0.026 (0.560%) iter 15, dt=0.002294: new neg 69, old_neg 71, delta 2, rms=0.026 (0.555%) iter 16, dt=0.002294: new neg 64, old_neg 69, delta 5, rms=0.025 (0.549%) iter 17, dt=0.002294: new neg 62, old_neg 64, delta 2, rms=0.025 (0.544%) iter 18, dt=0.002294: new neg 62, old_neg 62, delta 0, rms=0.025 (0.539%) iter 19, dt=0.002294: new neg 60, old_neg 62, delta 2, rms=0.025 (0.533%) iter 20, dt=0.002294: new neg 58, old_neg 60, delta 2, rms=0.025 (0.528%) iter 21, dt=0.002294: new neg 57, old_neg 58, delta 1, rms=0.025 (0.523%) iter 22, dt=0.002294: new neg 56, old_neg 57, delta 1, rms=0.025 (0.519%) iter 23, dt=0.002294: new neg 53, old_neg 56, delta 3, rms=0.024 (0.514%) iter 24, dt=0.002294: new neg 51, old_neg 53, delta 2, rms=0.024 (0.509%) iter 25, dt=0.002294: new neg 51, old_neg 51, delta 0, rms=0.024 (0.505%) iter 26, dt=0.002294: new neg 48, old_neg 51, delta 3, rms=0.024 (0.500%) iter 27, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.024 (0.496%) iter 28, dt=0.002294: new neg 43, old_neg 48, delta 5, rms=0.024 (0.491%) iter 29, dt=0.002294: new neg 43, old_neg 43, delta 0, rms=0.024 (0.487%) iter 30, dt=0.002294: new neg 42, old_neg 43, delta 1, rms=0.024 (0.483%) iter 31, dt=0.002294: new neg 42, old_neg 42, delta 0, rms=0.023 (0.478%) iter 32, dt=0.002294: new neg 41, old_neg 42, delta 1, rms=0.023 (0.474%) iter 33, dt=0.002294: new neg 40, old_neg 41, delta 1, rms=0.023 (0.470%) iter 34, dt=0.002294: new neg 38, old_neg 40, delta 2, rms=0.023 (0.466%) iter 35, dt=0.002294: new neg 36, old_neg 38, delta 2, rms=0.023 (0.461%) iter 36, dt=0.002294: new neg 32, old_neg 36, delta 4, rms=0.023 (0.457%) iter 37, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.023 (0.453%) iter 38, dt=0.002294: new neg 29, old_neg 32, delta 3, rms=0.023 (0.449%) iter 39, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.023 (0.444%) iter 40, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.023 (0.440%) iter 41, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.022 (0.436%) iter 42, dt=0.002294: new neg 24, old_neg 28, delta 4, rms=0.022 (0.432%) iter 43, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.022 (0.428%) iter 44, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.022 (0.423%) iter 45, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.022 (0.419%) iter 46, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.022 (0.415%) iter 47, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.022 (0.411%) iter 48, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.022 (0.407%) iter 49, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.022 (0.403%) iter 50, dt=0.002294: new neg 18, old_neg 20, delta 2, rms=0.022 (0.399%) iter 51, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.022 (0.395%) iter 52, dt=0.002294: new neg 16, old_neg 18, delta 2, rms=0.021 (0.392%) iter 53, dt=0.002294: new neg 15, old_neg 16, delta 1, rms=0.021 (0.388%) iter 54, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.021 (0.384%) iter 55, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.021 (0.380%) iter 56, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.021 (0.376%) iter 57, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.021 (0.373%) iter 58, dt=0.002294: new neg 10, old_neg 12, delta 2, rms=0.021 (0.369%) iter 59, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.021 (0.365%) iter 60, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.021 (0.361%) iter 61, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.021 (0.356%) iter 62, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.021 (0.352%) iter 63, dt=0.002294: new neg 5, old_neg 8, delta 3, rms=0.021 (0.347%) iter 64, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.021 (0.341%) iter 65, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.020 (0.335%) iter 66, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.329%) iter 67, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.324%) iter 68, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.318%) iter 69, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.314%) iter 70, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.309%) iter 71, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.306%) iter 72, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.020 (0.302%) iter 73, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.020 (0.299%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.020 (0.296%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.020 (0.293%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.020 (0.290%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.020 (0.287%) iter 78, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.020 (0.283%) iter 79, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.020 (0.280%) iter 80, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.020 (0.276%) iter 81, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.020 (0.272%) iter 82, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.268%) iter 83, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.264%) iter 84, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.260%) iter 85, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.256%) iter 86, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.253%) iter 87, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.250%) iter 88, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.248%) iter 89, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.245%) iter 90, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.243%) iter 91, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.241%) iter 92, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.239%) iter 93, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.237%) iter 94, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.236%) iter 95, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.234%) iter 96, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.232%) iter 97, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.231%) iter 98, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.230%) iter 99, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.228%) iter 100, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.019 (0.227%) ---------- unfolding failed - restoring original position -------------------- 0151: dt=30.870588, rms=1.003 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.004, neg=0, invalid=96777 iter 0, gcam->neg = 4672 after 200 iterations, nbhd size=1, neg = 10 starting rms=0.024, neg=10, removing folds in lattice.... iter 1, dt=0.194834: new neg 34, old_neg 10, delta -24, rms=0.016 (34.014%) iter 2, dt=0.002294: new neg 32, old_neg 34, delta 2, rms=0.016 (0.742%) iter 3, dt=0.002294: new neg 30, old_neg 32, delta 2, rms=0.016 (0.734%) iter 4, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.016 (0.727%) iter 5, dt=0.002294: new neg 27, old_neg 29, delta 2, rms=0.016 (0.720%) iter 6, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.015 (0.712%) iter 7, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.015 (0.704%) iter 8, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.015 (0.697%) iter 9, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.015 (0.689%) iter 10, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.015 (0.682%) iter 11, dt=0.002294: new neg 22, old_neg 24, delta 2, rms=0.015 (0.674%) iter 12, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.015 (0.666%) iter 13, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.015 (0.659%) iter 14, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.015 (0.651%) iter 15, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.015 (0.644%) iter 16, dt=0.002294: new neg 18, old_neg 19, delta 1, rms=0.014 (0.636%) iter 17, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.014 (0.629%) iter 18, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.014 (0.621%) iter 19, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.014 (0.614%) iter 20, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.014 (0.607%) iter 21, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.014 (0.599%) iter 22, dt=0.002294: new neg 11, old_neg 14, delta 3, rms=0.014 (0.592%) iter 23, dt=0.002294: new neg 9, old_neg 11, delta 2, rms=0.014 (0.585%) iter 24, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.014 (0.578%) iter 25, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.014 (0.571%) iter 26, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.014 (0.564%) iter 27, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.014 (0.558%) iter 28, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.013 (0.551%) iter 29, dt=0.002294: new neg 7, old_neg 9, delta 2, rms=0.013 (0.544%) iter 30, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.013 (0.538%) iter 31, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.013 (0.531%) iter 32, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.525%) iter 33, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.518%) iter 34, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.512%) iter 35, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.506%) iter 36, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.500%) iter 37, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.013 (0.494%) iter 38, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.489%) iter 39, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.013 (0.483%) iter 40, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.013 (0.477%) iter 41, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.013 (0.472%) iter 42, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.013 (0.467%) iter 43, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.012 (0.461%) iter 44, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.012 (0.456%) iter 45, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.012 (0.451%) iter 46, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.012 (0.446%) iter 47, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.442%) iter 48, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.437%) iter 49, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.433%) iter 50, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.428%) iter 51, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.424%) iter 52, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.420%) iter 53, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.012 (0.416%) iter 54, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.412%) iter 55, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.408%) iter 56, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.404%) iter 57, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.400%) iter 58, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.396%) iter 59, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.392%) iter 60, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.389%) iter 61, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.385%) iter 62, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.382%) iter 63, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.378%) iter 64, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.375%) iter 65, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.372%) iter 66, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.369%) iter 67, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.366%) iter 68, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.363%) iter 69, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.359%) iter 70, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.357%) iter 71, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.354%) iter 72, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.351%) iter 73, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.348%) iter 74, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.345%) iter 75, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.342%) iter 76, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.340%) iter 77, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.337%) iter 78, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.335%) iter 79, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.332%) iter 80, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.330%) iter 81, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.327%) iter 82, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.325%) iter 83, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.322%) iter 84, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.320%) iter 85, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.318%) iter 86, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.315%) iter 87, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.313%) iter 88, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.311%) iter 89, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.309%) iter 90, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.307%) iter 91, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.304%) iter 92, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.302%) iter 93, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.300%) iter 94, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.298%) iter 95, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.296%) iter 96, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.294%) iter 97, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.292%) iter 98, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.290%) iter 99, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.288%) iter 100, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.286%) ---------- unfolding failed - restoring original position -------------------- 0152: dt=28.568953, rms=1.003 (0.095%), neg=0, invalid=96777 iter 0, gcam->neg = 4672 after 200 iterations, nbhd size=1, neg = 10 starting rms=0.024, neg=10, removing folds in lattice.... iter 1, dt=0.194834: new neg 34, old_neg 10, delta -24, rms=0.016 (34.014%) iter 2, dt=0.002294: new neg 32, old_neg 34, delta 2, rms=0.016 (0.742%) iter 3, dt=0.002294: new neg 30, old_neg 32, delta 2, rms=0.016 (0.734%) iter 4, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.016 (0.727%) iter 5, dt=0.002294: new neg 27, old_neg 29, delta 2, rms=0.016 (0.720%) iter 6, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.015 (0.712%) iter 7, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.015 (0.704%) iter 8, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.015 (0.697%) iter 9, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.015 (0.689%) iter 10, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.015 (0.682%) iter 11, dt=0.002294: new neg 22, old_neg 24, delta 2, rms=0.015 (0.674%) iter 12, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.015 (0.666%) iter 13, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.015 (0.659%) iter 14, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.015 (0.651%) iter 15, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.015 (0.644%) iter 16, dt=0.002294: new neg 18, old_neg 19, delta 1, rms=0.014 (0.636%) iter 17, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.014 (0.629%) iter 18, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.014 (0.621%) iter 19, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.014 (0.614%) iter 20, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.014 (0.607%) iter 21, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.014 (0.599%) iter 22, dt=0.002294: new neg 11, old_neg 14, delta 3, rms=0.014 (0.592%) iter 23, dt=0.002294: new neg 9, old_neg 11, delta 2, rms=0.014 (0.585%) iter 24, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.014 (0.578%) iter 25, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.014 (0.571%) iter 26, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.014 (0.564%) iter 27, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.014 (0.558%) iter 28, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.013 (0.551%) iter 29, dt=0.002294: new neg 7, old_neg 9, delta 2, rms=0.013 (0.544%) iter 30, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.013 (0.538%) iter 31, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.013 (0.531%) iter 32, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.525%) iter 33, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.518%) iter 34, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.512%) iter 35, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.506%) iter 36, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.013 (0.500%) iter 37, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.013 (0.494%) iter 38, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.013 (0.489%) iter 39, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.013 (0.483%) iter 40, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.013 (0.477%) iter 41, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.013 (0.472%) iter 42, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.013 (0.467%) iter 43, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.012 (0.461%) iter 44, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.012 (0.456%) iter 45, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.012 (0.451%) iter 46, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.012 (0.446%) iter 47, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.442%) iter 48, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.437%) iter 49, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.433%) iter 50, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.428%) iter 51, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.424%) iter 52, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.012 (0.420%) iter 53, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.012 (0.416%) iter 54, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.412%) iter 55, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.408%) iter 56, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.404%) iter 57, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.400%) iter 58, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.396%) iter 59, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.392%) iter 60, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.389%) iter 61, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.385%) iter 62, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.012 (0.382%) iter 63, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.378%) iter 64, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.375%) iter 65, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.372%) iter 66, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.369%) iter 67, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.366%) iter 68, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.363%) iter 69, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.359%) iter 70, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.357%) iter 71, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.354%) iter 72, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.351%) iter 73, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.348%) iter 74, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.345%) iter 75, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.342%) iter 76, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.340%) iter 77, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.337%) iter 78, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.335%) iter 79, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.332%) iter 80, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.330%) iter 81, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.327%) iter 82, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.325%) iter 83, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.322%) iter 84, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.320%) iter 85, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.318%) iter 86, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.315%) iter 87, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.313%) iter 88, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.311%) iter 89, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.011 (0.309%) iter 90, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.307%) iter 91, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.304%) iter 92, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.302%) iter 93, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.300%) iter 94, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.298%) iter 95, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.296%) iter 96, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.294%) iter 97, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.292%) iter 98, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.290%) iter 99, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.288%) iter 100, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.010 (0.286%) ---------- unfolding failed - restoring original position -------------------- 0153: dt=28.568953, rms=1.003 (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=1.005, neg=0, invalid=96777 iter 0, gcam->neg = 437 after 200 iterations, nbhd size=2, neg = 3 starting rms=0.009, neg=3, removing folds in lattice.... iter 1, dt=0.278114: new neg 0, old_neg 3, delta 3, rms=0.004 (56.909%) 0154: dt=7.168000, rms=0.863 (14.082%), neg=0, invalid=96777 0155: dt=0.000000, rms=0.863 (0.013%), neg=0, invalid=96777 0156: dt=0.100000, rms=0.863 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.864, neg=0, invalid=96777 0157: dt=0.000000, rms=0.863 (0.093%), neg=0, invalid=96777 0158: dt=0.000000, rms=0.863 (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=0.844, neg=0, invalid=96777 iter 0, gcam->neg = 4059 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.013, neg=1, removing folds in lattice.... iter 1, dt=0.188037: new neg 4, old_neg 1, delta -3, rms=0.004 (66.355%) iter 2, dt=0.056641: new neg 0, old_neg 4, delta 4, rms=0.003 (27.549%) 0159: dt=2.842211, rms=0.778 (7.868%), neg=0, invalid=96777 iter 0, gcam->neg = 46 after 30 iterations, nbhd size=4, neg = 0 0160: dt=0.320000, rms=0.776 (0.265%), neg=0, invalid=96777 0161: dt=0.000000, rms=0.776 (-0.001%), neg=0, invalid=96777 0162: dt=0.050000, rms=0.776 (-0.007%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.777, neg=0, invalid=96777 iter 0, gcam->neg = 21 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... iter 1, dt=0.056000: new neg 0, old_neg 1, delta 1, rms=0.001 (79.955%) 0163: dt=0.256000, rms=0.775 (0.207%), neg=0, invalid=96777 0164: dt=0.028000, rms=0.775 (0.002%), neg=0, invalid=96777 0165: dt=0.028000, rms=0.775 (-0.002%), 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 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.761, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0166: dt=129.472000, rms=0.752 (1.222%), neg=0, invalid=96777 iter 0, gcam->neg = 38 after 200 iterations, nbhd size=4, neg = 9 starting rms=0.009, neg=9, removing folds in lattice.... iter 1, dt=0.160000: new neg 7, old_neg 9, delta 2, rms=0.004 (53.568%) iter 2, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (2.512%) iter 3, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (2.527%) iter 4, dt=0.002294: new neg 5, old_neg 7, delta 2, rms=0.004 (2.542%) iter 5, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.004 (2.559%) iter 6, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (2.577%) iter 7, dt=0.002294: new neg 2, old_neg 4, delta 2, rms=0.003 (2.597%) iter 8, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.620%) iter 9, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.648%) iter 10, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.680%) iter 11, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.718%) iter 12, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.762%) iter 13, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.812%) iter 14, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.870%) iter 15, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.934%) iter 16, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (3.005%) iter 17, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (3.083%) iter 18, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (3.169%) iter 19, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.002 (3.264%) iter 20, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.002 (3.369%) iter 21, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.002 (3.487%) iter 22, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (3.620%) iter 23, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (3.773%) iter 24, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (3.949%) iter 25, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (4.151%) iter 26, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (4.384%) iter 27, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (4.649%) iter 28, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (4.941%) iter 29, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (5.244%) iter 30, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (5.522%) iter 31, dt=0.070424: new neg 0, old_neg 1, delta 1, rms=0.001 (34.805%) 0167: dt=295.936000, rms=0.742 (1.376%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.739 (0.403%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.738 (0.090%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.738 (0.058%), neg=0, invalid=96777 0171: dt=32.368000, rms=0.737 (0.086%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 19 starting rms=0.010, neg=19, removing folds in lattice.... iter 1, dt=0.282942: new neg 5, old_neg 19, delta 14, rms=0.004 (56.739%) iter 2, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.004 (2.082%) iter 3, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (2.087%) iter 4, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (2.087%) iter 5, dt=0.207031: new neg 3, old_neg 4, delta 1, rms=0.002 (56.256%) iter 6, dt=0.120931: new neg 0, old_neg 3, delta 3, rms=0.001 (41.425%) 0172: dt=32.368000, rms=0.736 (0.084%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0173: dt=32.368000, rms=0.735 (0.147%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 1 iterations, nbhd size=0, neg = 0 0174: dt=32.368000, rms=0.734 (0.225%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.003, neg=4, removing folds in lattice.... iter 1, dt=0.056598: new neg 0, old_neg 4, delta 4, rms=0.001 (49.687%) 0175: dt=32.368000, rms=0.732 (0.246%), neg=0, invalid=96777 0176: dt=32.368000, rms=0.731 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0177: dt=32.368000, rms=0.731 (0.081%), neg=0, invalid=96777 0178: dt=32.368000, rms=0.730 (0.128%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 25 iterations, nbhd size=2, neg = 0 0179: dt=32.368000, rms=0.729 (0.174%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 200 iterations, nbhd size=1, neg = 36 starting rms=0.016, neg=36, removing folds in lattice.... iter 1, dt=0.224000: new neg 24, old_neg 36, delta 12, rms=0.010 (37.818%) iter 2, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.010 (1.287%) iter 3, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.010 (1.293%) iter 4, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.009 (1.299%) iter 5, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.009 (1.305%) iter 6, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.009 (1.310%) iter 7, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.009 (1.316%) iter 8, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.009 (1.322%) iter 9, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.009 (1.327%) iter 10, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (1.332%) iter 11, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (1.337%) iter 12, dt=0.002294: new neg 18, old_neg 20, delta 2, rms=0.008 (1.342%) iter 13, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.008 (1.346%) iter 14, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (1.350%) iter 15, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (1.353%) iter 16, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.008 (1.356%) iter 17, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (1.358%) iter 18, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (1.360%) iter 19, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (1.361%) iter 20, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.008 (1.362%) iter 21, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.007 (1.362%) iter 22, dt=0.002294: new neg 12, old_neg 14, delta 2, rms=0.007 (1.362%) iter 23, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.007 (1.361%) iter 24, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.007 (1.360%) iter 25, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (1.358%) iter 26, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (1.357%) iter 27, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.007 (1.355%) iter 28, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.007 (1.354%) iter 29, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.007 (1.351%) iter 30, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (1.349%) iter 31, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (1.347%) iter 32, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (1.345%) iter 33, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.345%) iter 34, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.345%) iter 35, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.346%) iter 36, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.348%) iter 37, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.351%) iter 38, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.355%) iter 39, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.361%) iter 40, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (1.367%) iter 41, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (1.375%) iter 42, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.384%) iter 43, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.394%) iter 44, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.404%) iter 45, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.416%) iter 46, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.428%) iter 47, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.440%) iter 48, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.454%) iter 49, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.005 (1.468%) iter 50, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.483%) iter 51, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.499%) iter 52, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.516%) iter 53, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.534%) iter 54, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.553%) iter 55, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.573%) iter 56, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.595%) iter 57, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.004 (1.618%) iter 58, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.642%) iter 59, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.668%) iter 60, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.695%) iter 61, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.724%) iter 62, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.755%) iter 63, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.787%) iter 64, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.821%) iter 65, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.856%) iter 66, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.893%) iter 67, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.004 (1.931%) iter 68, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.004 (1.972%) iter 69, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (2.014%) iter 70, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (2.058%) iter 71, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.104%) iter 72, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.152%) iter 73, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.202%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.253%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.306%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.360%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.415%) iter 78, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.469%) iter 79, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.003 (2.524%) iter 80, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.578%) iter 81, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.632%) iter 82, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.687%) iter 83, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (2.743%) iter 84, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.002 (2.801%) iter 85, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (2.864%) iter 86, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (2.931%) iter 87, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (3.003%) iter 88, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (3.078%) iter 89, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.002 (3.150%) iter 90, dt=0.195703: new neg 0, old_neg 1, delta 1, rms=0.002 (22.165%) 0180: dt=32.368000, rms=0.728 (0.145%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 6 starting rms=0.004, neg=6, removing folds in lattice.... iter 1, dt=0.066276: new neg 0, old_neg 6, delta 6, rms=0.002 (51.285%) 0181: dt=32.368000, rms=0.727 (0.056%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0182: dt=32.368000, rms=0.727 (0.051%), neg=0, invalid=96777 iter 0, gcam->neg = 549 after 200 iterations, nbhd size=4, neg = 166 starting rms=0.029, neg=166, removing folds in lattice.... iter 1, dt=0.291108: new neg 95, old_neg 166, delta 71, rms=0.019 (34.493%) iter 2, dt=0.002294: new neg 93, old_neg 95, delta 2, rms=0.019 (0.778%) iter 3, dt=0.002294: new neg 90, old_neg 93, delta 3, rms=0.019 (0.777%) iter 4, dt=0.002294: new neg 89, old_neg 90, delta 1, rms=0.019 (0.776%) iter 5, dt=0.002294: new neg 87, old_neg 89, delta 2, rms=0.019 (0.776%) iter 6, dt=0.002294: new neg 86, old_neg 87, delta 1, rms=0.018 (0.776%) iter 7, dt=0.002294: new neg 86, old_neg 86, delta 0, rms=0.018 (0.775%) iter 8, dt=0.002294: new neg 85, old_neg 86, delta 1, rms=0.018 (0.775%) iter 9, dt=0.002294: new neg 85, old_neg 85, delta 0, rms=0.018 (0.775%) iter 10, dt=0.002294: new neg 84, old_neg 85, delta 1, rms=0.018 (0.775%) iter 11, dt=0.002294: new neg 83, old_neg 84, delta 1, rms=0.018 (0.775%) iter 12, dt=0.002294: new neg 82, old_neg 83, delta 1, rms=0.018 (0.776%) iter 13, dt=0.002294: new neg 82, old_neg 82, delta 0, rms=0.018 (0.776%) iter 14, dt=0.002294: new neg 80, old_neg 82, delta 2, rms=0.017 (0.777%) iter 15, dt=0.002294: new neg 79, old_neg 80, delta 1, rms=0.017 (0.778%) iter 16, dt=0.002294: new neg 78, old_neg 79, delta 1, rms=0.017 (0.778%) iter 17, dt=0.002294: new neg 77, old_neg 78, delta 1, rms=0.017 (0.779%) iter 18, dt=0.002294: new neg 76, old_neg 77, delta 1, rms=0.017 (0.780%) iter 19, dt=0.002294: new neg 76, old_neg 76, delta 0, rms=0.017 (0.780%) iter 20, dt=0.002294: new neg 72, old_neg 76, delta 4, rms=0.017 (0.781%) iter 21, dt=0.002294: new neg 72, old_neg 72, delta 0, rms=0.016 (0.781%) iter 22, dt=0.002294: new neg 71, old_neg 72, delta 1, rms=0.016 (0.782%) iter 23, dt=0.002294: new neg 71, old_neg 71, delta 0, rms=0.016 (0.782%) iter 24, dt=0.002294: new neg 70, old_neg 71, delta 1, rms=0.016 (0.783%) iter 25, dt=0.002294: new neg 68, old_neg 70, delta 2, rms=0.016 (0.784%) iter 26, dt=0.002294: new neg 67, old_neg 68, delta 1, rms=0.016 (0.784%) iter 27, dt=0.002294: new neg 65, old_neg 67, delta 2, rms=0.016 (0.784%) iter 28, dt=0.002294: new neg 64, old_neg 65, delta 1, rms=0.016 (0.784%) iter 29, dt=0.002294: new neg 62, old_neg 64, delta 2, rms=0.015 (0.784%) iter 30, dt=0.002294: new neg 61, old_neg 62, delta 1, rms=0.015 (0.784%) iter 31, dt=0.002294: new neg 60, old_neg 61, delta 1, rms=0.015 (0.783%) iter 32, dt=0.002294: new neg 57, old_neg 60, delta 3, rms=0.015 (0.782%) iter 33, dt=0.002294: new neg 56, old_neg 57, delta 1, rms=0.015 (0.781%) iter 34, dt=0.002294: new neg 55, old_neg 56, delta 1, rms=0.015 (0.780%) iter 35, dt=0.002294: new neg 53, old_neg 55, delta 2, rms=0.015 (0.779%) iter 36, dt=0.002294: new neg 50, old_neg 53, delta 3, rms=0.015 (0.777%) iter 37, dt=0.002294: new neg 49, old_neg 50, delta 1, rms=0.014 (0.776%) iter 38, dt=0.002294: new neg 49, old_neg 49, delta 0, rms=0.014 (0.774%) iter 39, dt=0.002294: new neg 48, old_neg 49, delta 1, rms=0.014 (0.772%) iter 40, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.014 (0.769%) iter 41, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.014 (0.767%) iter 42, dt=0.002294: new neg 48, old_neg 48, delta 0, rms=0.014 (0.764%) iter 43, dt=0.002294: new neg 47, old_neg 48, delta 1, rms=0.014 (0.762%) iter 44, dt=0.002294: new neg 44, old_neg 47, delta 3, rms=0.014 (0.758%) iter 45, dt=0.002294: new neg 44, old_neg 44, delta 0, rms=0.014 (0.755%) iter 46, dt=0.002294: new neg 43, old_neg 44, delta 1, rms=0.014 (0.752%) iter 47, dt=0.002294: new neg 39, old_neg 43, delta 4, rms=0.013 (0.748%) iter 48, dt=0.002294: new neg 39, old_neg 39, delta 0, rms=0.013 (0.744%) iter 49, dt=0.002294: new neg 39, old_neg 39, delta 0, rms=0.013 (0.740%) iter 50, dt=0.002294: new neg 38, old_neg 39, delta 1, rms=0.013 (0.737%) iter 51, dt=0.002294: new neg 35, old_neg 38, delta 3, rms=0.013 (0.733%) iter 52, dt=0.002294: new neg 32, old_neg 35, delta 3, rms=0.013 (0.729%) iter 53, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.013 (0.725%) iter 54, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.013 (0.721%) iter 55, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.013 (0.718%) iter 56, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.013 (0.714%) iter 57, dt=0.002294: new neg 31, old_neg 32, delta 1, rms=0.012 (0.710%) iter 58, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.012 (0.707%) iter 59, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.012 (0.703%) iter 60, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.012 (0.700%) iter 61, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.012 (0.697%) iter 62, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.012 (0.693%) iter 63, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.012 (0.690%) iter 64, dt=0.002294: new neg 25, old_neg 28, delta 3, rms=0.012 (0.687%) iter 65, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.012 (0.684%) iter 66, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.012 (0.682%) iter 67, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.012 (0.680%) iter 68, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.012 (0.677%) iter 69, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.011 (0.675%) iter 70, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.011 (0.673%) iter 71, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.011 (0.671%) iter 72, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.011 (0.669%) iter 73, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.011 (0.667%) iter 74, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.011 (0.665%) iter 75, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.011 (0.663%) iter 76, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.011 (0.661%) iter 77, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.011 (0.659%) iter 78, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.011 (0.657%) iter 79, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.011 (0.656%) iter 80, dt=0.002294: new neg 19, old_neg 21, delta 2, rms=0.011 (0.654%) iter 81, dt=0.002294: new neg 18, old_neg 19, delta 1, rms=0.011 (0.652%) iter 82, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.011 (0.651%) iter 83, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.010 (0.650%) iter 84, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.010 (0.649%) iter 85, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.010 (0.648%) iter 86, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.648%) iter 87, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.648%) iter 88, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.648%) iter 89, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.648%) iter 90, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.648%) iter 91, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.647%) iter 92, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.647%) iter 93, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.646%) iter 94, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.010 (0.645%) iter 95, dt=0.002294: new neg 15, old_neg 16, delta 1, rms=0.010 (0.643%) iter 96, dt=0.002294: new neg 15, old_neg 15, delta 0, rms=0.010 (0.640%) iter 97, dt=0.002294: new neg 15, old_neg 15, delta 0, rms=0.010 (0.637%) iter 98, dt=0.002294: new neg 15, old_neg 15, delta 0, rms=0.010 (0.634%) iter 99, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.009 (0.629%) iter 100, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.009 (0.625%) ---------- unfolding failed - restoring original position -------------------- 0183: dt=1775.616000, rms=0.727 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.727, neg=0, invalid=96777 0184: dt=295.936000, rms=0.721 (0.757%), neg=0, invalid=96777 0185: dt=32.368000, rms=0.720 (0.155%), neg=0, invalid=96777 0186: dt=32.368000, rms=0.720 (0.048%), neg=0, invalid=96777 0187: dt=32.368000, rms=0.720 (0.003%), neg=0, invalid=96777 0188: dt=32.368000, rms=0.720 (-0.044%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.720, neg=0, invalid=96777 iter 0, gcam->neg = 582 after 200 iterations, nbhd size=1, neg = 135 starting rms=0.025, neg=135, removing folds in lattice.... iter 1, dt=0.224000: new neg 70, old_neg 135, delta 65, rms=0.015 (41.908%) iter 2, dt=0.002294: new neg 68, old_neg 70, delta 2, rms=0.014 (1.064%) iter 3, dt=0.002294: new neg 66, old_neg 68, delta 2, rms=0.014 (1.058%) iter 4, dt=0.002294: new neg 63, old_neg 66, delta 3, rms=0.014 (1.053%) iter 5, dt=0.002294: new neg 61, old_neg 63, delta 2, rms=0.014 (1.048%) iter 6, dt=0.002294: new neg 61, old_neg 61, delta 0, rms=0.014 (1.044%) iter 7, dt=0.002294: new neg 58, old_neg 61, delta 3, rms=0.014 (1.039%) iter 8, dt=0.002294: new neg 56, old_neg 58, delta 2, rms=0.014 (1.035%) iter 9, dt=0.002294: new neg 55, old_neg 56, delta 1, rms=0.013 (1.030%) iter 10, dt=0.002294: new neg 55, old_neg 55, delta 0, rms=0.013 (1.026%) iter 11, dt=0.002294: new neg 55, old_neg 55, delta 0, rms=0.013 (1.023%) iter 12, dt=0.002294: new neg 53, old_neg 55, delta 2, rms=0.013 (1.020%) iter 13, dt=0.002294: new neg 52, old_neg 53, delta 1, rms=0.013 (1.018%) iter 14, dt=0.002294: new neg 50, old_neg 52, delta 2, rms=0.013 (1.016%) iter 15, dt=0.002294: new neg 50, old_neg 50, delta 0, rms=0.013 (1.014%) iter 16, dt=0.002294: new neg 50, old_neg 50, delta 0, rms=0.013 (1.012%) iter 17, dt=0.002294: new neg 47, old_neg 50, delta 3, rms=0.012 (1.011%) iter 18, dt=0.002294: new neg 46, old_neg 47, delta 1, rms=0.012 (1.010%) iter 19, dt=0.002294: new neg 46, old_neg 46, delta 0, rms=0.012 (1.010%) iter 20, dt=0.002294: new neg 43, old_neg 46, delta 3, rms=0.012 (1.010%) iter 21, dt=0.002294: new neg 42, old_neg 43, delta 1, rms=0.012 (1.011%) iter 22, dt=0.002294: new neg 42, old_neg 42, delta 0, rms=0.012 (1.012%) iter 23, dt=0.002294: new neg 42, old_neg 42, delta 0, rms=0.012 (1.013%) iter 24, dt=0.002294: new neg 40, old_neg 42, delta 2, rms=0.012 (1.014%) iter 25, dt=0.002294: new neg 38, old_neg 40, delta 2, rms=0.011 (1.016%) iter 26, dt=0.002294: new neg 37, old_neg 38, delta 1, rms=0.011 (1.018%) iter 27, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.011 (1.021%) iter 28, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.011 (1.024%) iter 29, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.011 (1.027%) iter 30, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.011 (1.031%) iter 31, dt=0.002294: new neg 35, old_neg 37, delta 2, rms=0.011 (1.034%) iter 32, dt=0.002294: new neg 33, old_neg 35, delta 2, rms=0.011 (1.038%) iter 33, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.011 (1.042%) iter 34, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.010 (1.046%) iter 35, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.010 (1.052%) iter 36, dt=0.002294: new neg 32, old_neg 33, delta 1, rms=0.010 (1.057%) iter 37, dt=0.002294: new neg 29, old_neg 32, delta 3, rms=0.010 (1.062%) iter 38, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.010 (1.068%) iter 39, dt=0.002294: new neg 29, old_neg 28, delta -1, rms=0.010 (1.074%) iter 40, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.010 (1.080%) iter 41, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.010 (1.086%) iter 42, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.010 (1.092%) iter 43, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.009 (1.098%) iter 44, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.009 (1.103%) iter 45, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.009 (1.107%) iter 46, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.009 (1.111%) iter 47, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.009 (1.114%) iter 48, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.009 (1.116%) iter 49, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.009 (1.117%) iter 50, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.009 (1.118%) iter 51, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.009 (1.119%) iter 52, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.009 (1.119%) iter 53, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.008 (1.119%) iter 54, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.008 (1.118%) iter 55, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.008 (1.115%) iter 56, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.008 (1.112%) iter 57, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.008 (1.108%) iter 58, dt=0.002294: new neg 19, old_neg 19, delta 0, rms=0.008 (1.109%) iter 59, dt=0.002294: new neg 16, old_neg 19, delta 3, rms=0.008 (1.106%) iter 60, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (1.103%) iter 61, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.008 (1.101%) iter 62, dt=0.002294: new neg 15, old_neg 16, delta 1, rms=0.008 (1.102%) iter 63, dt=0.002294: new neg 15, old_neg 15, delta 0, rms=0.008 (1.102%) iter 64, dt=0.002294: new neg 15, old_neg 15, delta 0, rms=0.007 (1.101%) iter 65, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.007 (1.100%) iter 66, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.007 (1.103%) iter 67, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.007 (1.103%) iter 68, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.007 (1.103%) iter 69, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.101%) iter 70, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.104%) iter 71, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.102%) iter 72, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.101%) iter 73, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.007 (1.096%) iter 74, dt=0.002294: new neg 10, old_neg 12, delta 2, rms=0.007 (1.099%) iter 75, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.007 (1.094%) iter 76, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.007 (1.093%) iter 77, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (1.088%) iter 78, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (1.092%) iter 79, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (1.090%) iter 80, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (1.089%) iter 81, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.089%) iter 82, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.092%) iter 83, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.094%) iter 84, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (1.095%) iter 85, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.097%) iter 86, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.103%) iter 87, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (1.107%) iter 88, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.006 (1.116%) iter 89, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.122%) iter 90, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.129%) iter 91, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.136%) iter 92, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.146%) iter 93, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.159%) iter 94, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.171%) iter 95, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.181%) iter 96, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.005 (1.193%) iter 97, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.212%) iter 98, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.224%) iter 99, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.244%) iter 100, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.257%) ---------- unfolding failed - restoring original position -------------------- 0189: dt=103.680000, rms=0.720 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.720, neg=0, invalid=96777 iter 0, gcam->neg = 330 after 200 iterations, nbhd size=3, neg = 89 starting rms=0.021, neg=89, removing folds in lattice.... iter 1, dt=0.213532: new neg 41, old_neg 89, delta 48, rms=0.011 (45.544%) iter 2, dt=0.002294: new neg 40, old_neg 41, delta 1, rms=0.011 (1.205%) iter 3, dt=0.002294: new neg 36, old_neg 40, delta 4, rms=0.011 (1.206%) iter 4, dt=0.002294: new neg 36, old_neg 36, delta 0, rms=0.011 (1.207%) iter 5, dt=0.002294: new neg 36, old_neg 36, delta 0, rms=0.011 (1.209%) iter 6, dt=0.002294: new neg 34, old_neg 36, delta 2, rms=0.011 (1.213%) iter 7, dt=0.002294: new neg 34, old_neg 34, delta 0, rms=0.011 (1.217%) iter 8, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.010 (1.222%) iter 9, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.010 (1.227%) iter 10, dt=0.002294: new neg 31, old_neg 33, delta 2, rms=0.010 (1.233%) iter 11, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.010 (1.239%) iter 12, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.010 (1.246%) iter 13, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (1.253%) iter 14, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (1.261%) iter 15, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.010 (1.269%) iter 16, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.009 (1.277%) iter 17, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.009 (1.286%) iter 18, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.009 (1.295%) iter 19, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.009 (1.304%) iter 20, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.009 (1.312%) iter 21, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.009 (1.320%) iter 22, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.009 (1.328%) iter 23, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.009 (1.335%) iter 24, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.009 (1.340%) iter 25, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.008 (1.344%) iter 26, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.008 (1.347%) iter 27, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.008 (1.349%) iter 28, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.008 (1.348%) iter 29, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.008 (1.346%) iter 30, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.008 (1.343%) iter 31, dt=0.002294: new neg 19, old_neg 22, delta 3, rms=0.008 (1.337%) iter 32, dt=0.002294: new neg 16, old_neg 19, delta 3, rms=0.008 (1.330%) iter 33, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.008 (1.323%) iter 34, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.007 (1.314%) iter 35, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.007 (1.305%) iter 36, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.296%) iter 37, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.007 (1.288%) iter 38, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.007 (1.279%) iter 39, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.007 (1.271%) iter 40, dt=0.002294: new neg 9, old_neg 11, delta 2, rms=0.007 (1.263%) iter 41, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (1.256%) iter 42, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (1.249%) iter 43, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (1.243%) iter 44, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (1.238%) iter 45, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (1.232%) iter 46, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (1.227%) iter 47, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (1.222%) iter 48, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.006 (1.218%) iter 49, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (1.213%) iter 50, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (1.208%) iter 51, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.204%) iter 52, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.201%) iter 53, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.197%) iter 54, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.194%) iter 55, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (1.191%) iter 56, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.189%) iter 57, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.188%) iter 58, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.006 (1.188%) iter 59, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.005 (1.188%) iter 60, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.190%) iter 61, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.192%) iter 62, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.196%) iter 63, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.201%) iter 64, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.209%) iter 65, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.217%) iter 66, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.005 (1.227%) iter 67, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.240%) iter 68, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.253%) iter 69, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.268%) iter 70, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.285%) iter 71, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.304%) iter 72, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.324%) iter 73, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.345%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.369%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.394%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.420%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.449%) iter 78, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.478%) iter 79, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.509%) iter 80, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.540%) iter 81, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.573%) iter 82, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.606%) iter 83, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.640%) iter 84, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.672%) iter 85, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.705%) iter 86, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.735%) iter 87, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.764%) iter 88, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.789%) iter 89, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.811%) iter 90, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.003 (1.828%) iter 91, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (1.837%) iter 92, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (1.836%) iter 93, dt=0.292969: new neg 2, old_neg 2, delta 0, rms=0.003 (4.038%) iter 94, dt=0.183594: new neg 0, old_neg 2, delta 2, rms=0.003 (18.858%) 0190: dt=145.152000, rms=0.704 (2.232%), neg=0, invalid=96777 iter 0, gcam->neg = 50 after 200 iterations, nbhd size=1, neg = 81 starting rms=0.015, neg=81, removing folds in lattice.... iter 1, dt=0.155914: new neg 37, old_neg 81, delta 44, rms=0.009 (40.191%) iter 2, dt=0.002294: new neg 36, old_neg 37, delta 1, rms=0.009 (1.418%) iter 3, dt=0.002294: new neg 34, old_neg 36, delta 2, rms=0.009 (1.405%) iter 4, dt=0.002294: new neg 32, old_neg 34, delta 2, rms=0.009 (1.390%) iter 5, dt=0.002294: new neg 31, old_neg 32, delta 1, rms=0.009 (1.374%) iter 6, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.008 (1.357%) iter 7, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.008 (1.340%) iter 8, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.008 (1.321%) iter 9, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.008 (1.303%) iter 10, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.008 (1.285%) iter 11, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.008 (1.267%) iter 12, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.008 (1.249%) iter 13, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.008 (1.231%) iter 14, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.008 (1.214%) iter 15, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.007 (1.198%) iter 16, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.007 (1.183%) iter 17, dt=0.002294: new neg 24, old_neg 26, delta 2, rms=0.007 (1.167%) iter 18, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.007 (1.151%) iter 19, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.007 (1.135%) iter 20, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.007 (1.118%) iter 21, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.007 (1.100%) iter 22, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.007 (1.086%) iter 23, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.007 (1.071%) iter 24, dt=0.002294: new neg 18, old_neg 21, delta 3, rms=0.007 (1.056%) iter 25, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.007 (1.041%) iter 26, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (1.025%) iter 27, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (1.008%) iter 28, dt=0.002294: new neg 15, old_neg 17, delta 2, rms=0.007 (0.991%) iter 29, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.006 (0.974%) iter 30, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.956%) iter 31, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.942%) iter 32, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.929%) iter 33, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.916%) iter 34, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.907%) iter 35, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.894%) iter 36, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.880%) iter 37, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.006 (0.864%) iter 38, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.006 (0.854%) iter 39, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.006 (0.840%) iter 40, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.006 (0.825%) iter 41, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.006 (0.811%) iter 42, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.006 (0.801%) iter 43, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (0.790%) iter 44, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (0.774%) iter 45, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.006 (0.761%) iter 46, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.006 (0.751%) iter 47, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (0.741%) iter 48, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.005 (0.725%) iter 49, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.712%) iter 50, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.700%) iter 51, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.689%) iter 52, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.673%) iter 53, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.660%) iter 54, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.649%) iter 55, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.638%) iter 56, dt=0.002294: new neg 5, old_neg 7, delta 2, rms=0.005 (0.623%) iter 57, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.609%) iter 58, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.602%) iter 59, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.588%) iter 60, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.576%) iter 61, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.005 (0.559%) iter 62, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.005 (0.555%) iter 63, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.546%) iter 64, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.532%) iter 65, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.520%) iter 66, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.507%) iter 67, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.506%) iter 68, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.495%) iter 69, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.484%) iter 70, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.479%) iter 71, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.474%) iter 72, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.462%) iter 73, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.463%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.455%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.449%) iter 76, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.005 (0.442%) iter 77, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.442%) iter 78, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.430%) iter 79, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.433%) iter 80, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.419%) iter 81, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.419%) iter 82, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.415%) iter 83, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.409%) iter 84, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.401%) iter 85, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.401%) iter 86, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.394%) iter 87, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.392%) iter 88, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.387%) iter 89, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.383%) iter 90, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.376%) iter 91, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.376%) iter 92, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.371%) iter 93, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.369%) iter 94, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.366%) iter 95, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.360%) iter 96, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.358%) iter 97, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.356%) iter 98, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.352%) iter 99, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.350%) iter 100, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.347%) ---------- unfolding failed - restoring original position -------------------- 0191: dt=82.944000, rms=0.704 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 50 after 200 iterations, nbhd size=1, neg = 81 starting rms=0.015, neg=81, removing folds in lattice.... iter 1, dt=0.155914: new neg 37, old_neg 81, delta 44, rms=0.009 (40.191%) iter 2, dt=0.002294: new neg 36, old_neg 37, delta 1, rms=0.009 (1.418%) iter 3, dt=0.002294: new neg 34, old_neg 36, delta 2, rms=0.009 (1.405%) iter 4, dt=0.002294: new neg 32, old_neg 34, delta 2, rms=0.009 (1.390%) iter 5, dt=0.002294: new neg 31, old_neg 32, delta 1, rms=0.009 (1.374%) iter 6, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.008 (1.357%) iter 7, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.008 (1.340%) iter 8, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.008 (1.321%) iter 9, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.008 (1.303%) iter 10, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.008 (1.285%) iter 11, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.008 (1.267%) iter 12, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.008 (1.249%) iter 13, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.008 (1.231%) iter 14, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.008 (1.214%) iter 15, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.007 (1.198%) iter 16, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.007 (1.183%) iter 17, dt=0.002294: new neg 24, old_neg 26, delta 2, rms=0.007 (1.167%) iter 18, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.007 (1.151%) iter 19, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.007 (1.135%) iter 20, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.007 (1.118%) iter 21, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.007 (1.100%) iter 22, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.007 (1.086%) iter 23, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.007 (1.071%) iter 24, dt=0.002294: new neg 18, old_neg 21, delta 3, rms=0.007 (1.056%) iter 25, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.007 (1.041%) iter 26, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (1.025%) iter 27, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (1.008%) iter 28, dt=0.002294: new neg 15, old_neg 17, delta 2, rms=0.007 (0.991%) iter 29, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.006 (0.974%) iter 30, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.956%) iter 31, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.942%) iter 32, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.929%) iter 33, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.916%) iter 34, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.907%) iter 35, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.894%) iter 36, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.006 (0.880%) iter 37, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.006 (0.864%) iter 38, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.006 (0.854%) iter 39, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.006 (0.840%) iter 40, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.006 (0.825%) iter 41, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.006 (0.811%) iter 42, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.006 (0.801%) iter 43, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (0.790%) iter 44, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (0.774%) iter 45, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.006 (0.761%) iter 46, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.006 (0.751%) iter 47, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (0.741%) iter 48, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.005 (0.725%) iter 49, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.712%) iter 50, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.700%) iter 51, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.689%) iter 52, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.673%) iter 53, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.660%) iter 54, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.649%) iter 55, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (0.638%) iter 56, dt=0.002294: new neg 5, old_neg 7, delta 2, rms=0.005 (0.623%) iter 57, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.609%) iter 58, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.602%) iter 59, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.588%) iter 60, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (0.576%) iter 61, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.005 (0.559%) iter 62, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.005 (0.555%) iter 63, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.546%) iter 64, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.532%) iter 65, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.520%) iter 66, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.507%) iter 67, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.506%) iter 68, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.495%) iter 69, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.484%) iter 70, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.479%) iter 71, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.474%) iter 72, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.462%) iter 73, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.463%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.455%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.449%) iter 76, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.005 (0.442%) iter 77, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.442%) iter 78, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.430%) iter 79, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.433%) iter 80, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.419%) iter 81, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.419%) iter 82, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.415%) iter 83, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.409%) iter 84, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.401%) iter 85, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.005 (0.401%) iter 86, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.394%) iter 87, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.392%) iter 88, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.387%) iter 89, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.383%) iter 90, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.376%) iter 91, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.376%) iter 92, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.371%) iter 93, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.369%) iter 94, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.366%) iter 95, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.360%) iter 96, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.358%) iter 97, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.356%) iter 98, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.352%) iter 99, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.350%) iter 100, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (0.347%) ---------- unfolding failed - restoring original position -------------------- 0192: dt=82.944000, rms=0.704 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.706, neg=0, invalid=96777 iter 0, gcam->neg = 2637 after 205 iterations, nbhd size=3, neg = 231 starting rms=0.033, neg=231, removing folds in lattice.... iter 1, dt=0.193700: new neg 111, old_neg 231, delta 120, rms=0.018 (43.896%) iter 2, dt=0.002294: new neg 111, old_neg 111, delta 0, rms=0.018 (1.096%) iter 3, dt=0.002294: new neg 106, old_neg 111, delta 5, rms=0.018 (1.090%) iter 4, dt=0.002294: new neg 103, old_neg 106, delta 3, rms=0.018 (1.085%) iter 5, dt=0.002294: new neg 100, old_neg 103, delta 3, rms=0.018 (1.079%) iter 6, dt=0.002294: new neg 98, old_neg 100, delta 2, rms=0.017 (1.073%) iter 7, dt=0.002294: new neg 97, old_neg 98, delta 1, rms=0.017 (1.067%) iter 8, dt=0.002294: new neg 94, old_neg 97, delta 3, rms=0.017 (1.062%) iter 9, dt=0.002294: new neg 92, old_neg 94, delta 2, rms=0.017 (1.059%) iter 10, dt=0.002294: new neg 89, old_neg 92, delta 3, rms=0.017 (1.056%) iter 11, dt=0.002294: new neg 88, old_neg 89, delta 1, rms=0.016 (1.054%) iter 12, dt=0.002294: new neg 85, old_neg 88, delta 3, rms=0.016 (1.052%) iter 13, dt=0.002294: new neg 83, old_neg 85, delta 2, rms=0.016 (1.051%) iter 14, dt=0.002294: new neg 80, old_neg 83, delta 3, rms=0.016 (1.050%) iter 15, dt=0.002294: new neg 78, old_neg 80, delta 2, rms=0.016 (1.049%) iter 16, dt=0.002294: new neg 78, old_neg 78, delta 0, rms=0.016 (1.050%) iter 17, dt=0.002294: new neg 74, old_neg 78, delta 4, rms=0.015 (1.050%) iter 18, dt=0.002294: new neg 72, old_neg 74, delta 2, rms=0.015 (1.052%) iter 19, dt=0.002294: new neg 71, old_neg 72, delta 1, rms=0.015 (1.054%) iter 20, dt=0.002294: new neg 70, old_neg 71, delta 1, rms=0.015 (1.056%) iter 21, dt=0.002294: new neg 67, old_neg 70, delta 3, rms=0.015 (1.058%) iter 22, dt=0.002294: new neg 66, old_neg 67, delta 1, rms=0.015 (1.060%) iter 23, dt=0.002294: new neg 65, old_neg 66, delta 1, rms=0.015 (1.061%) iter 24, dt=0.002294: new neg 64, old_neg 65, delta 1, rms=0.014 (1.063%) iter 25, dt=0.002294: new neg 63, old_neg 64, delta 1, rms=0.014 (1.064%) iter 26, dt=0.002294: new neg 61, old_neg 63, delta 2, rms=0.014 (1.066%) iter 27, dt=0.002294: new neg 61, old_neg 61, delta 0, rms=0.014 (1.067%) iter 28, dt=0.002294: new neg 59, old_neg 61, delta 2, rms=0.014 (1.067%) iter 29, dt=0.002294: new neg 57, old_neg 59, delta 2, rms=0.014 (1.067%) iter 30, dt=0.002294: new neg 56, old_neg 57, delta 1, rms=0.013 (1.066%) iter 31, dt=0.002294: new neg 56, old_neg 56, delta 0, rms=0.013 (1.065%) iter 32, dt=0.002294: new neg 55, old_neg 56, delta 1, rms=0.013 (1.064%) iter 33, dt=0.002294: new neg 55, old_neg 55, delta 0, rms=0.013 (1.062%) iter 34, dt=0.002294: new neg 54, old_neg 55, delta 1, rms=0.013 (1.058%) iter 35, dt=0.002294: new neg 53, old_neg 54, delta 1, rms=0.013 (1.055%) iter 36, dt=0.002294: new neg 52, old_neg 53, delta 1, rms=0.013 (1.051%) iter 37, dt=0.002294: new neg 51, old_neg 52, delta 1, rms=0.013 (1.047%) iter 38, dt=0.002294: new neg 50, old_neg 51, delta 1, rms=0.012 (1.042%) iter 39, dt=0.002294: new neg 49, old_neg 50, delta 1, rms=0.012 (1.036%) iter 40, dt=0.002294: new neg 48, old_neg 49, delta 1, rms=0.012 (1.032%) iter 41, dt=0.002294: new neg 46, old_neg 48, delta 2, rms=0.012 (1.027%) iter 42, dt=0.002294: new neg 44, old_neg 46, delta 2, rms=0.012 (1.023%) iter 43, dt=0.002294: new neg 43, old_neg 44, delta 1, rms=0.012 (1.020%) iter 44, dt=0.002294: new neg 42, old_neg 43, delta 1, rms=0.012 (1.017%) iter 45, dt=0.002294: new neg 42, old_neg 42, delta 0, rms=0.012 (1.015%) iter 46, dt=0.002294: new neg 42, old_neg 42, delta 0, rms=0.011 (1.013%) iter 47, dt=0.002294: new neg 41, old_neg 42, delta 1, rms=0.011 (1.011%) iter 48, dt=0.002294: new neg 40, old_neg 41, delta 1, rms=0.011 (1.010%) iter 49, dt=0.002294: new neg 39, old_neg 40, delta 1, rms=0.011 (1.009%) iter 50, dt=0.002294: new neg 38, old_neg 39, delta 1, rms=0.011 (1.009%) iter 51, dt=0.002294: new neg 37, old_neg 38, delta 1, rms=0.011 (1.009%) iter 52, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.011 (1.009%) iter 53, dt=0.002294: new neg 37, old_neg 37, delta 0, rms=0.011 (1.009%) iter 54, dt=0.002294: new neg 36, old_neg 37, delta 1, rms=0.011 (1.009%) iter 55, dt=0.002294: new neg 34, old_neg 36, delta 2, rms=0.010 (1.009%) iter 56, dt=0.002294: new neg 34, old_neg 34, delta 0, rms=0.010 (1.008%) iter 57, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.010 (1.008%) iter 58, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.010 (1.007%) iter 59, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.010 (1.006%) iter 60, dt=0.002294: new neg 32, old_neg 33, delta 1, rms=0.010 (1.003%) iter 61, dt=0.002294: new neg 30, old_neg 32, delta 2, rms=0.010 (1.003%) iter 62, dt=0.002294: new neg 28, old_neg 30, delta 2, rms=0.010 (1.000%) iter 63, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.010 (1.000%) iter 64, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.010 (0.997%) iter 65, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.009 (0.999%) iter 66, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.009 (0.997%) iter 67, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.009 (0.996%) iter 68, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.009 (0.996%) iter 69, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.009 (0.993%) iter 70, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.009 (0.994%) iter 71, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.009 (0.992%) iter 72, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.009 (0.989%) iter 73, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.009 (0.985%) iter 74, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.009 (0.985%) iter 75, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.009 (0.980%) iter 76, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.008 (0.974%) iter 77, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.008 (0.972%) iter 78, dt=0.002294: new neg 20, old_neg 22, delta 2, rms=0.008 (0.964%) iter 79, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.008 (0.961%) iter 80, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.008 (0.952%) iter 81, dt=0.002294: new neg 19, old_neg 19, delta 0, rms=0.008 (0.954%) iter 82, dt=0.002294: new neg 18, old_neg 19, delta 1, rms=0.008 (0.947%) iter 83, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.008 (0.943%) iter 84, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.008 (0.938%) iter 85, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.008 (0.939%) iter 86, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (0.933%) iter 87, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (0.939%) iter 88, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (0.935%) iter 89, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (0.936%) iter 90, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (0.930%) iter 91, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (0.942%) iter 92, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (0.940%) iter 93, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.007 (0.941%) iter 94, dt=0.002294: new neg 17, old_neg 16, delta -1, rms=0.007 (0.941%) iter 95, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.007 (0.948%) iter 96, dt=0.002294: new neg 16, old_neg 16, delta 0, rms=0.007 (0.952%) iter 97, dt=0.002294: new neg 15, old_neg 16, delta 1, rms=0.007 (0.955%) iter 98, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.007 (0.955%) iter 99, dt=0.002294: new neg 15, old_neg 14, delta -1, rms=0.007 (0.965%) iter 100, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.007 (0.964%) ---------- unfolding failed - restoring original position -------------------- 0193: dt=26.137998, rms=0.706 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.706, neg=0, invalid=96777 iter 0, gcam->neg = 2834 after 201 iterations, nbhd size=4, neg = 163 starting rms=0.028, neg=163, removing folds in lattice.... iter 1, dt=0.194459: new neg 71, old_neg 163, delta 92, rms=0.014 (49.494%) iter 2, dt=0.002294: new neg 70, old_neg 71, delta 1, rms=0.014 (1.260%) iter 3, dt=0.002294: new neg 66, old_neg 70, delta 4, rms=0.014 (1.252%) iter 4, dt=0.002294: new neg 64, old_neg 66, delta 2, rms=0.014 (1.244%) iter 5, dt=0.002294: new neg 62, old_neg 64, delta 2, rms=0.013 (1.236%) iter 6, dt=0.002294: new neg 58, old_neg 62, delta 4, rms=0.013 (1.227%) iter 7, dt=0.002294: new neg 54, old_neg 58, delta 4, rms=0.013 (1.218%) iter 8, dt=0.002294: new neg 54, old_neg 54, delta 0, rms=0.013 (1.209%) iter 9, dt=0.002294: new neg 53, old_neg 54, delta 1, rms=0.013 (1.201%) iter 10, dt=0.002294: new neg 53, old_neg 53, delta 0, rms=0.013 (1.195%) iter 11, dt=0.002294: new neg 52, old_neg 53, delta 1, rms=0.013 (1.191%) iter 12, dt=0.002294: new neg 51, old_neg 52, delta 1, rms=0.012 (1.188%) iter 13, dt=0.002294: new neg 49, old_neg 51, delta 2, rms=0.012 (1.185%) iter 14, dt=0.002294: new neg 49, old_neg 49, delta 0, rms=0.012 (1.184%) iter 15, dt=0.002294: new neg 47, old_neg 49, delta 2, rms=0.012 (1.182%) iter 16, dt=0.002294: new neg 45, old_neg 47, delta 2, rms=0.012 (1.181%) iter 17, dt=0.002294: new neg 43, old_neg 45, delta 2, rms=0.012 (1.181%) iter 18, dt=0.002294: new neg 43, old_neg 43, delta 0, rms=0.012 (1.180%) iter 19, dt=0.002294: new neg 42, old_neg 43, delta 1, rms=0.011 (1.180%) iter 20, dt=0.002294: new neg 41, old_neg 42, delta 1, rms=0.011 (1.180%) iter 21, dt=0.002294: new neg 39, old_neg 41, delta 2, rms=0.011 (1.181%) iter 22, dt=0.002294: new neg 38, old_neg 39, delta 1, rms=0.011 (1.182%) iter 23, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.011 (1.184%) iter 24, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.011 (1.185%) iter 25, dt=0.002294: new neg 38, old_neg 38, delta 0, rms=0.011 (1.188%) iter 26, dt=0.002294: new neg 37, old_neg 38, delta 1, rms=0.010 (1.190%) iter 27, dt=0.002294: new neg 36, old_neg 37, delta 1, rms=0.010 (1.195%) iter 28, dt=0.002294: new neg 36, old_neg 36, delta 0, rms=0.010 (1.198%) iter 29, dt=0.002294: new neg 35, old_neg 36, delta 1, rms=0.010 (1.202%) iter 30, dt=0.002294: new neg 35, old_neg 35, delta 0, rms=0.010 (1.204%) iter 31, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.010 (1.208%) iter 32, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.010 (1.210%) iter 33, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.010 (1.212%) iter 34, dt=0.002294: new neg 30, old_neg 33, delta 3, rms=0.010 (1.213%) iter 35, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.009 (1.214%) iter 36, dt=0.002294: new neg 26, old_neg 29, delta 3, rms=0.009 (1.213%) iter 37, dt=0.002294: new neg 25, old_neg 26, delta 1, rms=0.009 (1.212%) iter 38, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.009 (1.210%) iter 39, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.009 (1.207%) iter 40, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.009 (1.202%) iter 41, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.009 (1.197%) iter 42, dt=0.002294: new neg 22, old_neg 24, delta 2, rms=0.009 (1.190%) iter 43, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.009 (1.183%) iter 44, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.008 (1.176%) iter 45, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.008 (1.169%) iter 46, dt=0.002294: new neg 18, old_neg 20, delta 2, rms=0.008 (1.164%) iter 47, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.008 (1.158%) iter 48, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.008 (1.152%) iter 49, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.008 (1.143%) iter 50, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.008 (1.136%) iter 51, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.008 (1.126%) iter 52, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.008 (1.119%) iter 53, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.008 (1.109%) iter 54, dt=0.002294: new neg 12, old_neg 14, delta 2, rms=0.008 (1.099%) iter 55, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.007 (1.086%) iter 56, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.007 (1.076%) iter 57, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (1.064%) iter 58, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.007 (1.052%) iter 59, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.007 (1.040%) iter 60, dt=0.002294: new neg 8, old_neg 10, delta 2, rms=0.007 (1.026%) iter 61, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.007 (1.015%) iter 62, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.007 (1.006%) iter 63, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.007 (0.996%) iter 64, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.007 (0.989%) iter 65, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.007 (0.982%) iter 66, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.007 (0.975%) iter 67, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.007 (0.973%) iter 68, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.007 (0.970%) iter 69, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (0.967%) iter 70, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (0.971%) iter 71, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (0.970%) iter 72, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.970%) iter 73, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.975%) iter 74, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.978%) iter 75, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.979%) iter 76, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.986%) iter 77, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.989%) iter 78, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.991%) iter 79, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (0.998%) iter 80, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.006 (1.001%) iter 81, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.002%) iter 82, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.008%) iter 83, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.010%) iter 84, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.011%) iter 85, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.005 (1.014%) iter 86, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.014%) iter 87, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.013%) iter 88, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.016%) iter 89, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.014%) iter 90, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.014%) iter 91, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.010%) iter 92, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.008%) iter 93, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.006%) iter 94, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.002%) iter 95, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (0.996%) iter 96, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.005 (0.991%) iter 97, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.986%) iter 98, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.980%) iter 99, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.973%) iter 100, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (0.964%) ---------- unfolding failed - restoring original position -------------------- 0194: dt=43.386503, rms=0.706 (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=0.711, neg=0, invalid=96777 iter 0, gcam->neg = 4125 after 200 iterations, nbhd size=2, neg = 113 starting rms=0.025, neg=113, removing folds in lattice.... iter 1, dt=0.189166: new neg 49, old_neg 113, delta 64, rms=0.012 (51.845%) iter 2, dt=0.002294: new neg 44, old_neg 49, delta 5, rms=0.012 (1.387%) iter 3, dt=0.002294: new neg 42, old_neg 44, delta 2, rms=0.012 (1.376%) iter 4, dt=0.002294: new neg 40, old_neg 42, delta 2, rms=0.012 (1.365%) iter 5, dt=0.002294: new neg 39, old_neg 40, delta 1, rms=0.011 (1.353%) iter 6, dt=0.002294: new neg 36, old_neg 39, delta 3, rms=0.011 (1.341%) iter 7, dt=0.002294: new neg 35, old_neg 36, delta 1, rms=0.011 (1.329%) iter 8, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.011 (1.317%) iter 9, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.011 (1.306%) iter 10, dt=0.002294: new neg 32, old_neg 33, delta 1, rms=0.011 (1.296%) iter 11, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.011 (1.288%) iter 12, dt=0.002294: new neg 30, old_neg 32, delta 2, rms=0.010 (1.282%) iter 13, dt=0.002294: new neg 30, old_neg 30, delta 0, rms=0.010 (1.276%) iter 14, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.010 (1.273%) iter 15, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (1.270%) iter 16, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (1.268%) iter 17, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.010 (1.268%) iter 18, dt=0.002294: new neg 26, old_neg 29, delta 3, rms=0.010 (1.268%) iter 19, dt=0.002294: new neg 24, old_neg 26, delta 2, rms=0.009 (1.268%) iter 20, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.009 (1.269%) iter 21, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.009 (1.271%) iter 22, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.009 (1.272%) iter 23, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.009 (1.274%) iter 24, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.009 (1.276%) iter 25, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.009 (1.278%) iter 26, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.009 (1.280%) iter 27, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.009 (1.282%) iter 28, dt=0.002294: new neg 18, old_neg 21, delta 3, rms=0.008 (1.284%) iter 29, dt=0.002294: new neg 18, old_neg 18, delta 0, rms=0.008 (1.286%) iter 30, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.008 (1.287%) iter 31, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (1.288%) iter 32, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.008 (1.288%) iter 33, dt=0.002294: new neg 15, old_neg 16, delta 1, rms=0.008 (1.287%) iter 34, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.008 (1.285%) iter 35, dt=0.002294: new neg 14, old_neg 14, delta 0, rms=0.008 (1.281%) iter 36, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.008 (1.278%) iter 37, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.008 (1.273%) iter 38, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.266%) iter 39, dt=0.002294: new neg 11, old_neg 13, delta 2, rms=0.007 (1.259%) iter 40, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (1.250%) iter 41, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (1.241%) iter 42, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.007 (1.232%) iter 43, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.007 (1.222%) iter 44, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.007 (1.213%) iter 45, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.007 (1.204%) iter 46, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.007 (1.196%) iter 47, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (1.189%) iter 48, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.007 (1.182%) iter 49, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (1.176%) iter 50, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (1.170%) iter 51, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.164%) iter 52, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.157%) iter 53, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.152%) iter 54, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.146%) iter 55, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.139%) iter 56, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.133%) iter 57, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (1.127%) iter 58, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.006 (1.123%) iter 59, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.118%) iter 60, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.114%) iter 61, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.112%) iter 62, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.110%) iter 63, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.112%) iter 64, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.113%) iter 65, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.116%) iter 66, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.122%) iter 67, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.128%) iter 68, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.135%) iter 69, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.144%) iter 70, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.152%) iter 71, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.161%) iter 72, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.170%) iter 73, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.177%) iter 74, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.184%) iter 75, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.189%) iter 76, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.192%) iter 77, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.193%) iter 78, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.191%) iter 79, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.186%) iter 80, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.179%) iter 81, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.004 (1.170%) iter 82, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.004 (1.160%) iter 83, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.148%) iter 84, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.138%) iter 85, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.127%) iter 86, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.119%) iter 87, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.113%) iter 88, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.109%) iter 89, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.108%) iter 90, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.110%) iter 91, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.114%) iter 92, dt=0.002294: new neg 2, old_neg 3, delta 1, rms=0.004 (1.120%) iter 93, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (1.129%) iter 94, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (1.140%) iter 95, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (1.152%) iter 96, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (1.165%) iter 97, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (1.179%) iter 98, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (1.193%) iter 99, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (1.205%) iter 100, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.004 (1.213%) ---------- unfolding failed - restoring original position -------------------- 0195: dt=12.419417, rms=0.711 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.711, neg=0, invalid=96777 iter 0, gcam->neg = 3964 after 200 iterations, nbhd size=3, neg = 91 starting rms=0.023, neg=91, removing folds in lattice.... iter 1, dt=0.199661: new neg 37, old_neg 91, delta 54, rms=0.011 (53.815%) iter 2, dt=0.002294: new neg 36, old_neg 37, delta 1, rms=0.011 (1.434%) iter 3, dt=0.002294: new neg 35, old_neg 36, delta 1, rms=0.010 (1.426%) iter 4, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.010 (1.417%) iter 5, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.010 (1.410%) iter 6, dt=0.002294: new neg 32, old_neg 33, delta 1, rms=0.010 (1.403%) iter 7, dt=0.002294: new neg 31, old_neg 32, delta 1, rms=0.010 (1.397%) iter 8, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.010 (1.393%) iter 9, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.010 (1.391%) iter 10, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.390%) iter 11, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.009 (1.389%) iter 12, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.009 (1.389%) iter 13, dt=0.002294: new neg 26, old_neg 27, delta 1, rms=0.009 (1.390%) iter 14, dt=0.002294: new neg 26, old_neg 26, delta 0, rms=0.009 (1.390%) iter 15, dt=0.002294: new neg 24, old_neg 26, delta 2, rms=0.009 (1.390%) iter 16, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.009 (1.389%) iter 17, dt=0.002294: new neg 21, old_neg 24, delta 3, rms=0.009 (1.388%) iter 18, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.008 (1.386%) iter 19, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.008 (1.383%) iter 20, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.008 (1.379%) iter 21, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.008 (1.373%) iter 22, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.008 (1.367%) iter 23, dt=0.002294: new neg 19, old_neg 19, delta 0, rms=0.008 (1.360%) iter 24, dt=0.002294: new neg 17, old_neg 19, delta 2, rms=0.008 (1.352%) iter 25, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.008 (1.344%) iter 26, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.008 (1.336%) iter 27, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.007 (1.329%) iter 28, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.007 (1.322%) iter 29, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.315%) iter 30, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.007 (1.308%) iter 31, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.007 (1.301%) iter 32, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.007 (1.293%) iter 33, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (1.285%) iter 34, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.007 (1.278%) iter 35, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.007 (1.269%) iter 36, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.007 (1.260%) iter 37, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.007 (1.250%) iter 38, dt=0.002294: new neg 8, old_neg 10, delta 2, rms=0.006 (1.239%) iter 39, dt=0.002294: new neg 6, old_neg 8, delta 2, rms=0.006 (1.229%) iter 40, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.219%) iter 41, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.209%) iter 42, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.200%) iter 43, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.192%) iter 44, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.184%) iter 45, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.178%) iter 46, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.173%) iter 47, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.170%) iter 48, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.167%) iter 49, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.167%) iter 50, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.006 (1.167%) iter 51, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.006 (1.170%) iter 52, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.173%) iter 53, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.176%) iter 54, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.180%) iter 55, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.184%) iter 56, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.187%) iter 57, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.190%) iter 58, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.191%) iter 59, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.191%) iter 60, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.189%) iter 61, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.184%) iter 62, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.178%) iter 63, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.169%) iter 64, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.005 (1.159%) iter 65, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.005 (1.148%) iter 66, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.137%) iter 67, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.126%) iter 68, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.117%) iter 69, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.109%) iter 70, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.104%) iter 71, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.101%) iter 72, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.101%) iter 73, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.104%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.109%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.117%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.126%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.138%) iter 78, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.151%) iter 79, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.165%) iter 80, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.178%) iter 81, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.190%) iter 82, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.197%) iter 83, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.196%) iter 84, dt=0.166504: new neg 0, old_neg 3, delta 3, rms=0.003 (17.833%) 0196: dt=17.218018, rms=0.682 (4.127%), neg=0, invalid=96777 iter 0, gcam->neg = 2204 after 200 iterations, nbhd size=4, neg = 101 starting rms=0.024, neg=101, removing folds in lattice.... iter 1, dt=0.185852: new neg 35, old_neg 101, delta 66, rms=0.010 (55.873%) iter 2, dt=0.002294: new neg 35, old_neg 35, delta 0, rms=0.010 (1.533%) iter 3, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.010 (1.519%) iter 4, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.010 (1.508%) iter 5, dt=0.002294: new neg 32, old_neg 33, delta 1, rms=0.010 (1.500%) iter 6, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.010 (1.494%) iter 7, dt=0.002294: new neg 31, old_neg 32, delta 1, rms=0.009 (1.490%) iter 8, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.009 (1.487%) iter 9, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.009 (1.486%) iter 10, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.485%) iter 11, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.485%) iter 12, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.486%) iter 13, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.487%) iter 14, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.009 (1.489%) iter 15, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.008 (1.490%) iter 16, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.008 (1.491%) iter 17, dt=0.002294: new neg 24, old_neg 27, delta 3, rms=0.008 (1.491%) iter 18, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.008 (1.490%) iter 19, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.008 (1.488%) iter 20, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.008 (1.485%) iter 21, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.008 (1.481%) iter 22, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.008 (1.476%) iter 23, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.007 (1.470%) iter 24, dt=0.002294: new neg 17, old_neg 20, delta 3, rms=0.007 (1.463%) iter 25, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (1.457%) iter 26, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.007 (1.449%) iter 27, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.007 (1.442%) iter 28, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.007 (1.433%) iter 29, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.423%) iter 30, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.414%) iter 31, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.007 (1.403%) iter 32, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.007 (1.391%) iter 33, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (1.379%) iter 34, dt=0.002294: new neg 8, old_neg 11, delta 3, rms=0.006 (1.366%) iter 35, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.354%) iter 36, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.342%) iter 37, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (1.331%) iter 38, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.320%) iter 39, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.309%) iter 40, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.299%) iter 41, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (1.289%) iter 42, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.279%) iter 43, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.271%) iter 44, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.262%) iter 45, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.254%) iter 46, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.245%) iter 47, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.235%) iter 48, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.005 (1.222%) iter 49, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.210%) iter 50, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.195%) iter 51, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.180%) iter 52, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.005 (1.162%) iter 53, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.145%) iter 54, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.005 (1.127%) iter 55, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.111%) iter 56, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.094%) iter 57, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.081%) iter 58, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.069%) iter 59, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.059%) iter 60, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.051%) iter 61, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.048%) iter 62, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.046%) iter 63, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.046%) iter 64, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.049%) iter 65, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.054%) iter 66, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.061%) iter 67, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.070%) iter 68, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.080%) iter 69, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.091%) iter 70, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.105%) iter 71, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.120%) iter 72, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.136%) iter 73, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.153%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.172%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.191%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.211%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.231%) iter 78, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.251%) iter 79, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.266%) iter 80, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.276%) iter 81, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.273%) iter 82, dt=0.335938: new neg 2, old_neg 3, delta 1, rms=0.003 (7.163%) iter 83, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (0.955%) iter 84, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (0.918%) iter 85, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (0.883%) iter 86, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.003 (0.850%) iter 87, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.820%) iter 88, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.793%) iter 89, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.767%) iter 90, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.744%) iter 91, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.723%) iter 92, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.703%) iter 93, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.685%) iter 94, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.669%) iter 95, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.654%) iter 96, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.641%) iter 97, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.628%) iter 98, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.617%) iter 99, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.607%) iter 100, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.598%) ---------- unfolding failed - restoring original position -------------------- 0197: dt=13.497674, rms=0.682 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 2204 after 200 iterations, nbhd size=4, neg = 101 starting rms=0.024, neg=101, removing folds in lattice.... iter 1, dt=0.185852: new neg 35, old_neg 101, delta 66, rms=0.010 (55.873%) iter 2, dt=0.002294: new neg 35, old_neg 35, delta 0, rms=0.010 (1.533%) iter 3, dt=0.002294: new neg 34, old_neg 35, delta 1, rms=0.010 (1.519%) iter 4, dt=0.002294: new neg 33, old_neg 34, delta 1, rms=0.010 (1.508%) iter 5, dt=0.002294: new neg 32, old_neg 33, delta 1, rms=0.010 (1.500%) iter 6, dt=0.002294: new neg 32, old_neg 32, delta 0, rms=0.010 (1.494%) iter 7, dt=0.002294: new neg 31, old_neg 32, delta 1, rms=0.009 (1.490%) iter 8, dt=0.002294: new neg 30, old_neg 31, delta 1, rms=0.009 (1.487%) iter 9, dt=0.002294: new neg 29, old_neg 30, delta 1, rms=0.009 (1.486%) iter 10, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.485%) iter 11, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.485%) iter 12, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.486%) iter 13, dt=0.002294: new neg 29, old_neg 29, delta 0, rms=0.009 (1.487%) iter 14, dt=0.002294: new neg 28, old_neg 29, delta 1, rms=0.009 (1.489%) iter 15, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.008 (1.490%) iter 16, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.008 (1.491%) iter 17, dt=0.002294: new neg 24, old_neg 27, delta 3, rms=0.008 (1.491%) iter 18, dt=0.002294: new neg 24, old_neg 24, delta 0, rms=0.008 (1.490%) iter 19, dt=0.002294: new neg 23, old_neg 24, delta 1, rms=0.008 (1.488%) iter 20, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.008 (1.485%) iter 21, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.008 (1.481%) iter 22, dt=0.002294: new neg 21, old_neg 21, delta 0, rms=0.008 (1.476%) iter 23, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.007 (1.470%) iter 24, dt=0.002294: new neg 17, old_neg 20, delta 3, rms=0.007 (1.463%) iter 25, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (1.457%) iter 26, dt=0.002294: new neg 16, old_neg 17, delta 1, rms=0.007 (1.449%) iter 27, dt=0.002294: new neg 14, old_neg 16, delta 2, rms=0.007 (1.442%) iter 28, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.007 (1.433%) iter 29, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.423%) iter 30, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.414%) iter 31, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.007 (1.403%) iter 32, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.007 (1.391%) iter 33, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (1.379%) iter 34, dt=0.002294: new neg 8, old_neg 11, delta 3, rms=0.006 (1.366%) iter 35, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.354%) iter 36, dt=0.002294: new neg 8, old_neg 8, delta 0, rms=0.006 (1.342%) iter 37, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (1.331%) iter 38, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.320%) iter 39, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.309%) iter 40, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.299%) iter 41, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.006 (1.289%) iter 42, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.279%) iter 43, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.271%) iter 44, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.262%) iter 45, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.006 (1.254%) iter 46, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.245%) iter 47, dt=0.002294: new neg 6, old_neg 6, delta 0, rms=0.005 (1.235%) iter 48, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.005 (1.222%) iter 49, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.210%) iter 50, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.195%) iter 51, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.005 (1.180%) iter 52, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.005 (1.162%) iter 53, dt=0.002294: new neg 4, old_neg 4, delta 0, rms=0.005 (1.145%) iter 54, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.005 (1.127%) iter 55, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.111%) iter 56, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.094%) iter 57, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.081%) iter 58, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.069%) iter 59, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.059%) iter 60, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.051%) iter 61, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.048%) iter 62, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.046%) iter 63, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.005 (1.046%) iter 64, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.049%) iter 65, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.054%) iter 66, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.061%) iter 67, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.070%) iter 68, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.080%) iter 69, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.091%) iter 70, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.105%) iter 71, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.120%) iter 72, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.136%) iter 73, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.153%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.172%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.191%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.211%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.231%) iter 78, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.251%) iter 79, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.266%) iter 80, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.276%) iter 81, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.004 (1.273%) iter 82, dt=0.335938: new neg 2, old_neg 3, delta 1, rms=0.003 (7.163%) iter 83, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (0.955%) iter 84, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (0.918%) iter 85, dt=0.002294: new neg 2, old_neg 2, delta 0, rms=0.003 (0.883%) iter 86, dt=0.002294: new neg 1, old_neg 2, delta 1, rms=0.003 (0.850%) iter 87, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.820%) iter 88, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.793%) iter 89, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.767%) iter 90, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.744%) iter 91, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.723%) iter 92, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.703%) iter 93, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.685%) iter 94, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.669%) iter 95, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.654%) iter 96, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.641%) iter 97, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.628%) iter 98, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.617%) iter 99, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.607%) iter 100, dt=0.002294: new neg 1, old_neg 1, delta 0, rms=0.003 (0.598%) ---------- unfolding failed - restoring original position -------------------- 0198: dt=13.497674, rms=0.682 (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=0.696, neg=0, invalid=96777 iter 0, gcam->neg = 113 after 200 iterations, nbhd size=2, neg = 61 starting rms=0.017, neg=61, removing folds in lattice.... iter 1, dt=0.144821: new neg 23, old_neg 61, delta 38, rms=0.006 (64.577%) iter 2, dt=0.135417: new neg 13, old_neg 23, delta 10, rms=0.005 (15.973%) iter 3, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.005 (2.297%) iter 4, dt=0.002294: new neg 11, old_neg 13, delta 2, rms=0.005 (2.291%) iter 5, dt=0.155469: new neg 11, old_neg 11, delta 0, rms=0.004 (7.479%) iter 6, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.004 (2.222%) iter 7, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.004 (2.253%) iter 8, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.004 (2.284%) iter 9, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.004 (2.315%) iter 10, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.004 (2.344%) iter 11, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.004 (2.372%) iter 12, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.004 (2.397%) iter 13, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.004 (2.419%) iter 14, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.004 (2.436%) iter 15, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.003 (2.448%) iter 16, dt=0.002294: new neg 7, old_neg 9, delta 2, rms=0.003 (2.453%) iter 17, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.003 (2.449%) iter 18, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.003 (2.437%) iter 19, dt=0.002294: new neg 4, old_neg 6, delta 2, rms=0.003 (2.415%) iter 20, dt=0.118707: new neg 3, old_neg 4, delta 1, rms=0.003 (8.763%) iter 21, dt=0.045166: new neg 0, old_neg 3, delta 3, rms=0.002 (23.724%) 0199: dt=1.536000, rms=0.696 (-0.116%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.696, neg=0, invalid=96777 iter 0, gcam->neg = 126 after 200 iterations, nbhd size=1, neg = 53 starting rms=0.017, neg=53, removing folds in lattice.... iter 1, dt=0.161917: new neg 27, old_neg 53, delta 26, rms=0.010 (40.632%) iter 2, dt=0.002294: new neg 27, old_neg 27, delta 0, rms=0.010 (1.412%) iter 3, dt=0.002294: new neg 25, old_neg 27, delta 2, rms=0.010 (1.389%) iter 4, dt=0.002294: new neg 23, old_neg 25, delta 2, rms=0.009 (1.384%) iter 5, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.009 (1.382%) iter 6, dt=0.002294: new neg 23, old_neg 23, delta 0, rms=0.009 (1.381%) iter 7, dt=0.002294: new neg 22, old_neg 23, delta 1, rms=0.009 (1.380%) iter 8, dt=0.002294: new neg 22, old_neg 22, delta 0, rms=0.009 (1.380%) iter 9, dt=0.002294: new neg 20, old_neg 22, delta 2, rms=0.009 (1.380%) iter 10, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.009 (1.378%) iter 11, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.009 (1.372%) iter 12, dt=0.211914: new neg 21, old_neg 19, delta -2, rms=0.006 (28.147%) iter 13, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.006 (2.104%) iter 14, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.006 (2.107%) iter 15, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.006 (2.117%) iter 16, dt=0.002294: new neg 20, old_neg 20, delta 0, rms=0.006 (2.131%) iter 17, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.006 (2.150%) iter 18, dt=0.002294: new neg 18, old_neg 19, delta 1, rms=0.005 (2.170%) iter 19, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.005 (2.192%) iter 20, dt=0.002294: new neg 15, old_neg 17, delta 2, rms=0.005 (2.215%) iter 21, dt=0.002294: new neg 13, old_neg 15, delta 2, rms=0.005 (2.239%) iter 22, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.005 (2.263%) iter 23, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.005 (2.289%) iter 24, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.005 (2.315%) iter 25, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.005 (2.342%) iter 26, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.004 (2.369%) iter 27, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.004 (2.400%) iter 28, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.004 (2.431%) iter 29, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.004 (2.460%) iter 30, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.004 (2.487%) iter 31, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.004 (2.511%) iter 32, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.004 (2.532%) iter 33, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.004 (2.548%) iter 34, dt=0.002294: new neg 9, old_neg 11, delta 2, rms=0.004 (2.560%) iter 35, dt=0.002294: new neg 9, old_neg 9, delta 0, rms=0.004 (2.567%) iter 36, dt=0.164307: new neg 3, old_neg 9, delta 6, rms=0.003 (19.944%) iter 37, dt=0.084570: new neg 0, old_neg 3, delta 3, rms=0.002 (27.840%) 0200: dt=1.792000, rms=0.695 (0.101%), neg=0, invalid=96777 iter 0, gcam->neg = 145 after 200 iterations, nbhd size=4, neg = 85 starting rms=0.021, neg=85, removing folds in lattice.... iter 1, dt=0.185362: new neg 35, old_neg 85, delta 50, rms=0.010 (51.283%) iter 2, dt=0.002294: new neg 33, old_neg 35, delta 2, rms=0.010 (1.470%) iter 3, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.010 (1.473%) iter 4, dt=0.002294: new neg 33, old_neg 33, delta 0, rms=0.010 (1.477%) iter 5, dt=0.002294: new neg 31, old_neg 33, delta 2, rms=0.009 (1.480%) iter 6, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.009 (1.483%) iter 7, dt=0.002294: new neg 31, old_neg 31, delta 0, rms=0.009 (1.486%) iter 8, dt=0.002294: new neg 28, old_neg 31, delta 3, rms=0.009 (1.489%) iter 9, dt=0.002294: new neg 28, old_neg 28, delta 0, rms=0.009 (1.490%) iter 10, dt=0.002294: new neg 27, old_neg 28, delta 1, rms=0.009 (1.491%) iter 11, dt=0.002294: new neg 25, old_neg 27, delta 2, rms=0.009 (1.490%) iter 12, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.008 (1.489%) iter 13, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.008 (1.488%) iter 14, dt=0.002294: new neg 25, old_neg 25, delta 0, rms=0.008 (1.486%) iter 15, dt=0.002294: new neg 24, old_neg 25, delta 1, rms=0.008 (1.485%) iter 16, dt=0.002294: new neg 22, old_neg 24, delta 2, rms=0.008 (1.483%) iter 17, dt=0.002294: new neg 21, old_neg 22, delta 1, rms=0.008 (1.482%) iter 18, dt=0.002294: new neg 20, old_neg 21, delta 1, rms=0.008 (1.481%) iter 19, dt=0.002294: new neg 19, old_neg 20, delta 1, rms=0.008 (1.479%) iter 20, dt=0.002294: new neg 18, old_neg 19, delta 1, rms=0.008 (1.477%) iter 21, dt=0.002294: new neg 17, old_neg 18, delta 1, rms=0.007 (1.473%) iter 22, dt=0.002294: new neg 17, old_neg 17, delta 0, rms=0.007 (1.469%) iter 23, dt=0.002294: new neg 15, old_neg 17, delta 2, rms=0.007 (1.465%) iter 24, dt=0.002294: new neg 14, old_neg 15, delta 1, rms=0.007 (1.460%) iter 25, dt=0.002294: new neg 13, old_neg 14, delta 1, rms=0.007 (1.455%) iter 26, dt=0.002294: new neg 13, old_neg 13, delta 0, rms=0.007 (1.450%) iter 27, dt=0.002294: new neg 12, old_neg 13, delta 1, rms=0.007 (1.445%) iter 28, dt=0.002294: new neg 12, old_neg 12, delta 0, rms=0.007 (1.439%) iter 29, dt=0.002294: new neg 11, old_neg 12, delta 1, rms=0.007 (1.434%) iter 30, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (1.430%) iter 31, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (1.426%) iter 32, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (1.422%) iter 33, dt=0.002294: new neg 11, old_neg 11, delta 0, rms=0.006 (1.418%) iter 34, dt=0.002294: new neg 10, old_neg 11, delta 1, rms=0.006 (1.415%) iter 35, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.006 (1.412%) iter 36, dt=0.002294: new neg 10, old_neg 10, delta 0, rms=0.006 (1.410%) iter 37, dt=0.002294: new neg 9, old_neg 10, delta 1, rms=0.006 (1.408%) iter 38, dt=0.002294: new neg 8, old_neg 9, delta 1, rms=0.006 (1.407%) iter 39, dt=0.002294: new neg 7, old_neg 8, delta 1, rms=0.006 (1.406%) iter 40, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.407%) iter 41, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.006 (1.410%) iter 42, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.414%) iter 43, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.420%) iter 44, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.428%) iter 45, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.438%) iter 46, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.451%) iter 47, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.467%) iter 48, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.485%) iter 49, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.505%) iter 50, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.527%) iter 51, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.551%) iter 52, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.576%) iter 53, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.602%) iter 54, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.005 (1.629%) iter 55, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (1.655%) iter 56, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (1.681%) iter 57, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (1.706%) iter 58, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (1.729%) iter 59, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (1.749%) iter 60, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (1.767%) iter 61, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (1.781%) iter 62, dt=0.002294: new neg 7, old_neg 7, delta 0, rms=0.004 (1.792%) iter 63, dt=0.002294: new neg 6, old_neg 7, delta 1, rms=0.004 (1.800%) iter 64, dt=0.002294: new neg 5, old_neg 6, delta 1, rms=0.004 (1.806%) iter 65, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.004 (1.811%) iter 66, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.004 (1.817%) iter 67, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.004 (1.823%) iter 68, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.004 (1.832%) iter 69, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.003 (1.844%) iter 70, dt=0.002294: new neg 5, old_neg 5, delta 0, rms=0.003 (1.859%) iter 71, dt=0.002294: new neg 4, old_neg 5, delta 1, rms=0.003 (1.879%) iter 72, dt=0.002294: new neg 3, old_neg 4, delta 1, rms=0.003 (1.904%) iter 73, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (1.933%) iter 74, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (1.968%) iter 75, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.008%) iter 76, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.053%) iter 77, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.103%) iter 78, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.158%) iter 79, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.217%) iter 80, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.278%) iter 81, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.337%) iter 82, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.387%) iter 83, dt=0.002294: new neg 3, old_neg 3, delta 0, rms=0.003 (2.417%) iter 84, dt=0.100477: new neg 0, old_neg 3, delta 3, rms=0.002 (23.278%) 0201: dt=1.792000, rms=0.695 (-0.279%), 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=0.674, neg=0, invalid=96777 iter 0, gcam->neg = 2086 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.009, neg=1, removing folds in lattice.... iter 1, dt=0.063783: new neg 3, old_neg 1, delta -2, rms=0.004 (55.491%) iter 2, dt=0.042011: new neg 0, old_neg 3, delta 3, rms=0.002 (44.399%) 0202: dt=1.629327, rms=0.635 (5.786%), neg=0, invalid=96777 0203: dt=0.000000, rms=0.635 (0.000%), neg=0, invalid=96777 0204: dt=0.050000, rms=0.635 (-0.051%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.635, neg=0, invalid=96777 0205: dt=0.080000, rms=0.635 (0.024%), neg=0, invalid=96777 0206: dt=0.005000, rms=0.635 (0.000%), neg=0, invalid=96777 0207: dt=0.005000, rms=0.635 (-0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... registration took 14 hours, 6 minutes and 18 seconds. #-------------------------------------- #@# CA Reg Inv Wed Jan 1 03:15:45 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Jan 1 03:16:37 CST 2014 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /soft/freesurfer/5.3.0_1/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_1/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... 10048168 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 52 seconds. #-------------------------------------- #@# SkullLTA Wed Jan 1 03:17:30 CST 2014 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /soft/freesurfer/5.3.0_1/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_1/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=10.0 skull bounding box = (45, 15, 34) --> (200, 184, 243) using (97, 71, 139) as brain centroid... mean wm in atlas = 126, using box (78,50,113) --> (116, 91,164) to find MRI wm before smoothing, mri peak at 102 after smoothing, mri peak at 101, scaling input intensities by 1.248 scaling channel 0 by 1.24752 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.7, old_max_log_p =-5750.1 (thresh=-5744.4) 0.757 -0.233 -0.451 113.036; 0.393 0.788 0.229 -34.190; 0.339 -0.549 0.855 -5.896; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.7, old_max_log_p =-4.7 (thresh=-4.7) 0.828 0.136 -0.535 88.954; 0.298 0.653 0.636 -58.708; 0.445 -0.827 0.671 39.466; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.6, old_max_log_p =-4.7 (thresh=-4.7) 0.915 0.335 -0.465 36.460; 0.445 0.135 1.085 -68.663; 0.349 -1.084 0.213 151.029; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.692 0.720 0.093 -39.944; -0.141 -0.054 1.080 20.434; 0.864 -0.934 0.256 70.103; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.731 0.523 0.231 -40.214; -0.141 -0.271 1.162 33.192; 0.777 -1.005 0.099 105.373; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.6, old_max_log_p =-4.6 (thresh=-4.6) 0.701 0.605 0.182 -37.298; -0.218 -0.124 1.167 23.063; 0.784 -0.976 0.255 78.346; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.5, old_max_log_p =-4.6 (thresh=-4.6) 0.581 0.714 0.144 -29.325; -0.231 -0.131 1.234 21.299; 0.852 -0.871 0.271 62.068; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 0.581 0.714 0.144 -29.325; -0.231 -0.131 1.234 21.299; 0.852 -0.871 0.271 62.068; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 0.584 0.714 0.124 -27.793; -0.235 -0.105 1.228 19.279; 0.847 -0.872 0.291 60.498; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 0.584 0.714 0.124 -27.793; -0.235 -0.105 1.228 19.279; 0.846 -0.871 0.291 60.551; 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 0.58364 0.71365 0.12403 -27.79274; -0.23466 -0.10455 1.22845 19.27895; 0.84599 -0.87132 0.29062 60.55095; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.58364 0.71365 0.12403 -27.79274; -0.23466 -0.10455 1.22845 19.27895; 0.84599 -0.87132 0.29062 60.55095; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.584 0.714 0.124 -27.793; -0.235 -0.105 1.228 19.279; 0.846 -0.871 0.291 60.551; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.5 (old=-5750.1) transform before final EM align: 0.584 0.714 0.124 -27.793; -0.235 -0.105 1.228 19.279; 0.846 -0.871 0.291 60.551; 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 0.58364 0.71365 0.12403 -27.79274; -0.23466 -0.10455 1.22845 19.27895; 0.84599 -0.87132 0.29062 60.55095; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.58364 0.71365 0.12403 -27.79274; -0.23466 -0.10455 1.22845 19.27895; 0.84599 -0.87132 0.29062 60.55095; 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: 013: -log(p) = 4.9 tol 0.000000 final transform: 0.584 0.714 0.124 -27.793; -0.235 -0.105 1.228 19.279; 0.846 -0.871 0.291 60.551; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 31 minutes and 33 seconds. #-------------------------------------- #@# SubCort Seg Wed Jan 1 03:49:04 CST 2014 mri_ca_label -align norm.mgz transforms/talairach.m3z /soft/freesurfer/5.3.0_1/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname node1108 machine x86_64 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis cd /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /soft/freesurfer/5.3.0_1/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_1/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_1/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 = 0.18045 (17) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (18379 voxels, overlap=0.003) Left_Lateral_Ventricle (4): linear fit = 0.62 x + 0.0 (18379 voxels, peak = 17), gca=16.6 gca peak = 0.14982 (20) mri peak = 0.14079 (15) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12110 voxels, overlap=0.155) Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12110 voxels, peak = 13), gca=12.9 gca peak = 0.28003 (97) mri peak = 0.11638 (85) Right_Pallidum (52): linear fit = 0.86 x + 0.0 (232 voxels, overlap=0.036) Right_Pallidum (52): linear fit = 0.86 x + 0.0 (232 voxels, peak = 83), gca=82.9 gca peak = 0.18160 (96) mri peak = 0.11012 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (332 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (332 voxels, peak = 96), gca=96.0 gca peak = 0.27536 (62) mri peak = 0.07503 (66) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1184 voxels, overlap=0.828) Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (1184 voxels, peak = 65), gca=64.8 gca peak = 0.32745 (63) mri peak = 0.06381 (70) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (637 voxels, overlap=0.534) Left_Hippocampus (17): linear fit = 1.07 x + 0.0 (637 voxels, peak = 67), gca=67.1 gca peak = 0.08597 (105) mri peak = 0.05098 (99) Right_Cerebral_White_Matter (41): linear fit = 0.96 x + 0.0 (53867 voxels, overlap=0.800) Right_Cerebral_White_Matter (41): linear fit = 0.96 x + 0.0 (53867 voxels, peak = 101), gca=101.3 gca peak = 0.09209 (106) mri peak = 0.04940 (99) Left_Cerebral_White_Matter (2): linear fit = 0.96 x + 0.0 (89056 voxels, overlap=0.872) Left_Cerebral_White_Matter (2): linear fit = 0.96 x + 0.0 (89056 voxels, peak = 102), gca=102.3 gca peak = 0.07826 (63) mri peak = 0.03975 (72) Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (28827 voxels, overlap=0.477) Left_Cerebral_Cortex (3): linear fit = 1.16 x + 0.0 (28827 voxels, peak = 73), gca=73.4 gca peak = 0.08598 (64) mri peak = 0.03026 (72) Right_Cerebral_Cortex (42): linear fit = 1.11 x + 0.0 (29516 voxels, overlap=0.598) Right_Cerebral_Cortex (42): linear fit = 1.11 x + 0.0 (29516 voxels, peak = 71), gca=70.7 gca peak = 0.24164 (71) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18227 (75) mri peak = 0.13692 (77) Left_Caudate (11): linear fit = 0.95 x + 0.0 (862 voxels, overlap=0.774) Left_Caudate (11): linear fit = 0.95 x + 0.0 (862 voxels, peak = 72), gca=71.6 gca peak = 0.10629 (62) mri peak = 0.05985 (72) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (25642 voxels, overlap=0.237) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (25642 voxels, peak = 73), gca=73.5 gca peak = 0.11668 (59) mri peak = 0.05489 (72) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (34453 voxels, overlap=0.151) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (34453 voxels, peak = 71), gca=70.5 gca peak = 0.17849 (88) mri peak = 0.06794 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (10679 voxels, overlap=0.980) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (10679 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.08860 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8057 voxels, overlap=0.973) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (8057 voxels, peak = 90), gca=89.9 gca peak = 0.41688 (64) mri peak = 0.20006 (69) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (540 voxels, overlap=0.041) Left_Amygdala (18): linear fit = 1.16 x + 0.0 (540 voxels, peak = 75), gca=74.6 gca peak = 0.42394 (62) mri peak = 0.12994 (65) Right_Amygdala (54): linear fit = 1.09 x + 0.0 (297 voxels, overlap=1.016) Right_Amygdala (54): linear fit = 1.09 x + 0.0 (297 voxels, peak = 67), gca=67.3 gca peak = 0.10041 (96) mri peak = 0.05417 (92) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4031 voxels, overlap=0.814) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (4031 voxels, peak = 92), gca=91.7 gca peak = 0.13978 (88) mri peak = 0.08546 (82) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (4581 voxels, overlap=0.754) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (4581 voxels, peak = 81), gca=81.4 gca peak = 0.08514 (81) mri peak = 0.07907 (88) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1611 voxels, overlap=0.884) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1611 voxels, peak = 83), gca=83.0 gca peak = 0.09624 (82) mri peak = 0.10233 (75) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1413 voxels, overlap=0.320) Right_Putamen (51): linear fit = 0.88 x + 0.0 (1413 voxels, peak = 73), gca=72.6 gca peak = 0.07543 (88) mri peak = 0.07490 (88) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12963 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12963 voxels, peak = 90), gca=90.2 gca peak = 0.12757 (95) mri peak = 0.08529 (92) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1004 voxels, overlap=0.817) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1004 voxels, peak = 95), gca=94.5 gca peak = 0.17004 (92) mri peak = 0.09936 (99) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1132 voxels, overlap=0.844) Left_VentralDC (28): linear fit = 1.04 x + 0.0 (1132 voxels, peak = 96), gca=96.1 gca peak = 0.21361 (36) mri peak = 0.16967 (20) Third_Ventricle (14): linear fit = 0.52 x + 0.0 (389 voxels, overlap=0.046) Third_Ventricle (14): linear fit = 0.52 x + 0.0 (389 voxels, peak = 19), gca=18.9 gca peak = 0.26069 (23) mri peak = 0.16325 (19) Fourth_Ventricle (15): linear fit = 0.80 x + 0.0 (318 voxels, overlap=0.432) Fourth_Ventricle (15): linear fit = 0.80 x + 0.0 (318 voxels, peak = 18), gca=18.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Caudate = 0.24164 (71) 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 setting label Right_Caudate based on Left_Caudate = 0.95 x + 0: 72 estimating mean gm scale to be 1.11 x + 0.0 estimating mean wm scale to be 0.96 x + 0.0 estimating mean csf scale to be 0.69 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.20670 (17) mri peak = 0.18045 (17) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (18379 voxels, overlap=0.929) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (18379 voxels, peak = 17), gca=16.6 gca peak = 0.22513 (13) mri peak = 0.14079 (15) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (12110 voxels, overlap=0.917) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (12110 voxels, peak = 13), gca=13.5 gca peak = 0.27285 (83) mri peak = 0.11638 (85) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (232 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (232 voxels, peak = 83), gca=83.0 gca peak = 0.18189 (96) mri peak = 0.11012 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (332 voxels, overlap=1.008) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (332 voxels, peak = 96), gca=96.0 gca peak = 0.26186 (65) mri peak = 0.07503 (66) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1184 voxels, overlap=0.933) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1184 voxels, peak = 65), gca=65.0 gca peak = 0.29387 (67) mri peak = 0.06381 (70) Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (637 voxels, overlap=1.013) Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (637 voxels, peak = 69), gca=69.3 gca peak = 0.08569 (103) mri peak = 0.05098 (99) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53867 voxels, overlap=0.916) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53867 voxels, peak = 104), gca=103.5 gca peak = 0.09568 (102) mri peak = 0.04940 (99) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (89056 voxels, overlap=0.947) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (89056 voxels, peak = 103), gca=102.5 gca peak = 0.06860 (73) mri peak = 0.03975 (72) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28827 voxels, overlap=0.945) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (28827 voxels, peak = 72), gca=71.9 gca peak = 0.07876 (70) mri peak = 0.03026 (72) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (29516 voxels, overlap=0.677) Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (29516 voxels, peak = 72), gca=72.4 gca peak = 0.27041 (70) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17332 (71) mri peak = 0.13692 (77) Left_Caudate (11): linear fit = 1.01 x + 0.0 (862 voxels, overlap=0.969) Left_Caudate (11): linear fit = 1.01 x + 0.0 (862 voxels, peak = 72), gca=72.1 gca peak = 0.09013 (74) mri peak = 0.05985 (72) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (25642 voxels, overlap=0.972) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (25642 voxels, peak = 74), gca=73.6 gca peak = 0.10665 (71) mri peak = 0.05489 (72) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (34453 voxels, overlap=0.965) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (34453 voxels, peak = 71), gca=70.6 gca peak = 0.17033 (92) mri peak = 0.06794 (93) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (10679 voxels, overlap=1.000) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (10679 voxels, peak = 91), gca=90.6 gca peak = 0.15955 (90) mri peak = 0.08860 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8057 voxels, overlap=1.000) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8057 voxels, peak = 90), gca=89.6 gca peak = 0.32112 (74) mri peak = 0.20006 (69) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (540 voxels, overlap=0.997) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (540 voxels, peak = 68), gca=68.5 gca peak = 0.38682 (68) mri peak = 0.12994 (65) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (297 voxels, overlap=1.006) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (297 voxels, peak = 67), gca=67.0 gca peak = 0.10507 (90) mri peak = 0.05417 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4031 voxels, overlap=0.996) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4031 voxels, peak = 90), gca=89.6 gca peak = 0.11027 (81) mri peak = 0.08546 (82) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4581 voxels, overlap=0.985) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4581 voxels, peak = 81), gca=81.0 gca peak = 0.08349 (83) mri peak = 0.07907 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1611 voxels, overlap=0.949) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1611 voxels, peak = 83), gca=83.0 gca peak = 0.12201 (67) mri peak = 0.10233 (75) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1413 voxels, overlap=0.924) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1413 voxels, peak = 67), gca=67.0 gca peak = 0.07238 (87) mri peak = 0.07490 (88) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12963 voxels, overlap=0.814) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12963 voxels, peak = 87), gca=86.6 gca peak = 0.14647 (94) mri peak = 0.08529 (92) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1004 voxels, overlap=0.804) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1004 voxels, peak = 95), gca=95.4 gca peak = 0.13208 (97) mri peak = 0.09936 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1132 voxels, overlap=0.838) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1132 voxels, peak = 97), gca=97.0 gca peak = 0.25895 (26) mri peak = 0.16967 (20) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (389 voxels, overlap=0.564) Third_Ventricle (14): linear fit = 0.77 x + 0.0 (389 voxels, peak = 20), gca=20.1 gca peak = 0.23743 (18) mri peak = 0.16325 (19) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (318 voxels, overlap=0.830) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (318 voxels, peak = 18), gca=18.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.20906 (38) gca peak CSF = 0.21162 (31) gca peak Left_Accumbens_area = 0.49607 (67) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63634 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31011 (33) gca peak Right_Caudate = 0.27041 (70) gca peak Right_Accumbens_area = 0.30875 (69) gca peak Right_vessel = 0.83781 (60) gca peak Right_choroid_plexus = 0.10190 (48) gca peak Fifth_Ventricle = 0.45329 (30) gca peak WM_hypointensities = 0.16741 (79) gca peak non_WM_hypointensities = 0.13024 (51) gca peak Optic_Chiasm = 0.34842 (76) not using caudate to estimate GM means setting label Right_Caudate based on Left_Caudate = 1.01 x + 0: 72 estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.95 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 51892 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 538 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 134067 changed. image ll: -2.966, PF=1.000 pass 2: 28173 changed. image ll: -2.959, PF=1.000 pass 3: 10932 changed. pass 4: 4896 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 12 minutes and 41 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/transforms/cc_up.lta MPS1036-1 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/MPS1036-1/mri/transforms/cc_up.lta reading aseg from /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aseg.auto_noCCseg.mgz reading norm from /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/norm.mgz 131595 voxels in left wm, 132004 in right wm, xrange [107, 135] searching rotation angles z=[-3 11], y=[-12 2] searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.7 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.7 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.2 searching scale 1 Z rot 9.5 searching scale 1 Z rot 9.7 searching scale 1 Z rot 10.0 searching scale 1 Z rot 10.2 searching scale 1 Z rot 10.5 searching scale 1 Z rot 10.7 searching scale 1 Z rot 11.0 searching scale 1 Z rot 11.2 searching scale 1 Z rot 11.5 searching scale 1 Z rot 11.7 searching scale 1 Z rot 12.0 searching scale 1 Z rot 12.2 searching scale 1 Z rot 12.5 searching scale 1 Z rot 12.7 searching scale 1 Z rot 13.0 global minimum found at slice 120.0, rotations (-4.48, 6.22) final transformation (x=120.0, yr=-4.484, zr=6.220): 0.991 -0.108 -0.078 26.700; 0.108 0.994 -0.008 53.586; 0.078 -0.000 0.997 -19.956; 0.000 0.000 0.000 1.000; updating x range to be [125, 134] in xformed coordinates best xformed slice 127 cc center is found at 127 154 104 eigenvectors: -0.010 0.017 1.000; -0.190 -0.982 0.015; 0.982 -0.190 0.013; writing aseg with callosum to /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 3.7 minutes #-------------------------------------- #@# Merge ASeg Wed Jan 1 04:05:27 CST 2014 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Jan 1 04:05:28 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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... 6441 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 43 (43) csf peak at 19, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 99 gm peak at 76 (76), valley at 42 (42) csf peak at 19, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 51 seconds. #-------------------------------------------- #@# Mask BFS Wed Jan 1 04:08:20 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2105835 voxels in mask (pct= 12.55) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Jan 1 04:08:22 CST 2014 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 (102.0): 101.7 +- 8.1 [80.0 --> 125.0] GM (73.0) : 69.9 +- 12.9 [30.0 --> 96.0] setting bottom of white matter range to 82.7 setting top of gray matter range to 95.6 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... 17556 sparsely connected voxels removed... thickening thin strands.... 20 segments, 8304 filled 1267 bright non-wm voxels segmented. 8956 diagonally connected voxels added... white matter segmentation took 2.0 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 1.17 minutes reading wm segmentation from wm.seg.mgz... 3199 voxels added to wm to prevent paths from MTL structures to cortex 24905 additional wm voxels added 0 additional wm voxels added SEG EDIT: 247342 voxels turned on, 68897 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 104 new 104 115,126,128 old 104 new 104 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 222 found - 222 modified | TOTAL: 222 pass 2 (xy+): 0 found - 222 modified | TOTAL: 222 pass 1 (xy-): 207 found - 207 modified | TOTAL: 429 pass 2 (xy-): 0 found - 207 modified | TOTAL: 429 pass 1 (yz+): 172 found - 172 modified | TOTAL: 601 pass 2 (yz+): 0 found - 172 modified | TOTAL: 601 pass 1 (yz-): 206 found - 206 modified | TOTAL: 807 pass 2 (yz-): 0 found - 206 modified | TOTAL: 807 pass 1 (xz+): 153 found - 153 modified | TOTAL: 960 pass 2 (xz+): 0 found - 153 modified | TOTAL: 960 pass 1 (xz-): 156 found - 156 modified | TOTAL: 1116 pass 2 (xz-): 0 found - 156 modified | TOTAL: 1116 Iteration Number : 1 pass 1 (+++): 89 found - 89 modified | TOTAL: 89 pass 2 (+++): 0 found - 89 modified | TOTAL: 89 pass 1 (+++): 100 found - 100 modified | TOTAL: 189 pass 2 (+++): 0 found - 100 modified | TOTAL: 189 pass 1 (+++): 80 found - 80 modified | TOTAL: 269 pass 2 (+++): 0 found - 80 modified | TOTAL: 269 pass 1 (+++): 84 found - 84 modified | TOTAL: 353 pass 2 (+++): 0 found - 84 modified | TOTAL: 353 Iteration Number : 1 pass 1 (++): 250 found - 250 modified | TOTAL: 250 pass 2 (++): 0 found - 250 modified | TOTAL: 250 pass 1 (+-): 276 found - 276 modified | TOTAL: 526 pass 2 (+-): 1 found - 277 modified | TOTAL: 527 pass 3 (+-): 0 found - 277 modified | TOTAL: 527 pass 1 (--): 266 found - 266 modified | TOTAL: 793 pass 2 (--): 1 found - 267 modified | TOTAL: 794 pass 3 (--): 0 found - 267 modified | TOTAL: 794 pass 1 (-+): 250 found - 250 modified | TOTAL: 1044 pass 2 (-+): 0 found - 250 modified | TOTAL: 1044 Iteration Number : 2 pass 1 (xy+): 28 found - 28 modified | TOTAL: 28 pass 2 (xy+): 0 found - 28 modified | TOTAL: 28 pass 1 (xy-): 26 found - 26 modified | TOTAL: 54 pass 2 (xy-): 0 found - 26 modified | TOTAL: 54 pass 1 (yz+): 21 found - 21 modified | TOTAL: 75 pass 2 (yz+): 0 found - 21 modified | TOTAL: 75 pass 1 (yz-): 27 found - 27 modified | TOTAL: 102 pass 2 (yz-): 0 found - 27 modified | TOTAL: 102 pass 1 (xz+): 23 found - 23 modified | TOTAL: 125 pass 2 (xz+): 0 found - 23 modified | TOTAL: 125 pass 1 (xz-): 30 found - 30 modified | TOTAL: 155 pass 2 (xz-): 0 found - 30 modified | TOTAL: 155 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 1 found - 1 modified | TOTAL: 9 pass 2 (+++): 0 found - 1 modified | TOTAL: 9 pass 1 (+++): 4 found - 4 modified | TOTAL: 13 pass 2 (+++): 0 found - 4 modified | TOTAL: 13 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 16 found - 16 modified | TOTAL: 22 pass 2 (+-): 0 found - 16 modified | TOTAL: 22 pass 1 (--): 17 found - 17 modified | TOTAL: 39 pass 2 (--): 0 found - 17 modified | TOTAL: 39 pass 1 (-+): 18 found - 18 modified | TOTAL: 57 pass 2 (-+): 0 found - 18 modified | TOTAL: 57 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 5 found - 5 modified | TOTAL: 10 pass 2 (yz-): 0 found - 5 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 1 found - 1 modified | TOTAL: 12 pass 2 (xz-): 0 found - 1 modified | TOTAL: 12 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 1 found - 1 modified | TOTAL: 5 pass 2 (-+): 0 found - 1 modified | TOTAL: 5 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2755 (out of 731549: 0.376598) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Jan 1 04:11:35 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2451 (min = 350, max = 1400), aspect = 0.64 (min = 0.10, max = 0.75) need search nearby using seed (121, 114, 148), TAL = (7.0, 20.0, 14.0) talairach voxel to voxel transform 1.086 -0.012 0.198 -27.718; -0.014 1.018 0.266 -57.126; -0.166 -0.240 1.172 65.007; 0.000 0.000 0.000 1.000; segmentation indicates cc at (121, 114, 148) --> (7.0, 20.0, 14.0) done. writing output to filled.mgz... filling took 0.6 minutes badRH = 1791/321714, badLH=10167/366630 Please check filled volume. Cerebellum may be included. talairach cc position changed to (7.00, 20.00, 14.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(25.00, 20.00, 14.00) SRC: (112.07, 96.76, 194.01) search lh wm seed point around talairach space (-11.00, 20.00, 14.00), SRC: (151.17, 96.23, 188.03) 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 Jan 1 04:12:12 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 21 found - 21 modified | TOTAL: 21 pass 2 (xy+): 0 found - 21 modified | TOTAL: 21 pass 1 (xy-): 13 found - 13 modified | TOTAL: 34 pass 2 (xy-): 0 found - 13 modified | TOTAL: 34 pass 1 (yz+): 16 found - 16 modified | TOTAL: 50 pass 2 (yz+): 0 found - 16 modified | TOTAL: 50 pass 1 (yz-): 24 found - 24 modified | TOTAL: 74 pass 2 (yz-): 0 found - 24 modified | TOTAL: 74 pass 1 (xz+): 20 found - 20 modified | TOTAL: 94 pass 2 (xz+): 0 found - 20 modified | TOTAL: 94 pass 1 (xz-): 12 found - 12 modified | TOTAL: 106 pass 2 (xz-): 0 found - 12 modified | TOTAL: 106 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 3 found - 3 modified | TOTAL: 9 pass 2 (+++): 0 found - 3 modified | TOTAL: 9 pass 1 (+++): 2 found - 2 modified | TOTAL: 11 pass 2 (+++): 0 found - 2 modified | TOTAL: 11 pass 1 (+++): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 11 found - 11 modified | TOTAL: 18 pass 2 (+-): 0 found - 11 modified | TOTAL: 18 pass 1 (--): 8 found - 8 modified | TOTAL: 26 pass 2 (--): 0 found - 8 modified | TOTAL: 26 pass 1 (-+): 6 found - 6 modified | TOTAL: 32 pass 2 (-+): 0 found - 6 modified | TOTAL: 32 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 2 found - 2 modified | TOTAL: 5 pass 2 (xy-): 0 found - 2 modified | TOTAL: 5 pass 1 (yz+): 2 found - 2 modified | TOTAL: 7 pass 2 (yz+): 0 found - 2 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 0 found - 0 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 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 = 160 (out of 366790: 0.043622) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 104 vertices, 121 faces slice 60: 4050 vertices, 4235 faces slice 70: 11346 vertices, 11645 faces slice 80: 19570 vertices, 19891 faces slice 90: 28915 vertices, 29278 faces slice 100: 38518 vertices, 38874 faces slice 110: 48200 vertices, 48647 faces slice 120: 60716 vertices, 61272 faces slice 130: 73984 vertices, 74597 faces slice 140: 88435 vertices, 89067 faces slice 150: 101768 vertices, 102423 faces slice 160: 114593 vertices, 115266 faces slice 170: 125176 vertices, 125749 faces slice 180: 133963 vertices, 134569 faces slice 190: 143309 vertices, 143927 faces slice 200: 152147 vertices, 152755 faces slice 210: 161456 vertices, 162090 faces slice 220: 167649 vertices, 168147 faces slice 230: 170373 vertices, 170738 faces slice 240: 170448 vertices, 170790 faces slice 250: 170448 vertices, 170790 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... 170408 voxel in cpt #1: X=-346 [v=170408,e=512262,f=341508] located at (-21.726509, 9.515985, 50.915520) 12 voxel in cpt #2: X=2 [v=12,e=30,f=20] located at (5.500000, 4.000000, 45.000000) 28 voxel in cpt #3: X=2 [v=28,e=78,f=52] located at (3.285714, 48.785713, 57.000000) For the whole surface: X=-342 [v=170448,e=512370,f=341580] 3 components have been found keeping component #1 with 170408 vertices done #-------------------------------------------- #@# Smooth1 lh Wed Jan 1 04:12:19 CST 2014 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Jan 1 04:12:23 CST 2014 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts avg radius = 52.2 mm, total surface area = 84838 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.126 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.066 (target=0.015) step 030: RMS=0.064 (target=0.015) step 035: RMS=0.061 (target=0.015) step 040: RMS=0.060 (target=0.015) step 045: RMS=0.059 (target=0.015) step 050: RMS=0.058 (target=0.015) step 055: RMS=0.058 (target=0.015) step 060: RMS=0.059 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Jan 1 04:12:52 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.89 +- 0.60 (0.00-->8.42) (max @ vno 68088 --> 68089) face area 0.02 +- 0.03 (-0.15-->0.83) scaling brain by 0.286... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.178, avgs=0 005/300: dt: 0.9000, rms radial error=176.920, avgs=0 010/300: dt: 0.9000, rms radial error=176.368, avgs=0 015/300: dt: 0.9000, rms radial error=175.642, avgs=0 020/300: dt: 0.9000, rms radial error=174.814, avgs=0 025/300: dt: 0.9000, rms radial error=173.929, avgs=0 030/300: dt: 0.9000, rms radial error=173.011, avgs=0 035/300: dt: 0.9000, rms radial error=172.076, avgs=0 040/300: dt: 0.9000, rms radial error=171.133, avgs=0 045/300: dt: 0.9000, rms radial error=170.187, avgs=0 050/300: dt: 0.9000, rms radial error=169.242, avgs=0 055/300: dt: 0.9000, rms radial error=168.299, avgs=0 060/300: dt: 0.9000, rms radial error=167.359, avgs=0 065/300: dt: 0.9000, rms radial error=166.424, avgs=0 070/300: dt: 0.9000, rms radial error=165.493, avgs=0 075/300: dt: 0.9000, rms radial error=164.565, avgs=0 080/300: dt: 0.9000, rms radial error=163.643, avgs=0 085/300: dt: 0.9000, rms radial error=162.725, avgs=0 090/300: dt: 0.9000, rms radial error=161.812, avgs=0 095/300: dt: 0.9000, rms radial error=160.904, avgs=0 100/300: dt: 0.9000, rms radial error=160.001, avgs=0 105/300: dt: 0.9000, rms radial error=159.103, avgs=0 110/300: dt: 0.9000, rms radial error=158.209, avgs=0 115/300: dt: 0.9000, rms radial error=157.321, avgs=0 120/300: dt: 0.9000, rms radial error=156.437, avgs=0 125/300: dt: 0.9000, rms radial error=155.558, avgs=0 130/300: dt: 0.9000, rms radial error=154.684, avgs=0 135/300: dt: 0.9000, rms radial error=153.814, avgs=0 140/300: dt: 0.9000, rms radial error=152.950, avgs=0 145/300: dt: 0.9000, rms radial error=152.090, avgs=0 150/300: dt: 0.9000, rms radial error=151.235, avgs=0 155/300: dt: 0.9000, rms radial error=150.385, avgs=0 160/300: dt: 0.9000, rms radial error=149.540, avgs=0 165/300: dt: 0.9000, rms radial error=148.699, avgs=0 170/300: dt: 0.9000, rms radial error=147.862, avgs=0 175/300: dt: 0.9000, rms radial error=147.030, avgs=0 180/300: dt: 0.9000, rms radial error=146.203, avgs=0 185/300: dt: 0.9000, rms radial error=145.381, avgs=0 190/300: dt: 0.9000, rms radial error=144.562, avgs=0 195/300: dt: 0.9000, rms radial error=143.749, avgs=0 200/300: dt: 0.9000, rms radial error=142.940, avgs=0 205/300: dt: 0.9000, rms radial error=142.135, avgs=0 210/300: dt: 0.9000, rms radial error=141.335, avgs=0 215/300: dt: 0.9000, rms radial error=140.538, avgs=0 220/300: dt: 0.9000, rms radial error=139.747, avgs=0 225/300: dt: 0.9000, rms radial error=138.960, avgs=0 230/300: dt: 0.9000, rms radial error=138.177, avgs=0 235/300: dt: 0.9000, rms radial error=137.398, avgs=0 240/300: dt: 0.9000, rms radial error=136.624, avgs=0 245/300: dt: 0.9000, rms radial error=135.855, avgs=0 250/300: dt: 0.9000, rms radial error=135.089, avgs=0 255/300: dt: 0.9000, rms radial error=134.328, avgs=0 260/300: dt: 0.9000, rms radial error=133.571, avgs=0 265/300: dt: 0.9000, rms radial error=132.819, avgs=0 270/300: dt: 0.9000, rms radial error=132.070, avgs=0 275/300: dt: 0.9000, rms radial error=131.326, avgs=0 280/300: dt: 0.9000, rms radial error=130.586, avgs=0 285/300: dt: 0.9000, rms radial error=129.850, avgs=0 290/300: dt: 0.9000, rms radial error=129.119, avgs=0 295/300: dt: 0.9000, rms radial error=128.391, avgs=0 300/300: dt: 0.9000, rms radial error=127.668, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20710.83 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3825.98 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00004 epoch 3 (K=160.0), pass 1, starting sse = 546.96 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00297 epoch 4 (K=640.0), pass 1, starting sse = 82.57 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00601 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.08 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Wed Jan 1 04:17:32 CST 2014 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS1036-1 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=-346 (nv=170408, nf=341508, ne=512262, g=174) 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... 47997 ambiguous faces found in tessellation segmenting defects... 164 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 22 into 16 -merging segment 57 into 55 -merging segment 129 into 66 -merging segment 160 into 66 -merging segment 72 into 71 -merging segment 81 into 84 -merging segment 100 into 94 -merging segment 126 into 104 -merging segment 120 into 113 -merging segment 157 into 156 154 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1064 (-4.5532) -vertex loglikelihood: -6.4231 (-3.2115) -normal dot loglikelihood: -3.5641 (-3.5641) -quad curv loglikelihood: -6.0869 (-3.0434) Total Loglikelihood : -25.1805 CORRECTING DEFECT 0 (vertices=59, convex hull=105) After retessellation of defect 0, euler #=-151 (143509,424408,280748) : difference with theory (-151) = 0 CORRECTING DEFECT 1 (vertices=42, convex hull=64) After retessellation of defect 1, euler #=-150 (143528,424491,280813) : difference with theory (-150) = 0 CORRECTING DEFECT 2 (vertices=18, convex hull=58) After retessellation of defect 2, euler #=-149 (143537,424540,280854) : difference with theory (-149) = 0 CORRECTING DEFECT 3 (vertices=8, convex hull=24) After retessellation of defect 3, euler #=-148 (143540,424557,280869) : difference with theory (-148) = 0 CORRECTING DEFECT 4 (vertices=77, convex hull=76) After retessellation of defect 4, euler #=-147 (143552,424625,280926) : difference with theory (-147) = 0 CORRECTING DEFECT 5 (vertices=27, convex hull=58) After retessellation of defect 5, euler #=-146 (143569,424698,280983) : difference with theory (-146) = 0 CORRECTING DEFECT 6 (vertices=49, convex hull=88) After retessellation of defect 6, euler #=-145 (143593,424806,281068) : difference with theory (-145) = 0 CORRECTING DEFECT 7 (vertices=32, convex hull=69) After retessellation of defect 7, euler #=-144 (143612,424888,281132) : difference with theory (-144) = 0 CORRECTING DEFECT 8 (vertices=103, convex hull=70) After retessellation of defect 8, euler #=-143 (143629,424968,281196) : difference with theory (-143) = 0 CORRECTING DEFECT 9 (vertices=29, convex hull=49) After retessellation of defect 9, euler #=-142 (143638,425016,281236) : difference with theory (-142) = 0 CORRECTING DEFECT 10 (vertices=27, convex hull=25) After retessellation of defect 10, euler #=-141 (143642,425036,281253) : difference with theory (-141) = 0 CORRECTING DEFECT 11 (vertices=12, convex hull=29) After retessellation of defect 11, euler #=-140 (143643,425049,281266) : difference with theory (-140) = 0 CORRECTING DEFECT 12 (vertices=187, convex hull=91) After retessellation of defect 12, euler #=-139 (143675,425182,281368) : difference with theory (-139) = 0 CORRECTING DEFECT 13 (vertices=30, convex hull=54) After retessellation of defect 13, euler #=-138 (143689,425247,281420) : difference with theory (-138) = 0 CORRECTING DEFECT 14 (vertices=21, convex hull=52) After retessellation of defect 14, euler #=-137 (143698,425294,281459) : difference with theory (-137) = 0 CORRECTING DEFECT 15 (vertices=7, convex hull=18) After retessellation of defect 15, euler #=-136 (143699,425302,281467) : difference with theory (-136) = 0 CORRECTING DEFECT 16 (vertices=67, convex hull=46) After retessellation of defect 16, euler #=-134 (143703,425332,281495) : difference with theory (-135) = -1 CORRECTING DEFECT 17 (vertices=28, convex hull=41) After retessellation of defect 17, euler #=-133 (143712,425377,281532) : difference with theory (-134) = -1 CORRECTING DEFECT 18 (vertices=229, convex hull=39) After retessellation of defect 18, euler #=-132 (143728,425439,281579) : difference with theory (-133) = -1 CORRECTING DEFECT 19 (vertices=56, convex hull=107) After retessellation of defect 19, euler #=-131 (143761,425583,281691) : difference with theory (-132) = -1 CORRECTING DEFECT 20 (vertices=52, convex hull=37) After retessellation of defect 20, euler #=-130 (143766,425609,281713) : difference with theory (-131) = -1 CORRECTING DEFECT 21 (vertices=24, convex hull=26) After retessellation of defect 21, euler #=-129 (143768,425623,281726) : difference with theory (-130) = -1 CORRECTING DEFECT 22 (vertices=60, convex hull=32) After retessellation of defect 22, euler #=-128 (143770,425643,281745) : difference with theory (-129) = -1 CORRECTING DEFECT 23 (vertices=23, convex hull=56) After retessellation of defect 23, euler #=-127 (143781,425699,281791) : difference with theory (-128) = -1 CORRECTING DEFECT 24 (vertices=43, convex hull=60) After retessellation of defect 24, euler #=-126 (143797,425769,281846) : difference with theory (-127) = -1 CORRECTING DEFECT 25 (vertices=19, convex hull=24) After retessellation of defect 25, euler #=-125 (143798,425780,281857) : difference with theory (-126) = -1 CORRECTING DEFECT 26 (vertices=100, convex hull=31) After retessellation of defect 26, euler #=-124 (143805,425810,281881) : difference with theory (-125) = -1 CORRECTING DEFECT 27 (vertices=24, convex hull=29) After retessellation of defect 27, euler #=-123 (143807,425825,281895) : difference with theory (-124) = -1 CORRECTING DEFECT 28 (vertices=7, convex hull=19) After retessellation of defect 28, euler #=-122 (143808,425833,281903) : difference with theory (-123) = -1 CORRECTING DEFECT 29 (vertices=40, convex hull=71) After retessellation of defect 29, euler #=-121 (143833,425936,281982) : difference with theory (-122) = -1 CORRECTING DEFECT 30 (vertices=35, convex hull=53) After retessellation of defect 30, euler #=-120 (143841,425980,282019) : difference with theory (-121) = -1 CORRECTING DEFECT 31 (vertices=44, convex hull=87) After retessellation of defect 31, euler #=-119 (143868,426096,282109) : difference with theory (-120) = -1 CORRECTING DEFECT 32 (vertices=32, convex hull=71) After retessellation of defect 32, euler #=-118 (143887,426182,282177) : difference with theory (-119) = -1 CORRECTING DEFECT 33 (vertices=85, convex hull=36) After retessellation of defect 33, euler #=-117 (143893,426216,282206) : difference with theory (-118) = -1 CORRECTING DEFECT 34 (vertices=314, convex hull=105) After retessellation of defect 34, euler #=-116 (143916,426330,282298) : difference with theory (-117) = -1 CORRECTING DEFECT 35 (vertices=47, convex hull=68) After retessellation of defect 35, euler #=-115 (143934,426411,282362) : difference with theory (-116) = -1 CORRECTING DEFECT 36 (vertices=48, convex hull=39) After retessellation of defect 36, euler #=-114 (143948,426467,282405) : difference with theory (-115) = -1 CORRECTING DEFECT 37 (vertices=45, convex hull=72) After retessellation of defect 37, euler #=-113 (143964,426550,282473) : difference with theory (-114) = -1 CORRECTING DEFECT 38 (vertices=27, convex hull=34) After retessellation of defect 38, euler #=-112 (143971,426583,282500) : difference with theory (-113) = -1 CORRECTING DEFECT 39 (vertices=98, convex hull=135) After retessellation of defect 39, euler #=-111 (144033,426835,282691) : difference with theory (-112) = -1 CORRECTING DEFECT 40 (vertices=70, convex hull=82) After retessellation of defect 40, euler #=-110 (144078,427005,282817) : difference with theory (-111) = -1 CORRECTING DEFECT 41 (vertices=29, convex hull=45) After retessellation of defect 41, euler #=-109 (144091,427064,282864) : difference with theory (-110) = -1 CORRECTING DEFECT 42 (vertices=418, convex hull=302) After retessellation of defect 42, euler #=-108 (144100,427238,283030) : difference with theory (-109) = -1 CORRECTING DEFECT 43 (vertices=390, convex hull=204) After retessellation of defect 43, euler #=-107 (144172,427546,283267) : difference with theory (-108) = -1 CORRECTING DEFECT 44 (vertices=36, convex hull=67) After retessellation of defect 44, euler #=-106 (144190,427624,283328) : difference with theory (-107) = -1 CORRECTING DEFECT 45 (vertices=926, convex hull=560) After retessellation of defect 45, euler #=-106 (144570,429052,284376) : difference with theory (-106) = 0 CORRECTING DEFECT 46 (vertices=45, convex hull=37) After retessellation of defect 46, euler #=-105 (144577,429087,284405) : difference with theory (-105) = 0 CORRECTING DEFECT 47 (vertices=17, convex hull=28) After retessellation of defect 47, euler #=-104 (144582,429109,284423) : difference with theory (-104) = 0 CORRECTING DEFECT 48 (vertices=46, convex hull=50) After retessellation of defect 48, euler #=-103 (144596,429172,284473) : difference with theory (-103) = 0 CORRECTING DEFECT 49 (vertices=25, convex hull=29) After retessellation of defect 49, euler #=-102 (144600,429193,284491) : difference with theory (-102) = 0 CORRECTING DEFECT 50 (vertices=12, convex hull=20) After retessellation of defect 50, euler #=-101 (144601,429202,284500) : difference with theory (-101) = 0 CORRECTING DEFECT 51 (vertices=29, convex hull=76) After retessellation of defect 51, euler #=-100 (144615,429271,284556) : difference with theory (-100) = 0 CORRECTING DEFECT 52 (vertices=23, convex hull=59) After retessellation of defect 52, euler #=-99 (144624,429323,284600) : difference with theory (-99) = 0 CORRECTING DEFECT 53 (vertices=436, convex hull=277) After retessellation of defect 53, euler #=-98 (144639,429501,284764) : difference with theory (-98) = 0 CORRECTING DEFECT 54 (vertices=796, convex hull=387) After retessellation of defect 54, euler #=-96 (144776,430117,285245) : difference with theory (-97) = -1 CORRECTING DEFECT 55 (vertices=46, convex hull=40) After retessellation of defect 55, euler #=-95 (144791,430176,285290) : difference with theory (-96) = -1 CORRECTING DEFECT 56 (vertices=20, convex hull=25) After retessellation of defect 56, euler #=-94 (144795,430193,285304) : difference with theory (-95) = -1 CORRECTING DEFECT 57 (vertices=32, convex hull=58) After retessellation of defect 57, euler #=-93 (144814,430272,285365) : difference with theory (-94) = -1 CORRECTING DEFECT 58 (vertices=13, convex hull=18) After retessellation of defect 58, euler #=-92 (144815,430279,285372) : difference with theory (-93) = -1 CORRECTING DEFECT 59 (vertices=55, convex hull=91) After retessellation of defect 59, euler #=-91 (144824,430341,285426) : difference with theory (-92) = -1 CORRECTING DEFECT 60 (vertices=21, convex hull=49) After retessellation of defect 60, euler #=-90 (144833,430382,285459) : difference with theory (-91) = -1 CORRECTING DEFECT 61 (vertices=225, convex hull=59) After retessellation of defect 61, euler #=-89 (144849,430454,285516) : difference with theory (-90) = -1 CORRECTING DEFECT 62 (vertices=18, convex hull=30) After retessellation of defect 62, euler #=-88 (144856,430484,285540) : difference with theory (-89) = -1 CORRECTING DEFECT 63 (vertices=21, convex hull=49) After retessellation of defect 63, euler #=-87 (144865,430526,285574) : difference with theory (-88) = -1 CORRECTING DEFECT 64 (vertices=12018, convex hull=2290) After retessellation of defect 64, euler #=-92 (147967,441099,293040) : difference with theory (-87) = 5 CORRECTING DEFECT 65 (vertices=5, convex hull=12) After retessellation of defect 65, euler #=-91 (147968,441104,293045) : difference with theory (-86) = 5 CORRECTING DEFECT 66 (vertices=14, convex hull=31) After retessellation of defect 66, euler #=-90 (147972,441124,293062) : difference with theory (-85) = 5 CORRECTING DEFECT 67 (vertices=160, convex hull=158) After retessellation of defect 67, euler #=-89 (148049,441427,293289) : difference with theory (-84) = 5 CORRECTING DEFECT 68 (vertices=26, convex hull=29) After retessellation of defect 68, euler #=-88 (148054,441451,293309) : difference with theory (-83) = 5 CORRECTING DEFECT 69 (vertices=565, convex hull=270) After retessellation of defect 69, euler #=-86 (148079,441672,293507) : difference with theory (-82) = 4 CORRECTING DEFECT 70 (vertices=36, convex hull=52) After retessellation of defect 70, euler #=-85 (148099,441752,293568) : difference with theory (-81) = 4 CORRECTING DEFECT 71 (vertices=1297, convex hull=515) After retessellation of defect 71, euler #=-84 (148139,442128,293905) : difference with theory (-80) = 4 CORRECTING DEFECT 72 (vertices=101, convex hull=108) After retessellation of defect 72, euler #=-83 (148187,442317,294047) : difference with theory (-79) = 4 CORRECTING DEFECT 73 (vertices=9, convex hull=20) After retessellation of defect 73, euler #=-82 (148188,442326,294056) : difference with theory (-78) = 4 CORRECTING DEFECT 74 (vertices=75, convex hull=80) After retessellation of defect 74, euler #=-81 (148229,442485,294175) : difference with theory (-77) = 4 CORRECTING DEFECT 75 (vertices=21, convex hull=55) After retessellation of defect 75, euler #=-80 (148239,442535,294216) : difference with theory (-76) = 4 CORRECTING DEFECT 76 (vertices=47, convex hull=101) After retessellation of defect 76, euler #=-79 (148266,442654,294309) : difference with theory (-75) = 4 CORRECTING DEFECT 77 (vertices=22, convex hull=24) After retessellation of defect 77, euler #=-78 (148271,442676,294327) : difference with theory (-74) = 4 CORRECTING DEFECT 78 (vertices=64, convex hull=32) After retessellation of defect 78, euler #=-77 (148276,442705,294352) : difference with theory (-73) = 4 CORRECTING DEFECT 79 (vertices=18, convex hull=30) After retessellation of defect 79, euler #=-76 (148281,442730,294373) : difference with theory (-72) = 4 CORRECTING DEFECT 80 (vertices=62, convex hull=92) After retessellation of defect 80, euler #=-74 (148305,442837,294458) : difference with theory (-71) = 3 CORRECTING DEFECT 81 (vertices=30, convex hull=64) After retessellation of defect 81, euler #=-73 (148323,442917,294521) : difference with theory (-70) = 3 CORRECTING DEFECT 82 (vertices=48, convex hull=77) After retessellation of defect 82, euler #=-72 (148333,442981,294576) : difference with theory (-69) = 3 CORRECTING DEFECT 83 (vertices=52, convex hull=31) After retessellation of defect 83, euler #=-71 (148337,443002,294594) : difference with theory (-68) = 3 CORRECTING DEFECT 84 (vertices=179, convex hull=41) After retessellation of defect 84, euler #=-70 (148350,443055,294635) : difference with theory (-67) = 3 CORRECTING DEFECT 85 (vertices=91, convex hull=91) After retessellation of defect 85, euler #=-69 (148389,443214,294756) : difference with theory (-66) = 3 CORRECTING DEFECT 86 (vertices=59, convex hull=80) After retessellation of defect 86, euler #=-68 (148400,443284,294816) : difference with theory (-65) = 3 CORRECTING DEFECT 87 (vertices=12, convex hull=30) After retessellation of defect 87, euler #=-67 (148402,443298,294829) : difference with theory (-64) = 3 CORRECTING DEFECT 88 (vertices=17, convex hull=35) After retessellation of defect 88, euler #=-66 (148402,443308,294840) : difference with theory (-63) = 3 CORRECTING DEFECT 89 (vertices=6, convex hull=14) After retessellation of defect 89, euler #=-65 (148403,443313,294845) : difference with theory (-62) = 3 CORRECTING DEFECT 90 (vertices=46, convex hull=46) After retessellation of defect 90, euler #=-63 (148411,443364,294890) : difference with theory (-61) = 2 CORRECTING DEFECT 91 (vertices=29, convex hull=69) After retessellation of defect 91, euler #=-62 (148421,443419,294936) : difference with theory (-60) = 2 CORRECTING DEFECT 92 (vertices=61, convex hull=52) After retessellation of defect 92, euler #=-61 (148428,443458,294969) : difference with theory (-59) = 2 CORRECTING DEFECT 93 (vertices=93, convex hull=67) After retessellation of defect 93, euler #=-60 (148447,443539,295032) : difference with theory (-58) = 2 CORRECTING DEFECT 94 (vertices=6, convex hull=10) After retessellation of defect 94, euler #=-59 (148448,443544,295037) : difference with theory (-57) = 2 CORRECTING DEFECT 95 (vertices=118, convex hull=21) After retessellation of defect 95, euler #=-58 (148453,443564,295053) : difference with theory (-56) = 2 CORRECTING DEFECT 96 (vertices=54, convex hull=79) After retessellation of defect 96, euler #=-57 (148480,443680,295143) : difference with theory (-55) = 2 CORRECTING DEFECT 97 (vertices=29, convex hull=69) After retessellation of defect 97, euler #=-56 (148497,443760,295207) : difference with theory (-54) = 2 CORRECTING DEFECT 98 (vertices=19, convex hull=46) After retessellation of defect 98, euler #=-55 (148506,443806,295245) : difference with theory (-53) = 2 CORRECTING DEFECT 99 (vertices=404, convex hull=244) After retessellation of defect 99, euler #=-53 (148607,444238,295578) : difference with theory (-52) = 1 CORRECTING DEFECT 100 (vertices=59, convex hull=72) After retessellation of defect 100, euler #=-52 (148623,444316,295641) : difference with theory (-51) = 1 CORRECTING DEFECT 101 (vertices=699, convex hull=303) After retessellation of defect 101, euler #=-51 (148789,444960,296120) : difference with theory (-50) = 1 CORRECTING DEFECT 102 (vertices=32, convex hull=25) After retessellation of defect 102, euler #=-50 (148792,444976,296134) : difference with theory (-49) = 1 CORRECTING DEFECT 103 (vertices=33, convex hull=67) After retessellation of defect 103, euler #=-49 (148812,445059,296198) : difference with theory (-48) = 1 CORRECTING DEFECT 104 (vertices=51, convex hull=76) After retessellation of defect 104, euler #=-48 (148833,445149,296268) : difference with theory (-47) = 1 CORRECTING DEFECT 105 (vertices=8, convex hull=35) After retessellation of defect 105, euler #=-47 (148835,445167,296285) : difference with theory (-46) = 1 CORRECTING DEFECT 106 (vertices=18, convex hull=32) After retessellation of defect 106, euler #=-46 (148840,445191,296305) : difference with theory (-45) = 1 CORRECTING DEFECT 107 (vertices=27, convex hull=54) After retessellation of defect 107, euler #=-45 (148854,445254,296355) : difference with theory (-44) = 1 CORRECTING DEFECT 108 (vertices=131, convex hull=130) After retessellation of defect 108, euler #=-43 (148862,445343,296438) : difference with theory (-43) = 0 CORRECTING DEFECT 109 (vertices=27, convex hull=54) After retessellation of defect 109, euler #=-42 (148872,445397,296483) : difference with theory (-42) = 0 CORRECTING DEFECT 110 (vertices=216, convex hull=108) After retessellation of defect 110, euler #=-41 (148889,445505,296575) : difference with theory (-41) = 0 CORRECTING DEFECT 111 (vertices=35, convex hull=71) After retessellation of defect 111, euler #=-40 (148907,445586,296639) : difference with theory (-40) = 0 CORRECTING DEFECT 112 (vertices=40, convex hull=48) After retessellation of defect 112, euler #=-39 (148926,445658,296693) : difference with theory (-39) = 0 CORRECTING DEFECT 113 (vertices=8, convex hull=16) After retessellation of defect 113, euler #=-38 (148928,445668,296702) : difference with theory (-38) = 0 CORRECTING DEFECT 114 (vertices=15, convex hull=20) After retessellation of defect 114, euler #=-37 (148930,445679,296712) : difference with theory (-37) = 0 CORRECTING DEFECT 115 (vertices=9, convex hull=14) After retessellation of defect 115, euler #=-36 (148930,445682,296716) : difference with theory (-36) = 0 CORRECTING DEFECT 116 (vertices=73, convex hull=49) After retessellation of defect 116, euler #=-35 (148940,445731,296756) : difference with theory (-35) = 0 CORRECTING DEFECT 117 (vertices=26, convex hull=28) After retessellation of defect 117, euler #=-34 (148947,445758,296777) : difference with theory (-34) = 0 CORRECTING DEFECT 118 (vertices=29, convex hull=59) After retessellation of defect 118, euler #=-33 (148961,445822,296828) : difference with theory (-33) = 0 CORRECTING DEFECT 119 (vertices=183, convex hull=45) After retessellation of defect 119, euler #=-32 (148971,445869,296866) : difference with theory (-32) = 0 CORRECTING DEFECT 120 (vertices=52, convex hull=65) After retessellation of defect 120, euler #=-31 (148995,445974,296948) : difference with theory (-31) = 0 CORRECTING DEFECT 121 (vertices=892, convex hull=200) After retessellation of defect 121, euler #=-30 (149028,446188,297130) : difference with theory (-30) = 0 CORRECTING DEFECT 122 (vertices=151, convex hull=74) After retessellation of defect 122, euler #=-29 (149051,446288,297208) : difference with theory (-29) = 0 CORRECTING DEFECT 123 (vertices=148, convex hull=97) After retessellation of defect 123, euler #=-29 (149080,446419,297310) : difference with theory (-28) = 1 CORRECTING DEFECT 124 (vertices=77, convex hull=60) After retessellation of defect 124, euler #=-28 (149111,446542,297403) : difference with theory (-27) = 1 CORRECTING DEFECT 125 (vertices=241, convex hull=115) After retessellation of defect 125, euler #=-27 (149135,446668,297506) : difference with theory (-26) = 1 CORRECTING DEFECT 126 (vertices=559, convex hull=368) After retessellation of defect 126, euler #=-26 (149289,447307,297992) : difference with theory (-25) = 1 CORRECTING DEFECT 127 (vertices=22, convex hull=45) After retessellation of defect 127, euler #=-25 (149302,447361,298034) : difference with theory (-24) = 1 CORRECTING DEFECT 128 (vertices=200, convex hull=202) After retessellation of defect 128, euler #=-24 (149409,447775,298342) : difference with theory (-23) = 1 CORRECTING DEFECT 129 (vertices=18, convex hull=21) After retessellation of defect 129, euler #=-23 (149409,447779,298347) : difference with theory (-22) = 1 CORRECTING DEFECT 130 (vertices=9, convex hull=14) After retessellation of defect 130, euler #=-22 (149409,447781,298350) : difference with theory (-21) = 1 CORRECTING DEFECT 131 (vertices=39, convex hull=91) After retessellation of defect 131, euler #=-21 (149423,447860,298416) : difference with theory (-20) = 1 CORRECTING DEFECT 132 (vertices=32, convex hull=72) After retessellation of defect 132, euler #=-20 (149440,447937,298477) : difference with theory (-19) = 1 CORRECTING DEFECT 133 (vertices=132, convex hull=116) After retessellation of defect 133, euler #=-19 (149475,448107,298613) : difference with theory (-18) = 1 CORRECTING DEFECT 134 (vertices=176, convex hull=49) After retessellation of defect 134, euler #=-18 (149491,448174,298665) : difference with theory (-17) = 1 CORRECTING DEFECT 135 (vertices=10, convex hull=23) After retessellation of defect 135, euler #=-17 (149494,448192,298681) : difference with theory (-16) = 1 CORRECTING DEFECT 136 (vertices=11, convex hull=21) After retessellation of defect 136, euler #=-16 (149495,448199,298688) : difference with theory (-15) = 1 CORRECTING DEFECT 137 (vertices=37, convex hull=83) After retessellation of defect 137, euler #=-15 (149522,448313,298776) : difference with theory (-14) = 1 CORRECTING DEFECT 138 (vertices=81, convex hull=105) After retessellation of defect 138, euler #=-14 (149547,448433,298872) : difference with theory (-13) = 1 CORRECTING DEFECT 139 (vertices=42, convex hull=75) After retessellation of defect 139, euler #=-13 (149560,448499,298926) : difference with theory (-12) = 1 CORRECTING DEFECT 140 (vertices=37, convex hull=26) Warning - incorrect dp selected!!!!(-76.496730 >= -76.496731 ) After retessellation of defect 140, euler #=-12 (149562,448512,298938) : difference with theory (-11) = 1 CORRECTING DEFECT 141 (vertices=60, convex hull=65) Warning - incorrect dp selected!!!!(-82.567083 >= -82.567088 ) After retessellation of defect 141, euler #=-11 (149568,448558,298979) : difference with theory (-10) = 1 CORRECTING DEFECT 142 (vertices=7, convex hull=27) After retessellation of defect 142, euler #=-10 (149570,448570,298990) : difference with theory (-9) = 1 CORRECTING DEFECT 143 (vertices=19, convex hull=20) After retessellation of defect 143, euler #=-9 (149571,448577,298997) : difference with theory (-8) = 1 CORRECTING DEFECT 144 (vertices=20, convex hull=30) After retessellation of defect 144, euler #=-8 (149573,448595,299014) : difference with theory (-7) = 1 CORRECTING DEFECT 145 (vertices=8, convex hull=21) After retessellation of defect 145, euler #=-7 (149574,448605,299024) : difference with theory (-6) = 1 CORRECTING DEFECT 146 (vertices=35, convex hull=42) After retessellation of defect 146, euler #=-6 (149582,448653,299065) : difference with theory (-5) = 1 CORRECTING DEFECT 147 (vertices=30, convex hull=63) After retessellation of defect 147, euler #=-5 (149592,448707,299110) : difference with theory (-4) = 1 CORRECTING DEFECT 148 (vertices=12, convex hull=39) After retessellation of defect 148, euler #=-3 (149594,448727,299130) : difference with theory (-3) = 0 CORRECTING DEFECT 149 (vertices=22, convex hull=52) After retessellation of defect 149, euler #=-2 (149602,448772,299168) : difference with theory (-2) = 0 CORRECTING DEFECT 150 (vertices=35, convex hull=37) After retessellation of defect 150, euler #=-1 (149607,448799,299191) : difference with theory (-1) = 0 CORRECTING DEFECT 151 (vertices=29, convex hull=27) Warning - incorrect dp selected!!!!(-75.193201 >= -75.193202 ) After retessellation of defect 151, euler #=0 (149609,448812,299203) : difference with theory (0) = 0 CORRECTING DEFECT 152 (vertices=13, convex hull=25) After retessellation of defect 152, euler #=1 (149609,448818,299210) : difference with theory (1) = 0 CORRECTING DEFECT 153 (vertices=5, convex hull=13) After retessellation of defect 153, euler #=2 (149610,448824,299216) : 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-->13.30) (max @ vno 86945 --> 88224) 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-->13.30) (max @ vno 86945 --> 88224) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 499 mutations (32.9%), 1016 crossovers (67.1%), 1335 vertices were eliminated building final representation... 20798 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=149610, nf=299216, ne=448824, g=0) writing corrected surface to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 157.5 minutes 0 defective edges removing intersecting faces 000: 3453 intersecting 001: 462 intersecting 002: 330 intersecting 003: 285 intersecting 004: 235 intersecting 005: 215 intersecting 006: 208 intersecting 007: 193 intersecting 008: 167 intersecting 009: 145 intersecting 010: 121 intersecting 011: 96 intersecting 012: 66 intersecting 013: 54 intersecting 014: 51 intersecting 015: 50 intersecting 016: 47 intersecting 017: 45 intersecting 018: 43 intersecting 019: 41 intersecting 020: 40 intersecting 021: 38 intersecting 022: 34 intersecting 023: 33 intersecting 024: 31 intersecting 025: 28 intersecting expanding nbhd size to 2 026: 29 intersecting expanding nbhd size to 3 027: 29 intersecting expanding nbhd size to 4 028: 29 intersecting expanding nbhd size to 5 029: 29 intersecting expanding nbhd size to 6 030: 32 intersecting 031: 29 intersecting 032: 26 intersecting 033: 14 intersecting 034: 9 intersecting 035: 3 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 149610 - 448824 + 299216 = 2 --> 0 holes F =2V-4: 299216 = 299220-4 (0) 2E=3F: 897648 = 897648 (0) total defect index = 0 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 1926 intersecting 001: 442 intersecting 002: 332 intersecting 003: 268 intersecting 004: 234 intersecting 005: 213 intersecting expanding nbhd size to 2 006: 216 intersecting 007: 193 intersecting 008: 155 intersecting 009: 137 intersecting 010: 111 intersecting 011: 76 intersecting 012: 54 intersecting 013: 50 intersecting 014: 47 intersecting 015: 42 intersecting 016: 38 intersecting 017: 32 intersecting 018: 30 intersecting expanding nbhd size to 3 019: 32 intersecting 020: 18 intersecting 021: 4 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Wed Jan 1 06:55:24 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 21087 bright wm thresholded. 1622 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (94.0): 94.3 +- 7.9 [70.0 --> 110.0] GM (82.0) : 78.4 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.3 (was 70) setting MAX_BORDER_WHITE to 106.9 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 91.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.01-->7.80) (max @ vno 147543 --> 147849) face area 0.27 +- 0.17 (0.00-->10.67) mean absolute distance = 0.84 +- 1.09 4848 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=99, GM=77 mean inside = 90.9, mean outside = 78.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.5, 3506 (3506) missing vertices, mean dist 0.2 [0.8 (%37.8)->0.9 (%62.2))] %66 local maxima, %22 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 0.90 +- 0.33 (0.06-->8.15) (max @ vno 146452 --> 146422) face area 0.27 +- 0.18 (0.00-->8.93) mean absolute distance = 0.49 +- 0.74 5461 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5303145.0, rms=9.33 001: dt: 0.5000, sse=6531451.5, rms=7.572 (0.000%) 002: dt: 0.5000, sse=6688228.0, rms=6.493 (0.000%) 003: dt: 0.5000, sse=7004955.5, rms=5.756 (0.000%) 004: dt: 0.5000, sse=7079984.5, rms=5.210 (0.000%) 005: dt: 0.5000, sse=7216182.5, rms=4.840 (0.000%) 006: dt: 0.5000, sse=7261460.5, rms=4.630 (0.000%) 007: dt: 0.5000, sse=7335171.0, rms=4.473 (0.000%) 008: dt: 0.5000, sse=7311855.0, rms=4.355 (0.000%) 009: dt: 0.5000, sse=7362247.5, rms=4.262 (0.000%) 010: dt: 0.5000, sse=7323530.0, rms=4.172 (0.000%) 011: dt: 0.5000, sse=7349716.5, rms=4.094 (0.000%) 012: dt: 0.5000, sse=7283919.0, rms=4.001 (0.000%) 013: dt: 0.5000, sse=7328449.0, rms=3.932 (0.000%) 014: dt: 0.5000, sse=7275054.5, rms=3.854 (0.000%) 015: dt: 0.5000, sse=7294568.5, rms=3.787 (0.000%) 016: dt: 0.5000, sse=7235222.0, rms=3.707 (0.000%) 017: dt: 0.5000, sse=7249834.0, rms=3.650 (0.000%) 018: dt: 0.5000, sse=7189831.0, rms=3.582 (0.000%) rms = 3.54, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=7235119.5, rms=3.545 (0.000%) 020: dt: 0.2500, sse=5097761.0, rms=3.126 (0.000%) 021: dt: 0.2500, sse=4874223.5, rms=3.029 (0.000%) rms = 3.01, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4776924.0, rms=3.008 (0.000%) rms = 2.96, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4701008.0, rms=2.958 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 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 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.9, 2964 (2315) missing vertices, mean dist -0.3 [0.6 (%69.2)->0.4 (%30.8))] %77 local maxima, %11 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 0.89 +- 0.32 (0.06-->8.65) (max @ vno 146452 --> 146422) face area 0.34 +- 0.23 (0.00-->11.42) mean absolute distance = 0.36 +- 0.53 4542 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5106683.5, rms=4.66 024: dt: 0.5000, sse=5560791.5, rms=3.680 (0.000%) 025: dt: 0.5000, sse=6259872.0, rms=3.437 (0.000%) 026: dt: 0.5000, sse=6344444.0, rms=3.384 (0.000%) 027: dt: 0.5000, sse=6887346.5, rms=3.314 (0.000%) rms = 3.34, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5790015.0, rms=3.023 (0.000%) 029: dt: 0.2500, sse=5346472.5, rms=2.901 (0.000%) rms = 2.90, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5255604.0, rms=2.897 (0.000%) 031: dt: 0.1250, sse=5173649.0, rms=2.833 (0.000%) rms = 2.81, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5130530.5, rms=2.805 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group 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 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.2, 2846 (2145) missing vertices, mean dist -0.1 [0.4 (%63.1)->0.3 (%36.9))] %81 local maxima, % 7 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 +- 0.32 (0.04-->8.90) (max @ vno 146452 --> 146422) face area 0.33 +- 0.22 (0.00-->11.08) mean absolute distance = 0.31 +- 0.45 3770 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5206026.5, rms=3.44 033: dt: 0.5000, sse=5677521.0, rms=3.099 (0.000%) 034: dt: 0.5000, sse=6255304.5, rms=3.014 (0.000%) rms = 3.11, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=5652057.5, rms=2.783 (0.000%) 036: dt: 0.2500, sse=5425327.5, rms=2.716 (0.000%) rms = 2.72, time step reduction 2 of 3 to 0.125... rms = 2.69, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=5366474.5, rms=2.688 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.7, 2873 (2067) missing vertices, mean dist -0.0 [0.3 (%54.2)->0.3 (%45.8))] %82 local maxima, % 5 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/MPS1036-1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5384865.5, rms=2.87 038: dt: 0.5000, sse=6897568.0, rms=2.760 (0.000%) rms = 2.90, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=6279512.0, rms=2.585 (0.000%) rms = 2.58, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=6040004.0, rms=2.579 (0.000%) 041: dt: 0.1250, sse=6038841.0, rms=2.493 (0.000%) rms = 2.46, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=6015350.0, rms=2.463 (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 generating cortex label... 36 non-cortical segments detected only using segment with 2169 vertices erasing segment 1 (vno[0] = 51821) erasing segment 2 (vno[0] = 53615) erasing segment 3 (vno[0] = 54839) erasing segment 4 (vno[0] = 55985) erasing segment 5 (vno[0] = 57096) erasing segment 6 (vno[0] = 62709) erasing segment 7 (vno[0] = 73951) erasing segment 8 (vno[0] = 73953) erasing segment 9 (vno[0] = 76180) erasing segment 10 (vno[0] = 76349) erasing segment 11 (vno[0] = 79942) erasing segment 12 (vno[0] = 82004) erasing segment 13 (vno[0] = 82338) erasing segment 14 (vno[0] = 85494) erasing segment 15 (vno[0] = 89087) erasing segment 16 (vno[0] = 93292) erasing segment 17 (vno[0] = 95315) erasing segment 18 (vno[0] = 98341) erasing segment 19 (vno[0] = 100341) erasing segment 20 (vno[0] = 100408) erasing segment 21 (vno[0] = 100440) erasing segment 22 (vno[0] = 101311) erasing segment 23 (vno[0] = 104042) erasing segment 24 (vno[0] = 106684) erasing segment 25 (vno[0] = 107428) erasing segment 26 (vno[0] = 107444) erasing segment 27 (vno[0] = 107466) erasing segment 28 (vno[0] = 109109) erasing segment 29 (vno[0] = 109928) erasing segment 30 (vno[0] = 110658) erasing segment 31 (vno[0] = 110673) erasing segment 32 (vno[0] = 111942) erasing segment 33 (vno[0] = 111948) erasing segment 34 (vno[0] = 111966) erasing segment 35 (vno[0] = 148894) writing cortex label to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label... writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.area vertex spacing 0.89 +- 0.34 (0.01-->9.22) (max @ vno 146422 --> 146452) face area 0.33 +- 0.22 (0.00-->11.30) refinement took 5.1 minutes #-------------------------------------------- #@# Smooth2 lh Wed Jan 1 07:00:30 CST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Wed Jan 1 07:00:34 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 52.5 mm, total surface area = 87354 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.125 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.070 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.050 (target=0.015) step 025: RMS=0.042 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.020 (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 220 vertices thresholded to be in k1 ~ [-0.40 1.32], k2 ~ [-0.15 0.10] total integrated curvature = 0.222*4pi (2.785) --> 1 handles ICI = 1.3, FI = 10.0, variation=166.184 152 vertices thresholded to be in [-0.05 0.03] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 138 vertices thresholded to be in [-0.21 0.59] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Wed Jan 1 07:02:13 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm MPS1036-1 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 [ MPS1036-1/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 [ 291 ] Gb_filter = 0 WARN: S lookup min: -0.237855 WARN: S explicit min: 0.000000 vertex = 238 #-------------------------------------------- #@# Sphere lh Wed Jan 1 07:02:16 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.278... 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 %20.06 pass 1: epoch 2 of 3 starting distance error %20.00 unfolding complete - removing small folds... starting distance error %19.83 removing remaining folds... final distance error %19.85 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.80 hours #-------------------------------------------- #@# Surf Reg lh Wed Jan 1 07:50:29 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_register -curv ../surf/lh.sphere /soft/freesurfer/5.3.0_1/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_1/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 = 0.543 curvature mean = 0.041, std = 0.935 curvature mean = 0.025, std = 0.843 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 345839.1, tmin=1.0108 d=32.00 min @ (-8.00, 0.00, 0.00) sse = 342484.1, tmin=2.0255 d=16.00 min @ (4.00, -4.00, -4.00) sse = 308239.8, tmin=3.0425 d=8.00 min @ (0.00, 2.00, 0.00) sse = 306974.8, tmin=4.1344 d=4.00 min @ (-1.00, -1.00, 0.00) sse = 305530.0, tmin=5.2437 d=2.00 min @ (0.00, 0.00, 0.50) sse = 305426.7, tmin=6.3639 d=1.00 min @ (0.25, 0.00, -0.25) sse = 305297.7, tmin=7.4587 d=0.50 min @ (0.00, 0.12, 0.12) sse = 305284.0, tmin=8.5303 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 8.53 min curvature mean = -0.019, std = 0.940 curvature mean = 0.008, std = 0.930 curvature mean = -0.034, std = 0.944 curvature mean = 0.003, std = 0.966 curvature mean = -0.035, std = 0.946 curvature mean = 0.001, std = 0.984 2 Reading smoothwm curvature mean = -0.034, std = 0.407 curvature mean = 0.005, std = 0.069 curvature mean = 0.047, std = 0.242 curvature mean = 0.004, std = 0.080 curvature mean = 0.029, std = 0.372 curvature mean = 0.003, std = 0.086 curvature mean = 0.016, std = 0.488 curvature mean = 0.003, std = 0.089 curvature mean = 0.005, std = 0.594 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Wed Jan 1 08:20:26 CST 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 Wed Jan 1 08:20:28 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mrisp_paint -a 5 /soft/freesurfer/5.3.0_1/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_1/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Jan 1 08:20:30 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 3684 labels changed using aseg relabeling using gibbs priors... 000: 3288 changed, 149610 examined... 001: 766 changed, 13917 examined... 002: 209 changed, 4145 examined... 003: 88 changed, 1272 examined... 004: 42 changed, 500 examined... 005: 14 changed, 235 examined... 006: 5 changed, 82 examined... 007: 2 changed, 22 examined... 008: 2 changed, 14 examined... 009: 2 changed, 13 examined... 010: 0 changed, 10 examined... 301 labels changed using aseg 000: 231 total segments, 185 labels (728 vertices) changed 001: 49 total segments, 4 labels (5 vertices) changed 002: 45 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 67 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2832 vertices marked for relabeling... 2832 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 38 seconds. #-------------------------------------------- #@# Make Pial Surf lh Wed Jan 1 08:21:08 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 21087 bright wm thresholded. 1622 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (94.0): 94.3 +- 7.9 [70.0 --> 110.0] GM (82.0) : 78.4 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.3 (was 70) setting MAX_BORDER_WHITE to 106.9 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 91.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.6 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99, GM=77 mean inside = 90.9, mean outside = 78.6 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/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.01-->7.80) (max @ vno 147543 --> 147849) face area 0.27 +- 0.17 (0.00-->10.67) mean absolute distance = 0.85 +- 1.13 4791 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 205 points - only 0.00% unknown deleting segment 2 with 22 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 71 points - only 0.00% unknown deleting segment 8 with 26 points - only 0.00% unknown deleting segment 9 with 58 points - only 3.45% unknown deleting segment 11 with 65 points - only 0.00% unknown deleting segment 12 with 44 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 2 points - only 0.00% unknown deleting segment 17 with 56 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown deleting segment 19 with 59 points - only 0.00% unknown deleting segment 20 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 23 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 24 with 3 points - only 0.00% unknown deleting segment 25 with 36 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 26 with 3 points - only 0.00% unknown deleting segment 27 with 29 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 28 with 3 points - only 0.00% unknown deleting segment 29 with 143 points - only 0.00% unknown deleting segment 30 with 15 points - only 0.00% unknown deleting segment 31 with 25 points - only 0.00% unknown deleting segment 32 with 11 points - only 0.00% unknown deleting segment 33 with 143 points - only 0.00% unknown deleting segment 34 with 203 points - only 0.00% unknown deleting segment 35 with 146 points - only 0.00% unknown deleting segment 36 with 21 points - only 0.00% unknown deleting segment 37 with 74 points - only 0.00% unknown deleting segment 38 with 17 points - only 0.00% unknown deleting segment 39 with 162 points - only 2.47% unknown mean border=85.5, 3772 (3628) missing vertices, mean dist 0.2 [0.8 (%38.3)->0.9 (%61.7))] %67 local maxima, %22 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 0.90 +- 0.33 (0.06-->7.05) (max @ vno 145904 --> 145920) face area 0.27 +- 0.18 (0.00-->8.92) mean absolute distance = 0.50 +- 0.77 5787 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5426009.0, rms=9.45 001: dt: 0.5000, sse=6661871.5, rms=7.716 (0.000%) 002: dt: 0.5000, sse=6808601.5, rms=6.647 (0.000%) 003: dt: 0.5000, sse=7123532.5, rms=5.915 (0.000%) 004: dt: 0.5000, sse=7195339.0, rms=5.371 (0.000%) 005: dt: 0.5000, sse=7331081.5, rms=4.998 (0.000%) 006: dt: 0.5000, sse=7386024.5, rms=4.776 (0.000%) 007: dt: 0.5000, sse=7453054.0, rms=4.610 (0.000%) 008: dt: 0.5000, sse=7420938.0, rms=4.486 (0.000%) 009: dt: 0.5000, sse=7478119.0, rms=4.383 (0.000%) 010: dt: 0.5000, sse=7439045.5, rms=4.291 (0.000%) 011: dt: 0.5000, sse=7467609.5, rms=4.202 (0.000%) 012: dt: 0.5000, sse=7409987.0, rms=4.111 (0.000%) 013: dt: 0.5000, sse=7437510.5, rms=4.038 (0.000%) 014: dt: 0.5000, sse=7397773.0, rms=3.959 (0.000%) 015: dt: 0.5000, sse=7407164.5, rms=3.899 (0.000%) 016: dt: 0.5000, sse=7342763.0, rms=3.826 (0.000%) 017: dt: 0.5000, sse=7360256.5, rms=3.766 (0.000%) 018: dt: 0.5000, sse=7305288.5, rms=3.711 (0.000%) rms = 3.67, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=7344013.5, rms=3.665 (0.000%) 020: dt: 0.2500, sse=5185325.0, rms=3.263 (0.000%) 021: dt: 0.2500, sse=4959077.0, rms=3.173 (0.000%) rms = 3.15, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4862290.0, rms=3.150 (0.000%) rms = 3.11, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4783885.5, rms=3.107 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown deleting segment 1 with 212 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 14 with 335 points - only 0.00% unknown deleting segment 15 with 70 points - only 0.00% unknown deleting segment 16 with 12 points - only 0.00% unknown deleting segment 17 with 9 points - only 0.00% unknown deleting segment 18 with 29 points - only 0.00% unknown deleting segment 20 with 7 points - only 0.00% unknown deleting segment 21 with 5 points - only 0.00% unknown deleting segment 22 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 24 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 25 with 4 points - only 0.00% unknown deleting segment 26 with 51 points - only 0.00% unknown deleting segment 27 with 35 points - only 0.00% unknown deleting segment 29 with 65 points - only 43.08% unknown deleting segment 30 with 7 points - only 0.00% unknown deleting segment 31 with 468 points - only 0.00% unknown deleting segment 32 with 81 points - only 0.00% unknown deleting segment 33 with 9 points - only 0.00% unknown deleting segment 36 with 58 points - only 8.62% unknown deleting segment 37 with 13 points - only 0.00% unknown deleting segment 38 with 478 points - only 0.00% unknown deleting segment 39 with 13 points - only 0.00% unknown deleting segment 40 with 183 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 42 with 211 points - only 0.00% unknown deleting segment 43 with 17 points - only 0.00% unknown deleting segment 44 with 66 points - only 0.00% unknown deleting segment 45 with 37 points - only 0.00% unknown deleting segment 47 with 178 points - only 1.69% unknown removing 3 vertex label from ripped group deleting segment 48 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 49 with 1 points - only 0.00% unknown deleting segment 50 with 6 points - only 0.00% unknown mean border=87.9, 3281 (2398) missing vertices, mean dist -0.3 [0.6 (%69.4)->0.4 (%30.6))] %78 local maxima, %11 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 0.89 +- 0.32 (0.04-->7.09) (max @ vno 111232 --> 110589) face area 0.34 +- 0.22 (0.00-->11.41) mean absolute distance = 0.37 +- 0.55 4153 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5277822.5, rms=4.81 024: dt: 0.5000, sse=5754622.5, rms=3.864 (0.000%) 025: dt: 0.5000, sse=6495274.5, rms=3.626 (0.000%) 026: dt: 0.5000, sse=6562577.0, rms=3.573 (0.000%) 027: dt: 0.5000, sse=7113262.5, rms=3.519 (0.000%) rms = 3.53, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5996687.5, rms=3.243 (0.000%) 029: dt: 0.2500, sse=5562744.5, rms=3.126 (0.000%) rms = 3.11, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5458044.5, rms=3.113 (0.000%) 031: dt: 0.1250, sse=5353800.5, rms=3.042 (0.000%) rms = 3.01, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5313307.0, rms=3.014 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 210 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 11 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 356 points - only 0.00% unknown deleting segment 11 with 72 points - only 0.00% unknown deleting segment 12 with 15 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown deleting segment 14 with 29 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown deleting segment 16 with 6 points - only 0.00% unknown deleting segment 17 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 19 with 4 points - only 0.00% unknown deleting segment 20 with 55 points - only 0.00% unknown deleting segment 21 with 30 points - only 0.00% unknown deleting segment 22 with 74 points - only 43.24% unknown removing 3 vertex label from ripped group deleting segment 23 with 3 points - only 0.00% unknown deleting segment 24 with 477 points - only 0.00% unknown deleting segment 25 with 78 points - only 0.00% unknown deleting segment 26 with 10 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 28 with 4 points - only 0.00% unknown deleting segment 29 with 501 points - only 0.00% unknown deleting segment 30 with 5 points - only 0.00% unknown deleting segment 31 with 10 points - only 0.00% unknown deleting segment 32 with 174 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 34 with 188 points - only 0.00% unknown deleting segment 35 with 20 points - only 0.00% unknown deleting segment 36 with 70 points - only 0.00% unknown deleting segment 37 with 39 points - only 0.00% unknown deleting segment 38 with 249 points - only 4.42% unknown deleting segment 39 with 6 points - only 0.00% unknown mean border=89.2, 3199 (2234) missing vertices, mean dist -0.1 [0.4 (%63.2)->0.3 (%36.8))] %82 local maxima, % 7 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 0.89 +- 0.32 (0.04-->7.30) (max @ vno 111232 --> 110589) face area 0.33 +- 0.22 (0.00-->11.07) mean absolute distance = 0.32 +- 0.46 4049 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5422358.0, rms=3.71 033: dt: 0.5000, sse=5912716.5, rms=3.375 (0.000%) 034: dt: 0.5000, sse=6501046.0, rms=3.295 (0.000%) rms = 3.38, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=5883348.0, rms=3.084 (0.000%) 036: dt: 0.2500, sse=5669357.5, rms=3.017 (0.000%) rms = 3.02, time step reduction 2 of 3 to 0.125... rms = 2.99, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=5602801.5, rms=2.991 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 24 points - only 4.17% unknown deleting segment 1 with 210 points - only 0.00% unknown deleting segment 2 with 13 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 20 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 11 with 60 points - only 0.00% unknown deleting segment 12 with 68 points - only 0.00% unknown deleting segment 13 with 16 points - only 0.00% unknown deleting segment 14 with 29 points - only 0.00% unknown deleting segment 15 with 5 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 6 points - only 0.00% unknown deleting segment 18 with 13 points - only 0.00% unknown deleting segment 19 with 275 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 21 with 5 points - only 0.00% unknown deleting segment 22 with 52 points - only 0.00% unknown deleting segment 23 with 26 points - only 0.00% unknown deleting segment 24 with 142 points - only 30.99% unknown removing 4 vertex label from ripped group deleting segment 25 with 4 points - only 0.00% unknown deleting segment 26 with 441 points - only 0.00% unknown deleting segment 27 with 76 points - only 0.00% unknown deleting segment 28 with 11 points - only 0.00% unknown deleting segment 29 with 58 points - only 8.62% unknown removing 4 vertex label from ripped group deleting segment 30 with 4 points - only 0.00% unknown deleting segment 31 with 496 points - only 0.00% unknown deleting segment 32 with 10 points - only 0.00% unknown deleting segment 33 with 173 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 35 with 188 points - only 0.00% unknown deleting segment 36 with 22 points - only 0.00% unknown deleting segment 37 with 73 points - only 0.00% unknown deleting segment 38 with 38 points - only 0.00% unknown deleting segment 40 with 268 points - only 4.10% unknown deleting segment 41 with 6 points - only 0.00% unknown mean border=89.7, 3296 (2159) missing vertices, mean dist -0.1 [0.3 (%54.3)->0.3 (%45.7))] %84 local maxima, % 5 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=5629355.5, rms=3.18 038: dt: 0.5000, sse=7207553.5, rms=3.078 (0.000%) rms = 3.19, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=6576349.5, rms=2.921 (0.000%) rms = 2.91, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=6344495.0, rms=2.909 (0.000%) 041: dt: 0.1250, sse=6335247.5, rms=2.842 (0.000%) rms = 2.81, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=6307879.5, rms=2.812 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 13 with 19 points - only 52.63% unknown smoothing surface for 5 iterations... mean border=64.2, 3003 (3003) missing vertices, mean dist 1.5 [3.0 (%2.0)->3.7 (%98.0))] %22 local maxima, %16 large gradients and %54 min vals, 3194 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=21593736.0, rms=26.17 001: dt: 0.5000, sse=17938038.0, rms=23.418 (0.000%) 002: dt: 0.5000, sse=15133758.0, rms=21.032 (0.000%) 003: dt: 0.5000, sse=12985256.0, rms=19.024 (0.000%) 004: dt: 0.5000, sse=11354953.0, rms=17.319 (0.000%) 005: dt: 0.5000, sse=10183133.0, rms=15.861 (0.000%) 006: dt: 0.5000, sse=9313321.0, rms=14.567 (0.000%) 007: dt: 0.5000, sse=8687917.0, rms=13.365 (0.000%) 008: dt: 0.5000, sse=8288513.5, rms=12.263 (0.000%) 009: dt: 0.5000, sse=8075837.0, rms=11.257 (0.000%) 010: dt: 0.5000, sse=7969174.0, rms=10.342 (0.000%) 011: dt: 0.5000, sse=7956420.0, rms=9.495 (0.000%) 012: dt: 0.5000, sse=7993899.5, rms=8.712 (0.000%) 013: dt: 0.5000, sse=8037459.0, rms=7.987 (0.000%) 014: dt: 0.5000, sse=8131728.5, rms=7.393 (0.000%) 015: dt: 0.5000, sse=8204601.5, rms=6.902 (0.000%) 016: dt: 0.5000, sse=8223722.0, rms=6.549 (0.000%) 017: dt: 0.5000, sse=8302908.0, rms=6.280 (0.000%) 018: dt: 0.5000, sse=8332429.0, rms=6.110 (0.000%) 019: dt: 0.5000, sse=8408161.0, rms=5.984 (0.000%) 020: dt: 0.5000, sse=8376178.5, rms=5.903 (0.000%) 021: dt: 0.5000, sse=8379730.5, rms=5.829 (0.000%) rms = 5.79, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=8399005.0, rms=5.793 (0.000%) 023: dt: 0.2500, sse=6558475.0, rms=5.279 (0.000%) 024: dt: 0.2500, sse=6456800.5, rms=5.168 (0.000%) rms = 5.16, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=6388496.0, rms=5.165 (0.000%) 026: dt: 0.1250, sse=5849490.0, rms=4.923 (0.000%) 027: dt: 0.1250, sse=5791396.5, rms=4.872 (0.000%) rms = 4.86, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5775820.0, rms=4.858 (0.000%) positioning took 2.5 minutes mean border=62.6, 5109 (1451) missing vertices, mean dist 0.2 [0.3 (%35.7)->0.8 (%64.3))] %30 local maxima, %14 large gradients and %46 min vals, 2312 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=6417863.0, rms=6.21 029: dt: 0.5000, sse=6906574.5, rms=6.080 (0.000%) 030: dt: 0.5000, sse=8132790.0, rms=5.774 (0.000%) rms = 5.86, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=7127347.0, rms=5.250 (0.000%) 032: dt: 0.2500, sse=6764967.5, rms=5.118 (0.000%) rms = 5.17, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=6615349.0, rms=5.023 (0.000%) 034: dt: 0.1250, sse=6385147.0, rms=4.901 (0.000%) 035: dt: 0.1250, sse=6317812.0, rms=4.845 (0.000%) rms = 4.82, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=6322061.5, rms=4.819 (0.000%) positioning took 0.9 minutes mean border=62.2, 6285 (1347) missing vertices, mean dist 0.1 [0.3 (%41.2)->0.6 (%58.8))] %32 local maxima, %11 large gradients and %46 min vals, 2126 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=6373055.5, rms=4.94 rms = 5.41, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=6246920.0, rms=4.791 (0.000%) rms = 4.76, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=6426086.0, rms=4.758 (0.000%) 039: dt: 0.1250, sse=6280743.5, rms=4.689 (0.000%) rms = 4.65, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=6321461.0, rms=4.646 (0.000%) positioning took 0.5 minutes mean border=61.9, 10916 (1310) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.4 (%55.4))] %32 local maxima, %10 large gradients and %44 min vals, 1966 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/MPS1036-1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6325675.5, rms=4.66 rms = 5.01, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=6293333.0, rms=4.566 (0.000%) rms = 4.52, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=6680503.5, rms=4.524 (0.000%) 043: dt: 0.1250, sse=6511756.0, rms=4.459 (0.000%) rms = 4.41, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=6565965.5, rms=4.411 (0.000%) positioning took 0.5 minutes writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.area.pial vertex spacing 0.98 +- 0.49 (0.01-->9.43) (max @ vno 100406 --> 99448) face area 0.38 +- 0.35 (0.00-->17.46) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 149610 vertices processed 25000 of 149610 vertices processed 50000 of 149610 vertices processed 75000 of 149610 vertices processed 100000 of 149610 vertices processed 125000 of 149610 vertices processed 0 of 149610 vertices processed 25000 of 149610 vertices processed 50000 of 149610 vertices processed 75000 of 149610 vertices processed 100000 of 149610 vertices processed 125000 of 149610 vertices processed thickness calculation complete, 2319:3171 truncations. 23874 vertices at 0 distance 73188 vertices at 1 distance 81386 vertices at 2 distance 52435 vertices at 3 distance 26633 vertices at 4 distance 11855 vertices at 5 distance 5161 vertices at 6 distance 2242 vertices at 7 distance 981 vertices at 8 distance 522 vertices at 9 distance 281 vertices at 10 distance 196 vertices at 11 distance 151 vertices at 12 distance 160 vertices at 13 distance 120 vertices at 14 distance 92 vertices at 15 distance 83 vertices at 16 distance 63 vertices at 17 distance 59 vertices at 18 distance 42 vertices at 19 distance 102 vertices at 20 distance writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.thickness positioning took 10.3 minutes #-------------------------------------------- #@# Surf Volume lh Wed Jan 1 08:31:27 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Wed Jan 1 08:31:27 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts pctsurfcon --s MPS1036-1 --lh-only Log file is /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts/pctsurfcon.log Wed Jan 1 08:31:27 CST 2014 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis cd /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts /soft/freesurfer/5.3.0_1/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node1108 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_1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.58296/lh.wm.mgh --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 78705 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.58296/lh.wm.mgh Dim: 149610 1 1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.58296/lh.gm.mgh --projfrac 0.3 --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Done reading source surface Reading thickness /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 90868 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.58296/lh.gm.mgh Dim: 149610 1 1 mri_concat /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.58296/lh.wm.mgh /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.58296/lh.gm.mgh --paired-diff-norm --mul 100 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh mri_segstats --in /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh --annot MPS1036-1 lh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh --annot MPS1036-1 lh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/stats/lh.w-g.pct.stats --snr sysname Linux hostname node1108 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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh Vertex Area is 0.649119 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1259 866.050 2 1002 caudalanteriorcingulate 1419 992.165 3 1003 caudalmiddlefrontal 4579 2940.448 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2068 1376.606 6 1006 entorhinal 468 322.712 7 1007 fusiform 3775 2592.411 8 1008 inferiorparietal 8095 5052.566 9 1009 inferiortemporal 5394 3617.709 10 1010 isthmuscingulate 3114 1722.324 11 1011 lateraloccipital 8126 5214.632 12 1012 lateralorbitofrontal 3300 2259.770 13 1013 lingual 3049 2367.006 14 1014 medialorbitofrontal 2608 1727.378 15 1015 middletemporal 5583 3652.630 16 1016 parahippocampal 908 607.917 17 1017 paracentral 2094 1420.875 18 1018 parsopercularis 2372 1415.041 19 1019 parsorbitalis 1276 700.414 20 1020 parstriangularis 2441 1548.441 21 1021 pericalcarine 1869 1211.572 22 1022 postcentral 6880 4351.542 23 1023 posteriorcingulate 2218 1471.197 24 1024 precentral 8527 5534.515 25 1025 precuneus 4927 3273.605 26 1026 rostralanteriorcingulate 998 863.752 27 1027 rostralmiddlefrontal 10601 6688.472 28 1028 superiorfrontal 11338 8131.938 29 1029 superiorparietal 8282 5175.878 30 1030 superiortemporal 6057 3728.289 31 1031 supramarginal 7396 4660.814 32 1032 frontalpole 484 270.350 33 1033 temporalpole 913 625.164 34 1034 transversetemporal 663 430.818 35 1035 insula 3911 2423.381 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Wed Jan 1 08:31:36 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1259 866 2445 3.118 0.637 0.142 0.070 19 3.9 bankssts 1419 992 3003 2.972 0.987 0.204 0.196 75 9.6 caudalanteriorcingulate 4579 2940 10271 3.391 0.688 0.192 0.237 325 51.4 caudalmiddlefrontal 2068 1377 3326 2.224 0.612 0.174 0.062 47 5.4 cuneus 468 323 1169 2.558 0.923 0.191 0.207 30 3.5 entorhinal 3775 2592 7906 2.720 0.626 0.187 0.130 148 22.8 fusiform 8095 5053 16345 2.966 0.668 0.170 0.150 545 40.8 inferiorparietal 5394 3618 13441 3.244 0.875 0.180 0.118 169 27.5 inferiortemporal 3114 1722 3344 1.888 0.865 0.155 0.245 164 31.6 isthmuscingulate 8126 5215 13767 2.441 0.732 0.181 0.120 223 36.2 lateraloccipital 3300 2260 8589 3.450 0.841 0.160 0.149 160 28.1 lateralorbitofrontal 3049 2367 6382 2.450 0.812 0.205 0.141 273 21.3 lingual 2608 1727 6294 3.123 1.050 0.157 0.081 80 7.7 medialorbitofrontal 5583 3653 14481 3.371 0.726 0.168 0.128 489 22.2 middletemporal 908 608 1358 1.952 0.544 0.127 0.089 19 1.8 parahippocampal 2094 1421 4239 2.717 0.612 0.157 0.114 80 6.2 paracentral 2372 1415 4893 3.050 0.722 0.175 0.204 120 12.5 parsopercularis 1276 700 2411 2.722 0.827 0.202 0.254 74 12.8 parsorbitalis 2441 1548 4638 2.716 0.782 0.177 0.169 295 13.4 parstriangularis 1869 1212 1978 1.784 0.653 0.207 0.148 78 13.4 pericalcarine 6880 4352 10754 2.354 0.783 0.170 0.205 326 29.6 postcentral 2218 1471 3337 2.186 0.893 0.179 0.160 338 10.6 posteriorcingulate 8527 5535 14383 2.577 0.926 0.181 0.165 375 59.1 precentral 4927 3274 10314 2.831 0.653 0.155 0.102 129 20.9 precuneus 998 864 2758 2.780 1.213 0.278 0.161 141 6.7 rostralanteriorcingulate 10601 6688 22318 3.017 0.776 0.178 0.132 436 58.7 rostralmiddlefrontal 11338 8132 29996 3.327 1.052 0.197 0.163 915 75.9 superiorfrontal 8282 5176 14484 2.650 0.561 0.166 0.136 395 55.0 superiorparietal 6057 3728 12320 2.933 0.681 0.137 0.096 196 20.4 superiortemporal 7396 4661 13401 2.728 0.715 0.177 0.276 783 50.1 supramarginal 484 270 1041 2.630 0.932 0.218 0.572 87 3.6 frontalpole 913 625 2896 2.879 0.830 0.247 0.174 64 7.4 temporalpole 663 431 1122 2.446 0.689 0.168 0.081 14 2.4 transversetemporal 3911 2423 7233 2.809 1.189 0.132 0.174 227 14.7 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Jan 1 08:31:50 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 294 labels changed using aseg relabeling using gibbs priors... 000: 10280 changed, 149610 examined... 001: 2495 changed, 39371 examined... 002: 821 changed, 12890 examined... 003: 347 changed, 4667 examined... 004: 188 changed, 2015 examined... 005: 115 changed, 1075 examined... 006: 59 changed, 610 examined... 007: 21 changed, 322 examined... 008: 11 changed, 120 examined... 009: 6 changed, 68 examined... 010: 3 changed, 36 examined... 011: 3 changed, 17 examined... 012: 2 changed, 14 examined... 013: 1 changed, 10 examined... 014: 1 changed, 7 examined... 015: 0 changed, 7 examined... 75 labels changed using aseg 000: 343 total segments, 257 labels (4060 vertices) changed 001: 112 total segments, 26 labels (181 vertices) changed 002: 86 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 185 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 2099 vertices marked for relabeling... 2099 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 44 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Jan 1 08:32:34 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1531 974 2990 2.757 0.796 0.206 0.159 92 9.8 G_and_S_frontomargin 1588 1198 3891 2.913 0.698 0.202 0.216 43 7.1 G_and_S_occipital_inf 1623 1030 3107 2.585 0.701 0.160 0.135 79 5.3 G_and_S_paracentral 1409 833 3201 3.178 0.799 0.169 0.122 66 8.6 G_and_S_subcentral 859 527 1788 2.434 0.926 0.250 0.525 191 13.2 G_and_S_transv_frontopol 2444 2282 4964 2.282 1.197 0.277 0.220 345 21.1 G_and_S_cingul-Ant 1634 1126 3198 2.884 0.640 0.164 0.113 69 5.1 G_and_S_cingul-Mid-Ant 1429 1008 2457 2.578 0.592 0.143 0.051 26 3.1 G_and_S_cingul-Mid-Post 1127 725 1581 1.857 0.891 0.173 0.104 39 4.4 G_cingul-Post-dorsal 719 377 679 1.699 0.736 0.187 0.509 57 12.7 G_cingul-Post-ventral 1894 1261 3008 2.044 0.635 0.187 0.106 75 9.7 G_cuneus 1288 701 3028 2.941 0.826 0.174 0.171 59 8.5 G_front_inf-Opercular 308 189 919 3.193 0.562 0.164 0.057 7 0.8 G_front_inf-Orbital 1482 865 3008 2.596 0.777 0.184 0.140 61 10.2 G_front_inf-Triangul 5865 3614 14454 3.222 0.791 0.190 0.201 331 57.8 G_front_middle 8038 5536 24741 3.568 0.962 0.197 0.156 481 54.1 G_front_sup 543 322 1071 2.620 1.153 0.118 0.094 14 2.1 G_Ins_lg_and_S_cent_ins 725 446 1678 3.070 1.314 0.101 0.084 16 3.1 G_insular_short 2182 1281 4542 2.792 0.560 0.164 0.095 57 8.7 G_occipital_middle 1683 1024 3063 2.493 0.493 0.173 0.084 54 6.0 G_occipital_sup 1327 917 3313 2.721 0.647 0.180 0.094 40 5.3 G_oc-temp_lat-fusifor 1982 1575 4791 2.440 0.887 0.237 0.190 260 18.7 G_oc-temp_med-Lingual 1148 731 2254 2.289 0.812 0.159 0.125 41 5.1 G_oc-temp_med-Parahip 2570 1596 6634 3.083 0.968 0.194 0.285 221 37.9 G_orbital 3669 2172 8036 2.865 0.752 0.184 0.146 152 23.5 G_pariet_inf-Angular 4034 2432 7894 2.773 0.752 0.181 0.510 588 31.4 G_pariet_inf-Supramar 3241 1846 6136 2.683 0.616 0.195 0.247 317 41.0 G_parietal_sup 3178 1895 4835 2.193 0.641 0.182 0.126 177 15.9 G_postcentral 3334 2006 6513 2.540 0.983 0.182 0.155 140 19.8 G_precentral 2495 1578 5765 2.884 0.725 0.183 0.140 101 13.8 G_precuneus 904 614 3151 3.557 0.973 0.203 0.117 38 3.5 G_rectus 517 252 515 1.793 1.178 0.130 0.087 17 1.9 G_subcallosal 504 316 977 2.591 0.643 0.158 0.086 11 1.9 G_temp_sup-G_T_transv 2358 1332 5887 3.064 0.785 0.179 0.188 166 14.9 G_temp_sup-Lateral 573 413 1318 2.729 0.650 0.122 0.039 5 0.9 G_temp_sup-Plan_polar 838 585 1619 2.611 0.581 0.144 0.066 13 2.3 G_temp_sup-Plan_tempo 3048 2085 9217 3.373 0.927 0.202 0.147 126 19.3 G_temporal_inf 3449 2255 10656 3.470 0.763 0.180 0.110 142 15.8 G_temporal_middle 450 298 877 2.912 0.587 0.174 0.217 221 1.2 Lat_Fis-ant-Horizont 333 216 532 2.976 0.917 0.158 0.189 16 2.2 Lat_Fis-ant-Vertical 945 613 1248 2.597 0.500 0.145 0.061 12 2.4 Lat_Fis-post 2755 1739 3521 1.914 0.617 0.193 0.110 84 14.4 Pole_occipital 2173 1416 5583 2.913 0.866 0.216 0.155 111 14.9 Pole_temporal 2033 1360 2413 2.019 0.775 0.175 0.088 43 8.0 S_calcarine 3060 2184 3179 1.811 0.576 0.205 0.224 196 29.9 S_central 1019 743 1788 2.615 0.460 0.111 0.031 7 1.4 S_cingul-Marginalis 505 344 913 3.178 0.542 0.112 0.032 6 0.7 S_circular_insula_ant 1651 1066 2880 3.086 0.562 0.090 0.023 8 1.7 S_circular_insula_inf 1687 1146 3133 3.188 0.762 0.193 0.417 199 8.2 S_circular_insula_sup 526 342 977 2.789 0.660 0.128 0.071 6 1.5 S_collat_transv_ant 251 197 429 2.472 0.410 0.142 0.039 2 0.4 S_collat_transv_post 2696 1774 5268 3.093 0.711 0.153 0.116 96 11.1 S_front_inf 2044 1307 3832 3.004 0.652 0.153 0.079 56 7.0 S_front_middle 2971 1927 6025 3.431 0.588 0.172 0.161 255 14.7 S_front_sup 540 339 909 2.985 0.782 0.142 0.076 9 1.5 S_interm_prim-Jensen 3176 2118 4851 2.683 0.498 0.147 0.066 44 9.1 S_intrapariet_and_P_trans 1390 860 1931 2.463 0.633 0.161 0.075 26 4.5 S_oc_middle_and_Lunatus 1220 832 1891 2.560 0.486 0.137 0.051 14 2.9 S_oc_sup_and_transversal 789 544 1461 3.036 0.662 0.142 0.057 9 1.7 S_occipital_ant 1261 846 2275 2.827 0.499 0.151 0.075 26 4.3 S_oc-temp_lat 1836 1346 2851 2.504 0.657 0.189 0.164 91 13.4 S_oc-temp_med_and_Lingual 713 446 1112 2.855 0.706 0.131 0.050 11 1.5 S_orbital_lateral 817 523 1674 2.676 1.540 0.123 0.095 21 2.4 S_orbital_med-olfact 1210 821 2432 3.386 0.893 0.158 0.072 22 3.7 S_orbital-H_Shaped 1834 1217 3263 2.650 0.549 0.143 0.053 24 4.2 S_parieto_occipital 2515 1355 2783 2.124 1.132 0.182 0.273 412 27.8 S_pericallosal 3200 2139 4886 2.750 0.562 0.155 0.191 209 14.8 S_postcentral 1967 1399 3680 3.269 0.566 0.168 0.090 45 7.8 S_precentral-inf-part 1689 1128 2634 3.195 0.720 0.157 0.098 37 5.7 S_precentral-sup-part 765 511 1399 3.044 1.016 0.145 0.077 24 2.4 S_suborbital 1062 720 2151 2.966 0.654 0.132 0.106 20 5.3 S_subparietal 1691 1118 3057 3.286 0.644 0.142 0.097 42 4.6 S_temporal_inf 6278 4115 11425 3.081 0.651 0.153 0.151 711 24.3 S_temporal_sup 400 269 493 2.203 0.520 0.152 0.050 6 0.8 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Wed Jan 1 08:32:48 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 433 labels changed using aseg relabeling using gibbs priors... 000: 3164 changed, 149610 examined... 001: 769 changed, 13186 examined... 002: 200 changed, 4149 examined... 003: 77 changed, 1164 examined... 004: 27 changed, 450 examined... 005: 17 changed, 136 examined... 006: 8 changed, 95 examined... 007: 3 changed, 42 examined... 008: 1 changed, 17 examined... 009: 1 changed, 6 examined... 010: 0 changed, 5 examined... 151 labels changed using aseg 000: 92 total segments, 57 labels (507 vertices) changed 001: 36 total segments, 1 labels (4 vertices) changed 002: 35 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 79 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2089 vertices marked for relabeling... 2089 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 38 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Wed Jan 1 08:33:26 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 2040 1507 4164 2.920 0.961 0.206 0.165 119 12.2 caudalanteriorcingulate 4751 3054 10870 3.393 0.684 0.193 0.232 329 52.3 caudalmiddlefrontal 2881 1934 4801 2.294 0.596 0.165 0.059 59 7.1 cuneus 448 315 1029 2.441 0.842 0.193 0.210 29 3.4 entorhinal 3353 2309 6845 2.735 0.614 0.182 0.130 135 20.8 fusiform 7573 4708 15135 2.958 0.669 0.168 0.151 527 37.8 inferiorparietal 5379 3625 13721 3.214 0.877 0.187 0.124 175 28.7 inferiortemporal 3056 1693 3261 1.872 0.862 0.154 0.247 163 31.2 isthmuscingulate 8632 5541 14595 2.444 0.733 0.182 0.119 237 38.3 lateraloccipital 3773 2505 9742 3.305 1.041 0.164 0.156 187 31.1 lateralorbitofrontal 3028 2350 6330 2.451 0.809 0.204 0.141 272 21.0 lingual 2594 1648 5918 2.910 1.218 0.169 0.110 117 9.4 medialorbitofrontal 6880 4522 17069 3.310 0.743 0.163 0.115 507 25.1 middletemporal 941 630 1413 1.960 0.552 0.130 0.090 21 2.0 parahippocampal 2356 1621 4996 2.804 0.660 0.155 0.112 84 6.7 paracentral 2092 1251 4214 3.059 0.716 0.176 0.217 110 10.7 parsopercularis 1050 672 2337 3.035 0.731 0.165 0.083 34 4.1 parsorbitalis 3070 1925 5777 2.713 0.774 0.175 0.162 322 17.6 parstriangularis 1825 1177 1907 1.787 0.661 0.208 0.149 77 13.3 pericalcarine 7693 4862 11954 2.393 0.769 0.170 0.199 359 32.7 postcentral 2378 1568 3508 2.218 0.875 0.177 0.152 340 10.8 posteriorcingulate 8470 5483 13941 2.567 0.920 0.181 0.199 479 57.4 precentral 4816 3176 10364 2.857 0.667 0.159 0.108 134 21.8 precuneus 1432 1189 3380 2.686 1.194 0.237 0.145 160 9.2 rostralanteriorcingulate 8192 4961 16623 3.016 0.796 0.179 0.154 375 51.5 rostralmiddlefrontal 12729 8877 33241 3.280 1.024 0.198 0.180 1001 87.0 superiorfrontal 6619 4108 11442 2.663 0.550 0.169 0.153 357 50.1 superiorparietal 8601 5430 18342 2.909 0.705 0.156 0.107 300 36.2 superiortemporal 6919 4358 12787 2.765 0.717 0.174 0.279 756 46.7 supramarginal 645 416 1089 2.441 0.690 0.167 0.080 14 2.3 transversetemporal 2776 1824 5841 3.103 1.011 0.110 0.068 59 8.2 insula #-------------------------------------------- #@# Tessellate rh Wed Jan 1 08:33:39 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 23 found - 23 modified | TOTAL: 45 pass 2 (xy-): 0 found - 23 modified | TOTAL: 45 pass 1 (yz+): 13 found - 13 modified | TOTAL: 58 pass 2 (yz+): 0 found - 13 modified | TOTAL: 58 pass 1 (yz-): 22 found - 22 modified | TOTAL: 80 pass 2 (yz-): 0 found - 22 modified | TOTAL: 80 pass 1 (xz+): 22 found - 22 modified | TOTAL: 102 pass 2 (xz+): 0 found - 22 modified | TOTAL: 102 pass 1 (xz-): 9 found - 9 modified | TOTAL: 111 pass 2 (xz-): 0 found - 9 modified | TOTAL: 111 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 7 found - 7 modified | TOTAL: 11 pass 2 (+++): 0 found - 7 modified | TOTAL: 11 Iteration Number : 1 pass 1 (++): 5 found - 5 modified | TOTAL: 5 pass 2 (++): 0 found - 5 modified | TOTAL: 5 pass 1 (+-): 7 found - 7 modified | TOTAL: 12 pass 2 (+-): 1 found - 8 modified | TOTAL: 13 pass 3 (+-): 0 found - 8 modified | TOTAL: 13 pass 1 (--): 22 found - 22 modified | TOTAL: 35 pass 2 (--): 0 found - 22 modified | TOTAL: 35 pass 1 (-+): 8 found - 8 modified | TOTAL: 43 pass 2 (-+): 0 found - 8 modified | TOTAL: 43 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 1 found - 1 modified | TOTAL: 3 pass 2 (yz+): 0 found - 1 modified | TOTAL: 3 pass 1 (yz-): 2 found - 2 modified | TOTAL: 5 pass 2 (yz-): 0 found - 2 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 2 found - 2 modified | TOTAL: 7 pass 2 (xz-): 0 found - 2 modified | TOTAL: 7 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 (++): 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 (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 = 175 (out of 321889: 0.054367) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 60: 1606 vertices, 1698 faces slice 70: 5521 vertices, 5711 faces slice 80: 12172 vertices, 12483 faces slice 90: 21258 vertices, 21683 faces slice 100: 32010 vertices, 32496 faces slice 110: 44322 vertices, 44888 faces slice 120: 58053 vertices, 58662 faces slice 130: 70554 vertices, 71152 faces slice 140: 83163 vertices, 83776 faces slice 150: 95439 vertices, 96048 faces slice 160: 106744 vertices, 107344 faces slice 170: 116234 vertices, 116787 faces slice 180: 122557 vertices, 123044 faces slice 190: 129199 vertices, 129743 faces slice 200: 136914 vertices, 137433 faces slice 210: 143589 vertices, 144076 faces slice 220: 150374 vertices, 150858 faces slice 230: 153901 vertices, 154244 faces slice 240: 154132 vertices, 154428 faces slice 250: 154132 vertices, 154428 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... 154132 voxel in cpt #1: X=-296 [v=154132,e=463284,f=308856] located at (33.574196, 9.733456, 44.507942) For the whole surface: X=-296 [v=154132,e=463284,f=308856] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Jan 1 08:33:44 CST 2014 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Wed Jan 1 08:33:48 CST 2014 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts avg radius = 50.4 mm, total surface area = 77522 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.125 (target=0.015) step 005: RMS=0.095 (target=0.015) step 010: RMS=0.080 (target=0.015) step 015: RMS=0.074 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.065 (target=0.015) step 030: RMS=0.062 (target=0.015) step 035: RMS=0.061 (target=0.015) step 040: RMS=0.060 (target=0.015) step 045: RMS=0.059 (target=0.015) step 050: RMS=0.059 (target=0.015) step 055: RMS=0.059 (target=0.015) step 060: RMS=0.059 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Wed Jan 1 08:34:14 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.93 +- 0.63 (0.00-->10.31) (max @ vno 62538 --> 62558) face area 0.02 +- 0.03 (-0.23-->0.90) scaling brain by 0.295... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.554, avgs=0 005/300: dt: 0.9000, rms radial error=177.300, avgs=0 010/300: dt: 0.9000, rms radial error=176.755, avgs=0 015/300: dt: 0.9000, rms radial error=176.039, avgs=0 020/300: dt: 0.9000, rms radial error=175.219, avgs=0 025/300: dt: 0.9000, rms radial error=174.338, avgs=0 030/300: dt: 0.9000, rms radial error=173.420, avgs=0 035/300: dt: 0.9000, rms radial error=172.482, avgs=0 040/300: dt: 0.9000, rms radial error=171.536, avgs=0 045/300: dt: 0.9000, rms radial error=170.587, avgs=0 050/300: dt: 0.9000, rms radial error=169.639, avgs=0 055/300: dt: 0.9000, rms radial error=168.696, avgs=0 060/300: dt: 0.9000, rms radial error=167.756, avgs=0 065/300: dt: 0.9000, rms radial error=166.820, avgs=0 070/300: dt: 0.9000, rms radial error=165.889, avgs=0 075/300: dt: 0.9000, rms radial error=164.963, avgs=0 080/300: dt: 0.9000, rms radial error=164.041, avgs=0 085/300: dt: 0.9000, rms radial error=163.124, avgs=0 090/300: dt: 0.9000, rms radial error=162.212, avgs=0 095/300: dt: 0.9000, rms radial error=161.306, avgs=0 100/300: dt: 0.9000, rms radial error=160.403, avgs=0 105/300: dt: 0.9000, rms radial error=159.506, avgs=0 110/300: dt: 0.9000, rms radial error=158.614, avgs=0 115/300: dt: 0.9000, rms radial error=157.726, avgs=0 120/300: dt: 0.9000, rms radial error=156.843, avgs=0 125/300: dt: 0.9000, rms radial error=155.965, avgs=0 130/300: dt: 0.9000, rms radial error=155.091, avgs=0 135/300: dt: 0.9000, rms radial error=154.222, avgs=0 140/300: dt: 0.9000, rms radial error=153.358, avgs=0 145/300: dt: 0.9000, rms radial error=152.499, avgs=0 150/300: dt: 0.9000, rms radial error=151.644, avgs=0 155/300: dt: 0.9000, rms radial error=150.794, avgs=0 160/300: dt: 0.9000, rms radial error=149.949, avgs=0 165/300: dt: 0.9000, rms radial error=149.108, avgs=0 170/300: dt: 0.9000, rms radial error=148.272, avgs=0 175/300: dt: 0.9000, rms radial error=147.440, avgs=0 180/300: dt: 0.9000, rms radial error=146.613, avgs=0 185/300: dt: 0.9000, rms radial error=145.790, avgs=0 190/300: dt: 0.9000, rms radial error=144.972, avgs=0 195/300: dt: 0.9000, rms radial error=144.159, avgs=0 200/300: dt: 0.9000, rms radial error=143.350, avgs=0 205/300: dt: 0.9000, rms radial error=142.545, avgs=0 210/300: dt: 0.9000, rms radial error=141.745, avgs=0 215/300: dt: 0.9000, rms radial error=140.950, avgs=0 220/300: dt: 0.9000, rms radial error=140.159, avgs=0 225/300: dt: 0.9000, rms radial error=139.372, avgs=0 230/300: dt: 0.9000, rms radial error=138.589, avgs=0 235/300: dt: 0.9000, rms radial error=137.811, avgs=0 240/300: dt: 0.9000, rms radial error=137.038, avgs=0 245/300: dt: 0.9000, rms radial error=136.268, avgs=0 250/300: dt: 0.9000, rms radial error=135.503, avgs=0 255/300: dt: 0.9000, rms radial error=134.742, avgs=0 260/300: dt: 0.9000, rms radial error=133.985, avgs=0 265/300: dt: 0.9000, rms radial error=133.233, avgs=0 270/300: dt: 0.9000, rms radial error=132.484, avgs=0 275/300: dt: 0.9000, rms radial error=131.740, avgs=0 280/300: dt: 0.9000, rms radial error=131.000, avgs=0 285/300: dt: 0.9000, rms radial error=130.264, avgs=0 290/300: dt: 0.9000, rms radial error=129.532, avgs=0 295/300: dt: 0.9000, rms radial error=128.805, avgs=0 300/300: dt: 0.9000, rms radial error=128.081, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18574.03 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 2 (K=40.0), pass 1, starting sse = 3404.11 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 = 479.19 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00264 epoch 4 (K=640.0), pass 1, starting sse = 81.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/12 = 0.00871 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Wed Jan 1 08:38:01 CST 2014 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS1036-1 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=-296 (nv=154132, nf=308856, ne=463284, g=149) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 39311 ambiguous faces found in tessellation segmenting defects... 141 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 4 into 2 -merging segment 6 into 2 -merging segment 8 into 2 -merging segment 5 into 2 -merging segment 15 into 2 -merging segment 19 into 13 -merging segment 63 into 46 -merging segment 60 into 46 -merging segment 2 into 48 -merging segment 56 into 55 -merging segment 74 into 70 -merging segment 83 into 85 -merging segment 100 into 92 -merging segment 106 into 103 127 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1490 (-4.5745) -vertex loglikelihood: -6.4987 (-3.2494) -normal dot loglikelihood: -3.5628 (-3.5628) -quad curv loglikelihood: -6.0727 (-3.0364) Total Loglikelihood : -25.2833 CORRECTING DEFECT 0 (vertices=580, convex hull=160) After retessellation of defect 0, euler #=-126 (131859,389977,257992) : difference with theory (-124) = 2 CORRECTING DEFECT 1 (vertices=15, convex hull=28) After retessellation of defect 1, euler #=-125 (131861,389991,258005) : difference with theory (-123) = 2 CORRECTING DEFECT 2 (vertices=62, convex hull=45) After retessellation of defect 2, euler #=-124 (131876,390053,258053) : difference with theory (-122) = 2 CORRECTING DEFECT 3 (vertices=38, convex hull=104) After retessellation of defect 3, euler #=-123 (131885,390122,258114) : difference with theory (-121) = 2 CORRECTING DEFECT 4 (vertices=21, convex hull=53) After retessellation of defect 4, euler #=-122 (131897,390174,258155) : difference with theory (-120) = 2 CORRECTING DEFECT 5 (vertices=40, convex hull=73) After retessellation of defect 5, euler #=-121 (131922,390277,258234) : difference with theory (-119) = 2 CORRECTING DEFECT 6 (vertices=24, convex hull=42) After retessellation of defect 6, euler #=-120 (131931,390318,258267) : difference with theory (-118) = 2 CORRECTING DEFECT 7 (vertices=11, convex hull=34) After retessellation of defect 7, euler #=-119 (131934,390338,258285) : difference with theory (-117) = 2 CORRECTING DEFECT 8 (vertices=63, convex hull=82) After retessellation of defect 8, euler #=-117 (131954,390437,258366) : difference with theory (-116) = 1 CORRECTING DEFECT 9 (vertices=50, convex hull=52) After retessellation of defect 9, euler #=-116 (131964,390484,258404) : difference with theory (-115) = 1 CORRECTING DEFECT 10 (vertices=65, convex hull=97) After retessellation of defect 10, euler #=-115 (131998,390629,258516) : difference with theory (-114) = 1 CORRECTING DEFECT 11 (vertices=76, convex hull=94) After retessellation of defect 11, euler #=-114 (132034,390778,258630) : difference with theory (-113) = 1 CORRECTING DEFECT 12 (vertices=59, convex hull=31) After retessellation of defect 12, euler #=-113 (132039,390803,258651) : difference with theory (-112) = 1 CORRECTING DEFECT 13 (vertices=106, convex hull=121) After retessellation of defect 13, euler #=-112 (132095,391024,258817) : difference with theory (-111) = 1 CORRECTING DEFECT 14 (vertices=6, convex hull=14) After retessellation of defect 14, euler #=-111 (132096,391031,258824) : difference with theory (-110) = 1 CORRECTING DEFECT 15 (vertices=45, convex hull=86) After retessellation of defect 15, euler #=-110 (132114,391124,258900) : difference with theory (-109) = 1 CORRECTING DEFECT 16 (vertices=14, convex hull=24) After retessellation of defect 16, euler #=-109 (132116,391136,258911) : difference with theory (-108) = 1 CORRECTING DEFECT 17 (vertices=180, convex hull=99) After retessellation of defect 17, euler #=-108 (132152,391291,259031) : difference with theory (-107) = 1 CORRECTING DEFECT 18 (vertices=37, convex hull=57) After retessellation of defect 18, euler #=-107 (132165,391351,259079) : difference with theory (-106) = 1 CORRECTING DEFECT 19 (vertices=77, convex hull=62) After retessellation of defect 19, euler #=-106 (132186,391445,259153) : difference with theory (-105) = 1 CORRECTING DEFECT 20 (vertices=6, convex hull=14) After retessellation of defect 20, euler #=-105 (132186,391447,259156) : difference with theory (-104) = 1 CORRECTING DEFECT 21 (vertices=48, convex hull=76) After retessellation of defect 21, euler #=-104 (132215,391561,259242) : difference with theory (-103) = 1 CORRECTING DEFECT 22 (vertices=76, convex hull=110) After retessellation of defect 22, euler #=-103 (132258,391739,259378) : difference with theory (-102) = 1 CORRECTING DEFECT 23 (vertices=12, convex hull=12) After retessellation of defect 23, euler #=-102 (132259,391746,259385) : difference with theory (-101) = 1 CORRECTING DEFECT 24 (vertices=1524, convex hull=762) After retessellation of defect 24, euler #=-101 (132724,393537,260712) : difference with theory (-100) = 1 CORRECTING DEFECT 25 (vertices=36, convex hull=49) After retessellation of defect 25, euler #=-100 (132736,393592,260756) : difference with theory (-99) = 1 CORRECTING DEFECT 26 (vertices=42, convex hull=51) After retessellation of defect 26, euler #=-99 (132749,393653,260805) : difference with theory (-98) = 1 CORRECTING DEFECT 27 (vertices=29, convex hull=42) After retessellation of defect 27, euler #=-98 (132751,393675,260826) : difference with theory (-97) = 1 CORRECTING DEFECT 28 (vertices=39, convex hull=68) After retessellation of defect 28, euler #=-97 (132770,393760,260893) : difference with theory (-96) = 1 CORRECTING DEFECT 29 (vertices=28, convex hull=23) After retessellation of defect 29, euler #=-96 (132773,393775,260906) : difference with theory (-95) = 1 CORRECTING DEFECT 30 (vertices=35, convex hull=66) After retessellation of defect 30, euler #=-95 (132782,393829,260952) : difference with theory (-94) = 1 CORRECTING DEFECT 31 (vertices=31, convex hull=33) After retessellation of defect 31, euler #=-94 (132786,393852,260972) : difference with theory (-93) = 1 CORRECTING DEFECT 32 (vertices=157, convex hull=80) After retessellation of defect 32, euler #=-94 (132830,394026,261102) : difference with theory (-92) = 2 CORRECTING DEFECT 33 (vertices=26, convex hull=26) After retessellation of defect 33, euler #=-93 (132837,394055,261125) : difference with theory (-91) = 2 CORRECTING DEFECT 34 (vertices=35, convex hull=75) After retessellation of defect 34, euler #=-92 (132850,394122,261180) : difference with theory (-90) = 2 CORRECTING DEFECT 35 (vertices=306, convex hull=232) After retessellation of defect 35, euler #=-91 (132944,394514,261479) : difference with theory (-89) = 2 CORRECTING DEFECT 36 (vertices=28, convex hull=62) After retessellation of defect 36, euler #=-90 (132953,394569,261526) : difference with theory (-88) = 2 CORRECTING DEFECT 37 (vertices=31, convex hull=75) After retessellation of defect 37, euler #=-89 (132972,394655,261594) : difference with theory (-87) = 2 CORRECTING DEFECT 38 (vertices=26, convex hull=21) After retessellation of defect 38, euler #=-88 (132974,394668,261606) : difference with theory (-86) = 2 CORRECTING DEFECT 39 (vertices=1148, convex hull=714) After retessellation of defect 39, euler #=-85 (133324,396080,262671) : difference with theory (-85) = 0 CORRECTING DEFECT 40 (vertices=54, convex hull=39) After retessellation of defect 40, euler #=-84 (133335,396125,262706) : difference with theory (-84) = 0 CORRECTING DEFECT 41 (vertices=10971, convex hull=2956) After retessellation of defect 41, euler #=-85 (136785,408169,271299) : difference with theory (-83) = 2 CORRECTING DEFECT 42 (vertices=61, convex hull=47) After retessellation of defect 42, euler #=-84 (136790,408202,271328) : difference with theory (-82) = 2 CORRECTING DEFECT 43 (vertices=7, convex hull=25) After retessellation of defect 43, euler #=-83 (136791,408212,271338) : difference with theory (-81) = 2 CORRECTING DEFECT 44 (vertices=37, convex hull=32) After retessellation of defect 44, euler #=-82 (136795,408236,271359) : difference with theory (-80) = 2 CORRECTING DEFECT 45 (vertices=64, convex hull=25) After retessellation of defect 45, euler #=-81 (136806,408279,271392) : difference with theory (-79) = 2 CORRECTING DEFECT 46 (vertices=29, convex hull=31) After retessellation of defect 46, euler #=-80 (136814,408313,271419) : difference with theory (-78) = 2 CORRECTING DEFECT 47 (vertices=8, convex hull=33) After retessellation of defect 47, euler #=-79 (136815,408323,271429) : difference with theory (-77) = 2 CORRECTING DEFECT 48 (vertices=53, convex hull=71) After retessellation of defect 48, euler #=-77 (136830,408399,271492) : difference with theory (-76) = 1 CORRECTING DEFECT 49 (vertices=23, convex hull=62) After retessellation of defect 49, euler #=-76 (136841,408457,271540) : difference with theory (-75) = 1 CORRECTING DEFECT 50 (vertices=80, convex hull=65) After retessellation of defect 50, euler #=-75 (136863,408553,271615) : difference with theory (-74) = 1 CORRECTING DEFECT 51 (vertices=31, convex hull=38) After retessellation of defect 51, euler #=-74 (136867,408579,271638) : difference with theory (-73) = 1 CORRECTING DEFECT 52 (vertices=42, convex hull=26) After retessellation of defect 52, euler #=-73 (136874,408605,271658) : difference with theory (-72) = 1 CORRECTING DEFECT 53 (vertices=67, convex hull=112) After retessellation of defect 53, euler #=-72 (136889,408699,271738) : difference with theory (-71) = 1 CORRECTING DEFECT 54 (vertices=7, convex hull=30) After retessellation of defect 54, euler #=-71 (136891,408714,271752) : difference with theory (-70) = 1 CORRECTING DEFECT 55 (vertices=148, convex hull=53) After retessellation of defect 55, euler #=-70 (136913,408797,271814) : difference with theory (-69) = 1 CORRECTING DEFECT 56 (vertices=252, convex hull=53) After retessellation of defect 56, euler #=-69 (136955,408947,271923) : difference with theory (-68) = 1 CORRECTING DEFECT 57 (vertices=24, convex hull=20) After retessellation of defect 57, euler #=-68 (136959,408962,271935) : difference with theory (-67) = 1 CORRECTING DEFECT 58 (vertices=220, convex hull=35) After retessellation of defect 58, euler #=-67 (136968,409000,271965) : difference with theory (-66) = 1 CORRECTING DEFECT 59 (vertices=51, convex hull=94) After retessellation of defect 59, euler #=-66 (136993,409117,272058) : difference with theory (-65) = 1 CORRECTING DEFECT 60 (vertices=80, convex hull=127) After retessellation of defect 60, euler #=-64 (137016,409242,272162) : difference with theory (-64) = 0 CORRECTING DEFECT 61 (vertices=9, convex hull=23) After retessellation of defect 61, euler #=-63 (137018,409254,272173) : difference with theory (-63) = 0 CORRECTING DEFECT 62 (vertices=28, convex hull=47) After retessellation of defect 62, euler #=-62 (137034,409321,272225) : difference with theory (-62) = 0 CORRECTING DEFECT 63 (vertices=55, convex hull=71) After retessellation of defect 63, euler #=-61 (137067,409455,272327) : difference with theory (-61) = 0 CORRECTING DEFECT 64 (vertices=31, convex hull=48) After retessellation of defect 64, euler #=-60 (137074,409500,272366) : difference with theory (-60) = 0 CORRECTING DEFECT 65 (vertices=26, convex hull=56) After retessellation of defect 65, euler #=-59 (137083,409549,272407) : difference with theory (-59) = 0 CORRECTING DEFECT 66 (vertices=235, convex hull=124) After retessellation of defect 66, euler #=-58 (137092,409632,272482) : difference with theory (-58) = 0 CORRECTING DEFECT 67 (vertices=21, convex hull=22) After retessellation of defect 67, euler #=-57 (137095,409648,272496) : difference with theory (-57) = 0 CORRECTING DEFECT 68 (vertices=32, convex hull=61) After retessellation of defect 68, euler #=-56 (137114,409730,272560) : difference with theory (-56) = 0 CORRECTING DEFECT 69 (vertices=66, convex hull=84) After retessellation of defect 69, euler #=-55 (137138,409840,272647) : difference with theory (-55) = 0 CORRECTING DEFECT 70 (vertices=662, convex hull=287) normal vector of length zero at vertex 150477 with 4 faces normal vector of length zero at vertex 150477 with 4 faces normal vector of length zero at vertex 150477 with 4 faces normal vector of length zero at vertex 150477 with 4 faces normal vector of length zero at vertex 150477 with 4 faces After retessellation of defect 70, euler #=-54 (137147,410007,272806) : difference with theory (-54) = 0 CORRECTING DEFECT 71 (vertices=591, convex hull=207) After retessellation of defect 71, euler #=-54 (137274,410492,273164) : difference with theory (-53) = 1 CORRECTING DEFECT 72 (vertices=560, convex hull=318) After retessellation of defect 72, euler #=-54 (137567,411551,273930) : difference with theory (-52) = 2 CORRECTING DEFECT 73 (vertices=22, convex hull=28) After retessellation of defect 73, euler #=-52 (137570,411569,273947) : difference with theory (-51) = 1 CORRECTING DEFECT 74 (vertices=21, convex hull=61) After retessellation of defect 74, euler #=-51 (137580,411624,273993) : difference with theory (-50) = 1 CORRECTING DEFECT 75 (vertices=20, convex hull=50) After retessellation of defect 75, euler #=-50 (137589,411665,274026) : difference with theory (-49) = 1 CORRECTING DEFECT 76 (vertices=29, convex hull=38) After retessellation of defect 76, euler #=-49 (137592,411687,274046) : difference with theory (-48) = 1 CORRECTING DEFECT 77 (vertices=61, convex hull=41) After retessellation of defect 77, euler #=-48 (137597,411718,274073) : difference with theory (-47) = 1 CORRECTING DEFECT 78 (vertices=173, convex hull=138) After retessellation of defect 78, euler #=-48 (137624,411872,274200) : difference with theory (-46) = 2 CORRECTING DEFECT 79 (vertices=138, convex hull=116) After retessellation of defect 79, euler #=-47 (137676,412084,274361) : difference with theory (-45) = 2 CORRECTING DEFECT 80 (vertices=126, convex hull=142) After retessellation of defect 80, euler #=-45 (137713,412263,274505) : difference with theory (-44) = 1 CORRECTING DEFECT 81 (vertices=23, convex hull=49) After retessellation of defect 81, euler #=-44 (137723,412310,274543) : difference with theory (-43) = 1 CORRECTING DEFECT 82 (vertices=10, convex hull=17) After retessellation of defect 82, euler #=-43 (137725,412320,274552) : difference with theory (-42) = 1 CORRECTING DEFECT 83 (vertices=201, convex hull=106) After retessellation of defect 83, euler #=-42 (137780,412556,274734) : difference with theory (-41) = 1 CORRECTING DEFECT 84 (vertices=8, convex hull=21) After retessellation of defect 84, euler #=-41 (137782,412568,274745) : difference with theory (-40) = 1 CORRECTING DEFECT 85 (vertices=82, convex hull=53) After retessellation of defect 85, euler #=-40 (137797,412637,274800) : difference with theory (-39) = 1 CORRECTING DEFECT 86 (vertices=9, convex hull=19) Warning - incorrect dp selected!!!!(-101.420758 >= -101.420765 ) After retessellation of defect 86, euler #=-39 (137799,412647,274809) : difference with theory (-38) = 1 CORRECTING DEFECT 87 (vertices=40, convex hull=59) After retessellation of defect 87, euler #=-38 (137819,412729,274872) : difference with theory (-37) = 1 CORRECTING DEFECT 88 (vertices=52, convex hull=31) After retessellation of defect 88, euler #=-37 (137823,412749,274889) : difference with theory (-36) = 1 CORRECTING DEFECT 89 (vertices=18, convex hull=63) After retessellation of defect 89, euler #=-36 (137836,412814,274942) : difference with theory (-35) = 1 CORRECTING DEFECT 90 (vertices=75, convex hull=119) After retessellation of defect 90, euler #=-34 (137847,412905,275024) : difference with theory (-34) = 0 CORRECTING DEFECT 91 (vertices=43, convex hull=90) After retessellation of defect 91, euler #=-33 (137863,412988,275092) : difference with theory (-33) = 0 CORRECTING DEFECT 92 (vertices=63, convex hull=84) After retessellation of defect 92, euler #=-32 (137874,413060,275154) : difference with theory (-32) = 0 CORRECTING DEFECT 93 (vertices=25, convex hull=20) After retessellation of defect 93, euler #=-31 (137874,413065,275160) : difference with theory (-31) = 0 CORRECTING DEFECT 94 (vertices=39, convex hull=33) After retessellation of defect 94, euler #=-30 (137880,413093,275183) : difference with theory (-30) = 0 CORRECTING DEFECT 95 (vertices=167, convex hull=33) After retessellation of defect 95, euler #=-29 (137890,413134,275215) : difference with theory (-29) = 0 CORRECTING DEFECT 96 (vertices=25, convex hull=19) After retessellation of defect 96, euler #=-28 (137891,413141,275222) : difference with theory (-28) = 0 CORRECTING DEFECT 97 (vertices=80, convex hull=78) After retessellation of defect 97, euler #=-27 (137903,413211,275281) : difference with theory (-27) = 0 CORRECTING DEFECT 98 (vertices=33, convex hull=25) After retessellation of defect 98, euler #=-26 (137907,413230,275297) : difference with theory (-26) = 0 CORRECTING DEFECT 99 (vertices=18, convex hull=39) After retessellation of defect 99, euler #=-25 (137913,413263,275325) : difference with theory (-25) = 0 CORRECTING DEFECT 100 (vertices=12, convex hull=21) After retessellation of defect 100, euler #=-24 (137915,413276,275337) : difference with theory (-24) = 0 CORRECTING DEFECT 101 (vertices=29, convex hull=60) After retessellation of defect 101, euler #=-23 (137924,413326,275379) : difference with theory (-23) = 0 CORRECTING DEFECT 102 (vertices=62, convex hull=43) After retessellation of defect 102, euler #=-22 (137932,413365,275411) : difference with theory (-22) = 0 CORRECTING DEFECT 103 (vertices=47, convex hull=42) After retessellation of defect 103, euler #=-21 (137938,413398,275439) : difference with theory (-21) = 0 CORRECTING DEFECT 104 (vertices=49, convex hull=50) After retessellation of defect 104, euler #=-20 (137947,413446,275479) : difference with theory (-20) = 0 CORRECTING DEFECT 105 (vertices=33, convex hull=84) After retessellation of defect 105, euler #=-19 (137956,413508,275533) : difference with theory (-19) = 0 CORRECTING DEFECT 106 (vertices=46, convex hull=31) After retessellation of defect 106, euler #=-18 (137960,413530,275552) : difference with theory (-18) = 0 CORRECTING DEFECT 107 (vertices=36, convex hull=66) After retessellation of defect 107, euler #=-17 (137971,413591,275603) : difference with theory (-17) = 0 CORRECTING DEFECT 108 (vertices=29, convex hull=51) After retessellation of defect 108, euler #=-16 (137978,413633,275639) : difference with theory (-16) = 0 CORRECTING DEFECT 109 (vertices=29, convex hull=66) After retessellation of defect 109, euler #=-15 (137989,413690,275686) : difference with theory (-15) = 0 CORRECTING DEFECT 110 (vertices=28, convex hull=50) After retessellation of defect 110, euler #=-14 (137996,413732,275722) : difference with theory (-14) = 0 CORRECTING DEFECT 111 (vertices=35, convex hull=75) After retessellation of defect 111, euler #=-13 (138006,413793,275774) : difference with theory (-13) = 0 CORRECTING DEFECT 112 (vertices=31, convex hull=52) After retessellation of defect 112, euler #=-12 (138014,413842,275816) : difference with theory (-12) = 0 CORRECTING DEFECT 113 (vertices=19, convex hull=20) After retessellation of defect 113, euler #=-11 (138014,413847,275822) : difference with theory (-11) = 0 CORRECTING DEFECT 114 (vertices=39, convex hull=74) After retessellation of defect 114, euler #=-10 (138026,413913,275877) : difference with theory (-10) = 0 CORRECTING DEFECT 115 (vertices=40, convex hull=36) After retessellation of defect 115, euler #=-9 (138029,413936,275898) : difference with theory (-9) = 0 CORRECTING DEFECT 116 (vertices=32, convex hull=51) After retessellation of defect 116, euler #=-8 (138038,413979,275933) : difference with theory (-8) = 0 CORRECTING DEFECT 117 (vertices=6, convex hull=27) After retessellation of defect 117, euler #=-7 (138039,413990,275944) : difference with theory (-7) = 0 CORRECTING DEFECT 118 (vertices=27, convex hull=58) After retessellation of defect 118, euler #=-6 (138048,414038,275984) : difference with theory (-6) = 0 CORRECTING DEFECT 119 (vertices=18, convex hull=17) After retessellation of defect 119, euler #=-5 (138048,414043,275990) : difference with theory (-5) = 0 CORRECTING DEFECT 120 (vertices=29, convex hull=29) After retessellation of defect 120, euler #=-4 (138050,414057,276003) : difference with theory (-4) = 0 CORRECTING DEFECT 121 (vertices=32, convex hull=31) After retessellation of defect 121, euler #=-3 (138051,414071,276017) : difference with theory (-3) = 0 CORRECTING DEFECT 122 (vertices=38, convex hull=84) After retessellation of defect 122, euler #=-2 (138066,414152,276084) : difference with theory (-2) = 0 CORRECTING DEFECT 123 (vertices=13, convex hull=24) After retessellation of defect 123, euler #=-1 (138067,414160,276092) : difference with theory (-1) = 0 CORRECTING DEFECT 124 (vertices=26, convex hull=50) After retessellation of defect 124, euler #=0 (138074,414197,276123) : difference with theory (0) = 0 CORRECTING DEFECT 125 (vertices=19, convex hull=18) After retessellation of defect 125, euler #=1 (138076,414207,276132) : difference with theory (1) = 0 CORRECTING DEFECT 126 (vertices=42, convex hull=40) After retessellation of defect 126, euler #=2 (138081,414237,276158) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.33 (0.02-->10.80) (max @ vno 27232 --> 145463) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.33 (0.02-->10.80) (max @ vno 27232 --> 145463) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 516 mutations (36.9%), 883 crossovers (63.1%), 671 vertices were eliminated building final representation... 16051 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138081, nf=276158, ne=414237, g=0) writing corrected surface to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 110.3 minutes 0 defective edges removing intersecting faces 000: 2477 intersecting 001: 228 intersecting 002: 121 intersecting 003: 80 intersecting expanding nbhd size to 2 004: 80 intersecting expanding nbhd size to 3 005: 92 intersecting 006: 70 intersecting 007: 48 intersecting 008: 38 intersecting 009: 37 intersecting 010: 5 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 138081 - 414237 + 276158 = 2 --> 0 holes F =2V-4: 276158 = 276162-4 (0) 2E=3F: 828474 = 828474 (0) total defect index = 0 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 1282 intersecting 001: 203 intersecting 002: 107 intersecting 003: 70 intersecting expanding nbhd size to 2 004: 86 intersecting expanding nbhd size to 3 005: 89 intersecting 006: 72 intersecting 007: 42 intersecting 008: 39 intersecting 009: 18 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Wed Jan 1 10:28:30 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 19762 bright wm thresholded. 1559 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (93.0): 94.0 +- 7.7 [70.0 --> 110.0] GM (82.0) : 78.7 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.3 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 47.6 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.02-->6.92) (max @ vno 133049 --> 133050) face area 0.27 +- 0.16 (0.00-->7.95) mean absolute distance = 0.81 +- 1.07 4148 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=100, GM=77 mean inside = 89.7, mean outside = 76.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.1, 3695 (3695) missing vertices, mean dist 0.2 [0.8 (%36.5)->0.8 (%63.5))] %63 local maxima, %23 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 0.91 +- 0.34 (0.05-->10.54) (max @ vno 134388 --> 135956) face area 0.27 +- 0.18 (0.00-->6.17) mean absolute distance = 0.47 +- 0.75 4813 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5014202.5, rms=9.95 001: dt: 0.5000, sse=5974493.5, rms=7.909 (0.000%) 002: dt: 0.5000, sse=6177714.0, rms=6.696 (0.000%) 003: dt: 0.5000, sse=6447428.0, rms=5.973 (0.000%) 004: dt: 0.5000, sse=6611053.5, rms=5.541 (0.000%) 005: dt: 0.5000, sse=6752580.5, rms=5.260 (0.000%) 006: dt: 0.5000, sse=6805220.5, rms=5.072 (0.000%) 007: dt: 0.5000, sse=6883308.5, rms=4.928 (0.000%) 008: dt: 0.5000, sse=6897991.0, rms=4.815 (0.000%) 009: dt: 0.5000, sse=6903231.0, rms=4.723 (0.000%) 010: dt: 0.5000, sse=6889856.5, rms=4.627 (0.000%) 011: dt: 0.5000, sse=6894091.0, rms=4.540 (0.000%) 012: dt: 0.5000, sse=6859914.5, rms=4.457 (0.000%) 013: dt: 0.5000, sse=6883189.5, rms=4.393 (0.000%) 014: dt: 0.5000, sse=6853099.5, rms=4.312 (0.000%) 015: dt: 0.5000, sse=6839382.0, rms=4.233 (0.000%) 016: dt: 0.5000, sse=6818582.0, rms=4.164 (0.000%) 017: dt: 0.5000, sse=6799882.0, rms=4.095 (0.000%) 018: dt: 0.5000, sse=6806158.0, rms=4.026 (0.000%) 019: dt: 0.5000, sse=6780790.0, rms=3.972 (0.000%) 020: dt: 0.5000, sse=6785969.0, rms=3.903 (0.000%) rms = 3.85, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=6788008.5, rms=3.854 (0.000%) 022: dt: 0.2500, sse=4740748.0, rms=3.452 (0.000%) 023: dt: 0.2500, sse=4517697.0, rms=3.365 (0.000%) rms = 3.34, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=4440406.0, rms=3.337 (0.000%) rms = 3.31, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4367969.5, rms=3.314 (0.000%) positioning took 1.9 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 removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.5, 3070 (2579) missing vertices, mean dist -0.3 [0.5 (%70.0)->0.4 (%30.0))] %75 local maxima, %11 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 0.89 +- 0.33 (0.07-->11.24) (max @ vno 134388 --> 135956) face area 0.34 +- 0.22 (0.00-->7.54) mean absolute distance = 0.33 +- 0.52 3567 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4765217.0, rms=4.93 026: dt: 0.5000, sse=5121282.0, rms=4.000 (0.000%) 027: dt: 0.5000, sse=5726999.0, rms=3.807 (0.000%) 028: dt: 0.5000, sse=5810190.0, rms=3.725 (0.000%) rms = 3.71, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=6341187.0, rms=3.713 (0.000%) 030: dt: 0.2500, sse=5074055.0, rms=3.377 (0.000%) 031: dt: 0.2500, sse=4914987.0, rms=3.305 (0.000%) rms = 3.27, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4844622.5, rms=3.271 (0.000%) rms = 3.25, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4794390.0, rms=3.249 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 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 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=89.0, 2890 (2305) missing vertices, mean dist -0.1 [0.4 (%65.4)->0.3 (%34.6))] %79 local maxima, % 7 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 0.89 +- 0.33 (0.01-->11.27) (max @ vno 134388 --> 135956) face area 0.33 +- 0.22 (0.00-->8.01) mean absolute distance = 0.29 +- 0.43 2997 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4871805.5, rms=3.84 034: dt: 0.5000, sse=5256385.5, rms=3.482 (0.000%) rms = 3.45, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=5770422.0, rms=3.455 (0.000%) 036: dt: 0.2500, sse=5111178.0, rms=3.206 (0.000%) 037: dt: 0.2500, sse=5025856.5, rms=3.149 (0.000%) rms = 3.13, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4967733.0, rms=3.128 (0.000%) rms = 3.11, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4923739.5, rms=3.106 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.6, 2912 (2224) missing vertices, mean dist -0.0 [0.3 (%54.8)->0.3 (%45.2))] %80 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/post_analysis/MPS1036-1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4937406.0, rms=3.26 040: dt: 0.5000, sse=6359287.0, rms=3.106 (0.000%) rms = 3.27, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=5853031.0, rms=3.018 (0.000%) rms = 3.02, time step reduction 2 of 3 to 0.125... rms = 3.01, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5792408.0, rms=3.006 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group generating cortex label... 27 non-cortical segments detected only using segment with 2153 vertices erasing segment 0 (vno[0] = 14791) erasing segment 1 (vno[0] = 17673) erasing segment 2 (vno[0] = 41085) erasing segment 3 (vno[0] = 42068) erasing segment 5 (vno[0] = 43135) erasing segment 6 (vno[0] = 44274) erasing segment 7 (vno[0] = 71289) erasing segment 8 (vno[0] = 73734) erasing segment 9 (vno[0] = 75965) erasing segment 10 (vno[0] = 79016) erasing segment 11 (vno[0] = 83583) erasing segment 12 (vno[0] = 85612) erasing segment 13 (vno[0] = 86314) erasing segment 14 (vno[0] = 86332) erasing segment 15 (vno[0] = 86344) erasing segment 16 (vno[0] = 88516) erasing segment 17 (vno[0] = 90300) erasing segment 18 (vno[0] = 91186) erasing segment 19 (vno[0] = 91993) erasing segment 20 (vno[0] = 92062) erasing segment 21 (vno[0] = 98918) erasing segment 22 (vno[0] = 99507) erasing segment 23 (vno[0] = 99530) erasing segment 24 (vno[0] = 100755) erasing segment 25 (vno[0] = 104807) erasing segment 26 (vno[0] = 137732) writing cortex label to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label... writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.curv writing smoothed area to rh.area writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.area vertex spacing 0.89 +- 0.34 (0.04-->11.35) (max @ vno 134388 --> 135956) face area 0.33 +- 0.22 (0.00-->7.95) refinement took 4.6 minutes #-------------------------------------------- #@# Smooth2 rh Wed Jan 1 10:33:05 CST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Wed Jan 1 10:33:08 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 50.7 mm, total surface area = 81675 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.125 (target=0.015) step 005: RMS=0.091 (target=0.015) step 010: RMS=0.071 (target=0.015) step 015: RMS=0.060 (target=0.015) step 020: RMS=0.051 (target=0.015) step 025: RMS=0.043 (target=0.015) step 030: RMS=0.037 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.024 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.020 (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 156 vertices thresholded to be in k1 ~ [-0.42 0.59], k2 ~ [-0.17 0.15] total integrated curvature = 0.280*4pi (3.513) --> 1 handles ICI = 1.3, FI = 10.0, variation=165.739 138 vertices thresholded to be in [-0.03 0.04] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 136 vertices thresholded to be in [-0.24 0.23] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.018, std = 0.027 done. #----------------------------------------- #@# Curvature Stats rh Wed Jan 1 10:34:40 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm MPS1036-1 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 [ MPS1036-1/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 [ 266 ] Gb_filter = 0 WARN: S lookup min: -3.417203 WARN: S explicit min: 0.000000 vertex = 425 #-------------------------------------------- #@# Sphere rh Wed Jan 1 10:34:43 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.278... 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 %19.10 pass 1: epoch 2 of 3 starting distance error %18.96 unfolding complete - removing small folds... starting distance error %18.75 removing remaining folds... final distance error %18.78 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.79 hours #-------------------------------------------- #@# Surf Reg rh Wed Jan 1 11:21:57 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_register -curv ../surf/rh.sphere /soft/freesurfer/5.3.0_1/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_1/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 = 0.566 curvature mean = 0.020, std = 0.916 curvature mean = 0.023, std = 0.864 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 379158.4, tmin=0.7601 d=32.00 min @ (8.00, 0.00, 0.00) sse = 337924.5, tmin=1.5341 d=16.00 min @ (-4.00, 0.00, 0.00) sse = 337042.9, tmin=2.4715 d=8.00 min @ (2.00, 0.00, 2.00) sse = 329195.4, tmin=3.4167 d=4.00 min @ (0.00, 0.00, -1.00) sse = 328285.9, tmin=4.3730 d=2.00 min @ (0.50, 0.50, 0.00) sse = 327871.7, tmin=5.3346 d=1.00 min @ (-0.25, 0.00, 0.00) sse = 327820.4, tmin=6.2908 d=0.50 min @ (0.12, 0.00, -0.12) sse = 327800.0, tmin=7.2501 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 7.25 min curvature mean = 0.002, std = 0.948 curvature mean = 0.009, std = 0.940 curvature mean = 0.000, std = 0.958 curvature mean = 0.004, std = 0.972 curvature mean = -0.000, std = 0.960 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.036, std = 0.405 curvature mean = 0.005, std = 0.070 curvature mean = 0.058, std = 0.247 curvature mean = 0.005, std = 0.083 curvature mean = 0.032, std = 0.383 curvature mean = 0.005, std = 0.089 curvature mean = 0.019, std = 0.496 curvature mean = 0.006, std = 0.092 curvature mean = 0.007, std = 0.614 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Wed Jan 1 11:50:00 CST 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 Wed Jan 1 11:50:02 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mrisp_paint -a 5 /soft/freesurfer/5.3.0_1/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_1/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Wed Jan 1 11:50:03 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 2889 labels changed using aseg relabeling using gibbs priors... 000: 2975 changed, 138081 examined... 001: 702 changed, 12755 examined... 002: 210 changed, 3924 examined... 003: 59 changed, 1180 examined... 004: 29 changed, 367 examined... 005: 23 changed, 172 examined... 006: 14 changed, 123 examined... 007: 6 changed, 91 examined... 008: 3 changed, 38 examined... 009: 2 changed, 17 examined... 010: 4 changed, 13 examined... 011: 0 changed, 18 examined... 249 labels changed using aseg 000: 196 total segments, 157 labels (1073 vertices) changed 001: 45 total segments, 6 labels (10 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 33 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1533 vertices marked for relabeling... 1533 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 36 seconds. #-------------------------------------------- #@# Make Pial Surf rh Wed Jan 1 11:50:39 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 19762 bright wm thresholded. 1559 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (93.0): 94.0 +- 7.7 [70.0 --> 110.0] GM (82.0) : 78.7 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.3 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 47.6 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 33.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100, GM=77 mean inside = 89.7, mean outside = 76.9 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/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.02-->6.92) (max @ vno 133049 --> 133050) face area 0.27 +- 0.16 (0.00-->7.95) mean absolute distance = 0.83 +- 1.09 4259 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 29 points - only 0.00% unknown deleting segment 2 with 87 points - only 0.00% unknown deleting segment 3 with 42 points - only 0.00% unknown deleting segment 8 with 151 points - only 0.00% unknown deleting segment 9 with 176 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 18 points - only 0.00% unknown deleting segment 12 with 812 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown deleting segment 16 with 6 points - only 0.00% unknown deleting segment 17 with 15 points - only 0.00% unknown deleting segment 18 with 19 points - only 0.00% unknown deleting segment 19 with 177 points - only 0.00% unknown deleting segment 20 with 222 points - only 0.00% unknown deleting segment 21 with 33 points - only 0.00% unknown deleting segment 22 with 142 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 23 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 24 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 25 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 26 with 4 points - only 0.00% unknown deleting segment 27 with 50 points - only 0.00% unknown mean border=85.1, 3703 (3699) missing vertices, mean dist 0.2 [0.9 (%36.8)->0.8 (%63.2))] %65 local maxima, %23 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 0.90 +- 0.33 (0.03-->10.54) (max @ vno 134388 --> 135956) face area 0.27 +- 0.18 (0.00-->6.17) mean absolute distance = 0.47 +- 0.75 4992 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5097934.0, rms=9.96 001: dt: 0.5000, sse=6067991.0, rms=7.942 (0.000%) 002: dt: 0.5000, sse=6270779.0, rms=6.736 (0.000%) 003: dt: 0.5000, sse=6540649.5, rms=6.013 (0.000%) 004: dt: 0.5000, sse=6716153.0, rms=5.578 (0.000%) 005: dt: 0.5000, sse=6858358.0, rms=5.290 (0.000%) 006: dt: 0.5000, sse=6914492.5, rms=5.098 (0.000%) 007: dt: 0.5000, sse=6991137.0, rms=4.947 (0.000%) 008: dt: 0.5000, sse=7015830.0, rms=4.827 (0.000%) 009: dt: 0.5000, sse=7002729.0, rms=4.729 (0.000%) 010: dt: 0.5000, sse=6987349.0, rms=4.629 (0.000%) 011: dt: 0.5000, sse=6984064.5, rms=4.540 (0.000%) 012: dt: 0.5000, sse=6952648.0, rms=4.454 (0.000%) 013: dt: 0.5000, sse=6965088.5, rms=4.388 (0.000%) 014: dt: 0.5000, sse=6933367.5, rms=4.307 (0.000%) 015: dt: 0.5000, sse=6935812.5, rms=4.227 (0.000%) 016: dt: 0.5000, sse=6902451.0, rms=4.156 (0.000%) 017: dt: 0.5000, sse=6894119.5, rms=4.086 (0.000%) 018: dt: 0.5000, sse=6877414.5, rms=4.017 (0.000%) 019: dt: 0.5000, sse=6875204.0, rms=3.962 (0.000%) 020: dt: 0.5000, sse=6847817.0, rms=3.893 (0.000%) rms = 3.84, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=6872352.0, rms=3.843 (0.000%) 022: dt: 0.2500, sse=4774258.5, rms=3.438 (0.000%) 023: dt: 0.2500, sse=4564727.5, rms=3.352 (0.000%) rms = 3.32, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=4468980.5, rms=3.323 (0.000%) rms = 3.30, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4414209.0, rms=3.300 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 4 with 191 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 88 points - only 0.00% unknown removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 16 with 76 points - only 0.00% unknown deleting segment 17 with 37 points - only 0.00% unknown deleting segment 18 with 222 points - only 0.00% unknown deleting segment 19 with 25 points - only 0.00% unknown deleting segment 20 with 16 points - only 0.00% unknown deleting segment 21 with 101 points - only 0.00% unknown deleting segment 22 with 202 points - only 0.00% unknown deleting segment 23 with 56 points - only 0.00% unknown deleting segment 25 with 218 points - only 0.00% unknown deleting segment 26 with 268 points - only 0.00% unknown deleting segment 27 with 12 points - only 0.00% unknown deleting segment 29 with 123 points - only 0.00% unknown deleting segment 30 with 24 points - only 0.00% unknown deleting segment 31 with 171 points - only 0.00% unknown deleting segment 32 with 15 points - only 0.00% unknown deleting segment 33 with 12 points - only 0.00% unknown deleting segment 34 with 39 points - only 0.00% unknown deleting segment 35 with 6 points - only 0.00% unknown deleting segment 36 with 10 points - only 0.00% unknown deleting segment 39 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 40 with 4 points - only 0.00% unknown deleting segment 41 with 50 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 43 with 3 points - only 33.33% unknown mean border=87.5, 3087 (2585) missing vertices, mean dist -0.3 [0.5 (%70.0)->0.4 (%30.0))] %77 local maxima, %12 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 0.89 +- 0.32 (0.07-->11.24) (max @ vno 134388 --> 135956) face area 0.34 +- 0.22 (0.00-->7.54) mean absolute distance = 0.33 +- 0.52 3695 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4845188.0, rms=4.91 026: dt: 0.5000, sse=5216437.0, rms=3.982 (0.000%) 027: dt: 0.5000, sse=5818710.5, rms=3.791 (0.000%) 028: dt: 0.5000, sse=5907548.5, rms=3.710 (0.000%) rms = 3.70, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=6446992.0, rms=3.698 (0.000%) 030: dt: 0.2500, sse=5158631.0, rms=3.361 (0.000%) 031: dt: 0.2500, sse=4993336.5, rms=3.289 (0.000%) rms = 3.26, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4920940.5, rms=3.255 (0.000%) rms = 3.23, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4867983.5, rms=3.233 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 194 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 88 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 8 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 14 with 76 points - only 0.00% unknown deleting segment 15 with 34 points - only 0.00% unknown deleting segment 17 with 214 points - only 0.00% unknown deleting segment 18 with 28 points - only 0.00% unknown deleting segment 19 with 13 points - only 0.00% unknown deleting segment 20 with 92 points - only 0.00% unknown deleting segment 21 with 205 points - only 0.00% unknown deleting segment 22 with 55 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 23 with 4 points - only 0.00% unknown deleting segment 24 with 226 points - only 0.00% unknown deleting segment 25 with 271 points - only 0.00% unknown deleting segment 27 with 12 points - only 0.00% unknown deleting segment 28 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 29 with 3 points - only 0.00% unknown deleting segment 30 with 126 points - only 0.00% unknown deleting segment 31 with 14 points - only 0.00% unknown deleting segment 32 with 160 points - only 0.00% unknown deleting segment 33 with 25 points - only 0.00% unknown deleting segment 34 with 19 points - only 0.00% unknown deleting segment 35 with 42 points - only 0.00% unknown deleting segment 36 with 17 points - only 0.00% unknown deleting segment 37 with 6 points - only 0.00% unknown deleting segment 39 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 41 with 3 points - only 0.00% unknown deleting segment 42 with 5 points - only 0.00% unknown deleting segment 43 with 44 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 45 with 3 points - only 33.33% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 48 with 3 points - only 0.00% unknown mean border=89.0, 2893 (2308) missing vertices, mean dist -0.1 [0.4 (%65.5)->0.3 (%34.5))] %81 local maxima, % 7 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 0.89 +- 0.32 (0.01-->11.27) (max @ vno 134388 --> 135956) face area 0.33 +- 0.22 (0.00-->8.01) mean absolute distance = 0.29 +- 0.44 3109 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4950055.0, rms=3.83 034: dt: 0.5000, sse=5327939.0, rms=3.473 (0.000%) rms = 3.45, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=5872228.0, rms=3.449 (0.000%) 036: dt: 0.2500, sse=5201269.5, rms=3.202 (0.000%) 037: dt: 0.2500, sse=5111088.5, rms=3.145 (0.000%) rms = 3.12, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5050061.5, rms=3.125 (0.000%) rms = 3.10, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=5007366.0, rms=3.103 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 195 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 32 points - only 0.00% unknown deleting segment 3 with 88 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 9 with 72 points - only 0.00% unknown deleting segment 10 with 34 points - only 0.00% unknown deleting segment 11 with 219 points - only 0.00% unknown deleting segment 12 with 13 points - only 0.00% unknown deleting segment 13 with 36 points - only 0.00% unknown deleting segment 14 with 19 points - only 0.00% unknown deleting segment 15 with 427 points - only 0.00% unknown deleting segment 16 with 93 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown deleting segment 18 with 55 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 20 with 225 points - only 0.00% unknown deleting segment 21 with 261 points - only 0.00% unknown deleting segment 22 with 12 points - only 0.00% unknown deleting segment 23 with 8 points - only 0.00% unknown deleting segment 24 with 26 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 25 with 4 points - only 0.00% unknown deleting segment 26 with 127 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 27 with 1 points - only 0.00% unknown deleting segment 28 with 159 points - only 0.00% unknown deleting segment 29 with 48 points - only 0.00% unknown deleting segment 30 with 19 points - only 0.00% unknown deleting segment 31 with 6 points - only 0.00% unknown deleting segment 32 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 33 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 34 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 35 with 4 points - only 0.00% unknown deleting segment 36 with 41 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 38 with 3 points - only 33.33% unknown removing 4 vertex label from ripped group mean border=89.5, 2931 (2228) missing vertices, mean dist -0.0 [0.3 (%54.9)->0.3 (%45.1))] %82 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=5029082.5, rms=3.28 040: dt: 0.5000, sse=6466313.0, rms=3.118 (0.000%) rms = 3.27, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=5953642.0, rms=3.030 (0.000%) rms = 3.03, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5735882.0, rms=3.027 (0.000%) rms = 2.99, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=5726806.0, rms=2.993 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 33.33% unknown removing 4 vertex label from ripped group smoothing surface for 5 iterations... mean border=63.3, 2436 (2436) missing vertices, mean dist 1.6 [3.4 (%1.6)->3.6 (%98.4))] %22 local maxima, %18 large gradients and %49 min vals, 3485 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=20264980.0, rms=26.75 001: dt: 0.5000, sse=16775350.0, rms=23.868 (0.000%) 002: dt: 0.5000, sse=14069075.0, rms=21.322 (0.000%) 003: dt: 0.5000, sse=11961010.0, rms=19.139 (0.000%) 004: dt: 0.5000, sse=10415980.0, rms=17.343 (0.000%) 005: dt: 0.5000, sse=9318216.0, rms=15.889 (0.000%) 006: dt: 0.5000, sse=8535862.0, rms=14.676 (0.000%) 007: dt: 0.5000, sse=8034975.5, rms=13.623 (0.000%) 008: dt: 0.5000, sse=7671830.5, rms=12.643 (0.000%) 009: dt: 0.5000, sse=7420069.5, rms=11.697 (0.000%) 010: dt: 0.5000, sse=7298432.5, rms=10.796 (0.000%) 011: dt: 0.5000, sse=7278302.0, rms=9.918 (0.000%) 012: dt: 0.5000, sse=7232910.0, rms=9.077 (0.000%) 013: dt: 0.5000, sse=7272533.0, rms=8.357 (0.000%) 014: dt: 0.5000, sse=7348256.5, rms=7.758 (0.000%) 015: dt: 0.5000, sse=7393509.0, rms=7.273 (0.000%) 016: dt: 0.5000, sse=7466983.5, rms=6.882 (0.000%) 017: dt: 0.5000, sse=7565868.0, rms=6.605 (0.000%) 018: dt: 0.5000, sse=7555332.0, rms=6.382 (0.000%) 019: dt: 0.5000, sse=7570302.0, rms=6.229 (0.000%) 020: dt: 0.5000, sse=7570749.5, rms=6.096 (0.000%) 021: dt: 0.5000, sse=7561897.5, rms=6.002 (0.000%) 022: dt: 0.5000, sse=7547231.0, rms=5.917 (0.000%) 023: dt: 0.5000, sse=7526595.0, rms=5.859 (0.000%) 024: dt: 0.5000, sse=7542453.0, rms=5.806 (0.000%) rms = 5.78, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=7496381.5, rms=5.776 (0.000%) 026: dt: 0.2500, sse=5874984.5, rms=5.241 (0.000%) 027: dt: 0.2500, sse=5763021.0, rms=5.117 (0.000%) rms = 5.13, time step reduction 2 of 3 to 0.125... 028: dt: 0.1250, sse=5590788.0, rms=5.019 (0.000%) 029: dt: 0.1250, sse=5301598.5, rms=4.885 (0.000%) rms = 4.85, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5223054.0, rms=4.851 (0.000%) positioning took 2.5 minutes mean border=61.7, 4619 (1409) missing vertices, mean dist 0.2 [0.3 (%37.6)->0.8 (%62.4))] %33 local maxima, %14 large gradients and %41 min vals, 1951 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=5869917.5, rms=6.34 031: dt: 0.5000, sse=6301270.5, rms=6.130 (0.000%) 032: dt: 0.5000, sse=7387240.0, rms=5.850 (0.000%) rms = 5.90, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=6471820.0, rms=5.309 (0.000%) 034: dt: 0.2500, sse=6173481.5, rms=5.176 (0.000%) rms = 5.22, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=6026199.5, rms=5.076 (0.000%) 036: dt: 0.1250, sse=5804373.5, rms=4.946 (0.000%) 037: dt: 0.1250, sse=5748581.0, rms=4.891 (0.000%) rms = 4.86, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5736423.0, rms=4.861 (0.000%) positioning took 0.8 minutes mean border=61.3, 5711 (1285) missing vertices, mean dist 0.1 [0.3 (%42.0)->0.6 (%58.0))] %36 local maxima, %10 large gradients and %41 min vals, 2001 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=5799581.0, rms=5.04 rms = 5.48, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=5698896.0, rms=4.881 (0.000%) 040: dt: 0.2500, sse=5892315.0, rms=4.829 (0.000%) rms = 4.85, time step reduction 2 of 3 to 0.125... rms = 4.79, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=5830875.0, rms=4.792 (0.000%) positioning took 0.4 minutes mean border=61.0, 9768 (1256) missing vertices, mean dist 0.1 [0.2 (%45.0)->0.5 (%55.0))] %35 local maxima, %10 large gradients and %39 min vals, 1909 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/MPS1036-1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5834756.5, rms=4.80 rms = 5.22, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=5790135.0, rms=4.679 (0.000%) 043: dt: 0.2500, sse=6175970.5, rms=4.614 (0.000%) rms = 4.63, time step reduction 2 of 3 to 0.125... rms = 4.57, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=6106726.0, rms=4.575 (0.000%) positioning took 0.4 minutes writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.area.pial vertex spacing 1.01 +- 0.51 (0.04-->15.16) (max @ vno 134480 --> 136237) face area 0.39 +- 0.37 (0.00-->15.37) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 138081 vertices processed 25000 of 138081 vertices processed 50000 of 138081 vertices processed 75000 of 138081 vertices processed 100000 of 138081 vertices processed 125000 of 138081 vertices processed 0 of 138081 vertices processed 25000 of 138081 vertices processed 50000 of 138081 vertices processed 75000 of 138081 vertices processed 100000 of 138081 vertices processed 125000 of 138081 vertices processed thickness calculation complete, 2766:4012 truncations. 20518 vertices at 0 distance 61912 vertices at 1 distance 74698 vertices at 2 distance 50800 vertices at 3 distance 24426 vertices at 4 distance 10416 vertices at 5 distance 4344 vertices at 6 distance 1958 vertices at 7 distance 853 vertices at 8 distance 415 vertices at 9 distance 233 vertices at 10 distance 141 vertices at 11 distance 89 vertices at 12 distance 90 vertices at 13 distance 89 vertices at 14 distance 58 vertices at 15 distance 52 vertices at 16 distance 60 vertices at 17 distance 42 vertices at 18 distance 44 vertices at 19 distance 44 vertices at 20 distance writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.thickness positioning took 9.5 minutes #-------------------------------------------- #@# Surf Volume rh Wed Jan 1 12:00:07 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Wed Jan 1 12:00:08 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts pctsurfcon --s MPS1036-1 --rh-only Log file is /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts/pctsurfcon.log Wed Jan 1 12:00:08 CST 2014 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis cd /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts /soft/freesurfer/5.3.0_1/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node1108 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_1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.63019/rh.wm.mgh --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 72806 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.63019/rh.wm.mgh Dim: 138081 1 1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.63019/rh.gm.mgh --projfrac 0.3 --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white Done reading source surface Reading thickness /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 84672 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.63019/rh.gm.mgh Dim: 138081 1 1 mri_concat /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.63019/rh.wm.mgh /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.63019/rh.gm.mgh --paired-diff-norm --mul 100 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh mri_segstats --in /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh --annot MPS1036-1 rh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh --annot MPS1036-1 rh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/stats/rh.w-g.pct.stats --snr sysname Linux hostname node1108 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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh Vertex Area is 0.656672 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1462 988.353 2 2002 caudalanteriorcingulate 1564 972.689 3 2003 caudalmiddlefrontal 3830 2525.041 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 1078 906.522 6 2006 entorhinal 640 402.578 7 2007 fusiform 4265 3094.153 8 2008 inferiorparietal 8491 5451.041 9 2009 inferiortemporal 3695 2664.847 10 2010 isthmuscingulate 887 499.099 11 2011 lateraloccipital 5736 4053.183 12 2012 lateralorbitofrontal 3223 2177.140 13 2013 lingual 1842 1233.768 14 2014 medialorbitofrontal 2325 1582.343 15 2015 middletemporal 4637 3126.240 16 2016 parahippocampal 2438 1468.391 17 2017 paracentral 2528 1628.686 18 2018 parsopercularis 1905 1305.243 19 2019 parsorbitalis 1147 800.497 20 2020 parstriangularis 1966 1370.787 21 2021 pericalcarine 754 502.912 22 2022 postcentral 5997 3761.652 23 2023 posteriorcingulate 1825 1278.755 24 2024 precentral 8494 5422.364 25 2025 precuneus 5348 4097.288 26 2026 rostralanteriorcingulate 953 653.186 27 2027 rostralmiddlefrontal 10973 7142.264 28 2028 superiorfrontal 10720 6922.190 29 2029 superiorparietal 7479 4703.218 30 2030 superiortemporal 5679 3692.323 31 2031 supramarginal 5771 3604.395 32 2032 frontalpole 575 327.161 33 2033 temporalpole 683 435.006 34 2034 transversetemporal 394 238.396 35 2035 insula 3269 2130.756 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Wed Jan 1 12:00:16 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1462 988 3078 3.386 0.629 0.164 0.119 44 5.3 bankssts 1564 973 2670 2.752 1.132 0.154 0.074 38 4.7 caudalanteriorcingulate 3830 2525 9831 3.428 0.658 0.173 0.302 429 20.2 caudalmiddlefrontal 1078 907 2598 2.537 0.733 0.243 0.139 47 4.9 cuneus 640 403 1712 2.910 0.840 0.268 0.540 181 9.3 entorhinal 4265 3094 8513 2.452 0.913 0.233 0.248 324 35.8 fusiform 8491 5451 19046 3.121 0.627 0.181 0.171 419 54.7 inferiorparietal 3695 2665 10920 3.425 0.771 0.178 0.127 144 17.7 inferiortemporal 887 499 942 1.827 0.829 0.148 0.194 46 6.0 isthmuscingulate 5736 4053 12862 2.762 0.693 0.193 0.109 191 27.5 lateraloccipital 3223 2177 7625 3.015 1.047 0.160 0.077 68 10.8 lateralorbitofrontal 1842 1234 1610 1.396 0.579 0.245 0.523 554 41.9 lingual 2325 1582 5329 2.797 1.166 0.168 0.134 125 12.8 medialorbitofrontal 4637 3126 13164 3.542 0.616 0.164 0.084 105 16.9 middletemporal 2438 1468 3553 2.045 0.701 0.221 0.289 294 27.2 parahippocampal 2528 1629 5347 2.940 0.766 0.157 0.105 57 12.9 paracentral 1905 1305 4671 2.976 0.586 0.144 0.126 166 5.5 parsopercularis 1147 800 3089 2.916 0.776 0.179 0.100 39 4.7 parsorbitalis 1966 1371 4454 2.738 0.585 0.157 0.083 40 5.9 parstriangularis 754 503 1502 2.318 0.974 0.238 0.294 68 8.8 pericalcarine 5997 3762 10303 2.465 0.812 0.146 0.093 257 24.3 postcentral 1825 1279 3214 2.343 0.692 0.182 0.077 174 6.8 posteriorcingulate 8494 5422 15360 2.645 0.900 0.172 0.152 541 50.9 precentral 5348 4097 11393 2.626 0.900 0.210 0.141 285 29.9 precuneus 953 653 2465 3.307 1.072 0.178 0.267 102 5.8 rostralanteriorcingulate 10973 7142 23063 2.913 0.752 0.184 0.156 535 79.7 rostralmiddlefrontal 10720 6922 26344 3.395 0.781 0.162 0.115 811 49.9 superiorfrontal 7479 4703 14104 2.706 0.631 0.165 0.160 337 36.5 superiorparietal 5679 3692 13786 3.159 0.622 0.146 0.069 114 17.8 superiortemporal 5771 3604 11182 2.917 0.645 0.169 0.427 349 38.3 supramarginal 575 327 1307 2.811 1.290 0.226 0.207 33 4.9 frontalpole 683 435 2209 3.412 0.848 0.222 0.188 25 5.7 temporalpole 394 238 690 2.678 0.611 0.189 0.135 11 2.4 transversetemporal 3269 2131 7162 3.360 0.822 0.151 0.240 260 16.8 insula #----------------------------------------- #@# Cortical Parc 2 rh Wed Jan 1 12:00:26 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 557 labels changed using aseg relabeling using gibbs priors... 000: 9934 changed, 138081 examined... 001: 2382 changed, 37562 examined... 002: 743 changed, 12134 examined... 003: 316 changed, 4097 examined... 004: 150 changed, 1800 examined... 005: 81 changed, 823 examined... 006: 39 changed, 442 examined... 007: 25 changed, 219 examined... 008: 13 changed, 133 examined... 009: 8 changed, 69 examined... 010: 4 changed, 45 examined... 011: 3 changed, 25 examined... 012: 1 changed, 19 examined... 013: 0 changed, 9 examined... 297 labels changed using aseg 000: 334 total segments, 251 labels (3365 vertices) changed 001: 102 total segments, 20 labels (109 vertices) changed 002: 83 total segments, 1 labels (1 vertices) changed 003: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 116 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1068 vertices marked for relabeling... 1068 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 41 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Wed Jan 1 12:01:08 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1482 962 3237 3.161 1.030 0.187 0.130 50 7.6 G_and_S_frontomargin 675 560 1742 2.711 0.507 0.222 0.126 26 3.7 G_and_S_occipital_inf 1233 803 2186 2.326 0.739 0.174 0.095 25 5.0 G_and_S_paracentral 953 653 2579 3.188 0.791 0.151 0.061 18 2.4 G_and_S_subcentral 1487 835 2348 2.430 0.808 0.224 0.211 137 14.8 G_and_S_transv_frontopol 2708 1827 6108 3.261 0.756 0.150 0.144 160 12.9 G_and_S_cingul-Ant 1697 1138 3324 2.914 0.785 0.156 0.127 480 11.5 G_and_S_cingul-Mid-Ant 1211 878 2374 2.704 0.656 0.156 0.057 34 2.9 G_and_S_cingul-Mid-Post 456 298 782 2.258 0.646 0.150 0.052 9 0.8 G_cingul-Post-dorsal 149 75 93 1.479 0.444 0.089 0.082 2 0.5 G_cingul-Post-ventral 867 650 2055 2.616 0.573 0.209 0.100 25 3.8 G_cuneus 1146 820 3745 3.166 0.600 0.182 0.210 179 4.9 G_front_inf-Opercular 311 236 1054 3.023 0.614 0.217 0.137 15 1.5 G_front_inf-Orbital 1227 809 3003 2.794 0.625 0.172 0.116 36 5.3 G_front_inf-Triangul 5776 3675 15414 3.167 0.765 0.202 0.217 427 58.5 G_front_middle 7788 4884 21749 3.536 0.837 0.180 0.144 320 43.9 G_front_sup 636 388 1452 3.454 0.808 0.181 0.157 50 4.2 G_Ins_lg_and_S_cent_ins 647 401 1982 3.903 0.912 0.135 0.202 88 5.5 G_insular_short 2363 1533 6415 3.212 0.565 0.205 0.175 137 13.4 G_occipital_middle 1464 1079 4294 2.912 0.831 0.220 0.149 91 9.3 G_occipital_sup 1585 1045 3292 2.390 0.778 0.246 0.222 132 15.4 G_oc-temp_lat-fusifor 1030 573 1167 1.600 0.697 0.312 0.708 382 37.8 G_oc-temp_med-Lingual 2227 1352 4173 2.534 0.779 0.212 0.344 336 19.8 G_oc-temp_med-Parahip 2520 1699 7635 3.252 0.986 0.194 0.112 87 12.7 G_orbital 3108 1806 7280 3.130 0.758 0.190 0.213 184 26.0 G_pariet_inf-Angular 2805 1687 6609 3.065 0.701 0.183 0.210 219 25.2 G_pariet_inf-Supramar 2408 1381 4483 2.712 0.559 0.163 0.166 111 15.4 G_parietal_sup 2446 1400 4395 2.456 0.754 0.155 0.135 75 15.1 G_postcentral 3157 1970 6964 2.698 1.081 0.174 0.139 169 16.1 G_precentral 2721 1785 6095 2.782 0.750 0.208 0.167 175 18.2 G_precuneus 640 448 1979 3.066 1.112 0.207 0.131 26 3.2 G_rectus 258 137 238 1.557 1.116 0.154 0.167 16 1.5 G_subcallosal 302 194 624 2.614 0.553 0.192 0.137 9 1.9 G_temp_sup-G_T_transv 2087 1234 6466 3.348 0.584 0.164 0.086 65 8.3 G_temp_sup-Lateral 784 527 1810 2.795 0.753 0.146 0.106 20 3.3 G_temp_sup-Plan_polar 792 571 1804 2.970 0.487 0.144 0.062 14 1.9 G_temp_sup-Plan_tempo 2313 1707 8007 3.503 0.736 0.202 0.165 112 13.0 G_temporal_inf 2921 1890 9460 3.630 0.641 0.181 0.100 87 12.8 G_temporal_middle 227 170 428 2.387 0.651 0.117 0.032 2 0.3 Lat_Fis-ant-Horizont 208 135 310 2.546 0.537 0.127 0.040 2 0.3 Lat_Fis-ant-Vertical 1284 862 1968 2.987 0.556 0.149 0.078 19 3.9 Lat_Fis-post 2728 2053 5637 2.320 0.699 0.217 0.117 105 14.4 Pole_occipital 1664 1142 5806 3.662 0.841 0.226 0.303 107 14.1 Pole_temporal 1435 926 1413 1.325 0.903 0.203 0.340 235 13.8 S_calcarine 3126 2057 3385 1.950 0.616 0.177 0.179 398 25.8 S_central 1341 971 2550 2.840 0.493 0.143 0.049 19 2.7 S_cingul-Marginalis 643 421 1174 3.029 0.664 0.108 0.041 5 1.1 S_circular_insula_ant 1237 803 2142 3.209 0.703 0.155 0.387 98 4.6 S_circular_insula_inf 1377 930 2289 2.788 0.468 0.106 0.040 11 2.5 S_circular_insula_sup 681 479 1302 2.912 0.407 0.131 0.047 7 1.5 S_collat_transv_ant 548 403 624 1.700 0.483 0.143 0.057 6 1.4 S_collat_transv_post 2120 1470 3798 2.899 0.581 0.161 0.091 55 7.0 S_front_inf 2471 1714 4538 2.975 0.634 0.143 0.051 29 5.1 S_front_middle 2820 1853 5504 3.063 0.583 0.141 0.327 347 10.2 S_front_sup 774 509 1224 2.830 0.418 0.132 0.049 8 1.8 S_interm_prim-Jensen 3165 2085 5357 2.795 0.517 0.153 0.176 127 12.6 S_intrapariet_and_P_trans 573 399 1099 3.129 0.612 0.157 0.067 10 1.5 S_oc_middle_and_Lunatus 1494 921 2193 2.636 0.640 0.133 0.075 31 4.4 S_oc_sup_and_transversal 611 429 1583 3.213 0.454 0.161 0.090 14 2.5 S_occipital_ant 431 353 1090 3.226 0.783 0.146 0.047 4 0.9 S_oc-temp_lat 2314 1759 2703 1.730 0.641 0.252 0.253 297 26.1 S_oc-temp_med_and_Lingual 419 291 758 2.741 0.782 0.126 0.047 4 0.7 S_orbital_lateral 596 423 1164 2.294 1.315 0.103 0.027 3 0.7 S_orbital_med-olfact 1213 819 2090 2.578 0.815 0.156 0.064 22 3.3 S_orbital-H_Shaped 1255 1306 2886 2.617 0.981 0.264 0.153 64 7.6 S_parieto_occipital 1696 1050 2087 2.415 1.145 0.178 0.157 187 11.2 S_pericallosal 2748 1775 4102 2.652 0.530 0.149 0.679 125 11.2 S_postcentral 2038 1331 3956 3.078 0.629 0.151 0.097 58 7.8 S_precentral-inf-part 1508 969 2528 3.143 0.664 0.141 0.102 47 4.7 S_precentral-sup-part 271 206 632 2.874 0.870 0.160 0.051 4 0.6 S_suborbital 1162 774 2480 2.852 0.533 0.165 0.087 27 4.3 S_subparietal 1096 768 2104 3.306 0.569 0.140 0.078 28 4.2 S_temporal_inf 6635 4522 13346 3.231 0.596 0.154 0.104 167 26.7 S_temporal_sup 284 177 436 2.625 0.637 0.174 0.129 9 1.6 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Wed Jan 1 12:01:20 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 895 labels changed using aseg relabeling using gibbs priors... 000: 2707 changed, 138081 examined... 001: 644 changed, 11837 examined... 002: 183 changed, 3523 examined... 003: 64 changed, 1068 examined... 004: 31 changed, 368 examined... 005: 14 changed, 182 examined... 006: 7 changed, 78 examined... 007: 4 changed, 42 examined... 008: 9 changed, 28 examined... 009: 4 changed, 32 examined... 010: 1 changed, 18 examined... 011: 0 changed, 7 examined... 192 labels changed using aseg 000: 120 total segments, 86 labels (682 vertices) changed 001: 36 total segments, 2 labels (7 vertices) changed 002: 34 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1051 vertices marked for relabeling... 1051 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 35 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Wed Jan 1 12:01:55 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1567 976 2770 2.804 1.097 0.154 0.074 39 4.7 caudalanteriorcingulate 4054 2662 10244 3.414 0.657 0.174 0.293 436 21.0 caudalmiddlefrontal 1494 1178 3372 2.657 0.769 0.225 0.127 68 6.5 cuneus 653 424 1782 2.880 0.852 0.272 0.545 183 9.8 entorhinal 3819 2752 7155 2.347 0.844 0.224 0.189 272 29.9 fusiform 7877 5031 17601 3.120 0.640 0.182 0.176 392 51.5 inferiorparietal 4141 2996 12445 3.437 0.791 0.190 0.192 188 23.0 inferiortemporal 1016 559 1070 1.876 0.817 0.172 0.237 75 9.4 isthmuscingulate 6006 4276 13486 2.758 0.701 0.192 0.107 195 28.3 lateraloccipital 3858 2594 9449 3.073 1.123 0.167 0.087 85 14.0 lateralorbitofrontal 1873 1235 1633 1.410 0.582 0.255 0.540 581 44.6 lingual 1681 1145 4115 2.756 1.292 0.174 0.114 64 7.9 medialorbitofrontal 5629 3790 15330 3.511 0.622 0.163 0.090 135 20.6 middletemporal 2307 1418 3445 2.043 0.712 0.210 0.259 246 21.5 parahippocampal 2683 1728 5740 2.993 0.781 0.154 0.101 58 13.1 paracentral 1935 1325 4690 2.964 0.583 0.142 0.125 167 5.6 parsopercularis 1270 893 3437 3.006 0.734 0.178 0.105 43 5.8 parsorbitalis 2275 1551 4951 2.678 0.603 0.167 0.093 56 8.5 parstriangularis 767 511 1512 2.291 0.976 0.242 0.302 71 9.3 pericalcarine 6597 4124 11371 2.491 0.807 0.150 0.335 329 28.8 postcentral 1892 1332 3306 2.350 0.685 0.180 0.075 175 6.8 posteriorcingulate 8018 5120 14526 2.594 0.884 0.175 0.156 532 49.8 precentral 5419 4163 11793 2.631 0.884 0.208 0.138 272 29.7 precuneus 1146 771 2827 3.215 1.109 0.185 0.292 142 10.4 rostralanteriorcingulate 7157 4721 15655 2.951 0.696 0.180 0.152 324 50.0 rostralmiddlefrontal 14459 9287 33086 3.236 0.830 0.168 0.129 1039 78.3 superiorfrontal 6465 4027 12032 2.694 0.627 0.166 0.174 317 33.3 superiorparietal 7410 4835 17959 3.196 0.655 0.152 0.081 162 26.1 superiortemporal 5582 3467 10776 2.930 0.625 0.169 0.156 302 36.4 supramarginal 407 244 662 2.639 0.596 0.208 0.172 17 3.1 transversetemporal 3116 2027 6879 3.366 0.796 0.145 0.243 248 15.3 insula #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 1 12:02:06 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon MPS1036-1 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 = 151 writing volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Wed Jan 1 12:08:52 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 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_1/ASegStatsLUT.txt --subject MPS1036-1 $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_1/ASegStatsLUT.txt --subject MPS1036-1 sysname Linux hostname node1108 machine x86_64 user kovacv UseRobust 0 atlas_icv (eTIV) = 2135681 mm^3 (det: 0.912171 ) Computing euler number orig.nofix lheno = -346, rheno = -296 orig.nofix lhholes = 174, rhholes = 149 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 257163.590 262056.000 diff=-4892.4 pctdiff=-1.902 rhCtxGM: 251277.810 253818.000 diff=-2540.2 pctdiff=-1.011 lhCtxWM: 267524.526 258502.500 diff= 9022.0 pctdiff= 3.372 rhCtxWM: 223342.936 235121.500 diff=-11778.6 pctdiff=-5.274 SubCortGMVol 71398.000 SupraTentVol 1229032.863 (1213139.000) diff=15893.863 pctdiff=1.293 SupraTentVolNotVent 1096901.863 (1081008.000) diff=15893.863 pctdiff=1.449 BrainSegVol 1418271.000 (1411030.000) diff=7241.000 pctdiff=0.511 BrainSegVolNotVent 1276673.000 (1266024.863) diff=10648.137 pctdiff=0.834 BrainSegVolNotVent 1276673.000 CerebellumVol 195206.000 VentChorVol 132131.000 3rd4th5thCSF 9467.000 CSFVol 2621.000, OptChiasmVol 64.000 MaskVol 2138819.000 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 67010 67009.617 4 5 Left-Inf-Lat-Vent 4716 4716.496 5 7 Left-Cerebellum-White-Matter 19922 19921.951 6 8 Left-Cerebellum-Cortex 72840 72839.742 7 10 Left-Thalamus-Proper 8228 8228.178 8 11 Left-Caudate 4580 4579.769 9 12 Left-Putamen 7302 7302.200 10 13 Left-Pallidum 1585 1584.526 11 14 3rd-Ventricle 4727 4726.834 12 15 4th-Ventricle 2364 2363.641 13 16 Brain-Stem 26137 26137.186 14 17 Left-Hippocampus 2875 2874.504 15 18 Left-Amygdala 1519 1518.600 16 24 CSF 2382 2382.016 17 26 Left-Accumbens-area 419 419.445 18 28 Left-VentralDC 3811 3811.076 19 30 Left-vessel 44 44.070 20 31 Left-choroid-plexus 1937 1936.549 23 43 Right-Lateral-Ventricle 52787 52787.492 24 44 Right-Inf-Lat-Vent 5673 5673.220 25 46 Right-Cerebellum-White-Matter 15961 15961.313 26 47 Right-Cerebellum-Cortex 88079 88078.992 27 49 Right-Thalamus-Proper 10287 10286.824 28 50 Right-Caudate 9351 9351.240 29 51 Right-Putamen 6480 6480.240 30 52 Right-Pallidum 2139 2138.611 31 53 Right-Hippocampus 3228 3228.436 32 54 Right-Amygdala 1528 1527.966 33 58 Right-Accumbens-area 605 605.002 34 60 Right-VentralDC 4858 4858.277 35 62 Right-vessel 74 74.138 36 63 Right-choroid-plexus 1887 1887.219 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 54791 54790.742 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 457 456.611 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 61 60.649 45 251 CC_Posterior 820 819.551 46 252 CC_Mid_Posterior 291 291.015 47 253 CC_Central 216 216.173 48 254 CC_Mid_Anterior 205 205.433 49 255 CC_Anterior 210 209.615 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Wed Jan 1 12:10:51 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --volmask SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 outvol /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/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/MPS1036-1/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 = 512993 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc+aseg.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --volmask --a2009s SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 outvol /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/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/MPS1036-1/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 = 512993 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Wed Jan 1 12:12:50 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 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/MPS1036-1/mri/aparc+aseg.mgz Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/mri/ribbon.mgz Loading filled from /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 12618 vertices from left hemi Ripped 15508 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/MPS1036-1/mri/aseg.mgz Loading Ctx Seg File /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 1006752 Used brute-force search on 930 voxels Fixing Parahip LH WM Found 13 clusters 0 k 2.000000 1 k 1.000000 2 k 2.000000 3 k 2.000000 4 k 1025.000000 5 k 1.000000 6 k 2.000000 7 k 1.000000 8 k 1.000000 9 k 1.000000 10 k 1.000000 11 k 2.000000 12 k 1.000000 Fixing Parahip RH WM Found 31 clusters 0 k 2.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 8 k 2.000000 9 k 1.000000 10 k 1.000000 11 k 2.000000 12 k 16.000000 13 k 1.000000 14 k 2.000000 15 k 9.000000 16 k 1.000000 17 k 2244.000000 18 k 1.000000 19 k 2.000000 20 k 1.000000 21 k 2.000000 22 k 3.000000 23 k 1.000000 24 k 1.000000 25 k 4.000000 26 k 1.000000 27 k 2.000000 28 k 1.000000 29 k 1.000000 30 k 1.000000 Writing output aseg to mri/wmparc.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1 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 MPS1036-1 --surf-wm-vol --ctab /soft/freesurfer/5.3.0_1/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 MPS1036-1 --surf-wm-vol --ctab /soft/freesurfer/5.3.0_1/WMParcStatsLUT.txt --etiv sysname Linux hostname node1108 machine x86_64 user kovacv UseRobust 0 atlas_icv (eTIV) = 2135681 mm^3 (det: 0.912171 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 257163.590 262056.000 diff=-4892.4 pctdiff=-1.902 rhCtxGM: 251277.810 253818.000 diff=-2540.2 pctdiff=-1.011 lhCtxWM: 267524.526 258502.500 diff= 9022.0 pctdiff= 3.372 rhCtxWM: 223342.936 235121.500 diff=-11778.6 pctdiff=-5.274 SubCortGMVol 71398.000 SupraTentVol 1229032.863 (1213139.000) diff=15893.863 pctdiff=1.293 SupraTentVolNotVent 1096901.863 (1081008.000) diff=15893.863 pctdiff=1.449 BrainSegVol 1418271.000 (1411030.000) diff=7241.000 pctdiff=0.511 BrainSegVolNotVent 1276673.000 (1266024.863) diff=10648.137 pctdiff=0.834 BrainSegVolNotVent 1276673.000 CerebellumVol 195206.000 VentChorVol 132131.000 3rd4th5thCSF 9467.000 CSFVol 2621.000, OptChiasmVol 64.000 MaskVol 2138819.000 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 3211 3210.777 2 3002 wm-lh-caudalanteriorcingulate 2924 2923.818 3 3003 wm-lh-caudalmiddlefrontal 9226 9225.692 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2644 2643.668 6 3006 wm-lh-entorhinal 653 652.741 7 3007 wm-lh-fusiform 4536 4536.052 8 3008 wm-lh-inferiorparietal 11893 11893.172 9 3009 wm-lh-inferiortemporal 6999 6999.079 10 3010 wm-lh-isthmuscingulate 6107 6106.753 11 3011 wm-lh-lateraloccipital 10006 10006.024 12 3012 wm-lh-lateralorbitofrontal 6682 6682.073 13 3013 wm-lh-lingual 4251 4251.469 14 3014 wm-lh-medialorbitofrontal 4078 4078.293 15 3015 wm-lh-middletemporal 7559 7559.004 16 3016 wm-lh-parahippocampal 1146 1145.833 17 3017 wm-lh-paracentral 4080 4079.789 18 3018 wm-lh-parsopercularis 3558 3557.871 19 3019 wm-lh-parsorbitalis 969 969.439 20 3020 wm-lh-parstriangularis 3266 3266.222 21 3021 wm-lh-pericalcarine 3011 3010.733 22 3022 wm-lh-postcentral 8732 8731.549 23 3023 wm-lh-posteriorcingulate 5711 5711.021 24 3024 wm-lh-precentral 17298 17298.338 25 3025 wm-lh-precuneus 8363 8362.749 26 3026 wm-lh-rostralanteriorcingulate 2541 2540.644 27 3027 wm-lh-rostralmiddlefrontal 18176 18175.914 28 3028 wm-lh-superiorfrontal 22014 22013.500 29 3029 wm-lh-superiorparietal 11873 11872.783 30 3030 wm-lh-superiortemporal 6600 6599.789 31 3031 wm-lh-supramarginal 10850 10849.888 32 3032 wm-lh-frontalpole 278 278.356 33 3033 wm-lh-temporalpole 827 826.568 34 3034 wm-lh-transversetemporal 723 723.237 35 3035 wm-lh-insula 7924 7923.779 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 2663 2662.768 120 4002 wm-rh-caudalanteriorcingulate 3433 3432.692 121 4003 wm-rh-caudalmiddlefrontal 7336 7336.432 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 1884 1884.455 124 4006 wm-rh-entorhinal 786 786.107 125 4007 wm-rh-fusiform 4914 4913.896 126 4008 wm-rh-inferiorparietal 11032 11031.827 127 4009 wm-rh-inferiortemporal 4842 4842.048 128 4010 wm-rh-isthmuscingulate 1597 1597.437 129 4011 wm-rh-lateraloccipital 5711 5710.558 130 4012 wm-rh-lateralorbitofrontal 6587 6587.465 131 4013 wm-rh-lingual 2832 2832.001 132 4014 wm-rh-medialorbitofrontal 3556 3556.232 133 4015 wm-rh-middletemporal 5369 5369.222 134 4016 wm-rh-parahippocampal 2488 2487.503 135 4017 wm-rh-paracentral 4933 4933.192 136 4018 wm-rh-parsopercularis 3142 3141.810 137 4019 wm-rh-parsorbitalis 1083 1082.856 138 4020 wm-rh-parstriangularis 2966 2966.142 139 4021 wm-rh-pericalcarine 955 954.595 140 4022 wm-rh-postcentral 6650 6650.462 141 4023 wm-rh-posteriorcingulate 4316 4316.132 142 4024 wm-rh-precentral 16492 16492.072 143 4025 wm-rh-precuneus 10109 10109.021 144 4026 wm-rh-rostralanteriorcingulate 2258 2257.734 145 4027 wm-rh-rostralmiddlefrontal 17054 17053.582 146 4028 wm-rh-superiorfrontal 17371 17371.389 147 4029 wm-rh-superiorparietal 9729 9729.076 148 4030 wm-rh-superiortemporal 7461 7461.395 149 4031 wm-rh-supramarginal 8565 8564.689 150 4032 wm-rh-frontalpole 413 412.840 151 4033 wm-rh-temporalpole 726 725.954 152 4034 wm-rh-transversetemporal 468 467.541 153 4035 wm-rh-insula 8047 8046.604 154 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 52509 52509.457 237 5002 Right-UnsegmentedWhiteMatter 39645 39645.148 238 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/post_analysis/MPS1036-1/label #-------------------------------------------- #@# BA Labels lh Wed Jan 1 12:22:18 CST 2014 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.label --trgsubject MPS1036-1 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 717 Checking for and removing duplicates Writing label file ./lh.BA1.label 4846 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.label --trgsubject MPS1036-1 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 1156 Checking for and removing duplicates Writing label file ./lh.BA2.label 9065 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.label --trgsubject MPS1036-1 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 432 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4509 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.label --trgsubject MPS1036-1 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 849 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6832 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.label --trgsubject MPS1036-1 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 603 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6387 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.label --trgsubject MPS1036-1 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 547 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4617 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.label --trgsubject MPS1036-1 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 2900 Checking for and removing duplicates Writing label file ./lh.BA6.label 16489 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.label --trgsubject MPS1036-1 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 619 Checking for and removing duplicates Writing label file ./lh.BA44.label 4800 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.label --trgsubject MPS1036-1 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 1734 Checking for and removing duplicates Writing label file ./lh.BA45.label 5156 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.label --trgsubject MPS1036-1 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 1369 Checking for and removing duplicates Writing label file ./lh.V1.label 6010 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.label --trgsubject MPS1036-1 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 2812 Checking for and removing duplicates Writing label file ./lh.V2.label 10926 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.label --trgsubject MPS1036-1 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 579 Checking for and removing duplicates Writing label file ./lh.MT.label 2597 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.perirhinal.label --trgsubject MPS1036-1 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1199 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 129 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1328 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1014 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 184 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1198 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2092 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 413 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2505 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1504 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 220 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1724 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1996 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 146 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2142 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2319 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 225 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2544 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1549 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 193 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1742 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 7035 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 1208 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8243 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1912 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 209 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2121 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1151 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 673 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1824 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3405 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 915 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4320 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3334 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 1273 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4607 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 513 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 149610 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 675 mri_label2label: Done mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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 node1108 machine x86_64 user kovacv subject MPS1036-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 104962 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.BA.annot mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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 node1108 machine x86_64 user kovacv subject MPS1036-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 124544 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab MPS1036-1 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 1292 704 2016 2.287 0.607 0.189 0.126 99 7.9 BA1 4591 2946 7430 2.683 0.614 0.158 0.148 174 16.6 BA2 1038 756 1038 1.944 0.538 0.243 0.281 75 10.0 BA3a 2321 1598 3040 1.974 0.726 0.182 0.463 166 10.7 BA3b 1842 1228 3260 2.471 0.867 0.174 0.135 53 12.9 BA4a 1422 968 1585 1.899 0.683 0.191 0.185 89 12.2 BA4p 11585 7400 28201 3.304 0.887 0.176 0.168 616 86.2 BA6 2243 1435 4722 2.983 0.696 0.168 0.142 94 12.8 BA44 4338 2657 7926 2.746 0.775 0.172 0.145 384 24.9 BA45 3140 2092 3636 1.690 0.568 0.211 0.140 125 19.9 V1 7780 5338 13790 2.324 0.703 0.192 0.108 407 40.6 V2 2188 1444 4348 2.925 0.631 0.160 0.157 42 7.6 MT 868 586 1665 2.237 0.798 0.213 0.216 51 9.5 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab MPS1036-1 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 867 465 1285 2.213 0.636 0.192 0.130 77 5.1 BA1 1956 1216 3186 2.496 0.557 0.166 0.112 72 8.3 BA2 873 628 824 1.814 0.478 0.272 0.334 73 9.5 BA3a 1336 1002 1630 1.655 0.564 0.155 0.069 27 3.3 BA3b 1632 1102 2838 2.348 0.852 0.162 0.131 42 10.8 BA4a 1172 820 1270 1.863 0.641 0.197 0.208 89 12.1 BA4p 6182 3961 14043 3.108 0.950 0.170 0.137 218 35.2 BA6 1427 885 3005 2.950 0.734 0.163 0.128 45 7.3 BA44 1712 967 3293 2.585 0.768 0.177 0.149 74 12.2 BA45 3346 2229 3940 1.696 0.576 0.210 0.136 130 21.0 V1 3962 2734 6882 2.265 0.750 0.200 0.138 308 27.8 V2 601 399 1240 2.905 0.630 0.161 0.103 10 3.1 MT #-------------------------------------------- #@# BA Labels rh Wed Jan 1 12:25:23 CST 2014 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.label --trgsubject MPS1036-1 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 443 Checking for and removing duplicates Writing label file ./rh.BA1.label 4405 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.label --trgsubject MPS1036-1 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 649 Checking for and removing duplicates Writing label file ./rh.BA2.label 7336 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.label --trgsubject MPS1036-1 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 249 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4229 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.label --trgsubject MPS1036-1 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 294 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4816 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.label --trgsubject MPS1036-1 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 800 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6547 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.label --trgsubject MPS1036-1 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 488 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4961 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.label --trgsubject MPS1036-1 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 1861 Checking for and removing duplicates Writing label file ./rh.BA6.label 14117 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.label --trgsubject MPS1036-1 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 1296 Checking for and removing duplicates Writing label file ./rh.BA44.label 8208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.label --trgsubject MPS1036-1 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 1349 Checking for and removing duplicates Writing label file ./rh.BA45.label 6704 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.label --trgsubject MPS1036-1 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 648 Checking for and removing duplicates Writing label file ./rh.V1.label 5375 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.label --trgsubject MPS1036-1 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 1800 Checking for and removing duplicates Writing label file ./rh.V2.label 9816 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.label --trgsubject MPS1036-1 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 395 Checking for and removing duplicates Writing label file ./rh.MT.label 2327 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.perirhinal.label --trgsubject MPS1036-1 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 752 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 232 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 984 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 876 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 115 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 991 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2688 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 286 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2974 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1698 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 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/post_analysis/fsaverage/label/rh.BA3b.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2183 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 173 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2356 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1388 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 150 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1538 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1489 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 202 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1691 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 6959 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 1029 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7988 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1012 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 191 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1178 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 302 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1480 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3232 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 314 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 3546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3437 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 718 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4155 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 268 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 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 138081 Number of reverse mapping hits = 77 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 345 mri_label2label: Done mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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 node1108 machine x86_64 user kovacv subject MPS1036-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 99562 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.BA.annot mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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 node1108 machine x86_64 user kovacv subject MPS1036-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 117604 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab MPS1036-1 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 970 522 1910 2.570 0.733 0.153 0.092 27 3.9 BA1 3388 2154 5615 2.646 0.618 0.146 0.582 129 17.9 BA2 1028 662 950 1.937 0.496 0.183 0.160 224 6.5 BA3a 1959 1311 2873 1.971 0.727 0.149 0.072 33 5.5 BA3b 1721 1158 3237 2.534 1.036 0.159 0.094 82 7.6 BA4a 1482 947 1716 2.027 0.757 0.192 0.243 168 17.8 BA4p 9188 5792 22027 3.260 0.857 0.170 0.147 365 49.2 BA6 3711 2487 9095 3.058 0.596 0.155 0.115 242 11.7 BA44 4586 3154 10771 2.854 0.658 0.166 0.094 124 17.3 BA45 2020 1413 3771 2.019 1.070 0.268 0.599 681 60.5 V1 5889 4185 8802 1.766 1.145 0.193 0.182 317 41.9 V2 1747 1211 4099 3.075 0.476 0.165 0.098 42 6.5 MT 830 548 1881 2.629 0.871 0.234 0.421 173 9.1 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab MPS1036-1 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 724 366 1395 2.576 0.540 0.151 0.089 23 2.8 BA1 2067 1299 3616 2.671 0.629 0.138 0.117 47 11.6 BA2 925 589 779 1.927 0.476 0.192 0.200 225 6.8 BA3a 1630 1108 2055 1.782 0.515 0.144 0.068 24 4.1 BA3b 993 674 2137 2.576 1.059 0.176 0.149 32 7.4 BA4a 1170 756 1234 1.865 0.700 0.192 0.253 158 15.5 BA4p 5886 3665 13711 3.176 0.884 0.170 0.155 274 28.7 BA6 936 656 2520 2.992 0.708 0.164 0.218 166 3.5 BA44 1167 773 2772 2.826 0.586 0.172 0.122 32 5.1 BA45 1822 1298 3491 2.033 1.096 0.265 0.558 476 47.0 V1 2867 2056 4321 1.821 1.020 0.207 0.229 343 27.3 V2 290 186 732 3.224 0.379 0.192 0.135 9 1.5 MT /lustre/kovacv/FS/post_analysis/MPS1036-1/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Wed Jan 1 12:28:16 CST 2014 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS1036-1 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject MPS1036-1. processing subject lh.EC_average... reading output surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 952 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label MPS1036-1 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 343 217 845 2.392 0.682 0.205 0.238 19 3.1 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Wed Jan 1 12:28:30 CST 2014 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS1036-1 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject MPS1036-1. processing subject rh.EC_average... reading output surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 995 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label MPS1036-1 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 385 208 830 2.603 0.652 0.194 0.607 109 3.6 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Tue Dec 31 12:16:18 CST 2013 Ended at Wed Jan 1 12:28:41 CST 2014 #@#%# recon-all-run-time-hours 24.206 recon-all -s MPS1036-1 finished without error at Wed Jan 1 12:28:41 CST 2014 New invocation of recon-all Thu Jan 2 18:38:47 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 /soft/freesurfer/5.3.0_1/bin/recon-all -autorecon2-cp -autorecon3 -subjid MPS1036-1 -bigventricles subjid MPS1036-1 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Actual FREESURFER_HOME /panfs/roc/itascasoft/freesurfer/5.3.0_1 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux node1108 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 1724396 64207848 0 9368 305780 -/+ buffers/cache: 1409248 64522996 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: 2014/01/03-00:38:47-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: node1108 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: 2014/01/03-00:38:48-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: node1108 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: 2014/01/03-00:38:48-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: node1108 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: 2014/01/03-00:38:48-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: node1108 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: 2014/01/03-00:38:48-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: node1108 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: 2014/01/03-00:38:48-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: node1108 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: 2014/01/03-00:38:49-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: node1108 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: 2014/01/03-00:38:49-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: node1108 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: 2014/01/03-00:38:49-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: node1108 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: 2014/01/03-00:38:49-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: node1108 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: $ TimeStamp: 2014/01/03-00:38:50-GMT BuildTimeStamp: Nov 16 2013 21:04:35 CVS: $Id: mri_ca_register.c,v 1.87 2013/11/14 16:15:12 fischl Exp $ User: kovacv Machine: node1108 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: 2014/01/03-00:38:50-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: node1108 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: 2014/01/03-00:38:50-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: node1108 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: 2014/01/03-00:38:50-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: node1108 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: 2014/01/03-00:38:50-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: node1108 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: 2014/01/03-00:38:50-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: node1108 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: 2014/01/03-00:38:51-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: node1108 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: 2014/01/03-00:38:51-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: node1108 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: 2014/01/03-00:38:51-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: node1108 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: 2014/01/03-00:38:51-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: node1108 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: 2014/01/03-00:38:51-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: node1108 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: 2014/01/03-00:38:52-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: node1108 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: 2014/01/03-00:38:52-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: node1108 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: 2014/01/03-00:38:52-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: node1108 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: 2014/01/03-00:38:53-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: node1108 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: 2014/01/03-00:38:53-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: node1108 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: 2014/01/03-00:38:53-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: node1108 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: 2014/01/03-00:38:53-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: node1108 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: 2014/01/03-00:38:53-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: node1108 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: 2014/01/03-00:38:54-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: node1108 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: 2014/01/03-00:38:54-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: node1108 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: 2014/01/03-00:38:54-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: node1108 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: 2014/01/03-00:38:55-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: node1108 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: 2014/01/03-00:38:55-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: node1108 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: 2014/01/03-00:38:55-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: node1108 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: 2014/01/03-00:38:55-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: node1108 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: 2014/01/03-00:38:55-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: node1108 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: 2014/01/03-00:38:55-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: node1108 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /soft/freesurfer/5.3.0_1/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_1/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Thu Jan 2 18:38:56 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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... 6441 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 43 (43) csf peak at 19, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 99 gm peak at 76 (76), valley at 42 (42) csf peak at 19, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 59 seconds. #-------------------------------------------- #@# Mask BFS Thu Jan 2 18:41:56 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2105835 voxels in mask (pct= 12.55) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Jan 2 18:41:58 CST 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/MPS1036-1/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname node1108 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/MPS1036-1/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname node1108 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 (102.0): 101.7 +- 8.1 [80.0 --> 125.0] GM (73.0) : 69.9 +- 12.9 [30.0 --> 96.0] setting bottom of white matter range to 82.7 setting top of gray matter range to 95.6 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... 17556 sparsely connected voxels removed... thickening thin strands.... 20 segments, 8304 filled 1267 bright non-wm voxels segmented. 8956 diagonally connected voxels added... white matter segmentation took 2.0 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 1.22 minutes reading wm segmentation from wm.seg.mgz... 3199 voxels added to wm to prevent paths from MTL structures to cortex 24905 additional wm voxels added 0 additional wm voxels added SEG EDIT: 247342 voxels turned on, 68897 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 104 new 104 115,126,128 old 104 new 104 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 222 found - 222 modified | TOTAL: 222 pass 2 (xy+): 0 found - 222 modified | TOTAL: 222 pass 1 (xy-): 207 found - 207 modified | TOTAL: 429 pass 2 (xy-): 0 found - 207 modified | TOTAL: 429 pass 1 (yz+): 172 found - 172 modified | TOTAL: 601 pass 2 (yz+): 0 found - 172 modified | TOTAL: 601 pass 1 (yz-): 206 found - 206 modified | TOTAL: 807 pass 2 (yz-): 0 found - 206 modified | TOTAL: 807 pass 1 (xz+): 153 found - 153 modified | TOTAL: 960 pass 2 (xz+): 0 found - 153 modified | TOTAL: 960 pass 1 (xz-): 156 found - 156 modified | TOTAL: 1116 pass 2 (xz-): 0 found - 156 modified | TOTAL: 1116 Iteration Number : 1 pass 1 (+++): 89 found - 89 modified | TOTAL: 89 pass 2 (+++): 0 found - 89 modified | TOTAL: 89 pass 1 (+++): 100 found - 100 modified | TOTAL: 189 pass 2 (+++): 0 found - 100 modified | TOTAL: 189 pass 1 (+++): 80 found - 80 modified | TOTAL: 269 pass 2 (+++): 0 found - 80 modified | TOTAL: 269 pass 1 (+++): 84 found - 84 modified | TOTAL: 353 pass 2 (+++): 0 found - 84 modified | TOTAL: 353 Iteration Number : 1 pass 1 (++): 250 found - 250 modified | TOTAL: 250 pass 2 (++): 0 found - 250 modified | TOTAL: 250 pass 1 (+-): 276 found - 276 modified | TOTAL: 526 pass 2 (+-): 1 found - 277 modified | TOTAL: 527 pass 3 (+-): 0 found - 277 modified | TOTAL: 527 pass 1 (--): 266 found - 266 modified | TOTAL: 793 pass 2 (--): 1 found - 267 modified | TOTAL: 794 pass 3 (--): 0 found - 267 modified | TOTAL: 794 pass 1 (-+): 250 found - 250 modified | TOTAL: 1044 pass 2 (-+): 0 found - 250 modified | TOTAL: 1044 Iteration Number : 2 pass 1 (xy+): 28 found - 28 modified | TOTAL: 28 pass 2 (xy+): 0 found - 28 modified | TOTAL: 28 pass 1 (xy-): 26 found - 26 modified | TOTAL: 54 pass 2 (xy-): 0 found - 26 modified | TOTAL: 54 pass 1 (yz+): 21 found - 21 modified | TOTAL: 75 pass 2 (yz+): 0 found - 21 modified | TOTAL: 75 pass 1 (yz-): 27 found - 27 modified | TOTAL: 102 pass 2 (yz-): 0 found - 27 modified | TOTAL: 102 pass 1 (xz+): 23 found - 23 modified | TOTAL: 125 pass 2 (xz+): 0 found - 23 modified | TOTAL: 125 pass 1 (xz-): 30 found - 30 modified | TOTAL: 155 pass 2 (xz-): 0 found - 30 modified | TOTAL: 155 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 1 found - 1 modified | TOTAL: 9 pass 2 (+++): 0 found - 1 modified | TOTAL: 9 pass 1 (+++): 4 found - 4 modified | TOTAL: 13 pass 2 (+++): 0 found - 4 modified | TOTAL: 13 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 16 found - 16 modified | TOTAL: 22 pass 2 (+-): 0 found - 16 modified | TOTAL: 22 pass 1 (--): 17 found - 17 modified | TOTAL: 39 pass 2 (--): 0 found - 17 modified | TOTAL: 39 pass 1 (-+): 18 found - 18 modified | TOTAL: 57 pass 2 (-+): 0 found - 18 modified | TOTAL: 57 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 5 found - 5 modified | TOTAL: 10 pass 2 (yz-): 0 found - 5 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 1 found - 1 modified | TOTAL: 12 pass 2 (xz-): 0 found - 1 modified | TOTAL: 12 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 1 found - 1 modified | TOTAL: 5 pass 2 (-+): 0 found - 1 modified | TOTAL: 5 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2755 (out of 731549: 0.376598) 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 Thu Jan 2 18:45:27 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 3366 (min = 350, max = 1400), aspect = 0.73 (min = 0.10, max = 0.75) need search nearby using seed (117, 99, 143), TAL = (11.0, 15.0, 29.0) talairach voxel to voxel transform 1.086 -0.012 0.198 -27.718; -0.014 1.018 0.266 -57.126; -0.166 -0.240 1.172 65.007; 0.000 0.000 0.000 1.000; segmentation indicates cc at (117, 99, 143) --> (11.0, 15.0, 29.0) done. writing output to filled.mgz... filling took 0.7 minutes badRH = 12703/323344, badLH=701/368281 Please check filled volume. Cerebellum may be included. talairach cc position changed to (11.00, 15.00, 29.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(29.00, 15.00, 29.00) SRC: (106.93, 80.22, 192.42) search lh wm seed point around talairach space (-7.00, 15.00, 29.00), SRC: (146.03, 79.70, 186.43) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu Jan 2 18:46:10 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 3 found - 3 modified | TOTAL: 16 pass 2 (xy-): 0 found - 3 modified | TOTAL: 16 pass 1 (yz+): 5 found - 5 modified | TOTAL: 21 pass 2 (yz+): 0 found - 5 modified | TOTAL: 21 pass 1 (yz-): 6 found - 6 modified | TOTAL: 27 pass 2 (yz-): 0 found - 6 modified | TOTAL: 27 pass 1 (xz+): 10 found - 10 modified | TOTAL: 37 pass 2 (xz+): 0 found - 10 modified | TOTAL: 37 pass 1 (xz-): 7 found - 7 modified | TOTAL: 44 pass 2 (xz-): 0 found - 7 modified | TOTAL: 44 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 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 3 found - 3 modified | TOTAL: 6 pass 2 (+-): 0 found - 3 modified | TOTAL: 6 pass 1 (--): 11 found - 11 modified | TOTAL: 17 pass 2 (--): 0 found - 11 modified | TOTAL: 17 pass 1 (-+): 3 found - 3 modified | TOTAL: 20 pass 2 (-+): 0 found - 3 modified | TOTAL: 20 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+): 2 found - 2 modified | TOTAL: 2 pass 2 (xz+): 0 found - 2 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 = 69 (out of 368350: 0.018732) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 104 vertices, 121 faces slice 60: 4109 vertices, 4298 faces slice 70: 11609 vertices, 11912 faces slice 80: 20061 vertices, 20393 faces slice 90: 29577 vertices, 29945 faces slice 100: 39211 vertices, 39568 faces slice 110: 48915 vertices, 49361 faces slice 120: 61430 vertices, 61992 faces slice 130: 74850 vertices, 75470 faces slice 140: 89190 vertices, 89822 faces slice 150: 102332 vertices, 102990 faces slice 160: 115110 vertices, 115779 faces slice 170: 125685 vertices, 126258 faces slice 180: 134538 vertices, 135147 faces slice 190: 143943 vertices, 144571 faces slice 200: 152892 vertices, 153508 faces slice 210: 162235 vertices, 162876 faces slice 220: 168439 vertices, 168943 faces slice 230: 171169 vertices, 171540 faces slice 240: 171244 vertices, 171592 faces slice 250: 171244 vertices, 171592 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... 171244 voxel in cpt #1: X=-348 [v=171244,e=514776,f=343184] located at (-21.646225, 9.320630, 50.872253) For the whole surface: X=-348 [v=171244,e=514776,f=343184] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Jan 2 18:46:17 CST 2014 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Thu Jan 2 18:46:21 CST 2014 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts avg radius = 52.3 mm, total surface area = 85246 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.126 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.066 (target=0.015) step 030: RMS=0.064 (target=0.015) step 035: RMS=0.062 (target=0.015) step 040: RMS=0.061 (target=0.015) step 045: RMS=0.060 (target=0.015) step 050: RMS=0.059 (target=0.015) step 055: RMS=0.060 (target=0.015) step 060: RMS=0.060 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Jan 2 18:46:54 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.89 +- 0.60 (0.00-->8.88) (max @ vno 59563 --> 59583) face area 0.02 +- 0.03 (-0.19-->0.82) scaling brain by 0.286... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.134, avgs=0 005/300: dt: 0.9000, rms radial error=176.877, avgs=0 010/300: dt: 0.9000, rms radial error=176.325, avgs=0 015/300: dt: 0.9000, rms radial error=175.599, avgs=0 020/300: dt: 0.9000, rms radial error=174.771, avgs=0 025/300: dt: 0.9000, rms radial error=173.886, avgs=0 030/300: dt: 0.9000, rms radial error=172.968, avgs=0 035/300: dt: 0.9000, rms radial error=172.033, avgs=0 040/300: dt: 0.9000, rms radial error=171.089, avgs=0 045/300: dt: 0.9000, rms radial error=170.143, avgs=0 050/300: dt: 0.9000, rms radial error=169.198, avgs=0 055/300: dt: 0.9000, rms radial error=168.255, avgs=0 060/300: dt: 0.9000, rms radial error=167.315, avgs=0 065/300: dt: 0.9000, rms radial error=166.378, avgs=0 070/300: dt: 0.9000, rms radial error=165.446, avgs=0 075/300: dt: 0.9000, rms radial error=164.518, avgs=0 080/300: dt: 0.9000, rms radial error=163.596, avgs=0 085/300: dt: 0.9000, rms radial error=162.678, avgs=0 090/300: dt: 0.9000, rms radial error=161.765, avgs=0 095/300: dt: 0.9000, rms radial error=160.857, avgs=0 100/300: dt: 0.9000, rms radial error=159.954, avgs=0 105/300: dt: 0.9000, rms radial error=159.056, avgs=0 110/300: dt: 0.9000, rms radial error=158.163, avgs=0 115/300: dt: 0.9000, rms radial error=157.275, avgs=0 120/300: dt: 0.9000, rms radial error=156.392, avgs=0 125/300: dt: 0.9000, rms radial error=155.513, avgs=0 130/300: dt: 0.9000, rms radial error=154.640, avgs=0 135/300: dt: 0.9000, rms radial error=153.771, avgs=0 140/300: dt: 0.9000, rms radial error=152.907, avgs=0 145/300: dt: 0.9000, rms radial error=152.047, avgs=0 150/300: dt: 0.9000, rms radial error=151.192, avgs=0 155/300: dt: 0.9000, rms radial error=150.342, avgs=0 160/300: dt: 0.9000, rms radial error=149.497, avgs=0 165/300: dt: 0.9000, rms radial error=148.657, avgs=0 170/300: dt: 0.9000, rms radial error=147.821, avgs=0 175/300: dt: 0.9000, rms radial error=146.990, avgs=0 180/300: dt: 0.9000, rms radial error=146.164, avgs=0 185/300: dt: 0.9000, rms radial error=145.342, avgs=0 190/300: dt: 0.9000, rms radial error=144.524, avgs=0 195/300: dt: 0.9000, rms radial error=143.712, avgs=0 200/300: dt: 0.9000, rms radial error=142.903, avgs=0 205/300: dt: 0.9000, rms radial error=142.098, avgs=0 210/300: dt: 0.9000, rms radial error=141.298, avgs=0 215/300: dt: 0.9000, rms radial error=140.502, avgs=0 220/300: dt: 0.9000, rms radial error=139.711, avgs=0 225/300: dt: 0.9000, rms radial error=138.924, avgs=0 230/300: dt: 0.9000, rms radial error=138.142, avgs=0 235/300: dt: 0.9000, rms radial error=137.364, avgs=0 240/300: dt: 0.9000, rms radial error=136.590, avgs=0 245/300: dt: 0.9000, rms radial error=135.820, avgs=0 250/300: dt: 0.9000, rms radial error=135.055, avgs=0 255/300: dt: 0.9000, rms radial error=134.294, avgs=0 260/300: dt: 0.9000, rms radial error=133.538, avgs=0 265/300: dt: 0.9000, rms radial error=132.785, avgs=0 270/300: dt: 0.9000, rms radial error=132.037, avgs=0 275/300: dt: 0.9000, rms radial error=131.293, avgs=0 280/300: dt: 0.9000, rms radial error=130.553, avgs=0 285/300: dt: 0.9000, rms radial error=129.817, avgs=0 290/300: dt: 0.9000, rms radial error=129.086, avgs=0 295/300: dt: 0.9000, rms radial error=128.358, avgs=0 300/300: dt: 0.9000, rms radial error=127.635, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20816.89 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 3852.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 3 (K=160.0), pass 1, starting sse = 549.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00287 epoch 4 (K=640.0), pass 1, starting sse = 84.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00616 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Jan 2 18:51:10 CST 2014 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS1036-1 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=-348 (nv=171244, nf=343184, ne=514776, g=175) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 49192 ambiguous faces found in tessellation segmenting defects... 160 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 157 into 71 -merging segment 93 into 86 -merging segment 97 into 96 -merging segment 107 into 104 156 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0107 (-4.5054) -vertex loglikelihood: -6.3883 (-3.1942) -normal dot loglikelihood: -3.4922 (-3.4922) -quad curv loglikelihood: -6.0829 (-3.0415) Total Loglikelihood : -24.9741 CORRECTING DEFECT 0 (vertices=60, convex hull=103) After retessellation of defect 0, euler #=-145 (143663,424793,280985) : difference with theory (-153) = -8 CORRECTING DEFECT 1 (vertices=38, convex hull=59) After retessellation of defect 1, euler #=-144 (143678,424859,281037) : difference with theory (-152) = -8 CORRECTING DEFECT 2 (vertices=19, convex hull=59) After retessellation of defect 2, euler #=-143 (143687,424910,281080) : difference with theory (-151) = -8 CORRECTING DEFECT 3 (vertices=51, convex hull=54) After retessellation of defect 3, euler #=-142 (143694,424957,281121) : difference with theory (-150) = -8 CORRECTING DEFECT 4 (vertices=30, convex hull=58) After retessellation of defect 4, euler #=-141 (143708,425023,281174) : difference with theory (-149) = -8 CORRECTING DEFECT 5 (vertices=45, convex hull=92) After retessellation of defect 5, euler #=-140 (143729,425126,281257) : difference with theory (-148) = -8 CORRECTING DEFECT 6 (vertices=27, convex hull=57) After retessellation of defect 6, euler #=-139 (143743,425191,281309) : difference with theory (-147) = -8 CORRECTING DEFECT 7 (vertices=5, convex hull=22) After retessellation of defect 7, euler #=-138 (143743,425194,281313) : difference with theory (-146) = -8 CORRECTING DEFECT 8 (vertices=33, convex hull=55) After retessellation of defect 8, euler #=-137 (143754,425250,281359) : difference with theory (-145) = -8 CORRECTING DEFECT 9 (vertices=15, convex hull=27) After retessellation of defect 9, euler #=-136 (143757,425271,281378) : difference with theory (-144) = -8 CORRECTING DEFECT 10 (vertices=6, convex hull=18) After retessellation of defect 10, euler #=-135 (143758,425279,281386) : difference with theory (-143) = -8 CORRECTING DEFECT 11 (vertices=200, convex hull=98) After retessellation of defect 11, euler #=-134 (143796,425439,281509) : difference with theory (-142) = -8 CORRECTING DEFECT 12 (vertices=10, convex hull=29) After retessellation of defect 12, euler #=-133 (143797,425452,281522) : difference with theory (-141) = -8 CORRECTING DEFECT 13 (vertices=39, convex hull=54) After retessellation of defect 13, euler #=-132 (143816,425530,281582) : difference with theory (-140) = -8 CORRECTING DEFECT 14 (vertices=23, convex hull=52) After retessellation of defect 14, euler #=-131 (143825,425576,281620) : difference with theory (-139) = -8 CORRECTING DEFECT 15 (vertices=15, convex hull=22) After retessellation of defect 15, euler #=-130 (143827,425589,281632) : difference with theory (-138) = -8 CORRECTING DEFECT 16 (vertices=27, convex hull=37) After retessellation of defect 16, euler #=-129 (143837,425637,281671) : difference with theory (-137) = -8 CORRECTING DEFECT 17 (vertices=75, convex hull=41) After retessellation of defect 17, euler #=-128 (143841,425664,281695) : difference with theory (-136) = -8 CORRECTING DEFECT 18 (vertices=226, convex hull=43) After retessellation of defect 18, euler #=-127 (143850,425707,281730) : difference with theory (-135) = -8 CORRECTING DEFECT 19 (vertices=65, convex hull=104) After retessellation of defect 19, euler #=-126 (143873,425819,281820) : difference with theory (-134) = -8 CORRECTING DEFECT 20 (vertices=51, convex hull=35) After retessellation of defect 20, euler #=-125 (143876,425836,281835) : difference with theory (-133) = -8 CORRECTING DEFECT 21 (vertices=22, convex hull=29) After retessellation of defect 21, euler #=-124 (143878,425853,281851) : difference with theory (-132) = -8 CORRECTING DEFECT 22 (vertices=68, convex hull=39) After retessellation of defect 22, euler #=-123 (143884,425888,281881) : difference with theory (-131) = -8 CORRECTING DEFECT 23 (vertices=23, convex hull=57) After retessellation of defect 23, euler #=-122 (143895,425945,281928) : difference with theory (-130) = -8 CORRECTING DEFECT 24 (vertices=39, convex hull=54) After retessellation of defect 24, euler #=-121 (143918,426034,281995) : difference with theory (-129) = -8 CORRECTING DEFECT 25 (vertices=16, convex hull=16) After retessellation of defect 25, euler #=-120 (143918,426037,281999) : difference with theory (-128) = -8 CORRECTING DEFECT 26 (vertices=100, convex hull=32) After retessellation of defect 26, euler #=-119 (143920,426052,282013) : difference with theory (-127) = -8 CORRECTING DEFECT 27 (vertices=10, convex hull=39) After retessellation of defect 27, euler #=-118 (143921,426066,282027) : difference with theory (-126) = -8 CORRECTING DEFECT 28 (vertices=6, convex hull=18) After retessellation of defect 28, euler #=-117 (143922,426074,282035) : difference with theory (-125) = -8 CORRECTING DEFECT 29 (vertices=14, convex hull=22) After retessellation of defect 29, euler #=-116 (143924,426088,282048) : difference with theory (-124) = -8 CORRECTING DEFECT 30 (vertices=39, convex hull=75) After retessellation of defect 30, euler #=-115 (143936,426152,282101) : difference with theory (-123) = -8 CORRECTING DEFECT 31 (vertices=34, convex hull=54) After retessellation of defect 31, euler #=-114 (143951,426217,282152) : difference with theory (-122) = -8 CORRECTING DEFECT 32 (vertices=52, convex hull=94) After retessellation of defect 32, euler #=-113 (143970,426312,282229) : difference with theory (-121) = -8 CORRECTING DEFECT 33 (vertices=40, convex hull=82) After retessellation of defect 33, euler #=-112 (143999,426438,282327) : difference with theory (-120) = -8 CORRECTING DEFECT 34 (vertices=85, convex hull=36) After retessellation of defect 34, euler #=-111 (144005,426472,282356) : difference with theory (-119) = -8 CORRECTING DEFECT 35 (vertices=316, convex hull=104) After retessellation of defect 35, euler #=-110 (144032,426591,282449) : difference with theory (-118) = -8 CORRECTING DEFECT 36 (vertices=50, convex hull=71) After retessellation of defect 36, euler #=-109 (144042,426649,282498) : difference with theory (-117) = -8 CORRECTING DEFECT 37 (vertices=52, convex hull=42) After retessellation of defect 37, euler #=-108 (144051,426690,282531) : difference with theory (-116) = -8 CORRECTING DEFECT 38 (vertices=41, convex hull=86) After retessellation of defect 38, euler #=-107 (144063,426767,282597) : difference with theory (-115) = -8 CORRECTING DEFECT 39 (vertices=30, convex hull=37) After retessellation of defect 39, euler #=-106 (144068,426794,282620) : difference with theory (-114) = -8 CORRECTING DEFECT 40 (vertices=81, convex hull=142) After retessellation of defect 40, euler #=-105 (144089,426922,282728) : difference with theory (-113) = -8 CORRECTING DEFECT 41 (vertices=57, convex hull=74) After retessellation of defect 41, euler #=-104 (144119,427047,282824) : difference with theory (-112) = -8 CORRECTING DEFECT 42 (vertices=31, convex hull=45) After retessellation of defect 42, euler #=-103 (144135,427116,282878) : difference with theory (-111) = -8 CORRECTING DEFECT 43 (vertices=5, convex hull=21) Warning - incorrect dp selected!!!!(-141.845340 >= -141.845341 ) After retessellation of defect 43, euler #=-102 (144136,427125,282887) : difference with theory (-110) = -8 CORRECTING DEFECT 44 (vertices=525, convex hull=343) After retessellation of defect 44, euler #=-101 (144145,427317,283071) : difference with theory (-109) = -8 CORRECTING DEFECT 45 (vertices=367, convex hull=213) After retessellation of defect 45, euler #=-100 (144246,427721,283375) : difference with theory (-108) = -8 CORRECTING DEFECT 46 (vertices=37, convex hull=65) After retessellation of defect 46, euler #=-99 (144265,427804,283440) : difference with theory (-107) = -8 CORRECTING DEFECT 47 (vertices=947, convex hull=576) After retessellation of defect 47, euler #=-98 (144690,429371,284583) : difference with theory (-106) = -8 CORRECTING DEFECT 48 (vertices=16, convex hull=18) After retessellation of defect 48, euler #=-97 (144691,429377,284589) : difference with theory (-105) = -8 CORRECTING DEFECT 49 (vertices=48, convex hull=35) After retessellation of defect 49, euler #=-96 (144700,429415,284619) : difference with theory (-104) = -8 CORRECTING DEFECT 50 (vertices=15, convex hull=27) After retessellation of defect 50, euler #=-95 (144703,429431,284633) : difference with theory (-103) = -8 CORRECTING DEFECT 51 (vertices=21, convex hull=36) After retessellation of defect 51, euler #=-94 (144712,429468,284662) : difference with theory (-102) = -8 CORRECTING DEFECT 52 (vertices=23, convex hull=41) After retessellation of defect 52, euler #=-94 (144721,429515,284700) : difference with theory (-101) = -7 CORRECTING DEFECT 53 (vertices=219, convex hull=54) After retessellation of defect 53, euler #=-93 (144737,429587,284757) : difference with theory (-100) = -7 CORRECTING DEFECT 54 (vertices=31, convex hull=90) After retessellation of defect 54, euler #=-92 (144756,429679,284831) : difference with theory (-99) = -7 CORRECTING DEFECT 55 (vertices=22, convex hull=52) After retessellation of defect 55, euler #=-91 (144766,429728,284871) : difference with theory (-98) = -7 CORRECTING DEFECT 56 (vertices=798, convex hull=351) After retessellation of defect 56, euler #=-90 (144966,430514,285458) : difference with theory (-97) = -7 CORRECTING DEFECT 57 (vertices=433, convex hull=286) After retessellation of defect 57, euler #=-89 (144992,430731,285650) : difference with theory (-96) = -7 CORRECTING DEFECT 58 (vertices=17, convex hull=25) Warning - incorrect dp selected!!!!(-71.049931 >= -71.049935 ) After retessellation of defect 58, euler #=-88 (144994,430743,285661) : difference with theory (-95) = -7 CORRECTING DEFECT 59 (vertices=31, convex hull=60) After retessellation of defect 59, euler #=-87 (145011,430817,285719) : difference with theory (-94) = -7 CORRECTING DEFECT 60 (vertices=13, convex hull=19) After retessellation of defect 60, euler #=-86 (145014,430829,285729) : difference with theory (-93) = -7 CORRECTING DEFECT 61 (vertices=61, convex hull=82) After retessellation of defect 61, euler #=-85 (145055,430987,285847) : difference with theory (-92) = -7 CORRECTING DEFECT 62 (vertices=155, convex hull=63) After retessellation of defect 62, euler #=-84 (145086,431106,285936) : difference with theory (-91) = -7 CORRECTING DEFECT 63 (vertices=5, convex hull=23) Warning - incorrect dp selected!!!!(-152.912833 >= -152.912835 ) After retessellation of defect 63, euler #=-83 (145088,431118,285947) : difference with theory (-90) = -7 CORRECTING DEFECT 64 (vertices=219, convex hull=54) After retessellation of defect 64, euler #=-82 (145097,431169,285990) : difference with theory (-89) = -7 CORRECTING DEFECT 65 (vertices=27, convex hull=54) After retessellation of defect 65, euler #=-81 (145111,431229,286037) : difference with theory (-88) = -7 CORRECTING DEFECT 66 (vertices=8, convex hull=28) After retessellation of defect 66, euler #=-80 (145114,431245,286051) : difference with theory (-87) = -7 CORRECTING DEFECT 67 (vertices=198, convex hull=136) After retessellation of defect 67, euler #=-80 (145131,431359,286148) : difference with theory (-86) = -6 CORRECTING DEFECT 68 (vertices=405, convex hull=135) After retessellation of defect 68, euler #=-79 (145208,431656,286369) : difference with theory (-85) = -6 CORRECTING DEFECT 69 (vertices=1344, convex hull=525) After retessellation of defect 69, euler #=-78 (145423,432568,287067) : difference with theory (-84) = -6 CORRECTING DEFECT 70 (vertices=143, convex hull=160) After retessellation of defect 70, euler #=-77 (145484,432831,287270) : difference with theory (-83) = -6 CORRECTING DEFECT 71 (vertices=11795, convex hull=2353) After retessellation of defect 71, euler #=-84 (148663,443668,294921) : difference with theory (-82) = 2 CORRECTING DEFECT 72 (vertices=33, convex hull=53) After retessellation of defect 72, euler #=-83 (148683,443747,294981) : difference with theory (-81) = 2 CORRECTING DEFECT 73 (vertices=100, convex hull=106) After retessellation of defect 73, euler #=-82 (148717,443891,295092) : difference with theory (-80) = 2 CORRECTING DEFECT 74 (vertices=6, convex hull=18) After retessellation of defect 74, euler #=-81 (148718,443899,295100) : difference with theory (-79) = 2 CORRECTING DEFECT 75 (vertices=69, convex hull=74) After retessellation of defect 75, euler #=-80 (148751,444031,295200) : difference with theory (-78) = 2 CORRECTING DEFECT 76 (vertices=22, convex hull=54) After retessellation of defect 76, euler #=-79 (148760,444078,295239) : difference with theory (-77) = 2 CORRECTING DEFECT 77 (vertices=49, convex hull=95) After retessellation of defect 77, euler #=-78 (148792,444208,295338) : difference with theory (-76) = 2 CORRECTING DEFECT 78 (vertices=20, convex hull=25) After retessellation of defect 78, euler #=-77 (148796,444226,295353) : difference with theory (-75) = 2 CORRECTING DEFECT 79 (vertices=9, convex hull=25) After retessellation of defect 79, euler #=-76 (148798,444238,295364) : difference with theory (-74) = 2 CORRECTING DEFECT 80 (vertices=77, convex hull=87) After retessellation of defect 80, euler #=-75 (148817,444332,295440) : difference with theory (-73) = 2 CORRECTING DEFECT 81 (vertices=76, convex hull=37) After retessellation of defect 81, euler #=-74 (148825,444372,295473) : difference with theory (-72) = 2 CORRECTING DEFECT 82 (vertices=7, convex hull=17) After retessellation of defect 82, euler #=-73 (148826,444379,295480) : difference with theory (-71) = 2 CORRECTING DEFECT 83 (vertices=17, convex hull=31) After retessellation of defect 83, euler #=-72 (148829,444399,295498) : difference with theory (-70) = 2 CORRECTING DEFECT 84 (vertices=30, convex hull=64) After retessellation of defect 84, euler #=-71 (148842,444464,295551) : difference with theory (-69) = 2 CORRECTING DEFECT 85 (vertices=48, convex hull=81) After retessellation of defect 85, euler #=-70 (148871,444586,295645) : difference with theory (-68) = 2 CORRECTING DEFECT 86 (vertices=81, convex hull=49) After retessellation of defect 86, euler #=-68 (148875,444619,295676) : difference with theory (-67) = 1 CORRECTING DEFECT 87 (vertices=183, convex hull=51) After retessellation of defect 87, euler #=-67 (148890,444682,295725) : difference with theory (-66) = 1 CORRECTING DEFECT 88 (vertices=5, convex hull=29) After retessellation of defect 88, euler #=-66 (148892,444697,295739) : difference with theory (-65) = 1 CORRECTING DEFECT 89 (vertices=5, convex hull=15) After retessellation of defect 89, euler #=-65 (148892,444702,295745) : difference with theory (-64) = 1 CORRECTING DEFECT 90 (vertices=93, convex hull=89) After retessellation of defect 90, euler #=-64 (148929,444855,295862) : difference with theory (-63) = 1 CORRECTING DEFECT 91 (vertices=73, convex hull=86) After retessellation of defect 91, euler #=-63 (148967,445006,295976) : difference with theory (-62) = 1 CORRECTING DEFECT 92 (vertices=7, convex hull=27) After retessellation of defect 92, euler #=-62 (148969,445020,295989) : difference with theory (-61) = 1 CORRECTING DEFECT 93 (vertices=9, convex hull=15) After retessellation of defect 93, euler #=-61 (148970,445033,296002) : difference with theory (-60) = 1 CORRECTING DEFECT 94 (vertices=59, convex hull=47) After retessellation of defect 94, euler #=-60 (148985,445095,296050) : difference with theory (-59) = 1 CORRECTING DEFECT 95 (vertices=92, convex hull=94) After retessellation of defect 95, euler #=-58 (149010,445210,296142) : difference with theory (-58) = 0 CORRECTING DEFECT 96 (vertices=86, convex hull=78) After retessellation of defect 96, euler #=-57 (149030,445298,296211) : difference with theory (-57) = 0 CORRECTING DEFECT 97 (vertices=6, convex hull=22) After retessellation of defect 97, euler #=-56 (149030,445302,296216) : difference with theory (-56) = 0 CORRECTING DEFECT 98 (vertices=21, convex hull=46) Warning - incorrect dp selected!!!!(-73.619855 >= -73.619859 ) After retessellation of defect 98, euler #=-55 (149031,445321,296235) : difference with theory (-55) = 0 CORRECTING DEFECT 99 (vertices=10, convex hull=20) After retessellation of defect 99, euler #=-54 (149033,445334,296247) : difference with theory (-54) = 0 CORRECTING DEFECT 100 (vertices=110, convex hull=35) After retessellation of defect 100, euler #=-53 (149037,445361,296271) : difference with theory (-53) = 0 CORRECTING DEFECT 101 (vertices=57, convex hull=84) After retessellation of defect 101, euler #=-52 (149056,445451,296343) : difference with theory (-52) = 0 CORRECTING DEFECT 102 (vertices=94, convex hull=114) After retessellation of defect 102, euler #=-50 (149103,445646,296493) : difference with theory (-51) = -1 CORRECTING DEFECT 103 (vertices=19, convex hull=56) After retessellation of defect 103, euler #=-49 (149113,445693,296531) : difference with theory (-50) = -1 CORRECTING DEFECT 104 (vertices=243, convex hull=136) After retessellation of defect 104, euler #=-48 (149129,445801,296624) : difference with theory (-49) = -1 CORRECTING DEFECT 105 (vertices=28, convex hull=36) After retessellation of defect 105, euler #=-48 (149137,445846,296661) : difference with theory (-48) = 0 CORRECTING DEFECT 106 (vertices=295, convex hull=116) After retessellation of defect 106, euler #=-47 (149202,446110,296861) : difference with theory (-47) = 0 CORRECTING DEFECT 107 (vertices=757, convex hull=298) After retessellation of defect 107, euler #=-46 (149343,446675,297286) : difference with theory (-46) = 0 CORRECTING DEFECT 108 (vertices=46, convex hull=76) After retessellation of defect 108, euler #=-45 (149367,446778,297366) : difference with theory (-45) = 0 CORRECTING DEFECT 109 (vertices=25, convex hull=48) After retessellation of defect 109, euler #=-44 (149378,446828,297406) : difference with theory (-44) = 0 CORRECTING DEFECT 110 (vertices=118, convex hull=128) After retessellation of defect 110, euler #=-43 (149412,446988,297533) : difference with theory (-43) = 0 CORRECTING DEFECT 111 (vertices=37, convex hull=56) After retessellation of defect 111, euler #=-42 (149433,447073,297598) : difference with theory (-42) = 0 CORRECTING DEFECT 112 (vertices=36, convex hull=68) After retessellation of defect 112, euler #=-41 (149451,447150,297658) : difference with theory (-41) = 0 CORRECTING DEFECT 113 (vertices=44, convex hull=61) After retessellation of defect 113, euler #=-40 (149465,447212,297707) : difference with theory (-40) = 0 CORRECTING DEFECT 114 (vertices=15, convex hull=19) After retessellation of defect 114, euler #=-39 (149467,447223,297717) : difference with theory (-39) = 0 CORRECTING DEFECT 115 (vertices=17, convex hull=25) After retessellation of defect 115, euler #=-38 (149470,447240,297732) : difference with theory (-38) = 0 CORRECTING DEFECT 116 (vertices=190, convex hull=127) After retessellation of defect 116, euler #=-37 (149506,447413,297870) : difference with theory (-37) = 0 CORRECTING DEFECT 117 (vertices=8, convex hull=15) After retessellation of defect 117, euler #=-36 (149506,447417,297875) : difference with theory (-36) = 0 CORRECTING DEFECT 118 (vertices=74, convex hull=43) After retessellation of defect 118, euler #=-35 (149515,447465,297915) : difference with theory (-35) = 0 CORRECTING DEFECT 119 (vertices=28, convex hull=32) After retessellation of defect 119, euler #=-34 (149524,447501,297943) : difference with theory (-34) = 0 CORRECTING DEFECT 120 (vertices=202, convex hull=30) After retessellation of defect 120, euler #=-33 (149528,447524,297963) : difference with theory (-33) = 0 CORRECTING DEFECT 121 (vertices=59, convex hull=60) After retessellation of defect 121, euler #=-32 (149542,447588,298014) : difference with theory (-32) = 0 CORRECTING DEFECT 122 (vertices=893, convex hull=176) After retessellation of defect 122, euler #=-31 (149608,447890,298251) : difference with theory (-31) = 0 CORRECTING DEFECT 123 (vertices=30, convex hull=32) After retessellation of defect 123, euler #=-30 (149615,447920,298275) : difference with theory (-30) = 0 CORRECTING DEFECT 124 (vertices=199, convex hull=85) After retessellation of defect 124, euler #=-29 (149629,448002,298344) : difference with theory (-29) = 0 CORRECTING DEFECT 125 (vertices=171, convex hull=95) After retessellation of defect 125, euler #=-28 (149656,448122,298438) : difference with theory (-28) = 0 CORRECTING DEFECT 126 (vertices=74, convex hull=48) After retessellation of defect 126, euler #=-27 (149676,448202,298499) : difference with theory (-27) = 0 CORRECTING DEFECT 127 (vertices=145, convex hull=76) After retessellation of defect 127, euler #=-26 (149700,448305,298579) : difference with theory (-26) = 0 CORRECTING DEFECT 128 (vertices=316, convex hull=124) After retessellation of defect 128, euler #=-25 (149751,448519,298743) : difference with theory (-25) = 0 CORRECTING DEFECT 129 (vertices=575, convex hull=356) After retessellation of defect 129, euler #=-24 (149899,449151,299228) : difference with theory (-24) = 0 CORRECTING DEFECT 130 (vertices=19, convex hull=39) After retessellation of defect 130, euler #=-23 (149910,449196,299263) : difference with theory (-23) = 0 CORRECTING DEFECT 131 (vertices=6, convex hull=26) After retessellation of defect 131, euler #=-22 (149912,449212,299278) : difference with theory (-22) = 0 CORRECTING DEFECT 132 (vertices=173, convex hull=205) After retessellation of defect 132, euler #=-21 (149966,449462,299475) : difference with theory (-21) = 0 CORRECTING DEFECT 133 (vertices=17, convex hull=21) After retessellation of defect 133, euler #=-20 (149967,449469,299482) : difference with theory (-20) = 0 CORRECTING DEFECT 134 (vertices=49, convex hull=101) After retessellation of defect 134, euler #=-19 (149995,449596,299582) : difference with theory (-19) = 0 CORRECTING DEFECT 135 (vertices=30, convex hull=69) After retessellation of defect 135, euler #=-18 (150007,449654,299629) : difference with theory (-18) = 0 CORRECTING DEFECT 136 (vertices=133, convex hull=97) After retessellation of defect 136, euler #=-17 (150024,449757,299716) : difference with theory (-17) = 0 CORRECTING DEFECT 137 (vertices=190, convex hull=58) After retessellation of defect 137, euler #=-16 (150043,449837,299778) : difference with theory (-16) = 0 CORRECTING DEFECT 138 (vertices=9, convex hull=27) After retessellation of defect 138, euler #=-15 (150044,449848,299789) : difference with theory (-15) = 0 CORRECTING DEFECT 139 (vertices=33, convex hull=80) After retessellation of defect 139, euler #=-14 (150063,449936,299859) : difference with theory (-14) = 0 CORRECTING DEFECT 140 (vertices=78, convex hull=99) After retessellation of defect 140, euler #=-13 (150076,450014,299925) : difference with theory (-13) = 0 CORRECTING DEFECT 141 (vertices=67, convex hull=68) After retessellation of defect 141, euler #=-12 (150095,450097,299990) : difference with theory (-12) = 0 CORRECTING DEFECT 142 (vertices=37, convex hull=29) After retessellation of defect 142, euler #=-11 (150100,450120,300009) : difference with theory (-11) = 0 CORRECTING DEFECT 143 (vertices=7, convex hull=24) After retessellation of defect 143, euler #=-10 (150102,450133,300021) : difference with theory (-10) = 0 CORRECTING DEFECT 144 (vertices=37, convex hull=66) After retessellation of defect 144, euler #=-9 (150113,450190,300068) : difference with theory (-9) = 0 CORRECTING DEFECT 145 (vertices=11, convex hull=31) After retessellation of defect 145, euler #=-8 (150115,450204,300081) : difference with theory (-8) = 0 CORRECTING DEFECT 146 (vertices=45, convex hull=40) After retessellation of defect 146, euler #=-7 (150126,450252,300119) : difference with theory (-7) = 0 CORRECTING DEFECT 147 (vertices=33, convex hull=33) After retessellation of defect 147, euler #=-6 (150129,450268,300133) : difference with theory (-6) = 0 CORRECTING DEFECT 148 (vertices=10, convex hull=18) After retessellation of defect 148, euler #=-5 (150130,450278,300143) : difference with theory (-5) = 0 CORRECTING DEFECT 149 (vertices=38, convex hull=40) After retessellation of defect 149, euler #=-4 (150134,450305,300167) : difference with theory (-4) = 0 CORRECTING DEFECT 150 (vertices=31, convex hull=49) After retessellation of defect 150, euler #=-3 (150142,450349,300204) : difference with theory (-3) = 0 CORRECTING DEFECT 151 (vertices=28, convex hull=64) After retessellation of defect 151, euler #=-2 (150152,450404,300250) : difference with theory (-2) = 0 CORRECTING DEFECT 152 (vertices=22, convex hull=47) After retessellation of defect 152, euler #=-1 (150161,450449,300287) : difference with theory (-1) = 0 CORRECTING DEFECT 153 (vertices=21, convex hull=27) After retessellation of defect 153, euler #=0 (150163,450465,300302) : difference with theory (0) = 0 CORRECTING DEFECT 154 (vertices=34, convex hull=21) After retessellation of defect 154, euler #=1 (150166,450482,300317) : difference with theory (1) = 0 CORRECTING DEFECT 155 (vertices=16, convex hull=33) After retessellation of defect 155, euler #=2 (150168,450498,300332) : 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-->14.29) (max @ vno 58860 --> 64507) 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-->14.29) (max @ vno 58860 --> 64507) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 593 mutations (35.8%), 1062 crossovers (64.2%), 1148 vertices were eliminated building final representation... 21076 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=150168, nf=300332, ne=450498, g=0) writing corrected surface to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 149.0 minutes 0 defective edges removing intersecting faces 000: 3379 intersecting 001: 632 intersecting 002: 473 intersecting 003: 413 intersecting 004: 284 intersecting 005: 204 intersecting 006: 172 intersecting expanding nbhd size to 2 007: 173 intersecting 008: 151 intersecting 009: 147 intersecting 010: 135 intersecting 011: 131 intersecting 012: 129 intersecting 013: 123 intersecting 014: 112 intersecting expanding nbhd size to 3 015: 112 intersecting expanding nbhd size to 4 016: 117 intersecting 017: 106 intersecting 018: 98 intersecting 019: 95 intersecting 020: 79 intersecting 021: 74 intersecting 022: 63 intersecting 023: 57 intersecting 024: 55 intersecting 025: 52 intersecting expanding nbhd size to 5 026: 53 intersecting 027: 51 intersecting 028: 50 intersecting 029: 45 intersecting 030: 42 intersecting 031: 40 intersecting expanding nbhd size to 6 032: 40 intersecting 033: 39 intersecting 034: 38 intersecting 035: 36 intersecting 036: 35 intersecting expanding nbhd size to 7 037: 36 intersecting 038: 33 intersecting expanding nbhd size to 8 039: 33 intersecting 040: 31 intersecting 041: 27 intersecting 042: 25 intersecting 043: 22 intersecting 044: 20 intersecting 045: 14 intersecting 046: 8 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 150168 - 450498 + 300332 = 2 --> 0 holes F =2V-4: 300332 = 300336-4 (0) 2E=3F: 900996 = 900996 (0) total defect index = 0 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.01 hours removing intersecting faces 000: 1866 intersecting 001: 565 intersecting 002: 450 intersecting 003: 387 intersecting 004: 265 intersecting 005: 211 intersecting 006: 170 intersecting 007: 168 intersecting 008: 152 intersecting 009: 141 intersecting 010: 137 intersecting 011: 128 intersecting 012: 116 intersecting 013: 114 intersecting expanding nbhd size to 2 014: 118 intersecting 015: 114 intersecting expanding nbhd size to 3 016: 115 intersecting 017: 108 intersecting expanding nbhd size to 4 018: 109 intersecting 019: 104 intersecting 020: 93 intersecting 021: 86 intersecting 022: 77 intersecting 023: 71 intersecting 024: 67 intersecting 025: 62 intersecting 026: 53 intersecting 027: 52 intersecting expanding nbhd size to 5 028: 54 intersecting 029: 50 intersecting 030: 45 intersecting expanding nbhd size to 6 031: 47 intersecting 032: 45 intersecting 033: 41 intersecting 034: 39 intersecting expanding nbhd size to 7 035: 39 intersecting 036: 38 intersecting 037: 37 intersecting 038: 36 intersecting 039: 35 intersecting 040: 31 intersecting 041: 29 intersecting expanding nbhd size to 8 042: 30 intersecting 043: 27 intersecting 044: 24 intersecting 045: 23 intersecting 046: 18 intersecting 047: 9 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Jan 2 21:20:53 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 21161 bright wm thresholded. 1636 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (94.0): 94.3 +- 7.9 [70.0 --> 110.0] GM (82.0) : 78.4 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.3 (was 70) setting MAX_BORDER_WHITE to 106.9 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 47.6 (was 40) setting MAX_GRAY to 91.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.01-->6.87) (max @ vno 147019 --> 147651) face area 0.27 +- 0.16 (0.00-->8.03) mean absolute distance = 0.83 +- 1.08 4485 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=99, GM=77 mean inside = 90.8, mean outside = 78.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.5, 3648 (3648) missing vertices, mean dist 0.2 [0.8 (%38.2)->0.8 (%61.8))] %67 local maxima, %22 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 0.90 +- 0.31 (0.04-->6.96) (max @ vno 58931 --> 57757) face area 0.27 +- 0.17 (0.00-->6.91) mean absolute distance = 0.50 +- 0.76 5508 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5233608.5, rms=9.27 001: dt: 0.5000, sse=6513731.5, rms=7.476 (0.000%) 002: dt: 0.5000, sse=6706423.5, rms=6.307 (0.000%) 003: dt: 0.5000, sse=7003605.0, rms=5.501 (0.000%) 004: dt: 0.5000, sse=7084486.5, rms=4.927 (0.000%) 005: dt: 0.5000, sse=7240545.0, rms=4.580 (0.000%) 006: dt: 0.5000, sse=7241173.0, rms=4.364 (0.000%) 007: dt: 0.5000, sse=7342248.5, rms=4.243 (0.000%) 008: dt: 0.5000, sse=7345578.5, rms=4.154 (0.000%) 009: dt: 0.5000, sse=7367017.5, rms=4.071 (0.000%) 010: dt: 0.5000, sse=7344674.0, rms=4.008 (0.000%) 011: dt: 0.5000, sse=7339942.0, rms=3.942 (0.000%) rms = 3.90, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=7336799.5, rms=3.903 (0.000%) 013: dt: 0.2500, sse=5198942.0, rms=3.523 (0.000%) 014: dt: 0.2500, sse=4965823.5, rms=3.455 (0.000%) rms = 3.44, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4883002.0, rms=3.440 (0.000%) rms = 3.39, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4792370.5, rms=3.391 (0.000%) positioning took 1.4 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 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.9, 3163 (2486) missing vertices, mean dist -0.3 [0.6 (%69.5)->0.4 (%30.5))] %77 local maxima, %11 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 +- 0.31 (0.02-->7.62) (max @ vno 58931 --> 57757) face area 0.33 +- 0.21 (0.00-->8.18) mean absolute distance = 0.36 +- 0.53 4614 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5174922.0, rms=4.84 017: dt: 0.5000, sse=5648101.0, rms=3.930 (0.000%) 018: dt: 0.5000, sse=6340446.0, rms=3.685 (0.000%) rms = 3.65, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6476945.0, rms=3.650 (0.000%) 020: dt: 0.2500, sse=5564828.0, rms=3.330 (0.000%) 021: dt: 0.2500, sse=5386251.5, rms=3.256 (0.000%) rms = 3.24, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5310478.5, rms=3.245 (0.000%) 023: dt: 0.1250, sse=5232859.0, rms=3.176 (0.000%) rms = 3.15, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5199694.5, rms=3.152 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.2, 3103 (2301) missing vertices, mean dist -0.1 [0.4 (%63.3)->0.3 (%36.7))] %81 local maxima, % 7 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 +- 0.31 (0.04-->7.74) (max @ vno 58931 --> 57757) face area 0.32 +- 0.21 (0.00-->8.23) mean absolute distance = 0.31 +- 0.44 3713 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5293151.0, rms=3.81 025: dt: 0.5000, sse=5790871.0, rms=3.501 (0.000%) 026: dt: 0.5000, sse=6382301.0, rms=3.405 (0.000%) rms = 3.48, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5762011.5, rms=3.197 (0.000%) 028: dt: 0.2500, sse=5537086.5, rms=3.127 (0.000%) rms = 3.13, time step reduction 2 of 3 to 0.125... rms = 3.10, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5468456.0, rms=3.101 (0.000%) positioning took 0.6 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 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 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 3 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 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 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.7, 3149 (2229) missing vertices, mean dist -0.0 [0.3 (%54.2)->0.3 (%45.8))] %83 local maxima, % 5 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/MPS1036-1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5484363.0, rms=3.25 030: dt: 0.5000, sse=7015162.0, rms=3.160 (0.000%) rms = 3.27, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=6398160.0, rms=2.999 (0.000%) rms = 3.00, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=6170094.5, rms=2.996 (0.000%) 033: dt: 0.1250, sse=6135512.0, rms=2.913 (0.000%) rms = 2.89, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=6113836.0, rms=2.885 (0.000%) positioning took 0.5 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 generating cortex label... 37 non-cortical segments detected only using segment with 2173 vertices erasing segment 0 (vno[0] = 53334) erasing segment 2 (vno[0] = 53549) erasing segment 3 (vno[0] = 54568) erasing segment 4 (vno[0] = 64533) erasing segment 5 (vno[0] = 72173) erasing segment 6 (vno[0] = 73422) erasing segment 7 (vno[0] = 74668) erasing segment 8 (vno[0] = 78273) erasing segment 9 (vno[0] = 80651) erasing segment 10 (vno[0] = 82705) erasing segment 11 (vno[0] = 84228) erasing segment 12 (vno[0] = 86083) erasing segment 13 (vno[0] = 86473) erasing segment 14 (vno[0] = 88490) erasing segment 15 (vno[0] = 95628) erasing segment 16 (vno[0] = 99855) erasing segment 17 (vno[0] = 100771) erasing segment 18 (vno[0] = 100781) erasing segment 19 (vno[0] = 100838) erasing segment 20 (vno[0] = 102619) erasing segment 21 (vno[0] = 103405) erasing segment 22 (vno[0] = 104332) erasing segment 23 (vno[0] = 105249) erasing segment 24 (vno[0] = 106054) erasing segment 25 (vno[0] = 106944) erasing segment 26 (vno[0] = 107688) erasing segment 27 (vno[0] = 107726) erasing segment 28 (vno[0] = 109318) erasing segment 29 (vno[0] = 109349) erasing segment 30 (vno[0] = 110168) erasing segment 31 (vno[0] = 110169) erasing segment 32 (vno[0] = 110926) erasing segment 33 (vno[0] = 111565) erasing segment 34 (vno[0] = 111577) erasing segment 35 (vno[0] = 112186) erasing segment 36 (vno[0] = 149055) writing cortex label to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label... writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.area vertex spacing 0.88 +- 0.32 (0.02-->7.73) (max @ vno 58931 --> 57757) face area 0.32 +- 0.21 (0.00-->8.31) refinement took 4.7 minutes #-------------------------------------------- #@# Smooth2 lh Thu Jan 2 21:25:34 CST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Jan 2 21:25:39 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 52.7 mm, total surface area = 86766 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.125 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.068 (target=0.015) step 015: RMS=0.057 (target=0.015) step 020: RMS=0.048 (target=0.015) step 025: RMS=0.041 (target=0.015) step 030: RMS=0.035 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.018 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 189 vertices thresholded to be in k1 ~ [-0.32 1.96], k2 ~ [-0.10 0.08] total integrated curvature = 0.361*4pi (4.537) --> 1 handles ICI = 1.3, FI = 9.9, variation=162.503 133 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 151 vertices thresholded to be in [-0.16 0.79] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.027 done. #----------------------------------------- #@# Curvature Stats lh Thu Jan 2 21:27:29 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm MPS1036-1 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 [ MPS1036-1/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 [ 315 ] Gb_filter = 0 WARN: S lookup min: -0.240089 WARN: S explicit min: 0.000000 vertex = 9 #-------------------------------------------- #@# Sphere lh Thu Jan 2 21:27:36 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.279... 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 %19.68 pass 1: epoch 2 of 3 starting distance error %19.66 unfolding complete - removing small folds... starting distance error %19.54 removing remaining folds... final distance error %19.56 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.78 hours #-------------------------------------------- #@# Surf Reg lh Thu Jan 2 22:14:22 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_register -curv ../surf/lh.sphere /soft/freesurfer/5.3.0_1/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_1/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 = 0.543 curvature mean = 0.042, std = 0.943 curvature mean = 0.023, std = 0.842 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 347564.7, tmin=0.8934 d=32.00 min @ (0.00, -8.00, 0.00) sse = 333847.8, tmin=1.7887 d=16.00 min @ (-4.00, 4.00, -4.00) sse = 300594.0, tmin=2.6945 d=8.00 min @ (2.00, 0.00, 0.00) sse = 296192.9, tmin=3.6862 d=4.00 min @ (-1.00, -1.00, 1.00) sse = 294667.9, tmin=4.7033 d=2.00 min @ (0.50, 0.00, -0.50) sse = 294280.8, tmin=5.7263 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 294272.0, tmin=7.6975 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 7.70 min curvature mean = -0.015, std = 0.941 curvature mean = 0.007, std = 0.931 curvature mean = -0.025, std = 0.948 curvature mean = 0.003, std = 0.968 curvature mean = -0.030, std = 0.947 curvature mean = 0.001, std = 0.984 2 Reading smoothwm curvature mean = -0.033, std = 0.388 curvature mean = 0.006, std = 0.069 curvature mean = 0.048, std = 0.255 curvature mean = 0.004, std = 0.079 curvature mean = 0.030, std = 0.391 curvature mean = 0.004, std = 0.085 curvature mean = 0.017, std = 0.508 curvature mean = 0.003, std = 0.087 curvature mean = 0.006, std = 0.613 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Jan 2 22:42:33 CST 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 Jan 2 22:42:35 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mrisp_paint -a 5 /soft/freesurfer/5.3.0_1/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_1/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Jan 2 22:42:36 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 3494 labels changed using aseg relabeling using gibbs priors... 000: 3176 changed, 150168 examined... 001: 762 changed, 13510 examined... 002: 185 changed, 4146 examined... 003: 63 changed, 1090 examined... 004: 31 changed, 402 examined... 005: 11 changed, 151 examined... 006: 10 changed, 73 examined... 007: 2 changed, 49 examined... 008: 2 changed, 12 examined... 009: 2 changed, 12 examined... 010: 1 changed, 11 examined... 011: 1 changed, 6 examined... 012: 2 changed, 7 examined... 013: 2 changed, 10 examined... 014: 1 changed, 10 examined... 015: 2 changed, 6 examined... 016: 1 changed, 12 examined... 017: 0 changed, 5 examined... 276 labels changed using aseg 000: 232 total segments, 183 labels (736 vertices) changed 001: 52 total segments, 4 labels (4 vertices) changed 002: 48 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 53 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2874 vertices marked for relabeling... 2874 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 41 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Jan 2 22:43:18 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 21161 bright wm thresholded. 1636 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (94.0): 94.3 +- 7.9 [70.0 --> 110.0] GM (82.0) : 78.4 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.3 (was 70) setting MAX_BORDER_WHITE to 106.9 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 47.6 (was 40) setting MAX_GRAY to 91.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99, GM=77 mean inside = 90.8, mean outside = 78.5 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/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.01-->6.87) (max @ vno 147019 --> 147651) face area 0.27 +- 0.16 (0.00-->8.03) mean absolute distance = 0.84 +- 1.11 4468 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 143 points - only 0.00% unknown deleting segment 2 with 20 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 8 with 22 points - only 0.00% unknown deleting segment 9 with 53 points - only 0.00% unknown deleting segment 10 with 51 points - only 0.00% unknown deleting segment 11 with 59 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 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown deleting segment 17 with 62 points - only 0.00% unknown deleting segment 18 with 74 points - only 0.00% unknown deleting segment 19 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 20 with 3 points - only 0.00% unknown deleting segment 22 with 39 points - only 0.00% unknown deleting segment 23 with 8 points - only 0.00% unknown deleting segment 24 with 7 points - only 0.00% unknown deleting segment 25 with 38 points - only 0.00% unknown deleting segment 26 with 122 points - only 0.00% unknown deleting segment 27 with 8 points - only 0.00% unknown deleting segment 28 with 83 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 29 with 2 points - only 0.00% unknown deleting segment 30 with 18 points - only 0.00% unknown deleting segment 31 with 145 points - only 0.00% unknown deleting segment 32 with 186 points - only 0.00% unknown deleting segment 33 with 154 points - only 0.00% unknown deleting segment 34 with 20 points - only 0.00% unknown deleting segment 35 with 76 points - only 0.00% unknown deleting segment 36 with 17 points - only 0.00% unknown deleting segment 37 with 14 points - only 0.00% unknown deleting segment 38 with 33 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 39 with 2 points - only 0.00% unknown deleting segment 40 with 24 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 41 with 4 points - only 0.00% unknown mean border=85.5, 3819 (3713) missing vertices, mean dist 0.2 [0.8 (%38.7)->0.8 (%61.3))] %67 local maxima, %22 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 0.90 +- 0.31 (0.03-->6.96) (max @ vno 58931 --> 57757) face area 0.27 +- 0.17 (0.00-->7.29) mean absolute distance = 0.51 +- 0.79 5329 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5346159.0, rms=9.39 001: dt: 0.5000, sse=6633900.5, rms=7.606 (0.000%) 002: dt: 0.5000, sse=6823738.0, rms=6.447 (0.000%) 003: dt: 0.5000, sse=7117860.0, rms=5.644 (0.000%) 004: dt: 0.5000, sse=7198064.0, rms=5.070 (0.000%) 005: dt: 0.5000, sse=7359454.0, rms=4.719 (0.000%) 006: dt: 0.5000, sse=7361677.0, rms=4.496 (0.000%) 007: dt: 0.5000, sse=7452761.5, rms=4.366 (0.000%) 008: dt: 0.5000, sse=7454219.5, rms=4.271 (0.000%) 009: dt: 0.5000, sse=7480977.0, rms=4.185 (0.000%) 010: dt: 0.5000, sse=7448255.5, rms=4.117 (0.000%) 011: dt: 0.5000, sse=7442724.5, rms=4.048 (0.000%) rms = 4.01, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=7453679.0, rms=4.008 (0.000%) 013: dt: 0.2500, sse=5263612.0, rms=3.632 (0.000%) 014: dt: 0.2500, sse=5032096.0, rms=3.562 (0.000%) rms = 3.54, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4945310.5, rms=3.536 (0.000%) rms = 3.49, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4855702.0, rms=3.492 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 183 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 24 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 8 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 15 with 5 points - only 0.00% unknown deleting segment 16 with 344 points - only 0.00% unknown deleting segment 18 with 73 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 19 with 2 points - only 0.00% unknown deleting segment 20 with 11 points - only 0.00% unknown deleting segment 21 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 22 with 4 points - only 0.00% unknown deleting segment 23 with 7 points - only 0.00% unknown deleting segment 24 with 9 points - only 0.00% unknown deleting segment 25 with 7 points - only 0.00% unknown deleting segment 26 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 29 with 3 points - only 0.00% unknown deleting segment 30 with 51 points - only 0.00% unknown deleting segment 31 with 46 points - only 0.00% unknown deleting segment 32 with 7 points - only 0.00% unknown deleting segment 34 with 428 points - only 0.00% unknown deleting segment 35 with 84 points - only 0.00% unknown deleting segment 36 with 11 points - only 0.00% unknown deleting segment 37 with 7 points - only 42.86% unknown removing 4 vertex label from ripped group deleting segment 40 with 544 points - only 0.00% unknown deleting segment 41 with 10 points - only 0.00% unknown deleting segment 43 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 44 with 2 points - only 0.00% unknown deleting segment 45 with 208 points - only 0.00% unknown deleting segment 46 with 218 points - only 0.00% unknown deleting segment 47 with 20 points - only 0.00% unknown deleting segment 49 with 75 points - only 0.00% unknown deleting segment 50 with 43 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 52 with 14 points - only 0.00% unknown deleting segment 53 with 176 points - only 0.00% unknown mean border=87.9, 3435 (2542) missing vertices, mean dist -0.3 [0.6 (%69.7)->0.4 (%30.3))] %79 local maxima, %11 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 +- 0.31 (0.06-->7.66) (max @ vno 58931 --> 57757) face area 0.33 +- 0.21 (0.00-->9.03) mean absolute distance = 0.37 +- 0.55 4269 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5338032.0, rms=5.05 017: dt: 0.5000, sse=5828669.5, rms=4.170 (0.000%) 018: dt: 0.5000, sse=6546468.0, rms=3.924 (0.000%) 019: dt: 0.5000, sse=6673098.0, rms=3.873 (0.000%) 020: dt: 0.5000, sse=7217985.5, rms=3.805 (0.000%) rms = 3.82, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=6077954.0, rms=3.543 (0.000%) 022: dt: 0.2500, sse=5653521.5, rms=3.431 (0.000%) rms = 3.42, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5531872.0, rms=3.420 (0.000%) 024: dt: 0.1250, sse=5421610.5, rms=3.354 (0.000%) rms = 3.32, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5381814.5, rms=3.325 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown deleting segment 1 with 49 points - only 0.00% unknown deleting segment 2 with 125 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 388 points - only 0.00% unknown deleting segment 14 with 103 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 25 points - only 0.00% unknown deleting segment 17 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 19 with 3 points - only 0.00% unknown deleting segment 20 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 24 with 4 points - only 0.00% unknown deleting segment 25 with 49 points - only 0.00% unknown deleting segment 26 with 52 points - only 0.00% unknown deleting segment 27 with 74 points - only 50.00% unknown deleting segment 28 with 6 points - only 0.00% unknown deleting segment 29 with 461 points - only 0.00% unknown deleting segment 31 with 89 points - only 0.00% unknown deleting segment 32 with 11 points - only 0.00% unknown deleting segment 33 with 7 points - only 42.86% unknown removing 4 vertex label from ripped group deleting segment 35 with 559 points - only 0.00% unknown deleting segment 36 with 9 points - only 0.00% unknown deleting segment 37 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 38 with 2 points - only 0.00% unknown deleting segment 39 with 190 points - only 0.00% unknown deleting segment 40 with 194 points - only 0.00% unknown deleting segment 41 with 20 points - only 0.00% unknown deleting segment 42 with 75 points - only 0.00% unknown deleting segment 43 with 41 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 45 with 16 points - only 0.00% unknown deleting segment 46 with 185 points - only 0.00% unknown mean border=89.3, 3453 (2372) missing vertices, mean dist -0.1 [0.4 (%63.4)->0.3 (%36.6))] %83 local maxima, % 7 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 +- 0.31 (0.03-->7.77) (max @ vno 58931 --> 57757) face area 0.32 +- 0.21 (0.00-->8.47) mean absolute distance = 0.32 +- 0.47 3403 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5493182.0, rms=3.97 026: dt: 0.5000, sse=5984089.5, rms=3.665 (0.000%) 027: dt: 0.5000, sse=6625040.5, rms=3.567 (0.000%) rms = 3.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5981118.5, rms=3.368 (0.000%) 029: dt: 0.2500, sse=5740574.0, rms=3.302 (0.000%) rms = 3.29, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5661442.5, rms=3.294 (0.000%) 031: dt: 0.1250, sse=5586683.5, rms=3.233 (0.000%) rms = 3.21, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5541591.0, rms=3.209 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 26 points - only 0.00% unknown deleting segment 1 with 51 points - only 0.00% unknown deleting segment 2 with 118 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 373 points - only 0.00% unknown deleting segment 13 with 110 points - only 0.00% unknown deleting segment 14 with 86 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown deleting segment 18 with 46 points - only 0.00% unknown deleting segment 19 with 41 points - only 0.00% unknown deleting segment 20 with 82 points - only 54.88% unknown deleting segment 21 with 5 points - only 0.00% unknown deleting segment 22 with 465 points - only 0.00% unknown deleting segment 23 with 83 points - only 0.00% unknown deleting segment 24 with 11 points - only 0.00% unknown deleting segment 25 with 19 points - only 15.79% unknown deleting segment 26 with 553 points - only 0.00% unknown deleting segment 27 with 8 points - only 0.00% unknown deleting segment 28 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 29 with 3 points - only 0.00% unknown deleting segment 30 with 182 points - only 0.00% unknown deleting segment 31 with 194 points - only 0.00% unknown deleting segment 32 with 20 points - only 0.00% unknown deleting segment 33 with 75 points - only 0.00% unknown deleting segment 34 with 38 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 36 with 18 points - only 0.00% unknown deleting segment 37 with 182 points - only 0.00% unknown mean border=89.7, 3461 (2262) missing vertices, mean dist -0.0 [0.3 (%54.3)->0.3 (%45.7))] %84 local maxima, % 5 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=5563111.0, rms=3.39 033: dt: 0.5000, sse=7183804.5, rms=3.293 (0.000%) rms = 3.37, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=6592945.0, rms=3.158 (0.000%) rms = 3.14, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=6337620.5, rms=3.143 (0.000%) 036: dt: 0.1250, sse=6301662.0, rms=3.071 (0.000%) rms = 3.05, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=6316444.0, rms=3.050 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=64.2, 3026 (3026) missing vertices, mean dist 1.5 [3.5 (%2.2)->3.7 (%97.8))] %22 local maxima, %16 large gradients and %54 min vals, 3121 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=21776984.0, rms=26.24 001: dt: 0.5000, sse=18108794.0, rms=23.493 (0.000%) 002: dt: 0.5000, sse=15290035.0, rms=21.120 (0.000%) 003: dt: 0.5000, sse=13106824.0, rms=19.111 (0.000%) 004: dt: 0.5000, sse=11493890.0, rms=17.408 (0.000%) 005: dt: 0.5000, sse=10277456.0, rms=15.941 (0.000%) 006: dt: 0.5000, sse=9401478.0, rms=14.653 (0.000%) 007: dt: 0.5000, sse=8799620.0, rms=13.468 (0.000%) 008: dt: 0.5000, sse=8360737.5, rms=12.353 (0.000%) 009: dt: 0.5000, sse=8169877.5, rms=11.348 (0.000%) 010: dt: 0.5000, sse=8023346.5, rms=10.416 (0.000%) 011: dt: 0.5000, sse=8036418.5, rms=9.559 (0.000%) 012: dt: 0.5000, sse=8040929.5, rms=8.760 (0.000%) 013: dt: 0.5000, sse=8110035.0, rms=8.055 (0.000%) 014: dt: 0.5000, sse=8139589.5, rms=7.456 (0.000%) 015: dt: 0.5000, sse=8223955.5, rms=6.967 (0.000%) 016: dt: 0.5000, sse=8267452.0, rms=6.596 (0.000%) 017: dt: 0.5000, sse=8335230.5, rms=6.335 (0.000%) 018: dt: 0.5000, sse=8338948.0, rms=6.166 (0.000%) 019: dt: 0.5000, sse=8388513.5, rms=6.041 (0.000%) 020: dt: 0.5000, sse=8353532.5, rms=5.954 (0.000%) 021: dt: 0.5000, sse=8408607.0, rms=5.894 (0.000%) 022: dt: 0.5000, sse=8392925.0, rms=5.836 (0.000%) rms = 5.79, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=8354063.5, rms=5.794 (0.000%) 024: dt: 0.2500, sse=6475170.0, rms=5.286 (0.000%) 025: dt: 0.2500, sse=6351686.0, rms=5.154 (0.000%) rms = 5.17, time step reduction 2 of 3 to 0.125... 026: dt: 0.1250, sse=6145760.0, rms=5.059 (0.000%) 027: dt: 0.1250, sse=5779848.5, rms=4.927 (0.000%) rms = 4.89, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5689459.0, rms=4.888 (0.000%) positioning took 2.8 minutes mean border=62.6, 5431 (1560) missing vertices, mean dist 0.2 [0.3 (%35.4)->0.8 (%64.6))] %30 local maxima, %14 large gradients and %46 min vals, 2235 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=6321019.0, rms=6.19 029: dt: 0.5000, sse=6892920.5, rms=6.038 (0.000%) 030: dt: 0.5000, sse=8082287.5, rms=5.763 (0.000%) rms = 5.84, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=7069456.0, rms=5.237 (0.000%) 032: dt: 0.2500, sse=6720642.5, rms=5.104 (0.000%) rms = 5.17, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=6570770.5, rms=5.010 (0.000%) 034: dt: 0.1250, sse=6342060.0, rms=4.886 (0.000%) rms = 4.84, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=6282797.0, rms=4.838 (0.000%) positioning took 0.9 minutes mean border=62.3, 6700 (1441) missing vertices, mean dist 0.1 [0.3 (%41.0)->0.6 (%59.0))] %32 local maxima, %11 large gradients and %46 min vals, 2134 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=6326381.0, rms=4.94 rms = 5.41, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=6205876.0, rms=4.772 (0.000%) rms = 4.74, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=6385645.5, rms=4.741 (0.000%) 038: dt: 0.1250, sse=6234392.5, rms=4.660 (0.000%) rms = 4.62, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=6267748.5, rms=4.617 (0.000%) positioning took 0.5 minutes mean border=62.0, 11298 (1408) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.4 (%55.3))] %32 local maxima, %10 large gradients and %44 min vals, 2034 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/MPS1036-1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6266447.0, rms=4.61 rms = 4.98, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=6246308.5, rms=4.514 (0.000%) 041: dt: 0.2500, sse=6635978.0, rms=4.463 (0.000%) rms = 4.50, time step reduction 2 of 3 to 0.125... rms = 4.43, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=6568963.0, rms=4.431 (0.000%) positioning took 0.5 minutes writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.area.pial vertex spacing 0.98 +- 0.48 (0.02-->9.22) (max @ vno 146918 --> 146971) face area 0.37 +- 0.34 (0.00-->9.57) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 150168 vertices processed 25000 of 150168 vertices processed 50000 of 150168 vertices processed 75000 of 150168 vertices processed 100000 of 150168 vertices processed 125000 of 150168 vertices processed 150000 of 150168 vertices processed 0 of 150168 vertices processed 25000 of 150168 vertices processed 50000 of 150168 vertices processed 75000 of 150168 vertices processed 100000 of 150168 vertices processed 125000 of 150168 vertices processed 150000 of 150168 vertices processed thickness calculation complete, 2173:3131 truncations. 23860 vertices at 0 distance 72961 vertices at 1 distance 82161 vertices at 2 distance 53446 vertices at 3 distance 26994 vertices at 4 distance 11998 vertices at 5 distance 4926 vertices at 6 distance 2094 vertices at 7 distance 938 vertices at 8 distance 489 vertices at 9 distance 308 vertices at 10 distance 217 vertices at 11 distance 175 vertices at 12 distance 137 vertices at 13 distance 105 vertices at 14 distance 100 vertices at 15 distance 78 vertices at 16 distance 80 vertices at 17 distance 49 vertices at 18 distance 31 vertices at 19 distance 67 vertices at 20 distance writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.thickness positioning took 10.7 minutes #-------------------------------------------- #@# Surf Volume lh Thu Jan 2 22:54:00 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Thu Jan 2 22:54:01 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts pctsurfcon --s MPS1036-1 --lh-only Log file is /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts/pctsurfcon.log Thu Jan 2 22:54:01 CST 2014 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis cd /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts /soft/freesurfer/5.3.0_1/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node1108 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_1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.1410/lh.wm.mgh --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 79135 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.1410/lh.wm.mgh Dim: 150168 1 1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.1410/lh.gm.mgh --projfrac 0.3 --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Done reading source surface Reading thickness /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 91088 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.1410/lh.gm.mgh Dim: 150168 1 1 mri_concat /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.1410/lh.wm.mgh /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.1410/lh.gm.mgh --paired-diff-norm --mul 100 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh mri_segstats --in /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh --annot MPS1036-1 lh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh --annot MPS1036-1 lh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/stats/lh.w-g.pct.stats --snr sysname Linux hostname node1108 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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh Vertex Area is 0.642548 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1436 980.109 2 1002 caudalanteriorcingulate 1544 1131.621 3 1003 caudalmiddlefrontal 4410 2830.203 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2071 1369.984 6 1006 entorhinal 539 356.259 7 1007 fusiform 3862 2608.408 8 1008 inferiorparietal 7566 4699.072 9 1009 inferiortemporal 5480 3662.999 10 1010 isthmuscingulate 3166 1777.736 11 1011 lateraloccipital 8173 5085.528 12 1012 lateralorbitofrontal 3193 2153.475 13 1013 lingual 3534 2544.161 14 1014 medialorbitofrontal 2633 1724.725 15 1015 middletemporal 5465 3564.127 16 1016 parahippocampal 1079 734.481 17 1017 paracentral 2238 1458.948 18 1018 parsopercularis 2333 1387.850 19 1019 parsorbitalis 1249 697.139 20 1020 parstriangularis 2527 1582.636 21 1021 pericalcarine 1827 1196.437 22 1022 postcentral 6891 4334.258 23 1023 posteriorcingulate 2109 1417.566 24 1024 precentral 8688 5673.733 25 1025 precuneus 4986 3303.581 26 1026 rostralanteriorcingulate 1023 728.234 27 1027 rostralmiddlefrontal 10482 6663.481 28 1028 superiorfrontal 11587 7917.416 29 1029 superiorparietal 8299 5154.621 30 1030 superiortemporal 6103 3772.483 31 1031 supramarginal 7444 4651.457 32 1032 frontalpole 549 299.445 33 1033 temporalpole 869 606.191 34 1034 transversetemporal 662 421.307 35 1035 insula 3899 2366.713 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Thu Jan 2 22:54:10 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1436 980 2786 3.073 0.686 0.145 0.072 22 4.5 bankssts 1544 1132 2855 2.660 1.083 0.272 0.287 292 17.1 caudalanteriorcingulate 4410 2830 10195 3.396 0.660 0.195 0.362 611 89.4 caudalmiddlefrontal 2071 1370 3260 2.184 0.623 0.172 0.066 43 5.4 cuneus 539 356 1277 2.777 0.831 0.252 0.379 75 4.9 entorhinal 3862 2608 8094 2.772 0.624 0.174 0.128 174 25.8 fusiform 7566 4699 15229 3.021 0.650 0.171 0.697 1809 60.6 inferiorparietal 5480 3663 13539 3.246 0.864 0.176 0.100 149 22.5 inferiortemporal 3166 1778 3315 1.817 0.842 0.155 1.666 526 19.2 isthmuscingulate 8173 5086 13137 2.413 0.694 0.177 0.097 254 32.8 lateraloccipital 3193 2153 8373 3.498 0.863 0.159 0.081 82 10.3 lateralorbitofrontal 3534 2544 6486 2.306 0.730 0.201 0.152 170 21.6 lingual 2633 1725 6020 2.976 1.086 0.158 0.105 89 9.2 medialorbitofrontal 5465 3564 14235 3.380 0.741 0.168 0.097 1127 23.6 middletemporal 1079 734 1567 1.946 0.548 0.158 0.095 32 4.4 parahippocampal 2238 1459 4403 2.726 0.645 0.157 0.189 248 8.1 paracentral 2333 1388 4824 3.071 0.717 0.159 0.215 237 17.1 parsopercularis 1249 697 2355 2.729 0.825 0.220 0.314 90 11.3 parsorbitalis 2527 1583 4828 2.758 0.780 0.174 0.128 161 13.7 parstriangularis 1827 1196 1840 1.706 0.616 0.196 0.106 54 8.3 pericalcarine 6891 4334 10692 2.344 0.812 0.173 0.131 964 34.5 postcentral 2109 1418 3344 2.244 0.858 0.157 0.147 229 7.9 posteriorcingulate 8688 5674 14649 2.584 0.922 0.190 0.263 664 64.1 precentral 4986 3304 10574 2.841 0.643 0.158 0.115 225 18.6 precuneus 1023 728 2705 2.816 1.253 0.236 0.380 133 9.7 rostralanteriorcingulate 10482 6663 22423 2.989 0.785 0.187 0.731 904 129.9 rostralmiddlefrontal 11587 7917 29719 3.329 1.042 0.194 0.329 1709 78.0 superiorfrontal 8299 5155 14553 2.662 0.578 0.169 0.148 435 54.5 superiorparietal 6103 3772 12574 2.974 0.672 0.134 0.110 287 21.6 superiortemporal 7444 4651 13895 2.751 0.730 0.181 0.567 3009 65.4 supramarginal 549 299 1080 2.561 0.836 0.226 0.332 256 9.4 frontalpole 869 606 2751 2.827 0.814 0.233 0.138 39 5.0 temporalpole 662 421 1101 2.425 0.675 0.170 0.083 13 2.4 transversetemporal 3899 2367 7126 2.859 1.134 0.121 0.111 109 17.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Jan 2 22:54:24 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 267 labels changed using aseg relabeling using gibbs priors... 000: 10262 changed, 150168 examined... 001: 2518 changed, 39348 examined... 002: 788 changed, 12976 examined... 003: 380 changed, 4362 examined... 004: 170 changed, 2019 examined... 005: 84 changed, 964 examined... 006: 53 changed, 483 examined... 007: 27 changed, 288 examined... 008: 16 changed, 150 examined... 009: 4 changed, 78 examined... 010: 1 changed, 24 examined... 011: 0 changed, 5 examined... 81 labels changed using aseg 000: 358 total segments, 277 labels (4309 vertices) changed 001: 107 total segments, 26 labels (282 vertices) changed 002: 84 total segments, 3 labels (9 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 135 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 2140 vertices marked for relabeling... 2140 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Jan 2 22:55:12 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1477 929 2884 2.772 0.809 0.212 2.271 205 10.6 G_and_S_frontomargin 1489 1065 3326 2.746 0.648 0.191 0.085 43 5.6 G_and_S_occipital_inf 1658 1038 3198 2.543 0.698 0.166 0.233 238 6.5 G_and_S_paracentral 1382 806 3104 3.168 0.792 0.167 0.169 65 12.4 G_and_S_subcentral 1041 663 1971 2.210 0.991 0.296 0.845 890 24.1 G_and_S_transv_frontopol 2743 2237 5135 2.190 1.281 0.300 0.930 891 29.9 G_and_S_cingul-Ant 1779 1190 3189 2.782 0.691 0.203 0.226 183 15.8 G_and_S_cingul-Mid-Ant 1428 1020 2546 2.573 0.561 0.139 0.053 24 3.0 G_and_S_cingul-Mid-Post 1065 684 1475 1.805 0.902 0.177 0.102 42 4.9 G_cingul-Post-dorsal 732 409 714 1.696 0.652 0.183 6.748 147 3.9 G_cingul-Post-ventral 1819 1197 2850 2.053 0.632 0.183 0.092 49 6.6 G_cuneus 1122 651 2771 2.927 0.861 0.181 0.214 179 13.1 G_front_inf-Opercular 254 149 690 2.933 0.625 0.192 0.135 10 1.9 G_front_inf-Orbital 1444 843 2966 2.674 0.799 0.195 0.167 132 10.1 G_front_inf-Triangul 5929 3652 14839 3.246 0.780 0.190 0.511 416 86.1 G_front_middle 8065 5203 24255 3.645 0.823 0.175 0.117 255 43.3 G_front_sup 596 350 1142 2.676 1.051 0.109 0.091 11 1.3 G_Ins_lg_and_S_cent_ins 733 447 1728 3.103 1.332 0.097 0.098 19 3.3 G_insular_short 2206 1286 4552 2.807 0.553 0.175 0.121 100 10.3 G_occipital_middle 1612 947 2900 2.480 0.514 0.177 0.093 55 6.2 G_occipital_sup 1318 916 3219 2.698 0.622 0.182 0.187 59 15.2 G_oc-temp_lat-fusifor 2372 1699 4682 2.219 0.774 0.223 0.197 152 18.3 G_oc-temp_med-Lingual 1388 860 2581 2.384 0.819 0.185 0.207 97 7.5 G_oc-temp_med-Parahip 2680 1647 6928 3.145 0.936 0.205 0.258 184 21.4 G_orbital 3588 2110 8068 2.979 0.750 0.196 1.375 1728 48.4 G_pariet_inf-Angular 4294 2569 8367 2.804 0.762 0.188 0.865 2859 36.8 G_pariet_inf-Supramar 3311 1871 6310 2.734 0.640 0.199 0.273 354 40.4 G_parietal_sup 3179 1853 4699 2.154 0.667 0.184 0.188 229 29.5 G_postcentral 3342 2096 6722 2.561 0.985 0.188 0.185 246 33.0 G_precentral 2601 1659 6255 2.925 0.706 0.187 0.128 121 14.2 G_precuneus 774 516 2598 3.454 1.025 0.206 0.110 36 3.3 G_rectus 502 259 542 1.983 1.147 0.142 0.130 22 2.4 G_subcallosal 561 353 1054 2.515 0.663 0.165 0.090 12 2.1 G_temp_sup-G_T_transv 2301 1325 5993 3.166 0.729 0.173 0.234 258 15.8 G_temp_sup-Lateral 602 399 1256 2.786 0.603 0.120 0.123 17 4.9 G_temp_sup-Plan_polar 804 557 1549 2.625 0.620 0.143 0.061 11 2.1 G_temp_sup-Plan_tempo 2994 2041 9012 3.350 0.927 0.203 0.137 108 16.8 G_temporal_inf 3430 2221 10650 3.482 0.760 0.180 0.097 91 13.7 G_temporal_middle 527 360 1028 2.896 0.588 0.134 0.053 5 1.2 Lat_Fis-ant-Horizont 393 240 653 3.073 0.976 0.168 0.140 23 2.8 Lat_Fis-ant-Vertical 951 618 1302 2.639 0.517 0.148 0.062 13 2.4 Lat_Fis-post 2691 1644 3232 1.913 0.593 0.188 0.101 71 11.5 Pole_occipital 2102 1390 5587 2.964 0.889 0.208 0.124 84 11.1 Pole_temporal 2149 1430 2560 1.993 0.769 0.168 0.072 45 6.4 S_calcarine 3027 2143 3074 1.798 0.599 0.212 0.238 890 21.0 S_central 1033 736 1763 2.596 0.464 0.113 0.030 8 1.4 S_cingul-Marginalis 446 309 758 3.046 0.546 0.111 0.035 4 0.7 S_circular_insula_ant 1700 1089 2923 3.052 0.579 0.091 0.028 10 1.8 S_circular_insula_inf 1718 1113 3227 3.225 0.681 0.148 0.179 71 6.3 S_circular_insula_sup 582 364 1040 2.831 0.646 0.128 0.059 7 1.5 S_collat_transv_ant 294 220 480 2.384 0.420 0.145 0.046 3 0.6 S_collat_transv_post 2860 1857 5622 3.012 0.635 0.156 0.432 296 36.5 S_front_inf 1712 1085 3292 2.939 0.656 0.161 0.255 168 24.3 S_front_middle 3112 2041 6255 3.390 0.602 0.164 0.284 328 44.3 S_front_sup 349 227 526 2.635 0.664 0.146 0.083 5 1.0 S_interm_prim-Jensen 3098 2072 4796 2.709 0.507 0.143 0.061 42 8.3 S_intrapariet_and_P_trans 1439 885 1990 2.455 0.653 0.158 0.069 25 4.3 S_oc_middle_and_Lunatus 1292 876 1981 2.501 0.469 0.135 0.053 16 2.7 S_oc_sup_and_transversal 751 521 1352 2.991 0.634 0.145 0.062 9 1.8 S_occipital_ant 1240 819 2217 2.857 0.545 0.143 0.061 19 3.3 S_oc-temp_lat 1936 1416 3072 2.527 0.633 0.178 0.103 106 8.8 S_oc-temp_med_and_Lingual 547 350 865 2.875 0.631 0.131 0.051 6 1.3 S_orbital_lateral 827 514 1629 2.609 1.570 0.110 0.066 15 1.5 S_orbital_med-olfact 1244 822 2448 3.425 0.984 0.161 0.091 30 4.2 S_orbital-H_Shaped 1839 1224 3210 2.585 0.567 0.147 0.068 61 5.4 S_parieto_occipital 2438 1380 2661 2.054 1.074 0.175 0.237 726 20.6 S_pericallosal 3323 2254 5140 2.728 0.605 0.159 0.101 113 13.1 S_postcentral 1912 1343 3494 3.238 0.587 0.203 0.540 236 13.5 S_precentral-inf-part 1755 1195 2810 3.181 0.675 0.161 0.102 35 7.6 S_precentral-sup-part 745 508 1410 2.902 1.106 0.141 0.054 11 1.9 S_suborbital 959 650 1860 2.861 0.640 0.119 0.191 62 2.2 S_subparietal 1773 1178 3159 3.272 0.652 0.139 0.071 22 5.5 S_temporal_inf 6132 4006 11203 3.124 0.655 0.146 0.083 1115 21.5 S_temporal_sup 405 261 465 2.207 0.488 0.142 0.047 4 0.8 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Thu Jan 2 22:55:26 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 278 labels changed using aseg relabeling using gibbs priors... 000: 3047 changed, 150168 examined... 001: 730 changed, 12957 examined... 002: 200 changed, 3969 examined... 003: 78 changed, 1156 examined... 004: 37 changed, 445 examined... 005: 15 changed, 210 examined... 006: 6 changed, 88 examined... 007: 5 changed, 32 examined... 008: 4 changed, 22 examined... 009: 3 changed, 18 examined... 010: 4 changed, 14 examined... 011: 1 changed, 8 examined... 012: 0 changed, 10 examined... 140 labels changed using aseg 000: 94 total segments, 58 labels (408 vertices) changed 001: 36 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 67 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2187 vertices marked for relabeling... 2187 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Thu Jan 2 22:56:13 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 2301 1710 4148 2.618 1.072 0.252 0.232 356 20.4 caudalanteriorcingulate 4571 2926 10679 3.392 0.656 0.195 0.354 616 90.4 caudalmiddlefrontal 2921 1932 4846 2.293 0.613 0.166 0.065 58 7.6 cuneus 535 349 1236 2.803 0.804 0.251 0.382 75 5.1 entorhinal 3333 2274 6817 2.762 0.606 0.161 0.119 148 21.5 fusiform 7238 4493 14529 2.990 0.670 0.171 0.723 1801 59.1 inferiorparietal 5467 3653 13778 3.226 0.856 0.185 0.111 164 24.7 inferiortemporal 3052 1725 3236 1.822 0.847 0.154 1.724 269 18.6 isthmuscingulate 8550 5319 13628 2.407 0.690 0.178 0.098 264 34.8 lateraloccipital 3700 2413 9480 3.340 1.078 0.160 0.093 105 12.5 lateralorbitofrontal 3556 2569 6563 2.302 0.729 0.201 0.152 170 21.6 lingual 2488 1593 5552 2.827 1.160 0.171 0.128 100 10.9 medialorbitofrontal 6892 4514 17164 3.329 0.752 0.164 0.089 1150 27.1 middletemporal 1093 744 1587 1.952 0.557 0.159 0.095 32 4.4 parahippocampal 2474 1621 4994 2.797 0.674 0.154 0.180 250 9.4 paracentral 1974 1201 4075 3.095 0.703 0.164 0.232 221 15.5 parsopercularis 1060 671 2444 3.106 0.646 0.162 0.079 27 3.9 parsorbitalis 3151 1940 5848 2.768 0.786 0.175 0.328 247 17.8 parstriangularis 1786 1158 1745 1.702 0.614 0.197 0.108 54 8.3 pericalcarine 7717 4856 11933 2.384 0.798 0.174 0.153 1062 53.3 postcentral 2342 1551 3561 2.242 0.847 0.160 0.140 487 8.8 posteriorcingulate 8534 5564 14152 2.576 0.923 0.190 0.265 659 62.7 precentral 4830 3203 10438 2.840 0.664 0.159 0.117 225 18.3 precuneus 1509 1035 3337 2.660 1.294 0.206 0.278 176 11.1 rostralanteriorcingulate 8243 5030 16910 2.974 0.805 0.191 0.623 740 122.6 rostralmiddlefrontal 12832 8668 33098 3.305 0.982 0.196 0.467 2004 92.5 superiorfrontal 6717 4137 11673 2.690 0.574 0.171 0.165 404 49.1 superiorparietal 8538 5379 18221 2.940 0.697 0.151 0.119 375 37.4 superiortemporal 6987 4378 13168 2.783 0.724 0.176 0.568 2915 47.8 supramarginal 664 422 1105 2.434 0.687 0.169 0.083 13 2.4 transversetemporal 2861 1827 5858 3.087 0.981 0.103 0.073 55 8.1 insula #-------------------------------------------- #@# Tessellate rh Thu Jan 2 22:56:27 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 1 found - 1 modified | TOTAL: 10 pass 2 (xy-): 0 found - 1 modified | TOTAL: 10 pass 1 (yz+): 8 found - 8 modified | TOTAL: 18 pass 2 (yz+): 0 found - 8 modified | TOTAL: 18 pass 1 (yz-): 6 found - 6 modified | TOTAL: 24 pass 2 (yz-): 0 found - 6 modified | TOTAL: 24 pass 1 (xz+): 9 found - 9 modified | TOTAL: 33 pass 2 (xz+): 0 found - 9 modified | TOTAL: 33 pass 1 (xz-): 4 found - 4 modified | TOTAL: 37 pass 2 (xz-): 0 found - 4 modified | TOTAL: 37 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 0 found - 0 modified | TOTAL: 8 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 6 found - 6 modified | TOTAL: 10 pass 2 (--): 0 found - 6 modified | TOTAL: 10 pass 1 (-+): 5 found - 5 modified | TOTAL: 15 pass 2 (-+): 0 found - 5 modified | TOTAL: 15 Iteration Number : 2 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+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 2 found - 2 modified | TOTAL: 5 pass 2 (xz-): 0 found - 2 modified | TOTAL: 5 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 3 found - 3 modified | TOTAL: 4 pass 2 (-+): 0 found - 3 modified | TOTAL: 4 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 = 69 (out of 323413: 0.021335) 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 50: 25 vertices, 34 faces slice 60: 2737 vertices, 2870 faces slice 70: 7809 vertices, 8022 faces slice 80: 14956 vertices, 15299 faces slice 90: 24377 vertices, 24823 faces slice 100: 35319 vertices, 35828 faces slice 110: 47923 vertices, 48511 faces slice 120: 61688 vertices, 62307 faces slice 130: 74074 vertices, 74691 faces slice 140: 86664 vertices, 87294 faces slice 150: 98767 vertices, 99392 faces slice 160: 110013 vertices, 110635 faces slice 170: 119513 vertices, 120077 faces slice 180: 125769 vertices, 126270 faces slice 190: 132435 vertices, 133001 faces slice 200: 139962 vertices, 140492 faces slice 210: 146633 vertices, 147134 faces slice 220: 153418 vertices, 153916 faces slice 230: 156945 vertices, 157302 faces slice 240: 157176 vertices, 157486 faces slice 250: 157176 vertices, 157486 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... 157168 voxel in cpt #1: X=-312 [v=157168,e=472440,f=314960] located at (33.342014, 8.070707, 44.216011) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (1.000000, 62.000000, 30.000000) For the whole surface: X=-310 [v=157176,e=472458,f=314972] 2 components have been found keeping component #1 with 157168 vertices done #-------------------------------------------- #@# Smooth1 rh Thu Jan 2 22:56:34 CST 2014 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Jan 2 22:56:42 CST 2014 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts avg radius = 50.9 mm, total surface area = 79058 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.124 (target=0.015) step 005: RMS=0.095 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.063 (target=0.015) step 030: RMS=0.061 (target=0.015) step 035: RMS=0.060 (target=0.015) step 040: RMS=0.059 (target=0.015) step 045: RMS=0.058 (target=0.015) step 050: RMS=0.058 (target=0.015) step 055: RMS=0.058 (target=0.015) step 060: RMS=0.058 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Jan 2 22:57:09 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.93 +- 0.63 (0.00-->11.97) (max @ vno 66129 --> 66149) face area 0.02 +- 0.03 (-0.36-->1.00) scaling brain by 0.291... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.672, avgs=0 005/300: dt: 0.9000, rms radial error=177.415, avgs=0 010/300: dt: 0.9000, rms radial error=176.864, avgs=0 015/300: dt: 0.9000, rms radial error=176.138, avgs=0 020/300: dt: 0.9000, rms radial error=175.311, avgs=0 025/300: dt: 0.9000, rms radial error=174.425, avgs=0 030/300: dt: 0.9000, rms radial error=173.505, avgs=0 035/300: dt: 0.9000, rms radial error=172.567, avgs=0 040/300: dt: 0.9000, rms radial error=171.621, avgs=0 045/300: dt: 0.9000, rms radial error=170.672, avgs=0 050/300: dt: 0.9000, rms radial error=169.726, avgs=0 055/300: dt: 0.9000, rms radial error=168.784, avgs=0 060/300: dt: 0.9000, rms radial error=167.844, avgs=0 065/300: dt: 0.9000, rms radial error=166.908, avgs=0 070/300: dt: 0.9000, rms radial error=165.977, avgs=0 075/300: dt: 0.9000, rms radial error=165.051, avgs=0 080/300: dt: 0.9000, rms radial error=164.129, avgs=0 085/300: dt: 0.9000, rms radial error=163.213, avgs=0 090/300: dt: 0.9000, rms radial error=162.301, avgs=0 095/300: dt: 0.9000, rms radial error=161.394, avgs=0 100/300: dt: 0.9000, rms radial error=160.492, avgs=0 105/300: dt: 0.9000, rms radial error=159.595, avgs=0 110/300: dt: 0.9000, rms radial error=158.702, avgs=0 115/300: dt: 0.9000, rms radial error=157.814, avgs=0 120/300: dt: 0.9000, rms radial error=156.931, avgs=0 125/300: dt: 0.9000, rms radial error=156.053, avgs=0 130/300: dt: 0.9000, rms radial error=155.179, avgs=0 135/300: dt: 0.9000, rms radial error=154.310, avgs=0 140/300: dt: 0.9000, rms radial error=153.446, avgs=0 145/300: dt: 0.9000, rms radial error=152.587, avgs=0 150/300: dt: 0.9000, rms radial error=151.732, avgs=0 155/300: dt: 0.9000, rms radial error=150.882, avgs=0 160/300: dt: 0.9000, rms radial error=150.036, avgs=0 165/300: dt: 0.9000, rms radial error=149.195, avgs=0 170/300: dt: 0.9000, rms radial error=148.358, avgs=0 175/300: dt: 0.9000, rms radial error=147.526, avgs=0 180/300: dt: 0.9000, rms radial error=146.699, avgs=0 185/300: dt: 0.9000, rms radial error=145.876, avgs=0 190/300: dt: 0.9000, rms radial error=145.057, avgs=0 195/300: dt: 0.9000, rms radial error=144.243, avgs=0 200/300: dt: 0.9000, rms radial error=143.434, avgs=0 205/300: dt: 0.9000, rms radial error=142.629, avgs=0 210/300: dt: 0.9000, rms radial error=141.828, avgs=0 215/300: dt: 0.9000, rms radial error=141.032, avgs=0 220/300: dt: 0.9000, rms radial error=140.241, avgs=0 225/300: dt: 0.9000, rms radial error=139.453, avgs=0 230/300: dt: 0.9000, rms radial error=138.670, avgs=0 235/300: dt: 0.9000, rms radial error=137.892, avgs=0 240/300: dt: 0.9000, rms radial error=137.117, avgs=0 245/300: dt: 0.9000, rms radial error=136.347, avgs=0 250/300: dt: 0.9000, rms radial error=135.581, avgs=0 255/300: dt: 0.9000, rms radial error=134.820, avgs=0 260/300: dt: 0.9000, rms radial error=134.062, avgs=0 265/300: dt: 0.9000, rms radial error=133.309, avgs=0 270/300: dt: 0.9000, rms radial error=132.560, avgs=0 275/300: dt: 0.9000, rms radial error=131.816, avgs=0 280/300: dt: 0.9000, rms radial error=131.075, avgs=0 285/300: dt: 0.9000, rms radial error=130.339, avgs=0 290/300: dt: 0.9000, rms radial error=129.606, avgs=0 295/300: dt: 0.9000, rms radial error=128.878, avgs=0 300/300: dt: 0.9000, rms radial error=128.154, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19012.88 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 2 (K=40.0), pass 1, starting sse = 3509.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 507.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00292 epoch 4 (K=640.0), pass 1, starting sse = 89.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/12 = 0.00896 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Jan 2 23:01:07 CST 2014 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS1036-1 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=-312 (nv=157168, nf=314960, ne=472440, g=157) 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... 44718 ambiguous faces found in tessellation segmenting defects... 132 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 4 into 0 -merging segment 46 into 0 -merging segment 5 into 3 -merging segment 0 into 19 -merging segment 53 into 35 -merging segment 44 into 43 -merging segment 50 into 49 -merging segment 58 into 55 -merging segment 94 into 87 -merging segment 96 into 88 -merging segment 98 into 91 121 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1237 (-4.5618) -vertex loglikelihood: -6.4722 (-3.2361) -normal dot loglikelihood: -3.5530 (-3.5530) -quad curv loglikelihood: -6.0720 (-3.0360) Total Loglikelihood : -25.2208 CORRECTING DEFECT 0 (vertices=27, convex hull=75) After retessellation of defect 0, euler #=-114 (132136,390760,258510) : difference with theory (-118) = -4 CORRECTING DEFECT 1 (vertices=79, convex hull=51) After retessellation of defect 1, euler #=-113 (132150,390820,258557) : difference with theory (-117) = -4 CORRECTING DEFECT 2 (vertices=2401, convex hull=998) After retessellation of defect 2, euler #=-111 (132893,393547,260543) : difference with theory (-116) = -5 CORRECTING DEFECT 3 (vertices=48, convex hull=104) After retessellation of defect 3, euler #=-110 (132913,393652,260629) : difference with theory (-115) = -5 CORRECTING DEFECT 4 (vertices=25, convex hull=56) After retessellation of defect 4, euler #=-109 (132929,393719,260681) : difference with theory (-114) = -5 CORRECTING DEFECT 5 (vertices=32, convex hull=64) After retessellation of defect 5, euler #=-108 (132949,393800,260743) : difference with theory (-113) = -5 CORRECTING DEFECT 6 (vertices=22, convex hull=42) After retessellation of defect 6, euler #=-107 (132955,393831,260769) : difference with theory (-112) = -5 CORRECTING DEFECT 7 (vertices=12, convex hull=24) After retessellation of defect 7, euler #=-106 (132956,393844,260782) : difference with theory (-111) = -5 CORRECTING DEFECT 8 (vertices=75, convex hull=124) After retessellation of defect 8, euler #=-105 (132998,394029,260926) : difference with theory (-110) = -5 CORRECTING DEFECT 9 (vertices=64, convex hull=103) After retessellation of defect 9, euler #=-104 (133034,394179,261041) : difference with theory (-109) = -5 CORRECTING DEFECT 10 (vertices=54, convex hull=25) After retessellation of defect 10, euler #=-103 (133037,394196,261056) : difference with theory (-108) = -5 CORRECTING DEFECT 11 (vertices=40, convex hull=70) After retessellation of defect 11, euler #=-102 (133059,394289,261128) : difference with theory (-107) = -5 CORRECTING DEFECT 12 (vertices=115, convex hull=138) After retessellation of defect 12, euler #=-101 (133122,394536,261313) : difference with theory (-106) = -5 CORRECTING DEFECT 13 (vertices=46, convex hull=86) After retessellation of defect 13, euler #=-100 (133145,394644,261399) : difference with theory (-105) = -5 CORRECTING DEFECT 14 (vertices=14, convex hull=26) Warning - incorrect dp selected!!!!(-112.092566 >= -112.092572 ) After retessellation of defect 14, euler #=-99 (133146,394654,261409) : difference with theory (-104) = -5 CORRECTING DEFECT 15 (vertices=191, convex hull=98) After retessellation of defect 15, euler #=-98 (133172,394777,261507) : difference with theory (-103) = -5 CORRECTING DEFECT 16 (vertices=11902, convex hull=2284) After retessellation of defect 16, euler #=-106 (136581,406367,269680) : difference with theory (-102) = 4 CORRECTING DEFECT 17 (vertices=33, convex hull=59) After retessellation of defect 17, euler #=-105 (136601,406450,269744) : difference with theory (-101) = 4 CORRECTING DEFECT 18 (vertices=85, convex hull=64) After retessellation of defect 18, euler #=-104 (136617,406524,269803) : difference with theory (-100) = 4 CORRECTING DEFECT 19 (vertices=13, convex hull=21) After retessellation of defect 19, euler #=-103 (136617,406528,269808) : difference with theory (-99) = 4 CORRECTING DEFECT 20 (vertices=46, convex hull=78) After retessellation of defect 20, euler #=-102 (136647,406654,269905) : difference with theory (-98) = 4 CORRECTING DEFECT 21 (vertices=69, convex hull=111) After retessellation of defect 21, euler #=-101 (136685,406819,270033) : difference with theory (-97) = 4 CORRECTING DEFECT 22 (vertices=16, convex hull=16) After retessellation of defect 22, euler #=-100 (136687,406829,270042) : difference with theory (-96) = 4 CORRECTING DEFECT 23 (vertices=1544, convex hull=701) After retessellation of defect 23, euler #=-99 (137182,408687,271406) : difference with theory (-95) = 4 CORRECTING DEFECT 24 (vertices=35, convex hull=58) After retessellation of defect 24, euler #=-98 (137191,408736,271447) : difference with theory (-94) = 4 CORRECTING DEFECT 25 (vertices=43, convex hull=44) After retessellation of defect 25, euler #=-97 (137200,408781,271484) : difference with theory (-93) = 4 CORRECTING DEFECT 26 (vertices=32, convex hull=40) After retessellation of defect 26, euler #=-96 (137205,408813,271512) : difference with theory (-92) = 4 CORRECTING DEFECT 27 (vertices=38, convex hull=34) After retessellation of defect 27, euler #=-95 (137208,408836,271533) : difference with theory (-91) = 4 CORRECTING DEFECT 28 (vertices=43, convex hull=70) After retessellation of defect 28, euler #=-94 (137230,408932,271608) : difference with theory (-90) = 4 CORRECTING DEFECT 29 (vertices=28, convex hull=22) After retessellation of defect 29, euler #=-93 (137233,408947,271621) : difference with theory (-89) = 4 CORRECTING DEFECT 30 (vertices=38, convex hull=65) After retessellation of defect 30, euler #=-92 (137242,409001,271667) : difference with theory (-88) = 4 CORRECTING DEFECT 31 (vertices=30, convex hull=40) After retessellation of defect 31, euler #=-91 (137256,409058,271711) : difference with theory (-87) = 4 CORRECTING DEFECT 32 (vertices=162, convex hull=90) After retessellation of defect 32, euler #=-89 (137281,409179,271809) : difference with theory (-86) = 3 CORRECTING DEFECT 33 (vertices=41, convex hull=84) After retessellation of defect 33, euler #=-88 (137290,409240,271862) : difference with theory (-85) = 3 CORRECTING DEFECT 34 (vertices=27, convex hull=25) After retessellation of defect 34, euler #=-87 (137296,409268,271885) : difference with theory (-84) = 3 CORRECTING DEFECT 35 (vertices=347, convex hull=254) After retessellation of defect 35, euler #=-86 (137436,409806,272284) : difference with theory (-83) = 3 CORRECTING DEFECT 36 (vertices=49, convex hull=77) After retessellation of defect 36, euler #=-85 (137475,409956,272396) : difference with theory (-82) = 3 CORRECTING DEFECT 37 (vertices=26, convex hull=58) After retessellation of defect 37, euler #=-84 (137484,410006,272438) : difference with theory (-81) = 3 CORRECTING DEFECT 38 (vertices=256, convex hull=131) After retessellation of defect 38, euler #=-83 (137570,410324,272671) : difference with theory (-80) = 3 CORRECTING DEFECT 39 (vertices=22, convex hull=31) After retessellation of defect 39, euler #=-82 (137572,410342,272688) : difference with theory (-79) = 3 CORRECTING DEFECT 40 (vertices=106, convex hull=71) After retessellation of defect 40, euler #=-80 (137581,410399,272738) : difference with theory (-78) = 2 CORRECTING DEFECT 41 (vertices=579, convex hull=392) After retessellation of defect 41, euler #=-79 (137605,410661,272977) : difference with theory (-77) = 2 CORRECTING DEFECT 42 (vertices=67, convex hull=52) After retessellation of defect 42, euler #=-78 (137613,410707,273016) : difference with theory (-76) = 2 CORRECTING DEFECT 43 (vertices=29, convex hull=36) After retessellation of defect 43, euler #=-77 (137615,410726,273034) : difference with theory (-75) = 2 CORRECTING DEFECT 44 (vertices=52, convex hull=70) After retessellation of defect 44, euler #=-75 (137633,410813,273105) : difference with theory (-74) = 1 CORRECTING DEFECT 45 (vertices=21, convex hull=63) After retessellation of defect 45, euler #=-74 (137642,410862,273146) : difference with theory (-73) = 1 CORRECTING DEFECT 46 (vertices=82, convex hull=68) After retessellation of defect 46, euler #=-73 (137667,410965,273225) : difference with theory (-72) = 1 CORRECTING DEFECT 47 (vertices=38, convex hull=40) After retessellation of defect 47, euler #=-72 (137670,410985,273243) : difference with theory (-71) = 1 CORRECTING DEFECT 48 (vertices=577, convex hull=386) After retessellation of defect 48, euler #=-70 (137844,411693,273779) : difference with theory (-70) = 0 CORRECTING DEFECT 49 (vertices=67, convex hull=127) After retessellation of defect 49, euler #=-69 (137854,411780,273857) : difference with theory (-69) = 0 CORRECTING DEFECT 50 (vertices=39, convex hull=23) After retessellation of defect 50, euler #=-68 (137863,411814,273883) : difference with theory (-68) = 0 CORRECTING DEFECT 51 (vertices=6, convex hull=31) After retessellation of defect 51, euler #=-67 (137865,411829,273897) : difference with theory (-67) = 0 CORRECTING DEFECT 52 (vertices=253, convex hull=54) After retessellation of defect 52, euler #=-66 (137882,411904,273956) : difference with theory (-66) = 0 CORRECTING DEFECT 53 (vertices=150, convex hull=58) After retessellation of defect 53, euler #=-65 (137907,412002,274030) : difference with theory (-65) = 0 CORRECTING DEFECT 54 (vertices=25, convex hull=32) After retessellation of defect 54, euler #=-64 (137910,412019,274045) : difference with theory (-64) = 0 CORRECTING DEFECT 55 (vertices=216, convex hull=32) After retessellation of defect 55, euler #=-63 (137919,412055,274073) : difference with theory (-63) = 0 CORRECTING DEFECT 56 (vertices=50, convex hull=94) After retessellation of defect 56, euler #=-62 (137949,412185,274174) : difference with theory (-62) = 0 CORRECTING DEFECT 57 (vertices=5, convex hull=17) After retessellation of defect 57, euler #=-61 (137950,412191,274180) : difference with theory (-61) = 0 CORRECTING DEFECT 58 (vertices=33, convex hull=54) After retessellation of defect 58, euler #=-60 (137966,412263,274237) : difference with theory (-60) = 0 CORRECTING DEFECT 59 (vertices=72, convex hull=96) After retessellation of defect 59, euler #=-59 (138002,412415,274354) : difference with theory (-59) = 0 CORRECTING DEFECT 60 (vertices=54, convex hull=76) After retessellation of defect 60, euler #=-58 (138013,412479,274408) : difference with theory (-58) = 0 CORRECTING DEFECT 61 (vertices=16, convex hull=18) After retessellation of defect 61, euler #=-57 (138014,412486,274415) : difference with theory (-57) = 0 CORRECTING DEFECT 62 (vertices=32, convex hull=48) After retessellation of defect 62, euler #=-56 (138029,412552,274467) : difference with theory (-56) = 0 CORRECTING DEFECT 63 (vertices=28, convex hull=70) After retessellation of defect 63, euler #=-55 (138045,412625,274525) : difference with theory (-55) = 0 CORRECTING DEFECT 64 (vertices=227, convex hull=97) After retessellation of defect 64, euler #=-54 (138063,412722,274605) : difference with theory (-54) = 0 CORRECTING DEFECT 65 (vertices=15, convex hull=26) After retessellation of defect 65, euler #=-53 (138068,412747,274626) : difference with theory (-53) = 0 CORRECTING DEFECT 66 (vertices=25, convex hull=57) After retessellation of defect 66, euler #=-52 (138081,412803,274670) : difference with theory (-52) = 0 CORRECTING DEFECT 67 (vertices=66, convex hull=79) After retessellation of defect 67, euler #=-51 (138098,412887,274738) : difference with theory (-51) = 0 CORRECTING DEFECT 68 (vertices=5, convex hull=21) After retessellation of defect 68, euler #=-50 (138099,412896,274747) : difference with theory (-50) = 0 CORRECTING DEFECT 69 (vertices=688, convex hull=297) After retessellation of defect 69, euler #=-49 (138221,413398,275128) : difference with theory (-49) = 0 CORRECTING DEFECT 70 (vertices=574, convex hull=187) After retessellation of defect 70, euler #=-48 (138370,413943,275525) : difference with theory (-48) = 0 CORRECTING DEFECT 71 (vertices=512, convex hull=285) After retessellation of defect 71, euler #=-48 (138587,414744,276109) : difference with theory (-47) = 1 CORRECTING DEFECT 72 (vertices=23, convex hull=56) After retessellation of defect 72, euler #=-47 (138600,414803,276156) : difference with theory (-46) = 1 CORRECTING DEFECT 73 (vertices=6, convex hull=25) After retessellation of defect 73, euler #=-46 (138602,414815,276167) : difference with theory (-45) = 1 CORRECTING DEFECT 74 (vertices=5, convex hull=14) After retessellation of defect 74, euler #=-45 (138603,414820,276172) : difference with theory (-44) = 1 CORRECTING DEFECT 75 (vertices=20, convex hull=55) After retessellation of defect 75, euler #=-44 (138612,414867,276211) : difference with theory (-43) = 1 CORRECTING DEFECT 76 (vertices=25, convex hull=19) Warning - incorrect dp selected!!!!(-78.091505 >= -78.091506 ) After retessellation of defect 76, euler #=-43 (138614,414881,276224) : difference with theory (-42) = 1 CORRECTING DEFECT 77 (vertices=58, convex hull=40) After retessellation of defect 77, euler #=-42 (138621,414917,276254) : difference with theory (-41) = 1 CORRECTING DEFECT 78 (vertices=167, convex hull=138) After retessellation of defect 78, euler #=-42 (138651,415083,276390) : difference with theory (-40) = 2 CORRECTING DEFECT 79 (vertices=128, convex hull=120) After retessellation of defect 79, euler #=-40 (138708,415313,276565) : difference with theory (-39) = 1 CORRECTING DEFECT 80 (vertices=125, convex hull=134) After retessellation of defect 80, euler #=-38 (138762,415539,276739) : difference with theory (-38) = 0 CORRECTING DEFECT 81 (vertices=23, convex hull=49) After retessellation of defect 81, euler #=-37 (138774,415592,276781) : difference with theory (-37) = 0 CORRECTING DEFECT 82 (vertices=9, convex hull=19) After retessellation of defect 82, euler #=-36 (138777,415606,276793) : difference with theory (-36) = 0 CORRECTING DEFECT 83 (vertices=172, convex hull=120) After retessellation of defect 83, euler #=-34 (138811,415774,276929) : difference with theory (-35) = -1 CORRECTING DEFECT 84 (vertices=6, convex hull=23) After retessellation of defect 84, euler #=-33 (138814,415790,276943) : difference with theory (-34) = -1 CORRECTING DEFECT 85 (vertices=81, convex hull=52) After retessellation of defect 85, euler #=-32 (138829,415857,276996) : difference with theory (-33) = -1 CORRECTING DEFECT 86 (vertices=41, convex hull=61) After retessellation of defect 86, euler #=-32 (138848,415941,277061) : difference with theory (-32) = 0 CORRECTING DEFECT 87 (vertices=49, convex hull=24) After retessellation of defect 87, euler #=-31 (138851,415957,277075) : difference with theory (-31) = 0 CORRECTING DEFECT 88 (vertices=16, convex hull=58) After retessellation of defect 88, euler #=-30 (138862,416014,277122) : difference with theory (-30) = 0 CORRECTING DEFECT 89 (vertices=40, convex hull=88) After retessellation of defect 89, euler #=-29 (138881,416107,277197) : difference with theory (-29) = 0 CORRECTING DEFECT 90 (vertices=52, convex hull=81) After retessellation of defect 90, euler #=-28 (138904,416213,277281) : difference with theory (-28) = 0 CORRECTING DEFECT 91 (vertices=23, convex hull=19) After retessellation of defect 91, euler #=-27 (138904,416219,277288) : difference with theory (-27) = 0 CORRECTING DEFECT 92 (vertices=170, convex hull=40) After retessellation of defect 92, euler #=-26 (138922,416288,277340) : difference with theory (-26) = 0 CORRECTING DEFECT 93 (vertices=24, convex hull=12) After retessellation of defect 93, euler #=-25 (138922,416289,277342) : difference with theory (-25) = 0 CORRECTING DEFECT 94 (vertices=9, convex hull=24) After retessellation of defect 94, euler #=-24 (138924,416303,277355) : difference with theory (-24) = 0 CORRECTING DEFECT 95 (vertices=75, convex hull=72) After retessellation of defect 95, euler #=-23 (138937,416371,277411) : difference with theory (-23) = 0 CORRECTING DEFECT 96 (vertices=33, convex hull=20) After retessellation of defect 96, euler #=-22 (138941,416390,277427) : difference with theory (-22) = 0 CORRECTING DEFECT 97 (vertices=20, convex hull=38) After retessellation of defect 97, euler #=-21 (138946,416417,277450) : difference with theory (-21) = 0 CORRECTING DEFECT 98 (vertices=38, convex hull=74) After retessellation of defect 98, euler #=-20 (138969,416515,277526) : difference with theory (-20) = 0 CORRECTING DEFECT 99 (vertices=54, convex hull=34) Warning - incorrect dp selected!!!!(-90.652627 >= -90.652633 ) After retessellation of defect 99, euler #=-19 (138972,416537,277546) : difference with theory (-19) = 0 CORRECTING DEFECT 100 (vertices=46, convex hull=55) After retessellation of defect 100, euler #=-18 (138989,416613,277606) : difference with theory (-18) = 0 CORRECTING DEFECT 101 (vertices=19, convex hull=81) After retessellation of defect 101, euler #=-17 (138996,416665,277652) : difference with theory (-17) = 0 CORRECTING DEFECT 102 (vertices=48, convex hull=25) After retessellation of defect 102, euler #=-16 (139001,416687,277670) : difference with theory (-16) = 0 CORRECTING DEFECT 103 (vertices=16, convex hull=24) After retessellation of defect 103, euler #=-15 (139002,416698,277681) : difference with theory (-15) = 0 CORRECTING DEFECT 104 (vertices=29, convex hull=63) After retessellation of defect 104, euler #=-14 (139011,416749,277724) : difference with theory (-14) = 0 CORRECTING DEFECT 105 (vertices=23, convex hull=57) Warning - incorrect dp selected!!!!(-80.430921 >= -80.430925 ) After retessellation of defect 105, euler #=-13 (139016,416786,277757) : difference with theory (-13) = 0 CORRECTING DEFECT 106 (vertices=21, convex hull=63) After retessellation of defect 106, euler #=-12 (139026,416839,277801) : difference with theory (-12) = 0 CORRECTING DEFECT 107 (vertices=32, convex hull=59) After retessellation of defect 107, euler #=-11 (139036,416893,277846) : difference with theory (-11) = 0 CORRECTING DEFECT 108 (vertices=35, convex hull=73) After retessellation of defect 108, euler #=-10 (139051,416969,277908) : difference with theory (-10) = 0 CORRECTING DEFECT 109 (vertices=34, convex hull=51) After retessellation of defect 109, euler #=-9 (139068,417040,277963) : difference with theory (-9) = 0 CORRECTING DEFECT 110 (vertices=5, convex hull=19) After retessellation of defect 110, euler #=-8 (139068,417044,277968) : difference with theory (-8) = 0 CORRECTING DEFECT 111 (vertices=42, convex hull=75) After retessellation of defect 111, euler #=-7 (139085,417127,278035) : difference with theory (-7) = 0 CORRECTING DEFECT 112 (vertices=35, convex hull=40) After retessellation of defect 112, euler #=-6 (139088,417150,278056) : difference with theory (-6) = 0 CORRECTING DEFECT 113 (vertices=35, convex hull=49) After retessellation of defect 113, euler #=-5 (139097,417194,278092) : difference with theory (-5) = 0 CORRECTING DEFECT 114 (vertices=22, convex hull=50) After retessellation of defect 114, euler #=-4 (139102,417227,278121) : difference with theory (-4) = 0 CORRECTING DEFECT 115 (vertices=24, convex hull=25) After retessellation of defect 115, euler #=-3 (139104,417244,278137) : difference with theory (-3) = 0 CORRECTING DEFECT 116 (vertices=29, convex hull=17) After retessellation of defect 116, euler #=-2 (139107,417257,278148) : difference with theory (-2) = 0 CORRECTING DEFECT 117 (vertices=36, convex hull=26) After retessellation of defect 117, euler #=-1 (139109,417273,278163) : difference with theory (-1) = 0 CORRECTING DEFECT 118 (vertices=43, convex hull=60) After retessellation of defect 118, euler #=0 (139118,417326,278208) : difference with theory (0) = 0 CORRECTING DEFECT 119 (vertices=29, convex hull=45) After retessellation of defect 119, euler #=1 (139127,417369,278243) : difference with theory (1) = 0 CORRECTING DEFECT 120 (vertices=45, convex hull=22) After retessellation of defect 120, euler #=2 (139129,417381,278254) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.91 +- 0.42 (0.02-->25.06) (max @ vno 21956 --> 136290) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.91 +- 0.42 (0.02-->25.06) (max @ vno 21956 --> 136290) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 408 mutations (33.7%), 801 crossovers (66.3%), 594 vertices were eliminated building final representation... 18039 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=139129, nf=278254, ne=417381, g=0) writing corrected surface to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 94.9 minutes 0 defective edges removing intersecting faces 000: 3536 intersecting 001: 472 intersecting 002: 216 intersecting 003: 157 intersecting 004: 111 intersecting 005: 89 intersecting 006: 82 intersecting 007: 80 intersecting 008: 66 intersecting 009: 61 intersecting 010: 55 intersecting expanding nbhd size to 2 011: 60 intersecting 012: 56 intersecting 013: 45 intersecting 014: 43 intersecting 015: 38 intersecting 016: 32 intersecting 017: 28 intersecting 018: 27 intersecting 019: 23 intersecting 020: 17 intersecting expanding nbhd size to 3 021: 17 intersecting expanding nbhd size to 4 022: 22 intersecting expanding nbhd size to 5 023: 22 intersecting 024: 19 intersecting expanding nbhd size to 6 025: 20 intersecting 026: 4 intersecting expanding nbhd size to 7 027: 5 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 139129 - 417381 + 278254 = 2 --> 0 holes F =2V-4: 278254 = 278258-4 (0) 2E=3F: 834762 = 834762 (0) total defect index = 0 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.01 hours removing intersecting faces 000: 2110 intersecting 001: 382 intersecting 002: 222 intersecting 003: 155 intersecting 004: 107 intersecting 005: 93 intersecting 006: 82 intersecting expanding nbhd size to 2 007: 82 intersecting 008: 72 intersecting 009: 65 intersecting 010: 58 intersecting 011: 48 intersecting 012: 44 intersecting 013: 33 intersecting 014: 28 intersecting 015: 23 intersecting 016: 17 intersecting 017: 15 intersecting expanding nbhd size to 3 018: 15 intersecting expanding nbhd size to 4 019: 26 intersecting expanding nbhd size to 5 020: 26 intersecting 021: 22 intersecting 022: 10 intersecting 023: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri Jan 3 00:36:21 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 19849 bright wm thresholded. 1516 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (93.0): 93.9 +- 7.7 [70.0 --> 110.0] GM (82.0) : 78.7 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.3 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.29 (0.01-->9.50) (max @ vno 133438 --> 134264) face area 0.28 +- 0.18 (0.00-->23.16) mean absolute distance = 0.81 +- 1.09 3880 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=100, GM=78 mean inside = 89.9, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.3, 3906 (3906) missing vertices, mean dist 0.2 [0.8 (%36.8)->0.8 (%63.2))] %61 local maxima, %26 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 0.91 +- 0.35 (0.05-->12.33) (max @ vno 134470 --> 29425) face area 0.28 +- 0.20 (0.00-->15.83) mean absolute distance = 0.46 +- 0.76 4749 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5247145.0, rms=10.04 001: dt: 0.5000, sse=6259453.5, rms=8.168 (0.000%) 002: dt: 0.5000, sse=6482712.5, rms=7.085 (0.000%) 003: dt: 0.5000, sse=6779956.5, rms=6.452 (0.000%) 004: dt: 0.5000, sse=6914660.0, rms=6.080 (0.000%) 005: dt: 0.5000, sse=7081885.0, rms=5.826 (0.000%) 006: dt: 0.5000, sse=7091013.5, rms=5.645 (0.000%) 007: dt: 0.5000, sse=7162657.5, rms=5.488 (0.000%) 008: dt: 0.5000, sse=7117804.0, rms=5.369 (0.000%) 009: dt: 0.5000, sse=7164841.5, rms=5.261 (0.000%) 010: dt: 0.5000, sse=7122625.5, rms=5.169 (0.000%) 011: dt: 0.5000, sse=7148906.5, rms=5.079 (0.000%) 012: dt: 0.5000, sse=7149645.5, rms=5.016 (0.000%) 013: dt: 0.5000, sse=7137562.5, rms=4.944 (0.000%) 014: dt: 0.5000, sse=7097359.0, rms=4.880 (0.000%) 015: dt: 0.5000, sse=7085315.5, rms=4.807 (0.000%) 016: dt: 0.5000, sse=7040418.0, rms=4.739 (0.000%) 017: dt: 0.5000, sse=7048367.5, rms=4.676 (0.000%) 018: dt: 0.5000, sse=7010542.0, rms=4.610 (0.000%) 019: dt: 0.5000, sse=7035936.0, rms=4.544 (0.000%) 020: dt: 0.5000, sse=6993679.5, rms=4.482 (0.000%) 021: dt: 0.5000, sse=6984102.5, rms=4.420 (0.000%) rms = 4.37, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=6944092.0, rms=4.374 (0.000%) 023: dt: 0.2500, sse=4888712.5, rms=4.033 (0.000%) 024: dt: 0.2500, sse=4695740.0, rms=3.972 (0.000%) rms = 3.95, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4576237.0, rms=3.948 (0.000%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 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 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.6, 3553 (2848) missing vertices, mean dist -0.3 [0.5 (%68.5)->0.3 (%31.5))] %74 local maxima, %13 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 0.89 +- 0.35 (0.03-->13.03) (max @ vno 134470 --> 29425) face area 0.34 +- 0.25 (0.00-->13.89) mean absolute distance = 0.33 +- 0.54 3734 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4953174.0, rms=5.35 026: dt: 0.5000, sse=5373015.0, rms=4.559 (0.000%) 027: dt: 0.5000, sse=5956628.5, rms=4.411 (0.000%) 028: dt: 0.5000, sse=6151772.0, rms=4.342 (0.000%) rms = 4.33, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=6610870.5, rms=4.325 (0.000%) 030: dt: 0.2500, sse=5308005.0, rms=4.031 (0.000%) 031: dt: 0.2500, sse=5129532.5, rms=3.961 (0.000%) rms = 3.94, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=5065990.5, rms=3.938 (0.000%) rms = 3.92, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5000326.0, rms=3.916 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 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=89.1, 3377 (2572) missing vertices, mean dist -0.1 [0.4 (%65.4)->0.3 (%34.6))] %79 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 0.89 +- 0.35 (0.03-->13.03) (max @ vno 134470 --> 29425) face area 0.33 +- 0.25 (0.00-->13.84) mean absolute distance = 0.29 +- 0.45 3091 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5085542.0, rms=4.43 034: dt: 0.5000, sse=5471091.5, rms=4.126 (0.000%) rms = 4.10, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=5994640.0, rms=4.100 (0.000%) 036: dt: 0.2500, sse=5362707.0, rms=3.898 (0.000%) rms = 3.86, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5276956.5, rms=3.859 (0.000%) rms = 3.83, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5184327.0, rms=3.831 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=89.7, 3432 (2467) missing vertices, mean dist -0.1 [0.3 (%55.0)->0.3 (%45.0))] %80 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/MPS1036-1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=5206261.5, rms=3.99 039: dt: 0.5000, sse=6491950.0, rms=3.842 (0.000%) rms = 3.96, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=6016112.0, rms=3.767 (0.000%) rms = 3.76, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=5825465.5, rms=3.757 (0.000%) rms = 3.73, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5812347.5, rms=3.725 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 30 non-cortical segments detected only using segment with 2182 vertices erasing segment 0 (vno[0] = 40544) erasing segment 2 (vno[0] = 55482) erasing segment 3 (vno[0] = 74007) erasing segment 4 (vno[0] = 76235) erasing segment 5 (vno[0] = 78263) erasing segment 6 (vno[0] = 83847) erasing segment 7 (vno[0] = 85684) erasing segment 8 (vno[0] = 85824) erasing segment 9 (vno[0] = 86576) erasing segment 10 (vno[0] = 86594) erasing segment 11 (vno[0] = 86606) erasing segment 12 (vno[0] = 87707) erasing segment 13 (vno[0] = 90595) erasing segment 14 (vno[0] = 91511) erasing segment 15 (vno[0] = 91541) erasing segment 16 (vno[0] = 92317) erasing segment 17 (vno[0] = 92378) erasing segment 18 (vno[0] = 93198) erasing segment 19 (vno[0] = 93981) erasing segment 20 (vno[0] = 95588) erasing segment 21 (vno[0] = 99292) erasing segment 22 (vno[0] = 99311) erasing segment 23 (vno[0] = 99872) erasing segment 24 (vno[0] = 101141) erasing segment 25 (vno[0] = 101148) erasing segment 26 (vno[0] = 102878) erasing segment 27 (vno[0] = 105837) erasing segment 28 (vno[0] = 106583) erasing segment 29 (vno[0] = 107249) writing cortex label to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label... writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.curv writing smoothed area to rh.area writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.area vertex spacing 0.89 +- 0.36 (0.04-->13.07) (max @ vno 134470 --> 29425) face area 0.33 +- 0.24 (0.00-->14.20) refinement took 4.7 minutes #-------------------------------------------- #@# Smooth2 rh Fri Jan 3 00:41:04 CST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Fri Jan 3 00:41:08 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.0 mm, total surface area = 81944 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.126 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.071 (target=0.015) step 015: RMS=0.060 (target=0.015) step 020: RMS=0.051 (target=0.015) step 025: RMS=0.043 (target=0.015) step 030: RMS=0.037 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (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 164 vertices thresholded to be in k1 ~ [-0.30 0.61], k2 ~ [-0.16 0.12] total integrated curvature = 0.387*4pi (4.861) --> 1 handles ICI = 1.3, FI = 10.0, variation=165.934 143 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 135 vertices thresholded to be in [-0.17 0.29] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025 done. #----------------------------------------- #@# Curvature Stats rh Fri Jan 3 00:42:43 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm MPS1036-1 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 [ MPS1036-1/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 [ 298 ] Gb_filter = 0 WARN: S lookup min: -0.083616 WARN: S explicit min: 0.000000 vertex = 15 #-------------------------------------------- #@# Sphere rh Fri Jan 3 00:42:48 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.278... 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 %18.98 pass 1: epoch 2 of 3 starting distance error %18.81 unfolding complete - removing small folds... starting distance error %18.52 removing remaining folds... final distance error %18.55 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.95 hours #-------------------------------------------- #@# Surf Reg rh Fri Jan 3 01:39:41 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_register -curv ../surf/rh.sphere /soft/freesurfer/5.3.0_1/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_1/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 = 0.564 curvature mean = 0.030, std = 0.920 curvature mean = 0.025, std = 0.862 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 367268.4, tmin=0.8724 d=32.00 min @ (8.00, 8.00, 0.00) sse = 351237.2, tmin=1.7273 d=16.00 min @ (-4.00, -4.00, 4.00) sse = 327558.5, tmin=2.6261 d=8.00 min @ (2.00, 0.00, 0.00) sse = 320100.8, tmin=3.6008 d=4.00 min @ (0.00, -1.00, 0.00) sse = 319156.0, tmin=4.6000 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 318586.9, tmin=5.5887 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 7.49 min curvature mean = 0.003, std = 0.948 curvature mean = 0.009, std = 0.940 curvature mean = 0.001, std = 0.957 curvature mean = 0.004, std = 0.972 curvature mean = 0.000, std = 0.960 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.037, std = 0.379 curvature mean = 0.006, std = 0.069 curvature mean = 0.065, std = 0.263 curvature mean = 0.005, std = 0.083 curvature mean = 0.036, std = 0.407 curvature mean = 0.005, std = 0.089 curvature mean = 0.022, std = 0.528 curvature mean = 0.006, std = 0.092 curvature mean = 0.008, std = 0.646 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Fri Jan 3 02:07:29 CST 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 Fri Jan 3 02:07:31 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mrisp_paint -a 5 /soft/freesurfer/5.3.0_1/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_1/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri Jan 3 02:07:33 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 2654 labels changed using aseg relabeling using gibbs priors... 000: 3144 changed, 139129 examined... 001: 760 changed, 13505 examined... 002: 184 changed, 4093 examined... 003: 73 changed, 1031 examined... 004: 39 changed, 395 examined... 005: 11 changed, 211 examined... 006: 3 changed, 57 examined... 007: 1 changed, 22 examined... 008: 1 changed, 5 examined... 009: 0 changed, 9 examined... 283 labels changed using aseg 000: 200 total segments, 160 labels (1085 vertices) changed 001: 44 total segments, 4 labels (36 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1927 vertices marked for relabeling... 1927 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 37 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri Jan 3 02:08:10 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 19849 bright wm thresholded. 1516 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (93.0): 93.9 +- 7.7 [70.0 --> 110.0] GM (82.0) : 78.7 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.3 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100, GM=78 mean inside = 89.9, 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/post_analysis/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.29 (0.01-->9.50) (max @ vno 133438 --> 134264) face area 0.28 +- 0.18 (0.00-->23.16) mean absolute distance = 0.83 +- 1.11 4053 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 28 points - only 0.00% unknown deleting segment 3 with 89 points - only 0.00% unknown deleting segment 4 with 45 points - only 0.00% unknown deleting segment 8 with 57 points - only 0.00% unknown deleting segment 9 with 180 points - only 0.00% unknown deleting segment 10 with 79 points - only 0.00% unknown deleting segment 12 with 15 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 3 points - only 0.00% unknown deleting segment 18 with 743 points - only 0.00% unknown deleting segment 19 with 22 points - only 0.00% unknown deleting segment 20 with 46 points - only 0.00% unknown deleting segment 21 with 177 points - only 0.00% unknown deleting segment 22 with 216 points - only 0.00% unknown deleting segment 23 with 46 points - only 0.00% unknown deleting segment 24 with 132 points - only 0.00% unknown deleting segment 25 with 6 points - only 0.00% unknown deleting segment 26 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 27 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 28 with 3 points - only 0.00% unknown deleting segment 29 with 57 points - only 0.00% unknown mean border=85.4, 3914 (3911) missing vertices, mean dist 0.2 [0.9 (%37.2)->0.8 (%62.8))] %62 local maxima, %26 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 0.90 +- 0.35 (0.05-->12.33) (max @ vno 134470 --> 29425) face area 0.28 +- 0.19 (0.00-->15.83) mean absolute distance = 0.46 +- 0.76 4921 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5332609.0, rms=10.06 001: dt: 0.5000, sse=6354687.0, rms=8.197 (0.000%) 002: dt: 0.5000, sse=6576443.5, rms=7.119 (0.000%) 003: dt: 0.5000, sse=6873440.0, rms=6.486 (0.000%) 004: dt: 0.5000, sse=7018464.0, rms=6.109 (0.000%) 005: dt: 0.5000, sse=7183313.5, rms=5.850 (0.000%) 006: dt: 0.5000, sse=7202937.0, rms=5.665 (0.000%) 007: dt: 0.5000, sse=7275325.0, rms=5.503 (0.000%) 008: dt: 0.5000, sse=7220239.5, rms=5.378 (0.000%) 009: dt: 0.5000, sse=7257502.5, rms=5.266 (0.000%) 010: dt: 0.5000, sse=7213987.0, rms=5.171 (0.000%) 011: dt: 0.5000, sse=7236876.5, rms=5.078 (0.000%) 012: dt: 0.5000, sse=7234324.0, rms=5.013 (0.000%) 013: dt: 0.5000, sse=7228608.0, rms=4.939 (0.000%) 014: dt: 0.5000, sse=7179347.0, rms=4.873 (0.000%) 015: dt: 0.5000, sse=7159506.5, rms=4.800 (0.000%) 016: dt: 0.5000, sse=7126886.0, rms=4.731 (0.000%) 017: dt: 0.5000, sse=7139816.5, rms=4.667 (0.000%) 018: dt: 0.5000, sse=7089806.5, rms=4.600 (0.000%) 019: dt: 0.5000, sse=7105219.5, rms=4.534 (0.000%) 020: dt: 0.5000, sse=7075496.5, rms=4.471 (0.000%) 021: dt: 0.5000, sse=7053379.5, rms=4.410 (0.000%) rms = 4.36, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=7029294.5, rms=4.364 (0.000%) 023: dt: 0.2500, sse=4926184.5, rms=4.020 (0.000%) 024: dt: 0.2500, sse=4730567.5, rms=3.957 (0.000%) rms = 3.93, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4597186.5, rms=3.933 (0.000%) positioning took 2.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 14 points - only 57.14% unknown removing 3 vertex label from ripped group deleting segment 6 with 213 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 93 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 70 points - only 0.00% unknown deleting segment 13 with 34 points - only 0.00% unknown deleting segment 14 with 231 points - only 0.00% unknown deleting segment 15 with 27 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 10 points - only 0.00% unknown deleting segment 18 with 197 points - only 0.00% unknown deleting segment 19 with 58 points - only 0.00% unknown deleting segment 20 with 120 points - only 0.00% unknown deleting segment 22 with 225 points - only 0.00% unknown deleting segment 24 with 259 points - only 0.00% unknown deleting segment 25 with 10 points - only 0.00% unknown deleting segment 27 with 165 points - only 0.00% unknown deleting segment 28 with 7 points - only 0.00% unknown deleting segment 29 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 30 with 4 points - only 0.00% unknown deleting segment 31 with 174 points - only 0.00% unknown deleting segment 32 with 18 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 33 with 2 points - only 0.00% unknown deleting segment 34 with 14 points - only 0.00% unknown deleting segment 35 with 57 points - only 0.00% unknown deleting segment 36 with 17 points - only 0.00% unknown deleting segment 37 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 40 with 4 points - only 0.00% unknown deleting segment 41 with 50 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.6, 3573 (2849) missing vertices, mean dist -0.3 [0.5 (%68.5)->0.3 (%31.5))] %76 local maxima, %13 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 0.89 +- 0.34 (0.03-->13.03) (max @ vno 134470 --> 29425) face area 0.34 +- 0.24 (0.00-->13.89) mean absolute distance = 0.34 +- 0.55 3921 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5031482.5, rms=5.32 026: dt: 0.5000, sse=5467506.5, rms=4.539 (0.000%) 027: dt: 0.5000, sse=6072256.5, rms=4.390 (0.000%) 028: dt: 0.5000, sse=6254818.0, rms=4.322 (0.000%) rms = 4.30, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=6728342.0, rms=4.304 (0.000%) 030: dt: 0.2500, sse=5399732.0, rms=4.008 (0.000%) 031: dt: 0.2500, sse=5215533.5, rms=3.939 (0.000%) rms = 3.91, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=5141523.0, rms=3.914 (0.000%) rms = 3.89, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5070795.5, rms=3.892 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 50.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 195 points - only 0.00% unknown deleting segment 4 with 36 points - only 0.00% unknown deleting segment 5 with 94 points - only 0.00% unknown deleting segment 8 with 7 points - only 42.86% unknown deleting segment 9 with 67 points - only 0.00% unknown deleting segment 10 with 34 points - only 0.00% unknown deleting segment 12 with 229 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown deleting segment 14 with 24 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 165 points - only 0.00% unknown deleting segment 18 with 55 points - only 0.00% unknown deleting segment 19 with 121 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 21 with 220 points - only 0.00% unknown deleting segment 22 with 260 points - only 0.00% unknown deleting segment 23 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 24 with 2 points - only 0.00% unknown deleting segment 25 with 134 points - only 0.00% unknown deleting segment 26 with 7 points - only 0.00% unknown deleting segment 27 with 5 points - only 0.00% unknown deleting segment 28 with 18 points - only 0.00% unknown deleting segment 29 with 10 points - only 0.00% unknown deleting segment 30 with 171 points - only 0.00% unknown deleting segment 31 with 22 points - only 0.00% unknown deleting segment 32 with 17 points - only 0.00% unknown deleting segment 33 with 57 points - only 0.00% unknown deleting segment 34 with 19 points - only 0.00% unknown deleting segment 35 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 36 with 3 points - only 0.00% unknown deleting segment 37 with 46 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=89.1, 3435 (2579) missing vertices, mean dist -0.1 [0.4 (%65.4)->0.3 (%34.6))] %81 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 0.89 +- 0.34 (0.03-->13.03) (max @ vno 134470 --> 29425) face area 0.33 +- 0.24 (0.00-->13.84) mean absolute distance = 0.29 +- 0.45 3168 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5172889.5, rms=4.45 034: dt: 0.5000, sse=5563910.5, rms=4.148 (0.000%) rms = 4.12, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=6113178.0, rms=4.117 (0.000%) 036: dt: 0.2500, sse=5454914.5, rms=3.914 (0.000%) rms = 3.87, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5363056.0, rms=3.875 (0.000%) rms = 3.85, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5277370.0, rms=3.845 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 50.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 191 points - only 0.00% unknown deleting segment 3 with 29 points - only 0.00% unknown deleting segment 4 with 94 points - only 0.00% unknown deleting segment 5 with 7 points - only 42.86% unknown deleting segment 7 with 68 points - only 0.00% unknown deleting segment 8 with 30 points - only 0.00% unknown deleting segment 9 with 236 points - only 0.00% unknown deleting segment 10 with 30 points - only 0.00% unknown deleting segment 11 with 29 points - only 0.00% unknown deleting segment 12 with 370 points - only 0.00% unknown deleting segment 13 with 54 points - only 0.00% unknown deleting segment 14 with 111 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 18 with 217 points - only 0.00% unknown deleting segment 19 with 256 points - only 0.00% unknown deleting segment 20 with 12 points - only 0.00% unknown deleting segment 21 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 22 with 3 points - only 0.00% unknown deleting segment 23 with 135 points - only 0.00% unknown deleting segment 24 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 25 with 1 points - only 0.00% unknown deleting segment 26 with 6 points - only 0.00% unknown deleting segment 27 with 172 points - only 0.00% unknown deleting segment 28 with 59 points - only 0.00% unknown deleting segment 29 with 19 points - only 0.00% unknown deleting segment 30 with 17 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 31 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 32 with 4 points - only 0.00% unknown deleting segment 33 with 46 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=89.7, 3502 (2473) missing vertices, mean dist -0.1 [0.3 (%55.0)->0.3 (%45.0))] %82 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=5301023.5, rms=4.01 039: dt: 0.5000, sse=6620296.0, rms=3.856 (0.000%) rms = 3.98, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=6132084.5, rms=3.783 (0.000%) rms = 3.77, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=5934949.0, rms=3.771 (0.000%) rms = 3.74, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5920614.5, rms=3.741 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=63.7, 2866 (2866) missing vertices, mean dist 1.7 [3.5 (%2.0)->3.6 (%98.0))] %23 local maxima, %20 large gradients and %47 min vals, 4166 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=20241062.0, rms=26.52 001: dt: 0.5000, sse=16790462.0, rms=23.656 (0.000%) 002: dt: 0.5000, sse=14109832.0, rms=21.131 (0.000%) 003: dt: 0.5000, sse=12016829.0, rms=18.973 (0.000%) 004: dt: 0.5000, sse=10511746.0, rms=17.213 (0.000%) 005: dt: 0.5000, sse=9432422.0, rms=15.776 (0.000%) 006: dt: 0.5000, sse=8696863.0, rms=14.576 (0.000%) 007: dt: 0.5000, sse=8190534.0, rms=13.506 (0.000%) 008: dt: 0.5000, sse=7832087.0, rms=12.515 (0.000%) 009: dt: 0.5000, sse=7550252.0, rms=11.566 (0.000%) 010: dt: 0.5000, sse=7359131.5, rms=10.658 (0.000%) 011: dt: 0.5000, sse=7332919.5, rms=9.806 (0.000%) 012: dt: 0.5000, sse=7301302.5, rms=8.995 (0.000%) 013: dt: 0.5000, sse=7313749.0, rms=8.292 (0.000%) 014: dt: 0.5000, sse=7342862.0, rms=7.679 (0.000%) 015: dt: 0.5000, sse=7430902.0, rms=7.204 (0.000%) 016: dt: 0.5000, sse=7490342.0, rms=6.818 (0.000%) 017: dt: 0.5000, sse=7537437.0, rms=6.559 (0.000%) 018: dt: 0.5000, sse=7583882.0, rms=6.345 (0.000%) 019: dt: 0.5000, sse=7617366.0, rms=6.194 (0.000%) 020: dt: 0.5000, sse=7625201.0, rms=6.052 (0.000%) 021: dt: 0.5000, sse=7666440.5, rms=5.968 (0.000%) 022: dt: 0.5000, sse=7627294.0, rms=5.881 (0.000%) rms = 5.84, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=7652614.5, rms=5.837 (0.000%) 024: dt: 0.2500, sse=6000558.0, rms=5.300 (0.000%) 025: dt: 0.2500, sse=5891087.5, rms=5.169 (0.000%) rms = 5.18, time step reduction 2 of 3 to 0.125... 026: dt: 0.1250, sse=5723993.0, rms=5.075 (0.000%) 027: dt: 0.1250, sse=5437575.0, rms=4.949 (0.000%) rms = 4.91, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5355485.0, rms=4.910 (0.000%) positioning took 2.3 minutes mean border=62.1, 4837 (1669) missing vertices, mean dist 0.2 [0.3 (%38.3)->0.8 (%61.7))] %35 local maxima, %15 large gradients and %39 min vals, 2242 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=6034838.0, rms=6.43 029: dt: 0.5000, sse=6532442.0, rms=6.234 (0.000%) 030: dt: 0.5000, sse=7656234.5, rms=5.987 (0.000%) rms = 6.02, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=6716884.5, rms=5.465 (0.000%) 032: dt: 0.2500, sse=6402137.0, rms=5.349 (0.000%) rms = 5.39, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=6259824.5, rms=5.251 (0.000%) 034: dt: 0.1250, sse=6036623.0, rms=5.122 (0.000%) 035: dt: 0.1250, sse=5978798.0, rms=5.066 (0.000%) rms = 5.04, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5968216.0, rms=5.042 (0.000%) positioning took 0.8 minutes mean border=61.7, 5877 (1504) missing vertices, mean dist 0.1 [0.3 (%41.3)->0.6 (%58.7))] %38 local maxima, %11 large gradients and %39 min vals, 2219 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=6037313.0, rms=5.22 rms = 5.64, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=5930653.5, rms=5.072 (0.000%) 038: dt: 0.2500, sse=6073213.5, rms=5.020 (0.000%) rms = 5.05, time step reduction 2 of 3 to 0.125... rms = 4.98, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=6011254.5, rms=4.982 (0.000%) positioning took 0.4 minutes mean border=61.3, 9855 (1466) missing vertices, mean dist 0.1 [0.3 (%44.9)->0.5 (%55.1))] %37 local maxima, %10 large gradients and %37 min vals, 2151 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/MPS1036-1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=6016870.0, rms=5.00 rms = 5.38, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5983969.0, rms=4.881 (0.000%) 041: dt: 0.2500, sse=6347468.5, rms=4.810 (0.000%) rms = 4.82, time step reduction 2 of 3 to 0.125... rms = 4.77, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=6286418.0, rms=4.771 (0.000%) positioning took 0.4 minutes writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.area.pial vertex spacing 1.01 +- 0.52 (0.02-->15.63) (max @ vno 134470 --> 29425) face area 0.39 +- 0.38 (0.00-->17.72) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 139129 vertices processed 25000 of 139129 vertices processed 50000 of 139129 vertices processed 75000 of 139129 vertices processed 100000 of 139129 vertices processed 125000 of 139129 vertices processed 0 of 139129 vertices processed 25000 of 139129 vertices processed 50000 of 139129 vertices processed 75000 of 139129 vertices processed 100000 of 139129 vertices processed 125000 of 139129 vertices processed thickness calculation complete, 2367:3600 truncations. 21964 vertices at 0 distance 64678 vertices at 1 distance 76597 vertices at 2 distance 50489 vertices at 3 distance 23870 vertices at 4 distance 10071 vertices at 5 distance 4119 vertices at 6 distance 1653 vertices at 7 distance 792 vertices at 8 distance 434 vertices at 9 distance 229 vertices at 10 distance 177 vertices at 11 distance 98 vertices at 12 distance 85 vertices at 13 distance 91 vertices at 14 distance 70 vertices at 15 distance 62 vertices at 16 distance 49 vertices at 17 distance 37 vertices at 18 distance 35 vertices at 19 distance 38 vertices at 20 distance writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.thickness positioning took 9.6 minutes #-------------------------------------------- #@# Surf Volume rh Fri Jan 3 02:17:47 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Fri Jan 3 02:17:48 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts pctsurfcon --s MPS1036-1 --rh-only Log file is /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts/pctsurfcon.log Fri Jan 3 02:17:48 CST 2014 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis cd /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts /soft/freesurfer/5.3.0_1/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node1108 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_1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.10650/rh.wm.mgh --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 72741 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.10650/rh.wm.mgh Dim: 139129 1 1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.10650/rh.gm.mgh --projfrac 0.3 --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white Done reading source surface Reading thickness /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 85290 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.10650/rh.gm.mgh Dim: 139129 1 1 mri_concat /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.10650/rh.wm.mgh /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.10650/rh.gm.mgh --paired-diff-norm --mul 100 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh mri_segstats --in /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh --annot MPS1036-1 rh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh --annot MPS1036-1 rh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/stats/rh.w-g.pct.stats --snr sysname Linux hostname node1108 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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh Vertex Area is 0.65446 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1568 1058.630 2 2002 caudalanteriorcingulate 1669 1029.129 3 2003 caudalmiddlefrontal 4164 2733.358 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 1737 1188.490 6 2006 entorhinal 611 387.161 7 2007 fusiform 4310 3085.285 8 2008 inferiorparietal 8511 5435.341 9 2009 inferiortemporal 3802 2639.895 10 2010 isthmuscingulate 924 515.971 11 2011 lateraloccipital 5713 3817.309 12 2012 lateralorbitofrontal 3109 2059.578 13 2013 lingual 1805 1641.471 14 2014 medialorbitofrontal 2252 1495.370 15 2015 middletemporal 4722 3165.253 16 2016 parahippocampal 2280 1387.319 17 2017 paracentral 2527 1618.983 18 2018 parsopercularis 1977 1335.873 19 2019 parsorbitalis 1098 750.764 20 2020 parstriangularis 1992 1355.890 21 2021 pericalcarine 1019 724.033 22 2022 postcentral 6219 3834.963 23 2023 posteriorcingulate 1828 1275.385 24 2024 precentral 8303 5311.877 25 2025 precuneus 6006 4406.081 26 2026 rostralanteriorcingulate 960 623.316 27 2027 rostralmiddlefrontal 10716 6910.543 28 2028 superiorfrontal 10902 6992.672 29 2029 superiorparietal 7498 4585.292 30 2030 superiortemporal 5604 3634.623 31 2031 supramarginal 5840 3663.642 32 2032 frontalpole 568 313.985 33 2033 temporalpole 676 426.373 34 2034 transversetemporal 424 252.924 35 2035 insula 3522 2247.050 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Fri Jan 3 02:17:58 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1568 1059 3277 3.336 0.610 0.162 0.106 46 6.6 bankssts 1669 1029 2795 2.715 1.157 0.152 0.090 42 5.2 caudalanteriorcingulate 4164 2733 10526 3.365 0.681 0.186 0.190 526 32.7 caudalmiddlefrontal 1737 1188 3233 2.330 0.604 0.226 0.160 181 10.8 cuneus 611 387 1707 3.003 0.768 0.220 0.207 30 6.5 entorhinal 4310 3085 8802 2.493 0.887 0.238 0.219 396 40.6 fusiform 8511 5435 19113 3.106 0.604 0.177 0.197 562 68.8 inferiorparietal 3802 2640 10762 3.397 0.811 0.180 0.145 1484 26.4 inferiortemporal 924 516 910 1.715 0.743 0.170 0.247 93 10.0 isthmuscingulate 5713 3817 11497 2.677 0.686 0.184 0.107 189 25.3 lateraloccipital 3109 2060 7397 2.997 1.057 0.155 0.064 59 8.6 lateralorbitofrontal 1805 1641 2320 1.404 0.658 0.377 0.896 938 28.4 lingual 2252 1495 5105 2.778 1.091 0.158 0.119 72 9.6 medialorbitofrontal 4722 3165 13234 3.505 0.614 0.160 0.088 117 17.4 middletemporal 2280 1387 3135 1.981 0.736 0.217 0.281 521 23.7 parahippocampal 2527 1619 5251 2.896 0.790 0.153 0.094 55 9.7 paracentral 1977 1336 4789 2.968 0.590 0.138 0.090 46 7.6 parsopercularis 1098 751 3003 2.898 0.771 0.173 0.090 33 4.8 parsorbitalis 1992 1356 4313 2.628 0.642 0.153 0.073 49 6.5 parstriangularis 1019 724 1524 1.793 0.743 0.394 1.141 523 35.7 pericalcarine 6219 3835 10569 2.459 0.802 0.143 0.114 159 21.8 postcentral 1828 1275 3203 2.335 0.704 0.176 0.107 74 6.1 posteriorcingulate 8303 5312 15275 2.667 0.884 0.168 0.143 348 44.2 precentral 6006 4406 11706 2.452 0.939 0.207 0.226 497 57.2 precuneus 960 623 2480 3.317 1.170 0.177 0.164 53 8.1 rostralanteriorcingulate 10716 6911 22109 2.870 0.748 0.179 0.142 419 66.6 rostralmiddlefrontal 10902 6993 26422 3.359 0.781 0.163 0.221 614 57.8 superiorfrontal 7498 4585 13865 2.734 0.573 0.156 0.102 367 34.4 superiorparietal 5604 3635 13535 3.142 0.626 0.145 0.087 142 22.8 superiortemporal 5840 3664 11193 2.881 0.643 0.182 0.261 1119 58.9 supramarginal 568 314 1254 2.693 1.198 0.220 0.272 33 5.6 frontalpole 676 426 2120 3.333 0.800 0.230 0.361 56 6.7 temporalpole 424 253 748 2.722 0.630 0.193 0.137 15 2.0 transversetemporal 3522 2247 7393 3.224 0.930 0.148 0.183 197 17.5 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri Jan 3 02:18:09 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 506 labels changed using aseg relabeling using gibbs priors... 000: 9805 changed, 139129 examined... 001: 2434 changed, 37289 examined... 002: 735 changed, 12610 examined... 003: 314 changed, 4037 examined... 004: 150 changed, 1761 examined... 005: 77 changed, 837 examined... 006: 47 changed, 431 examined... 007: 33 changed, 250 examined... 008: 20 changed, 163 examined... 009: 19 changed, 109 examined... 010: 16 changed, 106 examined... 011: 3 changed, 90 examined... 012: 3 changed, 14 examined... 013: 0 changed, 14 examined... 173 labels changed using aseg 000: 346 total segments, 264 labels (3213 vertices) changed 001: 105 total segments, 24 labels (339 vertices) changed 002: 83 total segments, 2 labels (2 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 128 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1309 vertices marked for relabeling... 1309 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 42 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri Jan 3 02:18:51 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1496 959 3211 3.082 1.042 0.190 0.133 54 7.9 G_and_S_frontomargin 751 548 1726 2.777 0.535 0.195 0.117 28 4.0 G_and_S_occipital_inf 1301 810 2204 2.292 0.706 0.165 0.086 25 4.7 G_and_S_paracentral 940 626 2435 3.199 0.789 0.144 0.061 15 2.3 G_and_S_subcentral 1449 806 2289 2.434 0.754 0.213 0.240 72 15.9 G_and_S_transv_frontopol 2711 1796 6095 3.212 0.805 0.137 0.067 47 8.4 G_and_S_cingul-Ant 1747 1168 3393 2.900 0.785 0.158 0.098 44 7.1 G_and_S_cingul-Mid-Ant 1355 971 2580 2.679 0.625 0.154 0.053 24 2.8 G_and_S_cingul-Mid-Post 407 263 681 2.260 0.660 0.153 0.070 14 0.8 G_cingul-Post-dorsal 162 79 105 1.452 0.588 0.157 0.213 22 2.0 G_cingul-Post-ventral 1752 1193 3254 2.250 0.721 0.295 0.504 396 26.9 G_cuneus 1248 872 3929 3.118 0.579 0.160 0.091 37 4.0 G_front_inf-Opercular 423 290 1438 3.180 0.738 0.184 0.089 16 1.9 G_front_inf-Orbital 1253 823 3053 2.765 0.637 0.175 0.111 54 6.6 G_front_inf-Triangul 5769 3553 14944 3.126 0.757 0.197 0.175 365 41.5 G_front_middle 7694 4792 21416 3.503 0.838 0.179 0.292 531 49.0 G_front_sup 629 361 1369 3.245 0.835 0.184 0.425 56 4.6 G_Ins_lg_and_S_cent_ins 649 403 2059 3.989 0.854 0.137 0.247 33 3.2 G_insular_short 2376 1529 6244 3.136 0.551 0.200 0.121 88 12.6 G_occipital_middle 1627 1081 4257 2.995 0.599 0.188 0.093 44 6.4 G_occipital_sup 1765 1156 4323 2.619 0.868 0.234 0.203 108 16.3 G_oc-temp_lat-fusifor 830 687 1355 1.706 0.811 0.497 1.501 738 16.3 G_oc-temp_med-Lingual 2228 1337 4011 2.493 0.804 0.207 0.207 160 19.1 G_oc-temp_med-Parahip 2526 1656 7419 3.165 1.010 0.181 0.138 84 19.3 G_orbital 3233 1876 7573 3.133 0.721 0.194 0.214 344 30.5 G_pariet_inf-Angular 2947 1796 6906 3.004 0.734 0.197 0.338 781 44.5 G_pariet_inf-Supramar 2366 1358 4168 2.728 0.529 0.151 0.115 176 12.2 G_parietal_sup 2507 1417 4519 2.487 0.745 0.153 0.104 81 12.9 G_postcentral 3284 2063 7277 2.706 1.034 0.179 0.161 149 20.4 G_precentral 3228 2058 7235 2.790 0.695 0.213 0.275 297 37.6 G_precuneus 620 417 1898 2.995 1.155 0.182 0.124 21 2.8 G_rectus 296 172 305 1.554 1.187 0.190 0.229 28 3.5 G_subcallosal 331 200 641 2.618 0.590 0.189 0.137 12 1.7 G_temp_sup-G_T_transv 2112 1246 6552 3.312 0.571 0.162 0.116 83 11.7 G_temp_sup-Lateral 821 534 1805 2.786 0.784 0.150 0.223 30 4.1 G_temp_sup-Plan_polar 804 567 1802 2.976 0.512 0.133 0.059 10 2.3 G_temp_sup-Plan_tempo 2287 1643 7825 3.498 0.788 0.197 0.168 89 15.9 G_temporal_inf 3039 1941 9641 3.591 0.631 0.178 0.106 103 13.5 G_temporal_middle 191 147 323 2.166 0.628 0.117 0.026 1 0.2 Lat_Fis-ant-Horizont 197 137 325 2.529 0.585 0.129 0.043 2 0.3 Lat_Fis-ant-Vertical 1275 853 1954 2.973 0.547 0.150 0.074 19 3.7 Lat_Fis-post 2624 1967 4629 2.161 0.643 0.229 0.185 266 18.3 Pole_occipital 1606 1072 5102 3.478 0.848 0.214 0.184 96 11.2 Pole_temporal 1218 726 878 1.093 0.584 0.257 0.693 555 31.9 S_calcarine 3163 2092 3610 2.048 0.653 0.160 0.134 108 15.7 S_central 1237 890 2315 2.787 0.493 0.138 0.043 16 2.1 S_cingul-Marginalis 619 402 1092 2.906 0.645 0.108 0.037 5 1.0 S_circular_insula_ant 1244 808 2141 3.229 0.726 0.153 0.097 89 6.3 S_circular_insula_inf 1327 896 2113 2.697 0.479 0.102 0.041 10 2.3 S_circular_insula_sup 594 417 1087 2.874 0.494 0.133 0.045 7 1.1 S_collat_transv_ant 511 376 616 1.793 0.556 0.129 0.057 4 1.1 S_collat_transv_post 2217 1523 3914 2.847 0.558 0.158 0.127 89 12.3 S_front_inf 2340 1623 4192 2.915 0.606 0.138 0.047 24 4.2 S_front_middle 2784 1867 5717 3.110 0.571 0.159 0.114 393 6.9 S_front_sup 733 479 1068 2.765 0.432 0.167 0.180 166 3.1 S_interm_prim-Jensen 2810 1827 4766 2.766 0.511 0.155 0.143 194 18.9 S_intrapariet_and_P_trans 588 413 1058 2.941 0.679 0.153 0.063 10 1.5 S_oc_middle_and_Lunatus 1681 1060 2584 2.627 0.594 0.130 0.226 36 13.5 S_oc_sup_and_transversal 477 323 1272 3.256 0.459 0.160 0.088 12 1.7 S_occipital_ant 515 383 1020 2.990 0.772 0.129 0.040 5 0.9 S_oc-temp_lat 2382 1849 2684 1.698 0.660 0.273 0.360 530 35.8 S_oc-temp_med_and_Lingual 403 269 696 2.642 0.884 0.129 0.052 7 0.8 S_orbital_lateral 650 421 1157 2.294 1.265 0.106 0.045 6 1.2 S_orbital_med-olfact 1197 796 2029 2.553 0.846 0.153 0.062 23 3.1 S_orbital-H_Shaped 1872 1730 3011 1.912 0.931 0.226 0.173 106 11.0 S_parieto_occipital 1775 1072 2159 2.414 1.209 0.172 0.182 108 12.5 S_pericallosal 2823 1822 4230 2.656 0.509 0.146 0.201 177 8.1 S_postcentral 1887 1234 3772 3.043 0.701 0.157 0.180 73 18.0 S_precentral-inf-part 1651 1062 2620 3.064 0.783 0.149 0.106 62 7.3 S_precentral-sup-part 281 199 547 2.783 0.866 0.157 0.209 10 0.6 S_suborbital 1055 693 2052 2.766 0.590 0.156 0.074 23 3.3 S_subparietal 1143 796 2165 3.322 0.593 0.162 0.129 1382 9.5 S_temporal_inf 6589 4483 13372 3.220 0.565 0.149 0.096 152 24.1 S_temporal_sup 234 148 356 2.466 0.574 0.184 0.288 25 3.6 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Fri Jan 3 02:19:05 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 857 labels changed using aseg relabeling using gibbs priors... 000: 2767 changed, 139129 examined... 001: 621 changed, 12198 examined... 002: 177 changed, 3472 examined... 003: 49 changed, 967 examined... 004: 38 changed, 300 examined... 005: 17 changed, 206 examined... 006: 4 changed, 95 examined... 007: 3 changed, 23 examined... 008: 3 changed, 19 examined... 009: 4 changed, 18 examined... 010: 5 changed, 19 examined... 011: 5 changed, 24 examined... 012: 7 changed, 29 examined... 013: 3 changed, 29 examined... 014: 7 changed, 16 examined... 015: 5 changed, 29 examined... 016: 1 changed, 21 examined... 017: 0 changed, 10 examined... 239 labels changed using aseg 000: 139 total segments, 104 labels (672 vertices) changed 001: 41 total segments, 6 labels (19 vertices) changed 002: 35 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1409 vertices marked for relabeling... 1409 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 37 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Fri Jan 3 02:19:42 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1630 1014 2876 2.802 1.103 0.155 0.092 42 5.2 caudalanteriorcingulate 4265 2774 10716 3.380 0.665 0.183 0.165 559 20.6 caudalmiddlefrontal 2142 1482 3945 2.336 0.669 0.207 0.163 98 10.2 cuneus 658 422 1722 2.861 0.841 0.243 0.241 41 9.0 entorhinal 3863 2800 7856 2.445 0.879 0.232 0.208 318 35.1 fusiform 7894 5033 17662 3.097 0.618 0.179 0.204 545 66.0 inferiorparietal 4215 2930 11781 3.358 0.819 0.187 0.155 1528 29.6 inferiortemporal 1059 571 1010 1.700 0.777 0.205 0.280 150 12.4 isthmuscingulate 6061 4030 12195 2.685 0.697 0.185 0.111 288 28.4 lateraloccipital 3841 2524 9420 3.034 1.136 0.164 0.110 101 21.6 lateralorbitofrontal 1804 1611 2273 1.404 0.647 0.370 0.893 956 27.6 lingual 1714 1128 3947 2.645 1.243 0.167 0.147 66 9.0 medialorbitofrontal 5702 3814 15297 3.485 0.619 0.159 0.087 135 21.6 middletemporal 2130 1329 3059 2.021 0.715 0.203 0.264 458 21.0 parahippocampal 2651 1698 5618 2.959 0.818 0.150 0.092 56 9.8 paracentral 1914 1310 4632 2.951 0.590 0.135 0.067 40 4.2 parsopercularis 1162 804 3125 2.910 0.754 0.169 0.073 30 4.1 parsorbitalis 2414 1611 5129 2.648 0.632 0.162 0.085 72 9.3 parstriangularis 1036 741 1556 1.783 0.748 0.399 1.126 530 35.7 pericalcarine 6766 4166 11496 2.476 0.789 0.146 0.115 192 25.0 postcentral 1873 1306 3247 2.332 0.697 0.175 0.105 74 6.2 posteriorcingulate 8004 5125 14662 2.619 0.865 0.172 0.167 357 56.5 precentral 6117 4468 12230 2.492 0.926 0.207 0.210 498 57.3 precuneus 1170 746 2805 3.169 1.232 0.166 0.142 56 8.4 rostralanteriorcingulate 6919 4490 14908 2.931 0.694 0.174 0.131 245 39.2 rostralmiddlefrontal 14699 9394 33079 3.184 0.826 0.168 0.199 732 80.3 superiorfrontal 6404 3917 11681 2.726 0.555 0.159 0.113 356 31.5 superiorparietal 7385 4795 17852 3.173 0.646 0.154 0.111 217 31.6 superiortemporal 5831 3630 11303 2.908 0.629 0.179 0.255 1096 58.4 supramarginal 457 267 755 2.686 0.617 0.212 0.243 37 5.2 transversetemporal 3076 1972 6730 3.331 0.824 0.143 0.188 182 14.7 insula #-------------------------------------------- #@# Cortical ribbon mask Fri Jan 3 02:19:54 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon MPS1036-1 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 = 144 writing volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Jan 3 02:26:38 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 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_1/ASegStatsLUT.txt --subject MPS1036-1 $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_1/ASegStatsLUT.txt --subject MPS1036-1 sysname Linux hostname node1108 machine x86_64 user kovacv UseRobust 0 atlas_icv (eTIV) = 2135681 mm^3 (det: 0.912171 ) Computing euler number orig.nofix lheno = -348, rheno = -312 orig.nofix lhholes = 175, rhholes = 157 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 256254.776 261368.000 diff=-5113.2 pctdiff=-1.995 rhCtxGM: 249294.421 252059.000 diff=-2764.6 pctdiff=-1.109 lhCtxWM: 266964.889 257877.500 diff= 9087.4 pctdiff= 3.404 rhCtxWM: 224612.591 236366.500 diff=-11753.9 pctdiff=-5.233 SubCortGMVol 71398.000 SupraTentVol 1228596.677 (1211312.000) diff=17284.677 pctdiff=1.407 SupraTentVolNotVent 1096465.677 (1079181.000) diff=17284.677 pctdiff=1.576 BrainSegVol 1416444.000 (1409203.000) diff=7241.000 pctdiff=0.511 BrainSegVolNotVent 1274846.000 (1263842.677) diff=11003.323 pctdiff=0.863 BrainSegVolNotVent 1274846.000 CerebellumVol 195206.000 VentChorVol 132131.000 3rd4th5thCSF 9467.000 CSFVol 2621.000, OptChiasmVol 64.000 MaskVol 2138819.000 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 67010 67009.617 4 5 Left-Inf-Lat-Vent 4716 4716.496 5 7 Left-Cerebellum-White-Matter 19922 19921.951 6 8 Left-Cerebellum-Cortex 72840 72839.742 7 10 Left-Thalamus-Proper 8228 8228.178 8 11 Left-Caudate 4580 4579.769 9 12 Left-Putamen 7302 7302.200 10 13 Left-Pallidum 1585 1584.526 11 14 3rd-Ventricle 4727 4726.834 12 15 4th-Ventricle 2364 2363.641 13 16 Brain-Stem 26137 26137.186 14 17 Left-Hippocampus 2875 2874.504 15 18 Left-Amygdala 1519 1518.600 16 24 CSF 2382 2382.016 17 26 Left-Accumbens-area 419 419.445 18 28 Left-VentralDC 3811 3811.076 19 30 Left-vessel 44 44.070 20 31 Left-choroid-plexus 1937 1936.549 23 43 Right-Lateral-Ventricle 52787 52787.492 24 44 Right-Inf-Lat-Vent 5673 5673.220 25 46 Right-Cerebellum-White-Matter 15961 15961.313 26 47 Right-Cerebellum-Cortex 88079 88078.992 27 49 Right-Thalamus-Proper 10287 10286.824 28 50 Right-Caudate 9351 9351.240 29 51 Right-Putamen 6480 6480.240 30 52 Right-Pallidum 2139 2138.611 31 53 Right-Hippocampus 3228 3228.436 32 54 Right-Amygdala 1528 1527.966 33 58 Right-Accumbens-area 605 605.002 34 60 Right-VentralDC 4858 4858.277 35 62 Right-vessel 74 74.138 36 63 Right-choroid-plexus 1887 1887.219 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 54791 54790.742 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 457 456.611 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 61 60.649 45 251 CC_Posterior 820 819.551 46 252 CC_Mid_Posterior 291 291.015 47 253 CC_Central 216 216.173 48 254 CC_Mid_Anterior 205 205.433 49 255 CC_Anterior 210 209.615 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Jan 3 02:28:35 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --volmask SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 outvol /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/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/MPS1036-1/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 = 510679 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc+aseg.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --volmask --a2009s SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 outvol /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/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/MPS1036-1/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 = 510679 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Jan 3 02:30:35 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 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/MPS1036-1/mri/aparc+aseg.mgz Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/mri/ribbon.mgz Loading filled from /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 12252 vertices from left hemi Ripped 14273 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/MPS1036-1/mri/aseg.mgz Loading Ctx Seg File /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 1004932 Used brute-force search on 949 voxels Fixing Parahip LH WM Found 22 clusters 0 k 2.000000 1 k 1.000000 2 k 4.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 5.000000 7 k 2.000000 8 k 1.000000 9 k 1.000000 10 k 3.000000 11 k 1.000000 12 k 14.000000 13 k 1.000000 14 k 1.000000 15 k 1141.000000 16 k 1.000000 17 k 1.000000 18 k 2.000000 19 k 2.000000 20 k 1.000000 21 k 1.000000 Fixing Parahip RH WM Found 32 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 8 k 23.000000 9 k 2.000000 10 k 1.000000 11 k 1.000000 12 k 2790.000000 13 k 1.000000 14 k 7.000000 15 k 1.000000 16 k 1.000000 17 k 1.000000 18 k 1.000000 19 k 2.000000 20 k 1.000000 21 k 1.000000 22 k 1.000000 23 k 1.000000 24 k 1.000000 25 k 4.000000 26 k 2.000000 27 k 1.000000 28 k 1.000000 29 k 1.000000 30 k 1.000000 31 k 12.000000 Writing output aseg to mri/wmparc.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1 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 MPS1036-1 --surf-wm-vol --ctab /soft/freesurfer/5.3.0_1/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 MPS1036-1 --surf-wm-vol --ctab /soft/freesurfer/5.3.0_1/WMParcStatsLUT.txt --etiv sysname Linux hostname node1108 machine x86_64 user kovacv UseRobust 0 atlas_icv (eTIV) = 2135681 mm^3 (det: 0.912171 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 256254.776 261368.000 diff=-5113.2 pctdiff=-1.995 rhCtxGM: 249294.421 252059.000 diff=-2764.6 pctdiff=-1.109 lhCtxWM: 266964.889 257877.500 diff= 9087.4 pctdiff= 3.404 rhCtxWM: 224612.591 236366.500 diff=-11753.9 pctdiff=-5.233 SubCortGMVol 71398.000 SupraTentVol 1228596.677 (1211312.000) diff=17284.677 pctdiff=1.407 SupraTentVolNotVent 1096465.677 (1079181.000) diff=17284.677 pctdiff=1.576 BrainSegVol 1416444.000 (1409203.000) diff=7241.000 pctdiff=0.511 BrainSegVolNotVent 1274846.000 (1263842.677) diff=11003.323 pctdiff=0.863 BrainSegVolNotVent 1274846.000 CerebellumVol 195206.000 VentChorVol 132131.000 3rd4th5thCSF 9467.000 CSFVol 2621.000, OptChiasmVol 64.000 MaskVol 2138819.000 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 3282 3281.789 2 3002 wm-lh-caudalanteriorcingulate 3564 3563.811 3 3003 wm-lh-caudalmiddlefrontal 8947 8947.027 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2593 2593.445 6 3006 wm-lh-entorhinal 655 654.760 7 3007 wm-lh-fusiform 4608 4607.688 8 3008 wm-lh-inferiorparietal 11380 11380.161 9 3009 wm-lh-inferiortemporal 7398 7397.763 10 3010 wm-lh-isthmuscingulate 6154 6153.518 11 3011 wm-lh-lateraloccipital 9683 9683.283 12 3012 wm-lh-lateralorbitofrontal 6285 6285.384 13 3013 wm-lh-lingual 4283 4282.742 14 3014 wm-lh-medialorbitofrontal 4155 4155.014 15 3015 wm-lh-middletemporal 7199 7198.575 16 3016 wm-lh-parahippocampal 1269 1268.619 17 3017 wm-lh-paracentral 4011 4010.517 18 3018 wm-lh-parsopercularis 3365 3365.262 19 3019 wm-lh-parsorbitalis 954 954.231 20 3020 wm-lh-parstriangularis 3414 3413.703 21 3021 wm-lh-pericalcarine 3000 3000.191 22 3022 wm-lh-postcentral 8082 8082.311 23 3023 wm-lh-posteriorcingulate 5645 5645.079 24 3024 wm-lh-precentral 17983 17982.912 25 3025 wm-lh-precuneus 8433 8433.099 26 3026 wm-lh-rostralanteriorcingulate 2616 2616.332 27 3027 wm-lh-rostralmiddlefrontal 17945 17944.547 28 3028 wm-lh-superiorfrontal 21910 21910.219 29 3029 wm-lh-superiorparietal 11806 11805.667 30 3030 wm-lh-superiortemporal 7014 7014.336 31 3031 wm-lh-supramarginal 10582 10582.073 32 3032 wm-lh-frontalpole 319 319.459 33 3033 wm-lh-temporalpole 828 828.194 34 3034 wm-lh-transversetemporal 701 700.567 35 3035 wm-lh-insula 7614 7614.173 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 2859 2859.242 120 4002 wm-rh-caudalanteriorcingulate 3822 3821.953 121 4003 wm-rh-caudalmiddlefrontal 8117 8116.793 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 1820 1820.050 124 4006 wm-rh-entorhinal 728 728.224 125 4007 wm-rh-fusiform 4663 4662.839 126 4008 wm-rh-inferiorparietal 10946 10946.172 127 4009 wm-rh-inferiortemporal 4703 4702.737 128 4010 wm-rh-isthmuscingulate 1528 1528.261 129 4011 wm-rh-lateraloccipital 5312 5311.938 130 4012 wm-rh-lateralorbitofrontal 6331 6331.444 131 4013 wm-rh-lingual 3069 3068.674 132 4014 wm-rh-medialorbitofrontal 3291 3290.704 133 4015 wm-rh-middletemporal 5438 5437.533 134 4016 wm-rh-parahippocampal 2941 2940.542 135 4017 wm-rh-paracentral 4836 4836.378 136 4018 wm-rh-parsopercularis 3224 3224.115 137 4019 wm-rh-parsorbitalis 989 989.412 138 4020 wm-rh-parstriangularis 2972 2971.586 139 4021 wm-rh-pericalcarine 884 884.300 140 4022 wm-rh-postcentral 7040 7040.164 141 4023 wm-rh-posteriorcingulate 4222 4222.451 142 4024 wm-rh-precentral 15875 15875.232 143 4025 wm-rh-precuneus 11422 11422.398 144 4026 wm-rh-rostralanteriorcingulate 2178 2177.915 145 4027 wm-rh-rostralmiddlefrontal 16540 16539.908 146 4028 wm-rh-superiorfrontal 17679 17678.924 147 4029 wm-rh-superiorparietal 9408 9408.209 148 4030 wm-rh-superiortemporal 7458 7458.024 149 4031 wm-rh-supramarginal 8749 8749.039 150 4032 wm-rh-frontalpole 353 353.228 151 4033 wm-rh-temporalpole 711 711.475 152 4034 wm-rh-transversetemporal 541 541.337 153 4035 wm-rh-insula 8220 8220.333 154 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 52776 52776.473 237 5002 Right-UnsegmentedWhiteMatter 39578 39578.223 238 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/post_analysis/MPS1036-1/label #-------------------------------------------- #@# BA Labels lh Fri Jan 3 02:38:29 CST 2014 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.label --trgsubject MPS1036-1 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 717 Checking for and removing duplicates Writing label file ./lh.BA1.label 4846 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.label --trgsubject MPS1036-1 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1210 Checking for and removing duplicates Writing label file ./lh.BA2.label 9119 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.label --trgsubject MPS1036-1 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 384 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4461 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.label --trgsubject MPS1036-1 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 769 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6752 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.label --trgsubject MPS1036-1 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 619 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.label --trgsubject MPS1036-1 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 523 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4593 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.label --trgsubject MPS1036-1 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 2730 Checking for and removing duplicates Writing label file ./lh.BA6.label 16319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.label --trgsubject MPS1036-1 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 508 Checking for and removing duplicates Writing label file ./lh.BA44.label 4689 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.label --trgsubject MPS1036-1 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1684 Checking for and removing duplicates Writing label file ./lh.BA45.label 5106 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.label --trgsubject MPS1036-1 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1451 Checking for and removing duplicates Writing label file ./lh.V1.label 6092 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.label --trgsubject MPS1036-1 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 2934 Checking for and removing duplicates Writing label file ./lh.V2.label 11048 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.label --trgsubject MPS1036-1 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 510 Checking for and removing duplicates Writing label file ./lh.MT.label 2528 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.perirhinal.label --trgsubject MPS1036-1 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1199 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1369 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1014 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 189 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2092 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 459 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2551 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1504 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1687 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1996 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2136 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2319 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2530 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1549 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 206 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1755 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 7035 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1254 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8289 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1912 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2064 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1151 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 660 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1811 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3405 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 992 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4397 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3334 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1305 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4639 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 513 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 672 mri_label2label: Done mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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 node1108 machine x86_64 user kovacv subject MPS1036-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 105118 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.BA.annot mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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 node1108 machine x86_64 user kovacv subject MPS1036-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 124691 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab MPS1036-1 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 1338 725 1978 2.184 0.619 0.180 0.170 58 7.3 BA1 4674 2993 7654 2.706 0.642 0.160 0.102 191 19.5 BA2 1041 727 962 1.873 0.533 0.265 0.270 101 9.1 BA3a 2328 1610 3015 1.931 0.737 0.197 0.244 835 29.8 BA3b 1912 1235 3306 2.462 0.825 0.169 0.267 240 7.3 BA4a 1385 994 1602 1.883 0.713 0.191 0.160 109 10.1 BA4p 11498 7268 27664 3.319 0.855 0.171 0.142 587 80.8 BA6 2231 1427 4646 2.962 0.706 0.171 0.230 184 31.5 BA44 4234 2593 7794 2.780 0.768 0.169 0.149 354 28.9 BA45 3296 2086 3449 1.665 0.537 0.196 0.127 110 17.1 V1 8011 5322 13242 2.254 0.653 0.189 0.107 289 35.6 V2 2137 1401 4189 2.871 0.596 0.160 0.090 70 6.5 MT 965 658 1949 2.381 0.798 0.220 0.245 80 6.1 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab MPS1036-1 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 899 480 1254 2.061 0.604 0.178 0.155 33 4.8 BA1 2020 1239 3295 2.554 0.587 0.174 0.141 140 9.6 BA2 868 591 729 1.775 0.458 0.285 0.325 113 9.6 BA3a 1291 983 1601 1.643 0.605 0.162 0.104 686 3.0 BA3b 1693 1118 2840 2.313 0.808 0.162 0.218 230 5.9 BA4a 1156 868 1327 1.807 0.662 0.205 0.174 93 8.8 BA4p 6352 3935 14091 3.128 0.900 0.167 0.142 314 46.2 BA6 1396 876 2983 2.980 0.737 0.157 0.090 31 5.3 BA44 1664 937 3249 2.638 0.781 0.192 0.225 290 17.9 BA45 3514 2228 3776 1.665 0.529 0.198 0.126 117 18.4 V1 4037 2673 6281 2.168 0.669 0.194 0.132 176 21.7 V2 587 391 1154 2.736 0.593 0.182 0.149 44 2.5 MT #-------------------------------------------- #@# BA Labels rh Fri Jan 3 02:41:33 CST 2014 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.label --trgsubject MPS1036-1 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 443 Checking for and removing duplicates Writing label file ./rh.BA1.label 4405 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.label --trgsubject MPS1036-1 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 693 Checking for and removing duplicates Writing label file ./rh.BA2.label 7380 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.label --trgsubject MPS1036-1 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 268 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4248 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.label --trgsubject MPS1036-1 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 316 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4838 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.label --trgsubject MPS1036-1 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 805 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.label --trgsubject MPS1036-1 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 470 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4943 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.label --trgsubject MPS1036-1 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1987 Checking for and removing duplicates Writing label file ./rh.BA6.label 14243 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.label --trgsubject MPS1036-1 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1238 Checking for and removing duplicates Writing label file ./rh.BA44.label 8150 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.label --trgsubject MPS1036-1 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1263 Checking for and removing duplicates Writing label file ./rh.BA45.label 6618 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.label --trgsubject MPS1036-1 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1040 Checking for and removing duplicates Writing label file ./rh.V1.label 5767 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.label --trgsubject MPS1036-1 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 2200 Checking for and removing duplicates Writing label file ./rh.V2.label 10216 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.label --trgsubject MPS1036-1 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 319 Checking for and removing duplicates Writing label file ./rh.MT.label 2251 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.perirhinal.label --trgsubject MPS1036-1 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 752 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 944 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 876 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 986 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2688 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3038 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1698 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1768 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2183 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2393 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1388 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1545 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1489 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1712 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 6959 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1178 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8137 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1012 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 175 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1187 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1178 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 332 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1510 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3232 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 619 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 3851 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3437 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 849 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4286 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 268 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 335 mri_label2label: Done mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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 node1108 machine x86_64 user kovacv subject MPS1036-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 99805 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.BA.annot mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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 node1108 machine x86_64 user kovacv subject MPS1036-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 117791 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab MPS1036-1 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 962 519 1914 2.615 0.695 0.150 0.077 23 3.4 BA1 3506 2187 5821 2.650 0.595 0.141 0.155 129 14.0 BA2 1023 660 943 1.934 0.492 0.154 0.070 14 3.0 BA3a 2007 1308 2903 1.966 0.733 0.147 0.064 31 5.8 BA3b 1702 1156 3249 2.538 1.011 0.163 0.150 71 8.3 BA4a 1452 948 1845 2.197 0.754 0.182 0.206 89 11.8 BA4p 9435 5919 22394 3.232 0.860 0.170 0.183 558 66.4 BA6 3630 2441 8909 3.024 0.610 0.149 0.081 94 9.8 BA44 4472 3041 10466 2.803 0.677 0.162 0.089 129 19.4 BA45 2190 1719 3468 1.731 0.923 0.386 1.131 1022 62.7 V1 6453 4629 9167 1.829 1.029 0.211 0.225 837 55.0 V2 1691 1159 3794 3.034 0.473 0.156 0.075 35 5.3 MT 801 534 1827 2.634 0.881 0.209 0.218 35 7.2 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab MPS1036-1 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 715 361 1392 2.610 0.532 0.151 0.095 20 3.1 BA1 2170 1319 3679 2.647 0.609 0.142 0.199 104 10.1 BA2 924 588 797 1.975 0.512 0.163 0.111 40 4.8 BA3a 1698 1120 2087 1.777 0.487 0.141 0.064 25 5.1 BA3b 1006 666 2073 2.538 1.017 0.173 0.122 29 5.0 BA4a 1204 785 1379 2.050 0.747 0.186 0.207 58 9.1 BA4p 6176 3818 14251 3.154 0.885 0.170 0.195 470 39.9 BA6 901 636 2447 2.974 0.711 0.149 0.088 25 2.2 BA44 1220 796 2856 2.766 0.609 0.172 0.096 42 5.2 BA45 2044 1595 3195 1.714 0.914 0.389 1.079 927 63.1 V1 2990 2189 4247 1.786 0.933 0.258 0.401 684 33.5 V2 290 184 695 3.223 0.367 0.178 0.102 8 1.1 MT /lustre/kovacv/FS/post_analysis/MPS1036-1/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Jan 3 02:44:27 CST 2014 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS1036-1 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject MPS1036-1. processing subject lh.EC_average... reading output surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1017 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label MPS1036-1 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 340 198 869 2.583 0.680 0.214 0.143 19 1.9 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Jan 3 02:44:38 CST 2014 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS1036-1 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject MPS1036-1. processing subject rh.EC_average... reading output surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 957 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label MPS1036-1 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 364 196 811 2.620 0.626 0.153 0.109 17 1.8 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Thu Jan 2 18:38:47 CST 2014 Ended at Fri Jan 3 02:44:49 CST 2014 #@#%# recon-all-run-time-hours 8.101 recon-all -s MPS1036-1 finished without error at Fri Jan 3 02:44:49 CST 2014 New invocation of recon-all Fri Jan 3 11:38:42 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 /soft/freesurfer/5.3.0_1/bin/recon-all -autorecon2-cp -autorecon3 -subjid MPS1036-1 -bigventricles subjid MPS1036-1 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Actual FREESURFER_HOME /panfs/roc/itascasoft/freesurfer/5.3.0_1 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux node1107 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 1171676 64760568 0 4880 33356 -/+ buffers/cache: 1133440 64798804 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: 2014/01/03-17:38:42-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: node1107 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: 2014/01/03-17:38:43-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: node1107 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: 2014/01/03-17:38:43-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: node1107 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: 2014/01/03-17:38:43-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: node1107 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: 2014/01/03-17:38:43-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: node1107 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: 2014/01/03-17:38:44-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: node1107 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: 2014/01/03-17:38:44-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: node1107 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: 2014/01/03-17:38:44-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: node1107 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: 2014/01/03-17:38:44-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: node1107 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: 2014/01/03-17:38:44-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: node1107 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: $ TimeStamp: 2014/01/03-17:38:46-GMT BuildTimeStamp: Nov 16 2013 21:04:35 CVS: $Id: mri_ca_register.c,v 1.87 2013/11/14 16:15:12 fischl Exp $ User: kovacv Machine: node1107 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: 2014/01/03-17:38:46-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: node1107 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: 2014/01/03-17:38:46-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: node1107 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: 2014/01/03-17:38:46-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: node1107 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: 2014/01/03-17:38:47-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: node1107 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: 2014/01/03-17:38:47-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: node1107 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: 2014/01/03-17:38:47-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: node1107 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: 2014/01/03-17:38:47-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: node1107 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: 2014/01/03-17:38:47-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: node1107 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: 2014/01/03-17:38:48-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: node1107 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: 2014/01/03-17:38:48-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: node1107 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: 2014/01/03-17:38:48-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: node1107 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: 2014/01/03-17:38:49-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: node1107 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: 2014/01/03-17:38:49-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: node1107 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: 2014/01/03-17:38:49-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: node1107 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: 2014/01/03-17:38:49-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: node1107 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: 2014/01/03-17:38:50-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: node1107 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: 2014/01/03-17:38:50-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: node1107 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: 2014/01/03-17:38:50-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: node1107 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: 2014/01/03-17:38:50-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: node1107 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: 2014/01/03-17:38:51-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: node1107 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: 2014/01/03-17:38:51-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: node1107 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: 2014/01/03-17:38:51-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: node1107 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: 2014/01/03-17:38:52-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: node1107 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: 2014/01/03-17:38:52-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: node1107 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: 2014/01/03-17:38:52-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: node1107 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: 2014/01/03-17:38:53-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: node1107 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: 2014/01/03-17:38:53-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: node1107 Platform: Linux PlatformVersion: 2.6.32-358.14.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /soft/freesurfer/5.3.0_1/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_1/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Fri Jan 3 11:38:53 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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... 6441 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 43 (43) csf peak at 19, setting threshold to 54 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 99 gm peak at 76 (76), valley at 42 (42) csf peak at 19, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 49 seconds. #-------------------------------------------- #@# Mask BFS Fri Jan 3 11:41:44 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2105835 voxels in mask (pct= 12.55) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Jan 3 11:41:46 CST 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/MPS1036-1/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname node1107 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/MPS1036-1/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname node1107 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 (102.0): 101.7 +- 8.1 [80.0 --> 125.0] GM (73.0) : 69.9 +- 12.9 [30.0 --> 96.0] setting bottom of white matter range to 82.7 setting top of gray matter range to 95.6 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... 17556 sparsely connected voxels removed... thickening thin strands.... 20 segments, 8304 filled 1267 bright non-wm voxels segmented. 8956 diagonally connected voxels added... white matter segmentation took 2.0 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 1.15 minutes reading wm segmentation from wm.seg.mgz... 3199 voxels added to wm to prevent paths from MTL structures to cortex 24905 additional wm voxels added 0 additional wm voxels added SEG EDIT: 247342 voxels turned on, 68897 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 104 new 104 115,126,128 old 104 new 104 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 222 found - 222 modified | TOTAL: 222 pass 2 (xy+): 0 found - 222 modified | TOTAL: 222 pass 1 (xy-): 207 found - 207 modified | TOTAL: 429 pass 2 (xy-): 0 found - 207 modified | TOTAL: 429 pass 1 (yz+): 172 found - 172 modified | TOTAL: 601 pass 2 (yz+): 0 found - 172 modified | TOTAL: 601 pass 1 (yz-): 206 found - 206 modified | TOTAL: 807 pass 2 (yz-): 0 found - 206 modified | TOTAL: 807 pass 1 (xz+): 153 found - 153 modified | TOTAL: 960 pass 2 (xz+): 0 found - 153 modified | TOTAL: 960 pass 1 (xz-): 156 found - 156 modified | TOTAL: 1116 pass 2 (xz-): 0 found - 156 modified | TOTAL: 1116 Iteration Number : 1 pass 1 (+++): 89 found - 89 modified | TOTAL: 89 pass 2 (+++): 0 found - 89 modified | TOTAL: 89 pass 1 (+++): 100 found - 100 modified | TOTAL: 189 pass 2 (+++): 0 found - 100 modified | TOTAL: 189 pass 1 (+++): 80 found - 80 modified | TOTAL: 269 pass 2 (+++): 0 found - 80 modified | TOTAL: 269 pass 1 (+++): 84 found - 84 modified | TOTAL: 353 pass 2 (+++): 0 found - 84 modified | TOTAL: 353 Iteration Number : 1 pass 1 (++): 250 found - 250 modified | TOTAL: 250 pass 2 (++): 0 found - 250 modified | TOTAL: 250 pass 1 (+-): 276 found - 276 modified | TOTAL: 526 pass 2 (+-): 1 found - 277 modified | TOTAL: 527 pass 3 (+-): 0 found - 277 modified | TOTAL: 527 pass 1 (--): 266 found - 266 modified | TOTAL: 793 pass 2 (--): 1 found - 267 modified | TOTAL: 794 pass 3 (--): 0 found - 267 modified | TOTAL: 794 pass 1 (-+): 250 found - 250 modified | TOTAL: 1044 pass 2 (-+): 0 found - 250 modified | TOTAL: 1044 Iteration Number : 2 pass 1 (xy+): 28 found - 28 modified | TOTAL: 28 pass 2 (xy+): 0 found - 28 modified | TOTAL: 28 pass 1 (xy-): 26 found - 26 modified | TOTAL: 54 pass 2 (xy-): 0 found - 26 modified | TOTAL: 54 pass 1 (yz+): 21 found - 21 modified | TOTAL: 75 pass 2 (yz+): 0 found - 21 modified | TOTAL: 75 pass 1 (yz-): 27 found - 27 modified | TOTAL: 102 pass 2 (yz-): 0 found - 27 modified | TOTAL: 102 pass 1 (xz+): 23 found - 23 modified | TOTAL: 125 pass 2 (xz+): 0 found - 23 modified | TOTAL: 125 pass 1 (xz-): 30 found - 30 modified | TOTAL: 155 pass 2 (xz-): 0 found - 30 modified | TOTAL: 155 Iteration Number : 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 1 found - 1 modified | TOTAL: 9 pass 2 (+++): 0 found - 1 modified | TOTAL: 9 pass 1 (+++): 4 found - 4 modified | TOTAL: 13 pass 2 (+++): 0 found - 4 modified | TOTAL: 13 Iteration Number : 2 pass 1 (++): 6 found - 6 modified | TOTAL: 6 pass 2 (++): 0 found - 6 modified | TOTAL: 6 pass 1 (+-): 16 found - 16 modified | TOTAL: 22 pass 2 (+-): 0 found - 16 modified | TOTAL: 22 pass 1 (--): 17 found - 17 modified | TOTAL: 39 pass 2 (--): 0 found - 17 modified | TOTAL: 39 pass 1 (-+): 18 found - 18 modified | TOTAL: 57 pass 2 (-+): 0 found - 18 modified | TOTAL: 57 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 5 found - 5 modified | TOTAL: 10 pass 2 (yz-): 0 found - 5 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 1 found - 1 modified | TOTAL: 12 pass 2 (xz-): 0 found - 1 modified | TOTAL: 12 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 2 found - 2 modified | TOTAL: 3 pass 2 (+-): 0 found - 2 modified | TOTAL: 3 pass 1 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 1 found - 1 modified | TOTAL: 5 pass 2 (-+): 0 found - 1 modified | TOTAL: 5 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2755 (out of 731549: 0.376598) 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 Fri Jan 3 11:45:06 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.898 -0.024 -0.147 33.072; -0.019 0.933 -0.209 66.331; 0.123 0.188 0.790 -37.202; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 3366 (min = 350, max = 1400), aspect = 0.73 (min = 0.10, max = 0.75) need search nearby using seed (117, 99, 143), TAL = (11.0, 15.0, 29.0) talairach voxel to voxel transform 1.086 -0.012 0.198 -27.718; -0.014 1.018 0.266 -57.126; -0.166 -0.240 1.172 65.007; 0.000 0.000 0.000 1.000; segmentation indicates cc at (117, 99, 143) --> (11.0, 15.0, 29.0) done. writing output to filled.mgz... filling took 0.6 minutes badRH = 12703/323344, badLH=701/368281 Please check filled volume. Cerebellum may be included. talairach cc position changed to (11.00, 15.00, 29.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(29.00, 15.00, 29.00) SRC: (106.93, 80.22, 192.42) search lh wm seed point around talairach space (-7.00, 15.00, 29.00), SRC: (146.03, 79.70, 186.43) 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 Jan 3 11:45:45 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 3 found - 3 modified | TOTAL: 16 pass 2 (xy-): 0 found - 3 modified | TOTAL: 16 pass 1 (yz+): 5 found - 5 modified | TOTAL: 21 pass 2 (yz+): 0 found - 5 modified | TOTAL: 21 pass 1 (yz-): 6 found - 6 modified | TOTAL: 27 pass 2 (yz-): 0 found - 6 modified | TOTAL: 27 pass 1 (xz+): 10 found - 10 modified | TOTAL: 37 pass 2 (xz+): 0 found - 10 modified | TOTAL: 37 pass 1 (xz-): 7 found - 7 modified | TOTAL: 44 pass 2 (xz-): 0 found - 7 modified | TOTAL: 44 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 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 3 found - 3 modified | TOTAL: 6 pass 2 (+-): 0 found - 3 modified | TOTAL: 6 pass 1 (--): 11 found - 11 modified | TOTAL: 17 pass 2 (--): 0 found - 11 modified | TOTAL: 17 pass 1 (-+): 3 found - 3 modified | TOTAL: 20 pass 2 (-+): 0 found - 3 modified | TOTAL: 20 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+): 2 found - 2 modified | TOTAL: 2 pass 2 (xz+): 0 found - 2 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 = 69 (out of 368350: 0.018732) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 50: 104 vertices, 121 faces slice 60: 4109 vertices, 4298 faces slice 70: 11609 vertices, 11912 faces slice 80: 20061 vertices, 20393 faces slice 90: 29577 vertices, 29945 faces slice 100: 39211 vertices, 39568 faces slice 110: 48915 vertices, 49361 faces slice 120: 61430 vertices, 61992 faces slice 130: 74850 vertices, 75470 faces slice 140: 89190 vertices, 89822 faces slice 150: 102332 vertices, 102990 faces slice 160: 115110 vertices, 115779 faces slice 170: 125685 vertices, 126258 faces slice 180: 134538 vertices, 135147 faces slice 190: 143943 vertices, 144571 faces slice 200: 152892 vertices, 153508 faces slice 210: 162235 vertices, 162876 faces slice 220: 168439 vertices, 168943 faces slice 230: 171169 vertices, 171540 faces slice 240: 171244 vertices, 171592 faces slice 250: 171244 vertices, 171592 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... 171244 voxel in cpt #1: X=-348 [v=171244,e=514776,f=343184] located at (-21.646225, 9.320630, 50.872253) For the whole surface: X=-348 [v=171244,e=514776,f=343184] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Jan 3 11:45:50 CST 2014 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Jan 3 11:45:54 CST 2014 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts avg radius = 52.3 mm, total surface area = 85246 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.126 (target=0.015) step 005: RMS=0.096 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.066 (target=0.015) step 030: RMS=0.064 (target=0.015) step 035: RMS=0.062 (target=0.015) step 040: RMS=0.061 (target=0.015) step 045: RMS=0.060 (target=0.015) step 050: RMS=0.059 (target=0.015) step 055: RMS=0.060 (target=0.015) step 060: RMS=0.060 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Jan 3 11:46:23 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.89 +- 0.60 (0.00-->8.88) (max @ vno 59563 --> 59583) face area 0.02 +- 0.03 (-0.19-->0.82) scaling brain by 0.286... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.134, avgs=0 005/300: dt: 0.9000, rms radial error=176.877, avgs=0 010/300: dt: 0.9000, rms radial error=176.325, avgs=0 015/300: dt: 0.9000, rms radial error=175.599, avgs=0 020/300: dt: 0.9000, rms radial error=174.771, avgs=0 025/300: dt: 0.9000, rms radial error=173.886, avgs=0 030/300: dt: 0.9000, rms radial error=172.968, avgs=0 035/300: dt: 0.9000, rms radial error=172.033, avgs=0 040/300: dt: 0.9000, rms radial error=171.089, avgs=0 045/300: dt: 0.9000, rms radial error=170.143, avgs=0 050/300: dt: 0.9000, rms radial error=169.198, avgs=0 055/300: dt: 0.9000, rms radial error=168.255, avgs=0 060/300: dt: 0.9000, rms radial error=167.315, avgs=0 065/300: dt: 0.9000, rms radial error=166.378, avgs=0 070/300: dt: 0.9000, rms radial error=165.446, avgs=0 075/300: dt: 0.9000, rms radial error=164.518, avgs=0 080/300: dt: 0.9000, rms radial error=163.596, avgs=0 085/300: dt: 0.9000, rms radial error=162.678, avgs=0 090/300: dt: 0.9000, rms radial error=161.765, avgs=0 095/300: dt: 0.9000, rms radial error=160.857, avgs=0 100/300: dt: 0.9000, rms radial error=159.954, avgs=0 105/300: dt: 0.9000, rms radial error=159.056, avgs=0 110/300: dt: 0.9000, rms radial error=158.163, avgs=0 115/300: dt: 0.9000, rms radial error=157.275, avgs=0 120/300: dt: 0.9000, rms radial error=156.392, avgs=0 125/300: dt: 0.9000, rms radial error=155.513, avgs=0 130/300: dt: 0.9000, rms radial error=154.640, avgs=0 135/300: dt: 0.9000, rms radial error=153.771, avgs=0 140/300: dt: 0.9000, rms radial error=152.907, avgs=0 145/300: dt: 0.9000, rms radial error=152.047, avgs=0 150/300: dt: 0.9000, rms radial error=151.192, avgs=0 155/300: dt: 0.9000, rms radial error=150.342, avgs=0 160/300: dt: 0.9000, rms radial error=149.497, avgs=0 165/300: dt: 0.9000, rms radial error=148.657, avgs=0 170/300: dt: 0.9000, rms radial error=147.821, avgs=0 175/300: dt: 0.9000, rms radial error=146.990, avgs=0 180/300: dt: 0.9000, rms radial error=146.164, avgs=0 185/300: dt: 0.9000, rms radial error=145.342, avgs=0 190/300: dt: 0.9000, rms radial error=144.524, avgs=0 195/300: dt: 0.9000, rms radial error=143.712, avgs=0 200/300: dt: 0.9000, rms radial error=142.903, avgs=0 205/300: dt: 0.9000, rms radial error=142.098, avgs=0 210/300: dt: 0.9000, rms radial error=141.298, avgs=0 215/300: dt: 0.9000, rms radial error=140.502, avgs=0 220/300: dt: 0.9000, rms radial error=139.711, avgs=0 225/300: dt: 0.9000, rms radial error=138.924, avgs=0 230/300: dt: 0.9000, rms radial error=138.142, avgs=0 235/300: dt: 0.9000, rms radial error=137.364, avgs=0 240/300: dt: 0.9000, rms radial error=136.590, avgs=0 245/300: dt: 0.9000, rms radial error=135.820, avgs=0 250/300: dt: 0.9000, rms radial error=135.055, avgs=0 255/300: dt: 0.9000, rms radial error=134.294, avgs=0 260/300: dt: 0.9000, rms radial error=133.538, avgs=0 265/300: dt: 0.9000, rms radial error=132.785, avgs=0 270/300: dt: 0.9000, rms radial error=132.037, avgs=0 275/300: dt: 0.9000, rms radial error=131.293, avgs=0 280/300: dt: 0.9000, rms radial error=130.553, avgs=0 285/300: dt: 0.9000, rms radial error=129.817, avgs=0 290/300: dt: 0.9000, rms radial error=129.086, avgs=0 295/300: dt: 0.9000, rms radial error=128.358, avgs=0 300/300: dt: 0.9000, rms radial error=127.635, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20816.89 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 2 (K=40.0), pass 1, starting sse = 3852.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 3 (K=160.0), pass 1, starting sse = 549.73 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00287 epoch 4 (K=640.0), pass 1, starting sse = 84.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00616 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri Jan 3 11:50:05 CST 2014 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS1036-1 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=-348 (nv=171244, nf=343184, ne=514776, g=175) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 49192 ambiguous faces found in tessellation segmenting defects... 160 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 157 into 71 -merging segment 93 into 86 -merging segment 97 into 96 -merging segment 107 into 104 156 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0107 (-4.5054) -vertex loglikelihood: -6.3883 (-3.1942) -normal dot loglikelihood: -3.4922 (-3.4922) -quad curv loglikelihood: -6.0829 (-3.0415) Total Loglikelihood : -24.9741 CORRECTING DEFECT 0 (vertices=60, convex hull=103) After retessellation of defect 0, euler #=-145 (143663,424793,280985) : difference with theory (-153) = -8 CORRECTING DEFECT 1 (vertices=38, convex hull=59) After retessellation of defect 1, euler #=-144 (143678,424859,281037) : difference with theory (-152) = -8 CORRECTING DEFECT 2 (vertices=19, convex hull=59) After retessellation of defect 2, euler #=-143 (143687,424910,281080) : difference with theory (-151) = -8 CORRECTING DEFECT 3 (vertices=51, convex hull=54) After retessellation of defect 3, euler #=-142 (143694,424957,281121) : difference with theory (-150) = -8 CORRECTING DEFECT 4 (vertices=30, convex hull=58) After retessellation of defect 4, euler #=-141 (143708,425023,281174) : difference with theory (-149) = -8 CORRECTING DEFECT 5 (vertices=45, convex hull=92) After retessellation of defect 5, euler #=-140 (143729,425126,281257) : difference with theory (-148) = -8 CORRECTING DEFECT 6 (vertices=27, convex hull=57) After retessellation of defect 6, euler #=-139 (143743,425191,281309) : difference with theory (-147) = -8 CORRECTING DEFECT 7 (vertices=5, convex hull=22) After retessellation of defect 7, euler #=-138 (143743,425194,281313) : difference with theory (-146) = -8 CORRECTING DEFECT 8 (vertices=33, convex hull=55) After retessellation of defect 8, euler #=-137 (143754,425250,281359) : difference with theory (-145) = -8 CORRECTING DEFECT 9 (vertices=15, convex hull=27) After retessellation of defect 9, euler #=-136 (143757,425271,281378) : difference with theory (-144) = -8 CORRECTING DEFECT 10 (vertices=6, convex hull=18) After retessellation of defect 10, euler #=-135 (143758,425279,281386) : difference with theory (-143) = -8 CORRECTING DEFECT 11 (vertices=200, convex hull=98) After retessellation of defect 11, euler #=-134 (143796,425439,281509) : difference with theory (-142) = -8 CORRECTING DEFECT 12 (vertices=10, convex hull=29) After retessellation of defect 12, euler #=-133 (143797,425452,281522) : difference with theory (-141) = -8 CORRECTING DEFECT 13 (vertices=39, convex hull=54) After retessellation of defect 13, euler #=-132 (143816,425530,281582) : difference with theory (-140) = -8 CORRECTING DEFECT 14 (vertices=23, convex hull=52) After retessellation of defect 14, euler #=-131 (143825,425576,281620) : difference with theory (-139) = -8 CORRECTING DEFECT 15 (vertices=15, convex hull=22) After retessellation of defect 15, euler #=-130 (143827,425589,281632) : difference with theory (-138) = -8 CORRECTING DEFECT 16 (vertices=27, convex hull=37) After retessellation of defect 16, euler #=-129 (143837,425637,281671) : difference with theory (-137) = -8 CORRECTING DEFECT 17 (vertices=75, convex hull=41) After retessellation of defect 17, euler #=-128 (143841,425664,281695) : difference with theory (-136) = -8 CORRECTING DEFECT 18 (vertices=226, convex hull=43) After retessellation of defect 18, euler #=-127 (143850,425707,281730) : difference with theory (-135) = -8 CORRECTING DEFECT 19 (vertices=65, convex hull=104) After retessellation of defect 19, euler #=-126 (143873,425819,281820) : difference with theory (-134) = -8 CORRECTING DEFECT 20 (vertices=51, convex hull=35) After retessellation of defect 20, euler #=-125 (143876,425836,281835) : difference with theory (-133) = -8 CORRECTING DEFECT 21 (vertices=22, convex hull=29) After retessellation of defect 21, euler #=-124 (143878,425853,281851) : difference with theory (-132) = -8 CORRECTING DEFECT 22 (vertices=68, convex hull=39) After retessellation of defect 22, euler #=-123 (143884,425888,281881) : difference with theory (-131) = -8 CORRECTING DEFECT 23 (vertices=23, convex hull=57) After retessellation of defect 23, euler #=-122 (143895,425945,281928) : difference with theory (-130) = -8 CORRECTING DEFECT 24 (vertices=39, convex hull=54) After retessellation of defect 24, euler #=-121 (143918,426034,281995) : difference with theory (-129) = -8 CORRECTING DEFECT 25 (vertices=16, convex hull=16) After retessellation of defect 25, euler #=-120 (143918,426037,281999) : difference with theory (-128) = -8 CORRECTING DEFECT 26 (vertices=100, convex hull=32) After retessellation of defect 26, euler #=-119 (143920,426052,282013) : difference with theory (-127) = -8 CORRECTING DEFECT 27 (vertices=10, convex hull=39) After retessellation of defect 27, euler #=-118 (143921,426066,282027) : difference with theory (-126) = -8 CORRECTING DEFECT 28 (vertices=6, convex hull=18) After retessellation of defect 28, euler #=-117 (143922,426074,282035) : difference with theory (-125) = -8 CORRECTING DEFECT 29 (vertices=14, convex hull=22) After retessellation of defect 29, euler #=-116 (143924,426088,282048) : difference with theory (-124) = -8 CORRECTING DEFECT 30 (vertices=39, convex hull=75) After retessellation of defect 30, euler #=-115 (143936,426152,282101) : difference with theory (-123) = -8 CORRECTING DEFECT 31 (vertices=34, convex hull=54) After retessellation of defect 31, euler #=-114 (143951,426217,282152) : difference with theory (-122) = -8 CORRECTING DEFECT 32 (vertices=52, convex hull=94) After retessellation of defect 32, euler #=-113 (143970,426312,282229) : difference with theory (-121) = -8 CORRECTING DEFECT 33 (vertices=40, convex hull=82) After retessellation of defect 33, euler #=-112 (143999,426438,282327) : difference with theory (-120) = -8 CORRECTING DEFECT 34 (vertices=85, convex hull=36) After retessellation of defect 34, euler #=-111 (144005,426472,282356) : difference with theory (-119) = -8 CORRECTING DEFECT 35 (vertices=316, convex hull=104) After retessellation of defect 35, euler #=-110 (144032,426591,282449) : difference with theory (-118) = -8 CORRECTING DEFECT 36 (vertices=50, convex hull=71) After retessellation of defect 36, euler #=-109 (144042,426649,282498) : difference with theory (-117) = -8 CORRECTING DEFECT 37 (vertices=52, convex hull=42) After retessellation of defect 37, euler #=-108 (144051,426690,282531) : difference with theory (-116) = -8 CORRECTING DEFECT 38 (vertices=41, convex hull=86) After retessellation of defect 38, euler #=-107 (144063,426767,282597) : difference with theory (-115) = -8 CORRECTING DEFECT 39 (vertices=30, convex hull=37) After retessellation of defect 39, euler #=-106 (144068,426794,282620) : difference with theory (-114) = -8 CORRECTING DEFECT 40 (vertices=81, convex hull=142) After retessellation of defect 40, euler #=-105 (144089,426922,282728) : difference with theory (-113) = -8 CORRECTING DEFECT 41 (vertices=57, convex hull=74) After retessellation of defect 41, euler #=-104 (144119,427047,282824) : difference with theory (-112) = -8 CORRECTING DEFECT 42 (vertices=31, convex hull=45) After retessellation of defect 42, euler #=-103 (144135,427116,282878) : difference with theory (-111) = -8 CORRECTING DEFECT 43 (vertices=5, convex hull=21) Warning - incorrect dp selected!!!!(-141.845340 >= -141.845341 ) After retessellation of defect 43, euler #=-102 (144136,427125,282887) : difference with theory (-110) = -8 CORRECTING DEFECT 44 (vertices=525, convex hull=343) After retessellation of defect 44, euler #=-101 (144145,427317,283071) : difference with theory (-109) = -8 CORRECTING DEFECT 45 (vertices=367, convex hull=213) After retessellation of defect 45, euler #=-100 (144246,427721,283375) : difference with theory (-108) = -8 CORRECTING DEFECT 46 (vertices=37, convex hull=65) After retessellation of defect 46, euler #=-99 (144265,427804,283440) : difference with theory (-107) = -8 CORRECTING DEFECT 47 (vertices=947, convex hull=576) After retessellation of defect 47, euler #=-98 (144690,429371,284583) : difference with theory (-106) = -8 CORRECTING DEFECT 48 (vertices=16, convex hull=18) After retessellation of defect 48, euler #=-97 (144691,429377,284589) : difference with theory (-105) = -8 CORRECTING DEFECT 49 (vertices=48, convex hull=35) After retessellation of defect 49, euler #=-96 (144700,429415,284619) : difference with theory (-104) = -8 CORRECTING DEFECT 50 (vertices=15, convex hull=27) After retessellation of defect 50, euler #=-95 (144703,429431,284633) : difference with theory (-103) = -8 CORRECTING DEFECT 51 (vertices=21, convex hull=36) After retessellation of defect 51, euler #=-94 (144712,429468,284662) : difference with theory (-102) = -8 CORRECTING DEFECT 52 (vertices=23, convex hull=41) After retessellation of defect 52, euler #=-94 (144721,429515,284700) : difference with theory (-101) = -7 CORRECTING DEFECT 53 (vertices=219, convex hull=54) After retessellation of defect 53, euler #=-93 (144737,429587,284757) : difference with theory (-100) = -7 CORRECTING DEFECT 54 (vertices=31, convex hull=90) After retessellation of defect 54, euler #=-92 (144756,429679,284831) : difference with theory (-99) = -7 CORRECTING DEFECT 55 (vertices=22, convex hull=52) After retessellation of defect 55, euler #=-91 (144766,429728,284871) : difference with theory (-98) = -7 CORRECTING DEFECT 56 (vertices=798, convex hull=351) After retessellation of defect 56, euler #=-90 (144966,430514,285458) : difference with theory (-97) = -7 CORRECTING DEFECT 57 (vertices=433, convex hull=286) After retessellation of defect 57, euler #=-89 (144992,430731,285650) : difference with theory (-96) = -7 CORRECTING DEFECT 58 (vertices=17, convex hull=25) Warning - incorrect dp selected!!!!(-71.049931 >= -71.049935 ) After retessellation of defect 58, euler #=-88 (144994,430743,285661) : difference with theory (-95) = -7 CORRECTING DEFECT 59 (vertices=31, convex hull=60) After retessellation of defect 59, euler #=-87 (145011,430817,285719) : difference with theory (-94) = -7 CORRECTING DEFECT 60 (vertices=13, convex hull=19) After retessellation of defect 60, euler #=-86 (145014,430829,285729) : difference with theory (-93) = -7 CORRECTING DEFECT 61 (vertices=61, convex hull=82) After retessellation of defect 61, euler #=-85 (145055,430987,285847) : difference with theory (-92) = -7 CORRECTING DEFECT 62 (vertices=155, convex hull=63) After retessellation of defect 62, euler #=-84 (145086,431106,285936) : difference with theory (-91) = -7 CORRECTING DEFECT 63 (vertices=5, convex hull=23) Warning - incorrect dp selected!!!!(-152.912833 >= -152.912835 ) After retessellation of defect 63, euler #=-83 (145088,431118,285947) : difference with theory (-90) = -7 CORRECTING DEFECT 64 (vertices=219, convex hull=54) After retessellation of defect 64, euler #=-82 (145097,431169,285990) : difference with theory (-89) = -7 CORRECTING DEFECT 65 (vertices=27, convex hull=54) After retessellation of defect 65, euler #=-81 (145111,431229,286037) : difference with theory (-88) = -7 CORRECTING DEFECT 66 (vertices=8, convex hull=28) After retessellation of defect 66, euler #=-80 (145114,431245,286051) : difference with theory (-87) = -7 CORRECTING DEFECT 67 (vertices=198, convex hull=136) After retessellation of defect 67, euler #=-80 (145131,431359,286148) : difference with theory (-86) = -6 CORRECTING DEFECT 68 (vertices=405, convex hull=135) After retessellation of defect 68, euler #=-79 (145208,431656,286369) : difference with theory (-85) = -6 CORRECTING DEFECT 69 (vertices=1344, convex hull=525) After retessellation of defect 69, euler #=-78 (145423,432568,287067) : difference with theory (-84) = -6 CORRECTING DEFECT 70 (vertices=143, convex hull=160) After retessellation of defect 70, euler #=-77 (145484,432831,287270) : difference with theory (-83) = -6 CORRECTING DEFECT 71 (vertices=11795, convex hull=2353) After retessellation of defect 71, euler #=-84 (148663,443668,294921) : difference with theory (-82) = 2 CORRECTING DEFECT 72 (vertices=33, convex hull=53) After retessellation of defect 72, euler #=-83 (148683,443747,294981) : difference with theory (-81) = 2 CORRECTING DEFECT 73 (vertices=100, convex hull=106) After retessellation of defect 73, euler #=-82 (148717,443891,295092) : difference with theory (-80) = 2 CORRECTING DEFECT 74 (vertices=6, convex hull=18) After retessellation of defect 74, euler #=-81 (148718,443899,295100) : difference with theory (-79) = 2 CORRECTING DEFECT 75 (vertices=69, convex hull=74) After retessellation of defect 75, euler #=-80 (148751,444031,295200) : difference with theory (-78) = 2 CORRECTING DEFECT 76 (vertices=22, convex hull=54) After retessellation of defect 76, euler #=-79 (148760,444078,295239) : difference with theory (-77) = 2 CORRECTING DEFECT 77 (vertices=49, convex hull=95) After retessellation of defect 77, euler #=-78 (148792,444208,295338) : difference with theory (-76) = 2 CORRECTING DEFECT 78 (vertices=20, convex hull=25) After retessellation of defect 78, euler #=-77 (148796,444226,295353) : difference with theory (-75) = 2 CORRECTING DEFECT 79 (vertices=9, convex hull=25) After retessellation of defect 79, euler #=-76 (148798,444238,295364) : difference with theory (-74) = 2 CORRECTING DEFECT 80 (vertices=77, convex hull=87) After retessellation of defect 80, euler #=-75 (148817,444332,295440) : difference with theory (-73) = 2 CORRECTING DEFECT 81 (vertices=76, convex hull=37) After retessellation of defect 81, euler #=-74 (148825,444372,295473) : difference with theory (-72) = 2 CORRECTING DEFECT 82 (vertices=7, convex hull=17) After retessellation of defect 82, euler #=-73 (148826,444379,295480) : difference with theory (-71) = 2 CORRECTING DEFECT 83 (vertices=17, convex hull=31) After retessellation of defect 83, euler #=-72 (148829,444399,295498) : difference with theory (-70) = 2 CORRECTING DEFECT 84 (vertices=30, convex hull=64) After retessellation of defect 84, euler #=-71 (148842,444464,295551) : difference with theory (-69) = 2 CORRECTING DEFECT 85 (vertices=48, convex hull=81) After retessellation of defect 85, euler #=-70 (148871,444586,295645) : difference with theory (-68) = 2 CORRECTING DEFECT 86 (vertices=81, convex hull=49) After retessellation of defect 86, euler #=-68 (148875,444619,295676) : difference with theory (-67) = 1 CORRECTING DEFECT 87 (vertices=183, convex hull=51) After retessellation of defect 87, euler #=-67 (148890,444682,295725) : difference with theory (-66) = 1 CORRECTING DEFECT 88 (vertices=5, convex hull=29) After retessellation of defect 88, euler #=-66 (148892,444697,295739) : difference with theory (-65) = 1 CORRECTING DEFECT 89 (vertices=5, convex hull=15) After retessellation of defect 89, euler #=-65 (148892,444702,295745) : difference with theory (-64) = 1 CORRECTING DEFECT 90 (vertices=93, convex hull=89) After retessellation of defect 90, euler #=-64 (148929,444855,295862) : difference with theory (-63) = 1 CORRECTING DEFECT 91 (vertices=73, convex hull=86) After retessellation of defect 91, euler #=-63 (148967,445006,295976) : difference with theory (-62) = 1 CORRECTING DEFECT 92 (vertices=7, convex hull=27) After retessellation of defect 92, euler #=-62 (148969,445020,295989) : difference with theory (-61) = 1 CORRECTING DEFECT 93 (vertices=9, convex hull=15) After retessellation of defect 93, euler #=-61 (148970,445033,296002) : difference with theory (-60) = 1 CORRECTING DEFECT 94 (vertices=59, convex hull=47) After retessellation of defect 94, euler #=-60 (148985,445095,296050) : difference with theory (-59) = 1 CORRECTING DEFECT 95 (vertices=92, convex hull=94) After retessellation of defect 95, euler #=-58 (149010,445210,296142) : difference with theory (-58) = 0 CORRECTING DEFECT 96 (vertices=86, convex hull=78) After retessellation of defect 96, euler #=-57 (149030,445298,296211) : difference with theory (-57) = 0 CORRECTING DEFECT 97 (vertices=6, convex hull=22) After retessellation of defect 97, euler #=-56 (149030,445302,296216) : difference with theory (-56) = 0 CORRECTING DEFECT 98 (vertices=21, convex hull=46) Warning - incorrect dp selected!!!!(-73.619855 >= -73.619859 ) After retessellation of defect 98, euler #=-55 (149031,445321,296235) : difference with theory (-55) = 0 CORRECTING DEFECT 99 (vertices=10, convex hull=20) After retessellation of defect 99, euler #=-54 (149033,445334,296247) : difference with theory (-54) = 0 CORRECTING DEFECT 100 (vertices=110, convex hull=35) After retessellation of defect 100, euler #=-53 (149037,445361,296271) : difference with theory (-53) = 0 CORRECTING DEFECT 101 (vertices=57, convex hull=84) After retessellation of defect 101, euler #=-52 (149056,445451,296343) : difference with theory (-52) = 0 CORRECTING DEFECT 102 (vertices=94, convex hull=114) After retessellation of defect 102, euler #=-50 (149103,445646,296493) : difference with theory (-51) = -1 CORRECTING DEFECT 103 (vertices=19, convex hull=56) After retessellation of defect 103, euler #=-49 (149113,445693,296531) : difference with theory (-50) = -1 CORRECTING DEFECT 104 (vertices=243, convex hull=136) After retessellation of defect 104, euler #=-48 (149129,445801,296624) : difference with theory (-49) = -1 CORRECTING DEFECT 105 (vertices=28, convex hull=36) After retessellation of defect 105, euler #=-48 (149137,445846,296661) : difference with theory (-48) = 0 CORRECTING DEFECT 106 (vertices=295, convex hull=116) After retessellation of defect 106, euler #=-47 (149202,446110,296861) : difference with theory (-47) = 0 CORRECTING DEFECT 107 (vertices=757, convex hull=298) After retessellation of defect 107, euler #=-46 (149343,446675,297286) : difference with theory (-46) = 0 CORRECTING DEFECT 108 (vertices=46, convex hull=76) After retessellation of defect 108, euler #=-45 (149367,446778,297366) : difference with theory (-45) = 0 CORRECTING DEFECT 109 (vertices=25, convex hull=48) After retessellation of defect 109, euler #=-44 (149378,446828,297406) : difference with theory (-44) = 0 CORRECTING DEFECT 110 (vertices=118, convex hull=128) After retessellation of defect 110, euler #=-43 (149412,446988,297533) : difference with theory (-43) = 0 CORRECTING DEFECT 111 (vertices=37, convex hull=56) After retessellation of defect 111, euler #=-42 (149433,447073,297598) : difference with theory (-42) = 0 CORRECTING DEFECT 112 (vertices=36, convex hull=68) After retessellation of defect 112, euler #=-41 (149451,447150,297658) : difference with theory (-41) = 0 CORRECTING DEFECT 113 (vertices=44, convex hull=61) After retessellation of defect 113, euler #=-40 (149465,447212,297707) : difference with theory (-40) = 0 CORRECTING DEFECT 114 (vertices=15, convex hull=19) After retessellation of defect 114, euler #=-39 (149467,447223,297717) : difference with theory (-39) = 0 CORRECTING DEFECT 115 (vertices=17, convex hull=25) After retessellation of defect 115, euler #=-38 (149470,447240,297732) : difference with theory (-38) = 0 CORRECTING DEFECT 116 (vertices=190, convex hull=127) After retessellation of defect 116, euler #=-37 (149506,447413,297870) : difference with theory (-37) = 0 CORRECTING DEFECT 117 (vertices=8, convex hull=15) After retessellation of defect 117, euler #=-36 (149506,447417,297875) : difference with theory (-36) = 0 CORRECTING DEFECT 118 (vertices=74, convex hull=43) After retessellation of defect 118, euler #=-35 (149515,447465,297915) : difference with theory (-35) = 0 CORRECTING DEFECT 119 (vertices=28, convex hull=32) After retessellation of defect 119, euler #=-34 (149524,447501,297943) : difference with theory (-34) = 0 CORRECTING DEFECT 120 (vertices=202, convex hull=30) After retessellation of defect 120, euler #=-33 (149528,447524,297963) : difference with theory (-33) = 0 CORRECTING DEFECT 121 (vertices=59, convex hull=60) After retessellation of defect 121, euler #=-32 (149542,447588,298014) : difference with theory (-32) = 0 CORRECTING DEFECT 122 (vertices=893, convex hull=176) After retessellation of defect 122, euler #=-31 (149608,447890,298251) : difference with theory (-31) = 0 CORRECTING DEFECT 123 (vertices=30, convex hull=32) After retessellation of defect 123, euler #=-30 (149615,447920,298275) : difference with theory (-30) = 0 CORRECTING DEFECT 124 (vertices=199, convex hull=85) After retessellation of defect 124, euler #=-29 (149629,448002,298344) : difference with theory (-29) = 0 CORRECTING DEFECT 125 (vertices=171, convex hull=95) After retessellation of defect 125, euler #=-28 (149656,448122,298438) : difference with theory (-28) = 0 CORRECTING DEFECT 126 (vertices=74, convex hull=48) After retessellation of defect 126, euler #=-27 (149676,448202,298499) : difference with theory (-27) = 0 CORRECTING DEFECT 127 (vertices=145, convex hull=76) After retessellation of defect 127, euler #=-26 (149700,448305,298579) : difference with theory (-26) = 0 CORRECTING DEFECT 128 (vertices=316, convex hull=124) After retessellation of defect 128, euler #=-25 (149751,448519,298743) : difference with theory (-25) = 0 CORRECTING DEFECT 129 (vertices=575, convex hull=356) After retessellation of defect 129, euler #=-24 (149899,449151,299228) : difference with theory (-24) = 0 CORRECTING DEFECT 130 (vertices=19, convex hull=39) After retessellation of defect 130, euler #=-23 (149910,449196,299263) : difference with theory (-23) = 0 CORRECTING DEFECT 131 (vertices=6, convex hull=26) After retessellation of defect 131, euler #=-22 (149912,449212,299278) : difference with theory (-22) = 0 CORRECTING DEFECT 132 (vertices=173, convex hull=205) After retessellation of defect 132, euler #=-21 (149966,449462,299475) : difference with theory (-21) = 0 CORRECTING DEFECT 133 (vertices=17, convex hull=21) After retessellation of defect 133, euler #=-20 (149967,449469,299482) : difference with theory (-20) = 0 CORRECTING DEFECT 134 (vertices=49, convex hull=101) After retessellation of defect 134, euler #=-19 (149995,449596,299582) : difference with theory (-19) = 0 CORRECTING DEFECT 135 (vertices=30, convex hull=69) After retessellation of defect 135, euler #=-18 (150007,449654,299629) : difference with theory (-18) = 0 CORRECTING DEFECT 136 (vertices=133, convex hull=97) After retessellation of defect 136, euler #=-17 (150024,449757,299716) : difference with theory (-17) = 0 CORRECTING DEFECT 137 (vertices=190, convex hull=58) After retessellation of defect 137, euler #=-16 (150043,449837,299778) : difference with theory (-16) = 0 CORRECTING DEFECT 138 (vertices=9, convex hull=27) After retessellation of defect 138, euler #=-15 (150044,449848,299789) : difference with theory (-15) = 0 CORRECTING DEFECT 139 (vertices=33, convex hull=80) After retessellation of defect 139, euler #=-14 (150063,449936,299859) : difference with theory (-14) = 0 CORRECTING DEFECT 140 (vertices=78, convex hull=99) After retessellation of defect 140, euler #=-13 (150076,450014,299925) : difference with theory (-13) = 0 CORRECTING DEFECT 141 (vertices=67, convex hull=68) After retessellation of defect 141, euler #=-12 (150095,450097,299990) : difference with theory (-12) = 0 CORRECTING DEFECT 142 (vertices=37, convex hull=29) After retessellation of defect 142, euler #=-11 (150100,450120,300009) : difference with theory (-11) = 0 CORRECTING DEFECT 143 (vertices=7, convex hull=24) After retessellation of defect 143, euler #=-10 (150102,450133,300021) : difference with theory (-10) = 0 CORRECTING DEFECT 144 (vertices=37, convex hull=66) After retessellation of defect 144, euler #=-9 (150113,450190,300068) : difference with theory (-9) = 0 CORRECTING DEFECT 145 (vertices=11, convex hull=31) After retessellation of defect 145, euler #=-8 (150115,450204,300081) : difference with theory (-8) = 0 CORRECTING DEFECT 146 (vertices=45, convex hull=40) After retessellation of defect 146, euler #=-7 (150126,450252,300119) : difference with theory (-7) = 0 CORRECTING DEFECT 147 (vertices=33, convex hull=33) After retessellation of defect 147, euler #=-6 (150129,450268,300133) : difference with theory (-6) = 0 CORRECTING DEFECT 148 (vertices=10, convex hull=18) After retessellation of defect 148, euler #=-5 (150130,450278,300143) : difference with theory (-5) = 0 CORRECTING DEFECT 149 (vertices=38, convex hull=40) After retessellation of defect 149, euler #=-4 (150134,450305,300167) : difference with theory (-4) = 0 CORRECTING DEFECT 150 (vertices=31, convex hull=49) After retessellation of defect 150, euler #=-3 (150142,450349,300204) : difference with theory (-3) = 0 CORRECTING DEFECT 151 (vertices=28, convex hull=64) After retessellation of defect 151, euler #=-2 (150152,450404,300250) : difference with theory (-2) = 0 CORRECTING DEFECT 152 (vertices=22, convex hull=47) After retessellation of defect 152, euler #=-1 (150161,450449,300287) : difference with theory (-1) = 0 CORRECTING DEFECT 153 (vertices=21, convex hull=27) After retessellation of defect 153, euler #=0 (150163,450465,300302) : difference with theory (0) = 0 CORRECTING DEFECT 154 (vertices=34, convex hull=21) After retessellation of defect 154, euler #=1 (150166,450482,300317) : difference with theory (1) = 0 CORRECTING DEFECT 155 (vertices=16, convex hull=33) After retessellation of defect 155, euler #=2 (150168,450498,300332) : 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-->14.29) (max @ vno 58860 --> 64507) 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-->14.29) (max @ vno 58860 --> 64507) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 593 mutations (35.8%), 1062 crossovers (64.2%), 1148 vertices were eliminated building final representation... 21076 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=150168, nf=300332, ne=450498, g=0) writing corrected surface to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 132.3 minutes 0 defective edges removing intersecting faces 000: 3379 intersecting 001: 632 intersecting 002: 473 intersecting 003: 413 intersecting 004: 284 intersecting 005: 204 intersecting 006: 172 intersecting expanding nbhd size to 2 007: 173 intersecting 008: 151 intersecting 009: 147 intersecting 010: 135 intersecting 011: 131 intersecting 012: 129 intersecting 013: 123 intersecting 014: 112 intersecting expanding nbhd size to 3 015: 112 intersecting expanding nbhd size to 4 016: 117 intersecting 017: 106 intersecting 018: 98 intersecting 019: 95 intersecting 020: 79 intersecting 021: 74 intersecting 022: 63 intersecting 023: 57 intersecting 024: 55 intersecting 025: 52 intersecting expanding nbhd size to 5 026: 53 intersecting 027: 51 intersecting 028: 50 intersecting 029: 45 intersecting 030: 42 intersecting 031: 40 intersecting expanding nbhd size to 6 032: 40 intersecting 033: 39 intersecting 034: 38 intersecting 035: 36 intersecting 036: 35 intersecting expanding nbhd size to 7 037: 36 intersecting 038: 33 intersecting expanding nbhd size to 8 039: 33 intersecting 040: 31 intersecting 041: 27 intersecting 042: 25 intersecting 043: 22 intersecting 044: 20 intersecting 045: 14 intersecting 046: 8 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 150168 - 450498 + 300332 = 2 --> 0 holes F =2V-4: 300332 = 300336-4 (0) 2E=3F: 900996 = 900996 (0) total defect index = 0 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.01 hours removing intersecting faces 000: 1866 intersecting 001: 565 intersecting 002: 450 intersecting 003: 387 intersecting 004: 265 intersecting 005: 211 intersecting 006: 170 intersecting 007: 168 intersecting 008: 152 intersecting 009: 141 intersecting 010: 137 intersecting 011: 128 intersecting 012: 116 intersecting 013: 114 intersecting expanding nbhd size to 2 014: 118 intersecting 015: 114 intersecting expanding nbhd size to 3 016: 115 intersecting 017: 108 intersecting expanding nbhd size to 4 018: 109 intersecting 019: 104 intersecting 020: 93 intersecting 021: 86 intersecting 022: 77 intersecting 023: 71 intersecting 024: 67 intersecting 025: 62 intersecting 026: 53 intersecting 027: 52 intersecting expanding nbhd size to 5 028: 54 intersecting 029: 50 intersecting 030: 45 intersecting expanding nbhd size to 6 031: 47 intersecting 032: 45 intersecting 033: 41 intersecting 034: 39 intersecting expanding nbhd size to 7 035: 39 intersecting 036: 38 intersecting 037: 37 intersecting 038: 36 intersecting 039: 35 intersecting 040: 31 intersecting 041: 29 intersecting expanding nbhd size to 8 042: 30 intersecting 043: 27 intersecting 044: 24 intersecting 045: 23 intersecting 046: 18 intersecting 047: 9 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Jan 3 14:03:02 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 21161 bright wm thresholded. 1636 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (94.0): 94.3 +- 7.9 [70.0 --> 110.0] GM (82.0) : 78.4 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.3 (was 70) setting MAX_BORDER_WHITE to 106.9 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 47.6 (was 40) setting MAX_GRAY to 91.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.9 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.01-->6.87) (max @ vno 147019 --> 147651) face area 0.27 +- 0.16 (0.00-->8.03) mean absolute distance = 0.83 +- 1.08 4485 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=99, GM=77 mean inside = 90.8, mean outside = 78.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=85.5, 3648 (3648) missing vertices, mean dist 0.2 [0.8 (%38.2)->0.8 (%61.8))] %67 local maxima, %22 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 0.90 +- 0.31 (0.04-->6.96) (max @ vno 58931 --> 57757) face area 0.27 +- 0.17 (0.00-->6.91) mean absolute distance = 0.50 +- 0.76 5508 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5233608.5, rms=9.27 001: dt: 0.5000, sse=6513731.5, rms=7.476 (0.000%) 002: dt: 0.5000, sse=6706423.5, rms=6.307 (0.000%) 003: dt: 0.5000, sse=7003605.0, rms=5.501 (0.000%) 004: dt: 0.5000, sse=7084486.5, rms=4.927 (0.000%) 005: dt: 0.5000, sse=7240545.0, rms=4.580 (0.000%) 006: dt: 0.5000, sse=7241173.0, rms=4.364 (0.000%) 007: dt: 0.5000, sse=7342248.5, rms=4.243 (0.000%) 008: dt: 0.5000, sse=7345578.5, rms=4.154 (0.000%) 009: dt: 0.5000, sse=7367017.5, rms=4.071 (0.000%) 010: dt: 0.5000, sse=7344674.0, rms=4.008 (0.000%) 011: dt: 0.5000, sse=7339942.0, rms=3.942 (0.000%) rms = 3.90, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=7336799.5, rms=3.903 (0.000%) 013: dt: 0.2500, sse=5198942.0, rms=3.523 (0.000%) 014: dt: 0.2500, sse=4965823.5, rms=3.455 (0.000%) rms = 3.44, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4883002.0, rms=3.440 (0.000%) rms = 3.39, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4792370.5, rms=3.391 (0.000%) positioning took 1.4 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 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=87.9, 3163 (2486) missing vertices, mean dist -0.3 [0.6 (%69.5)->0.4 (%30.5))] %77 local maxima, %11 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 +- 0.31 (0.02-->7.62) (max @ vno 58931 --> 57757) face area 0.33 +- 0.21 (0.00-->8.18) mean absolute distance = 0.36 +- 0.53 4614 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5174922.0, rms=4.84 017: dt: 0.5000, sse=5648101.0, rms=3.930 (0.000%) 018: dt: 0.5000, sse=6340446.0, rms=3.685 (0.000%) rms = 3.65, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6476945.0, rms=3.650 (0.000%) 020: dt: 0.2500, sse=5564828.0, rms=3.330 (0.000%) 021: dt: 0.2500, sse=5386251.5, rms=3.256 (0.000%) rms = 3.24, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5310478.5, rms=3.245 (0.000%) 023: dt: 0.1250, sse=5232859.0, rms=3.176 (0.000%) rms = 3.15, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=5199694.5, rms=3.152 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.2, 3103 (2301) missing vertices, mean dist -0.1 [0.4 (%63.3)->0.3 (%36.7))] %81 local maxima, % 7 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 +- 0.31 (0.04-->7.74) (max @ vno 58931 --> 57757) face area 0.32 +- 0.21 (0.00-->8.23) mean absolute distance = 0.31 +- 0.44 3713 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5293151.0, rms=3.81 025: dt: 0.5000, sse=5790871.0, rms=3.501 (0.000%) 026: dt: 0.5000, sse=6382301.0, rms=3.405 (0.000%) rms = 3.48, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5762011.5, rms=3.197 (0.000%) 028: dt: 0.2500, sse=5537086.5, rms=3.127 (0.000%) rms = 3.13, time step reduction 2 of 3 to 0.125... rms = 3.10, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5468456.0, rms=3.101 (0.000%) positioning took 0.5 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 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 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 3 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 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 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.7, 3149 (2229) missing vertices, mean dist -0.0 [0.3 (%54.2)->0.3 (%45.8))] %83 local maxima, % 5 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/MPS1036-1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5484363.0, rms=3.25 030: dt: 0.5000, sse=7015162.0, rms=3.160 (0.000%) rms = 3.27, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=6398160.0, rms=2.999 (0.000%) rms = 3.00, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=6170094.5, rms=2.996 (0.000%) 033: dt: 0.1250, sse=6135512.0, rms=2.913 (0.000%) rms = 2.89, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=6113836.0, rms=2.885 (0.000%) positioning took 0.5 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 generating cortex label... 37 non-cortical segments detected only using segment with 2173 vertices erasing segment 0 (vno[0] = 53334) erasing segment 2 (vno[0] = 53549) erasing segment 3 (vno[0] = 54568) erasing segment 4 (vno[0] = 64533) erasing segment 5 (vno[0] = 72173) erasing segment 6 (vno[0] = 73422) erasing segment 7 (vno[0] = 74668) erasing segment 8 (vno[0] = 78273) erasing segment 9 (vno[0] = 80651) erasing segment 10 (vno[0] = 82705) erasing segment 11 (vno[0] = 84228) erasing segment 12 (vno[0] = 86083) erasing segment 13 (vno[0] = 86473) erasing segment 14 (vno[0] = 88490) erasing segment 15 (vno[0] = 95628) erasing segment 16 (vno[0] = 99855) erasing segment 17 (vno[0] = 100771) erasing segment 18 (vno[0] = 100781) erasing segment 19 (vno[0] = 100838) erasing segment 20 (vno[0] = 102619) erasing segment 21 (vno[0] = 103405) erasing segment 22 (vno[0] = 104332) erasing segment 23 (vno[0] = 105249) erasing segment 24 (vno[0] = 106054) erasing segment 25 (vno[0] = 106944) erasing segment 26 (vno[0] = 107688) erasing segment 27 (vno[0] = 107726) erasing segment 28 (vno[0] = 109318) erasing segment 29 (vno[0] = 109349) erasing segment 30 (vno[0] = 110168) erasing segment 31 (vno[0] = 110169) erasing segment 32 (vno[0] = 110926) erasing segment 33 (vno[0] = 111565) erasing segment 34 (vno[0] = 111577) erasing segment 35 (vno[0] = 112186) erasing segment 36 (vno[0] = 149055) writing cortex label to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label... writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.curv writing smoothed area to lh.area writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.area vertex spacing 0.88 +- 0.32 (0.02-->7.73) (max @ vno 58931 --> 57757) face area 0.32 +- 0.21 (0.00-->8.31) refinement took 4.5 minutes #-------------------------------------------- #@# Smooth2 lh Fri Jan 3 14:07:34 CST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Fri Jan 3 14:07:38 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 52.7 mm, total surface area = 86766 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.125 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.068 (target=0.015) step 015: RMS=0.057 (target=0.015) step 020: RMS=0.048 (target=0.015) step 025: RMS=0.041 (target=0.015) step 030: RMS=0.035 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.018 (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 212 vertices thresholded to be in k1 ~ [-0.32 1.75], k2 ~ [-0.10 0.06] total integrated curvature = 0.361*4pi (4.535) --> 1 handles ICI = 1.3, FI = 9.8, variation=162.410 138 vertices thresholded to be in [-0.02 0.03] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 156 vertices thresholded to be in [-0.17 0.75] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.027 done. #----------------------------------------- #@# Curvature Stats lh Fri Jan 3 14:09:17 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm MPS1036-1 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 [ MPS1036-1/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 [ 315 ] Gb_filter = 0 WARN: S lookup min: -0.240089 WARN: S explicit min: 0.000000 vertex = 9 #-------------------------------------------- #@# Sphere lh Fri Jan 3 14:09:22 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.279... 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 %19.68 pass 1: epoch 2 of 3 starting distance error %19.66 unfolding complete - removing small folds... starting distance error %19.54 removing remaining folds... final distance error %19.56 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.66 hours #-------------------------------------------- #@# Surf Reg lh Fri Jan 3 14:49:15 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_register -curv ../surf/lh.sphere /soft/freesurfer/5.3.0_1/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_1/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 = 0.543 curvature mean = 0.042, std = 0.943 curvature mean = 0.023, std = 0.842 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 347564.7, tmin=0.8058 d=32.00 min @ (0.00, -8.00, 0.00) sse = 333847.8, tmin=1.6193 d=16.00 min @ (-4.00, 4.00, -4.00) sse = 300594.0, tmin=2.4356 d=8.00 min @ (2.00, 0.00, 0.00) sse = 296192.9, tmin=3.3424 d=4.00 min @ (-1.00, -1.00, 1.00) sse = 294667.9, tmin=4.2704 d=2.00 min @ (0.50, 0.00, -0.50) sse = 294280.8, tmin=5.1942 d=0.50 min @ (-0.12, 0.00, 0.12) sse = 294272.0, tmin=6.9656 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 6.97 min curvature mean = -0.015, std = 0.941 curvature mean = 0.007, std = 0.931 curvature mean = -0.025, std = 0.948 curvature mean = 0.003, std = 0.968 curvature mean = -0.030, std = 0.947 curvature mean = 0.001, std = 0.984 2 Reading smoothwm curvature mean = -0.033, std = 0.388 curvature mean = 0.006, std = 0.069 curvature mean = 0.048, std = 0.255 curvature mean = 0.004, std = 0.079 curvature mean = 0.030, std = 0.391 curvature mean = 0.004, std = 0.085 curvature mean = 0.017, std = 0.508 curvature mean = 0.003, std = 0.087 curvature mean = 0.006, std = 0.613 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri Jan 3 15:15:16 CST 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 Fri Jan 3 15:15:18 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mrisp_paint -a 5 /soft/freesurfer/5.3.0_1/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_1/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Jan 3 15:15:20 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 3494 labels changed using aseg relabeling using gibbs priors... 000: 3176 changed, 150168 examined... 001: 762 changed, 13510 examined... 002: 185 changed, 4146 examined... 003: 63 changed, 1090 examined... 004: 31 changed, 402 examined... 005: 11 changed, 151 examined... 006: 10 changed, 73 examined... 007: 2 changed, 49 examined... 008: 2 changed, 12 examined... 009: 2 changed, 12 examined... 010: 1 changed, 11 examined... 011: 1 changed, 6 examined... 012: 2 changed, 7 examined... 013: 2 changed, 10 examined... 014: 1 changed, 10 examined... 015: 2 changed, 6 examined... 016: 1 changed, 12 examined... 017: 0 changed, 5 examined... 276 labels changed using aseg 000: 232 total segments, 183 labels (736 vertices) changed 001: 52 total segments, 4 labels (4 vertices) changed 002: 48 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 53 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2874 vertices marked for relabeling... 2874 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 38 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Jan 3 15:15:58 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 21161 bright wm thresholded. 1636 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (94.0): 94.3 +- 7.9 [70.0 --> 110.0] GM (82.0) : 78.4 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.3 (was 70) setting MAX_BORDER_WHITE to 106.9 (was 105) setting MIN_BORDER_WHITE to 77.0 (was 85) setting MAX_CSF to 47.6 (was 40) setting MAX_GRAY to 91.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 32.9 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=99, GM=77 mean inside = 90.8, mean outside = 78.5 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/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.27 (0.01-->6.87) (max @ vno 147019 --> 147651) face area 0.27 +- 0.16 (0.00-->8.03) mean absolute distance = 0.84 +- 1.11 4468 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 143 points - only 0.00% unknown deleting segment 2 with 20 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 8 with 22 points - only 0.00% unknown deleting segment 9 with 53 points - only 0.00% unknown deleting segment 10 with 51 points - only 0.00% unknown deleting segment 11 with 59 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 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown deleting segment 17 with 62 points - only 0.00% unknown deleting segment 18 with 74 points - only 0.00% unknown deleting segment 19 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 20 with 3 points - only 0.00% unknown deleting segment 22 with 39 points - only 0.00% unknown deleting segment 23 with 8 points - only 0.00% unknown deleting segment 24 with 7 points - only 0.00% unknown deleting segment 25 with 38 points - only 0.00% unknown deleting segment 26 with 122 points - only 0.00% unknown deleting segment 27 with 8 points - only 0.00% unknown deleting segment 28 with 83 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 29 with 2 points - only 0.00% unknown deleting segment 30 with 18 points - only 0.00% unknown deleting segment 31 with 145 points - only 0.00% unknown deleting segment 32 with 186 points - only 0.00% unknown deleting segment 33 with 154 points - only 0.00% unknown deleting segment 34 with 20 points - only 0.00% unknown deleting segment 35 with 76 points - only 0.00% unknown deleting segment 36 with 17 points - only 0.00% unknown deleting segment 37 with 14 points - only 0.00% unknown deleting segment 38 with 33 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 39 with 2 points - only 0.00% unknown deleting segment 40 with 24 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 41 with 4 points - only 0.00% unknown mean border=85.5, 3819 (3713) missing vertices, mean dist 0.2 [0.8 (%38.7)->0.8 (%61.3))] %67 local maxima, %22 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 0.90 +- 0.31 (0.03-->6.96) (max @ vno 58931 --> 57757) face area 0.27 +- 0.17 (0.00-->7.29) mean absolute distance = 0.51 +- 0.79 5329 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5346159.0, rms=9.39 001: dt: 0.5000, sse=6633900.5, rms=7.606 (0.000%) 002: dt: 0.5000, sse=6823738.0, rms=6.447 (0.000%) 003: dt: 0.5000, sse=7117860.0, rms=5.644 (0.000%) 004: dt: 0.5000, sse=7198064.0, rms=5.070 (0.000%) 005: dt: 0.5000, sse=7359454.0, rms=4.719 (0.000%) 006: dt: 0.5000, sse=7361677.0, rms=4.496 (0.000%) 007: dt: 0.5000, sse=7452761.5, rms=4.366 (0.000%) 008: dt: 0.5000, sse=7454219.5, rms=4.271 (0.000%) 009: dt: 0.5000, sse=7480977.0, rms=4.185 (0.000%) 010: dt: 0.5000, sse=7448255.5, rms=4.117 (0.000%) 011: dt: 0.5000, sse=7442724.5, rms=4.048 (0.000%) rms = 4.01, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=7453679.0, rms=4.008 (0.000%) 013: dt: 0.2500, sse=5263612.0, rms=3.632 (0.000%) 014: dt: 0.2500, sse=5032096.0, rms=3.562 (0.000%) rms = 3.54, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4945310.5, rms=3.536 (0.000%) rms = 3.49, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4855702.0, rms=3.492 (0.000%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 183 points - only 0.00% unknown deleting segment 2 with 11 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 24 points - only 0.00% unknown removing 2 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 8 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 15 with 5 points - only 0.00% unknown deleting segment 16 with 344 points - only 0.00% unknown deleting segment 18 with 73 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 19 with 2 points - only 0.00% unknown deleting segment 20 with 11 points - only 0.00% unknown deleting segment 21 with 8 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 22 with 4 points - only 0.00% unknown deleting segment 23 with 7 points - only 0.00% unknown deleting segment 24 with 9 points - only 0.00% unknown deleting segment 25 with 7 points - only 0.00% unknown deleting segment 26 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 29 with 3 points - only 0.00% unknown deleting segment 30 with 51 points - only 0.00% unknown deleting segment 31 with 46 points - only 0.00% unknown deleting segment 32 with 7 points - only 0.00% unknown deleting segment 34 with 428 points - only 0.00% unknown deleting segment 35 with 84 points - only 0.00% unknown deleting segment 36 with 11 points - only 0.00% unknown deleting segment 37 with 7 points - only 42.86% unknown removing 4 vertex label from ripped group deleting segment 40 with 544 points - only 0.00% unknown deleting segment 41 with 10 points - only 0.00% unknown deleting segment 43 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 44 with 2 points - only 0.00% unknown deleting segment 45 with 208 points - only 0.00% unknown deleting segment 46 with 218 points - only 0.00% unknown deleting segment 47 with 20 points - only 0.00% unknown deleting segment 49 with 75 points - only 0.00% unknown deleting segment 50 with 43 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 52 with 14 points - only 0.00% unknown deleting segment 53 with 176 points - only 0.00% unknown mean border=87.9, 3435 (2542) missing vertices, mean dist -0.3 [0.6 (%69.7)->0.4 (%30.3))] %79 local maxima, %11 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 +- 0.31 (0.06-->7.66) (max @ vno 58931 --> 57757) face area 0.33 +- 0.21 (0.00-->9.03) mean absolute distance = 0.37 +- 0.55 4269 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5338032.0, rms=5.05 017: dt: 0.5000, sse=5828669.5, rms=4.170 (0.000%) 018: dt: 0.5000, sse=6546468.0, rms=3.924 (0.000%) 019: dt: 0.5000, sse=6673098.0, rms=3.873 (0.000%) 020: dt: 0.5000, sse=7217985.5, rms=3.805 (0.000%) rms = 3.82, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=6077954.0, rms=3.543 (0.000%) 022: dt: 0.2500, sse=5653521.5, rms=3.431 (0.000%) rms = 3.42, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5531872.0, rms=3.420 (0.000%) 024: dt: 0.1250, sse=5421610.5, rms=3.354 (0.000%) rms = 3.32, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5381814.5, rms=3.325 (0.000%) positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown deleting segment 1 with 49 points - only 0.00% unknown deleting segment 2 with 125 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 388 points - only 0.00% unknown deleting segment 14 with 103 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 15 with 2 points - only 0.00% unknown deleting segment 16 with 25 points - only 0.00% unknown deleting segment 17 with 9 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 19 with 3 points - only 0.00% unknown deleting segment 20 with 10 points - only 0.00% unknown removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 24 with 4 points - only 0.00% unknown deleting segment 25 with 49 points - only 0.00% unknown deleting segment 26 with 52 points - only 0.00% unknown deleting segment 27 with 74 points - only 50.00% unknown deleting segment 28 with 6 points - only 0.00% unknown deleting segment 29 with 461 points - only 0.00% unknown deleting segment 31 with 89 points - only 0.00% unknown deleting segment 32 with 11 points - only 0.00% unknown deleting segment 33 with 7 points - only 42.86% unknown removing 4 vertex label from ripped group deleting segment 35 with 559 points - only 0.00% unknown deleting segment 36 with 9 points - only 0.00% unknown deleting segment 37 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 38 with 2 points - only 0.00% unknown deleting segment 39 with 190 points - only 0.00% unknown deleting segment 40 with 194 points - only 0.00% unknown deleting segment 41 with 20 points - only 0.00% unknown deleting segment 42 with 75 points - only 0.00% unknown deleting segment 43 with 41 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 45 with 16 points - only 0.00% unknown deleting segment 46 with 185 points - only 0.00% unknown mean border=89.3, 3453 (2372) missing vertices, mean dist -0.1 [0.4 (%63.4)->0.3 (%36.6))] %83 local maxima, % 7 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 +- 0.31 (0.03-->7.77) (max @ vno 58931 --> 57757) face area 0.32 +- 0.21 (0.00-->8.47) mean absolute distance = 0.32 +- 0.47 3403 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5493182.0, rms=3.97 026: dt: 0.5000, sse=5984089.5, rms=3.665 (0.000%) 027: dt: 0.5000, sse=6625040.5, rms=3.567 (0.000%) rms = 3.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=5981118.5, rms=3.368 (0.000%) 029: dt: 0.2500, sse=5740574.0, rms=3.302 (0.000%) rms = 3.29, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5661442.5, rms=3.294 (0.000%) 031: dt: 0.1250, sse=5586683.5, rms=3.233 (0.000%) rms = 3.21, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5541591.0, rms=3.209 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 26 points - only 0.00% unknown deleting segment 1 with 51 points - only 0.00% unknown deleting segment 2 with 118 points - only 0.00% unknown deleting segment 3 with 11 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 10 with 4 points - only 0.00% unknown deleting segment 11 with 373 points - only 0.00% unknown deleting segment 13 with 110 points - only 0.00% unknown deleting segment 14 with 86 points - only 0.00% unknown removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown deleting segment 18 with 46 points - only 0.00% unknown deleting segment 19 with 41 points - only 0.00% unknown deleting segment 20 with 82 points - only 54.88% unknown deleting segment 21 with 5 points - only 0.00% unknown deleting segment 22 with 465 points - only 0.00% unknown deleting segment 23 with 83 points - only 0.00% unknown deleting segment 24 with 11 points - only 0.00% unknown deleting segment 25 with 19 points - only 15.79% unknown deleting segment 26 with 553 points - only 0.00% unknown deleting segment 27 with 8 points - only 0.00% unknown deleting segment 28 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 29 with 3 points - only 0.00% unknown deleting segment 30 with 182 points - only 0.00% unknown deleting segment 31 with 194 points - only 0.00% unknown deleting segment 32 with 20 points - only 0.00% unknown deleting segment 33 with 75 points - only 0.00% unknown deleting segment 34 with 38 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 36 with 18 points - only 0.00% unknown deleting segment 37 with 182 points - only 0.00% unknown mean border=89.7, 3461 (2262) missing vertices, mean dist -0.0 [0.3 (%54.3)->0.3 (%45.7))] %84 local maxima, % 5 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=5563111.0, rms=3.39 033: dt: 0.5000, sse=7183804.5, rms=3.293 (0.000%) rms = 3.37, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=6592945.0, rms=3.158 (0.000%) rms = 3.14, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=6337620.5, rms=3.143 (0.000%) 036: dt: 0.1250, sse=6301662.0, rms=3.071 (0.000%) rms = 3.05, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=6316444.0, rms=3.050 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=64.2, 3026 (3026) missing vertices, mean dist 1.5 [3.5 (%2.2)->3.7 (%97.8))] %22 local maxima, %16 large gradients and %54 min vals, 3121 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=21776984.0, rms=26.24 001: dt: 0.5000, sse=18108794.0, rms=23.493 (0.000%) 002: dt: 0.5000, sse=15290035.0, rms=21.120 (0.000%) 003: dt: 0.5000, sse=13106824.0, rms=19.111 (0.000%) 004: dt: 0.5000, sse=11493890.0, rms=17.408 (0.000%) 005: dt: 0.5000, sse=10277456.0, rms=15.941 (0.000%) 006: dt: 0.5000, sse=9401478.0, rms=14.653 (0.000%) 007: dt: 0.5000, sse=8799620.0, rms=13.468 (0.000%) 008: dt: 0.5000, sse=8360737.5, rms=12.353 (0.000%) 009: dt: 0.5000, sse=8169877.5, rms=11.348 (0.000%) 010: dt: 0.5000, sse=8023346.5, rms=10.416 (0.000%) 011: dt: 0.5000, sse=8036418.5, rms=9.559 (0.000%) 012: dt: 0.5000, sse=8040929.5, rms=8.760 (0.000%) 013: dt: 0.5000, sse=8110035.0, rms=8.055 (0.000%) 014: dt: 0.5000, sse=8139589.5, rms=7.456 (0.000%) 015: dt: 0.5000, sse=8223955.5, rms=6.967 (0.000%) 016: dt: 0.5000, sse=8267452.0, rms=6.596 (0.000%) 017: dt: 0.5000, sse=8335230.5, rms=6.335 (0.000%) 018: dt: 0.5000, sse=8338948.0, rms=6.166 (0.000%) 019: dt: 0.5000, sse=8388513.5, rms=6.041 (0.000%) 020: dt: 0.5000, sse=8353532.5, rms=5.954 (0.000%) 021: dt: 0.5000, sse=8408607.0, rms=5.894 (0.000%) 022: dt: 0.5000, sse=8392925.0, rms=5.836 (0.000%) rms = 5.79, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=8354063.5, rms=5.794 (0.000%) 024: dt: 0.2500, sse=6475170.0, rms=5.286 (0.000%) 025: dt: 0.2500, sse=6351686.0, rms=5.154 (0.000%) rms = 5.17, time step reduction 2 of 3 to 0.125... 026: dt: 0.1250, sse=6145760.0, rms=5.059 (0.000%) 027: dt: 0.1250, sse=5779848.5, rms=4.927 (0.000%) rms = 4.89, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5689459.0, rms=4.888 (0.000%) positioning took 2.5 minutes mean border=62.6, 5431 (1560) missing vertices, mean dist 0.2 [0.3 (%35.4)->0.8 (%64.6))] %30 local maxima, %14 large gradients and %46 min vals, 2235 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=6321019.0, rms=6.19 029: dt: 0.5000, sse=6892920.5, rms=6.038 (0.000%) 030: dt: 0.5000, sse=8082287.5, rms=5.763 (0.000%) rms = 5.84, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=7069456.0, rms=5.237 (0.000%) 032: dt: 0.2500, sse=6720642.5, rms=5.104 (0.000%) rms = 5.17, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=6570770.5, rms=5.010 (0.000%) 034: dt: 0.1250, sse=6342060.0, rms=4.886 (0.000%) rms = 4.84, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=6282797.0, rms=4.838 (0.000%) positioning took 0.8 minutes mean border=62.3, 6700 (1441) missing vertices, mean dist 0.1 [0.3 (%41.0)->0.6 (%59.0))] %32 local maxima, %11 large gradients and %46 min vals, 2134 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=6326381.0, rms=4.94 rms = 5.41, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=6205876.0, rms=4.772 (0.000%) rms = 4.74, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=6385645.5, rms=4.741 (0.000%) 038: dt: 0.1250, sse=6234392.5, rms=4.660 (0.000%) rms = 4.62, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=6267748.5, rms=4.617 (0.000%) positioning took 0.5 minutes mean border=62.0, 11298 (1408) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.4 (%55.3))] %32 local maxima, %10 large gradients and %44 min vals, 2034 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/MPS1036-1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6266447.0, rms=4.61 rms = 4.98, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=6246308.5, rms=4.514 (0.000%) 041: dt: 0.2500, sse=6635978.0, rms=4.463 (0.000%) rms = 4.50, time step reduction 2 of 3 to 0.125... rms = 4.43, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=6568963.0, rms=4.431 (0.000%) positioning took 0.4 minutes writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.area.pial vertex spacing 0.98 +- 0.48 (0.02-->9.22) (max @ vno 146918 --> 146971) face area 0.37 +- 0.34 (0.00-->9.57) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 150168 vertices processed 25000 of 150168 vertices processed 50000 of 150168 vertices processed 75000 of 150168 vertices processed 100000 of 150168 vertices processed 125000 of 150168 vertices processed 150000 of 150168 vertices processed 0 of 150168 vertices processed 25000 of 150168 vertices processed 50000 of 150168 vertices processed 75000 of 150168 vertices processed 100000 of 150168 vertices processed 125000 of 150168 vertices processed 150000 of 150168 vertices processed thickness calculation complete, 2173:3131 truncations. 23860 vertices at 0 distance 72961 vertices at 1 distance 82161 vertices at 2 distance 53446 vertices at 3 distance 26994 vertices at 4 distance 11998 vertices at 5 distance 4926 vertices at 6 distance 2094 vertices at 7 distance 938 vertices at 8 distance 489 vertices at 9 distance 308 vertices at 10 distance 217 vertices at 11 distance 175 vertices at 12 distance 137 vertices at 13 distance 105 vertices at 14 distance 100 vertices at 15 distance 78 vertices at 16 distance 80 vertices at 17 distance 49 vertices at 18 distance 31 vertices at 19 distance 67 vertices at 20 distance writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.thickness positioning took 9.7 minutes #-------------------------------------------- #@# Surf Volume lh Fri Jan 3 15:25:39 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Fri Jan 3 15:25:40 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts pctsurfcon --s MPS1036-1 --lh-only Log file is /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts/pctsurfcon.log Fri Jan 3 15:25:40 CST 2014 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis cd /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts /soft/freesurfer/5.3.0_1/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node1107 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_1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.16322/lh.wm.mgh --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 79135 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.16322/lh.wm.mgh Dim: 150168 1 1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.16322/lh.gm.mgh --projfrac 0.3 --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Done reading source surface Reading thickness /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 91088 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.16322/lh.gm.mgh Dim: 150168 1 1 mri_concat /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.16322/lh.wm.mgh /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.16322/lh.gm.mgh --paired-diff-norm --mul 100 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh mri_segstats --in /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh --annot MPS1036-1 lh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh --annot MPS1036-1 lh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/stats/lh.w-g.pct.stats --snr sysname Linux hostname node1107 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/post_analysis/MPS1036-1/surf/lh.w-g.pct.mgh Vertex Area is 0.642548 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1436 980.109 2 1002 caudalanteriorcingulate 1544 1131.621 3 1003 caudalmiddlefrontal 4410 2830.203 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2071 1369.984 6 1006 entorhinal 539 356.259 7 1007 fusiform 3862 2608.408 8 1008 inferiorparietal 7566 4699.072 9 1009 inferiortemporal 5480 3662.999 10 1010 isthmuscingulate 3166 1777.736 11 1011 lateraloccipital 8173 5085.528 12 1012 lateralorbitofrontal 3193 2153.475 13 1013 lingual 3534 2544.161 14 1014 medialorbitofrontal 2633 1724.725 15 1015 middletemporal 5465 3564.127 16 1016 parahippocampal 1079 734.481 17 1017 paracentral 2238 1458.948 18 1018 parsopercularis 2333 1387.850 19 1019 parsorbitalis 1249 697.139 20 1020 parstriangularis 2527 1582.636 21 1021 pericalcarine 1827 1196.437 22 1022 postcentral 6891 4334.258 23 1023 posteriorcingulate 2109 1417.566 24 1024 precentral 8688 5673.733 25 1025 precuneus 4986 3303.581 26 1026 rostralanteriorcingulate 1023 728.234 27 1027 rostralmiddlefrontal 10482 6663.481 28 1028 superiorfrontal 11587 7917.416 29 1029 superiorparietal 8299 5154.621 30 1030 superiortemporal 6103 3772.483 31 1031 supramarginal 7444 4651.457 32 1032 frontalpole 549 299.445 33 1033 temporalpole 869 606.191 34 1034 transversetemporal 662 421.307 35 1035 insula 3899 2366.713 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Fri Jan 3 15:25:48 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1436 980 2786 3.073 0.686 0.145 0.072 22 4.5 bankssts 1544 1132 2855 2.660 1.083 0.272 0.287 292 17.1 caudalanteriorcingulate 4410 2830 10195 3.396 0.660 0.195 0.362 611 89.4 caudalmiddlefrontal 2071 1370 3260 2.184 0.623 0.172 0.066 43 5.4 cuneus 539 356 1277 2.777 0.831 0.252 0.379 75 4.9 entorhinal 3862 2608 8094 2.772 0.624 0.174 0.128 174 25.8 fusiform 7566 4699 15229 3.021 0.650 0.171 0.697 1809 60.6 inferiorparietal 5480 3663 13539 3.246 0.864 0.176 0.100 149 22.5 inferiortemporal 3166 1778 3315 1.817 0.842 0.155 1.666 526 19.2 isthmuscingulate 8173 5086 13137 2.413 0.694 0.177 0.097 254 32.8 lateraloccipital 3193 2153 8373 3.498 0.863 0.159 0.081 82 10.3 lateralorbitofrontal 3534 2544 6486 2.306 0.730 0.201 0.152 170 21.6 lingual 2633 1725 6020 2.976 1.086 0.158 0.105 89 9.2 medialorbitofrontal 5465 3564 14235 3.380 0.741 0.168 0.097 1127 23.6 middletemporal 1079 734 1567 1.946 0.548 0.158 0.095 32 4.4 parahippocampal 2238 1459 4403 2.726 0.645 0.157 0.189 248 8.1 paracentral 2333 1388 4824 3.071 0.717 0.159 0.215 237 17.1 parsopercularis 1249 697 2355 2.729 0.825 0.220 0.314 90 11.3 parsorbitalis 2527 1583 4828 2.758 0.780 0.174 0.128 161 13.7 parstriangularis 1827 1196 1840 1.706 0.616 0.196 0.106 54 8.3 pericalcarine 6891 4334 10692 2.344 0.812 0.173 0.131 964 34.5 postcentral 2109 1418 3344 2.244 0.858 0.157 0.147 229 7.9 posteriorcingulate 8688 5674 14649 2.584 0.922 0.190 0.263 664 64.1 precentral 4986 3304 10574 2.841 0.643 0.158 0.115 225 18.6 precuneus 1023 728 2705 2.816 1.253 0.236 0.380 133 9.7 rostralanteriorcingulate 10482 6663 22423 2.989 0.785 0.187 0.731 904 129.9 rostralmiddlefrontal 11587 7917 29719 3.329 1.042 0.194 0.329 1709 78.0 superiorfrontal 8299 5155 14553 2.662 0.578 0.169 0.148 435 54.5 superiorparietal 6103 3772 12574 2.974 0.672 0.134 0.110 287 21.6 superiortemporal 7444 4651 13895 2.751 0.730 0.181 0.567 3009 65.4 supramarginal 549 299 1080 2.561 0.836 0.226 0.332 256 9.4 frontalpole 869 606 2751 2.827 0.814 0.233 0.138 39 5.0 temporalpole 662 421 1101 2.425 0.675 0.170 0.083 13 2.4 transversetemporal 3899 2367 7126 2.859 1.134 0.121 0.111 109 17.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Jan 3 15:26:01 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 267 labels changed using aseg relabeling using gibbs priors... 000: 10262 changed, 150168 examined... 001: 2518 changed, 39348 examined... 002: 788 changed, 12976 examined... 003: 380 changed, 4362 examined... 004: 170 changed, 2019 examined... 005: 84 changed, 964 examined... 006: 53 changed, 483 examined... 007: 27 changed, 288 examined... 008: 16 changed, 150 examined... 009: 4 changed, 78 examined... 010: 1 changed, 24 examined... 011: 0 changed, 5 examined... 81 labels changed using aseg 000: 358 total segments, 277 labels (4309 vertices) changed 001: 107 total segments, 26 labels (282 vertices) changed 002: 84 total segments, 3 labels (9 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 135 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 2140 vertices marked for relabeling... 2140 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 45 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Jan 3 15:26:46 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1477 929 2884 2.772 0.809 0.212 2.271 205 10.6 G_and_S_frontomargin 1489 1065 3326 2.746 0.648 0.191 0.085 43 5.6 G_and_S_occipital_inf 1658 1038 3198 2.543 0.698 0.166 0.233 238 6.5 G_and_S_paracentral 1382 806 3104 3.168 0.792 0.167 0.169 65 12.4 G_and_S_subcentral 1041 663 1971 2.210 0.991 0.296 0.845 890 24.1 G_and_S_transv_frontopol 2743 2237 5135 2.190 1.281 0.300 0.930 891 29.9 G_and_S_cingul-Ant 1779 1190 3189 2.782 0.691 0.203 0.226 183 15.8 G_and_S_cingul-Mid-Ant 1428 1020 2546 2.573 0.561 0.139 0.053 24 3.0 G_and_S_cingul-Mid-Post 1065 684 1475 1.805 0.902 0.177 0.102 42 4.9 G_cingul-Post-dorsal 732 409 714 1.696 0.652 0.183 6.748 147 3.9 G_cingul-Post-ventral 1819 1197 2850 2.053 0.632 0.183 0.092 49 6.6 G_cuneus 1122 651 2771 2.927 0.861 0.181 0.214 179 13.1 G_front_inf-Opercular 254 149 690 2.933 0.625 0.192 0.135 10 1.9 G_front_inf-Orbital 1444 843 2966 2.674 0.799 0.195 0.167 132 10.1 G_front_inf-Triangul 5929 3652 14839 3.246 0.780 0.190 0.511 416 86.1 G_front_middle 8065 5203 24255 3.645 0.823 0.175 0.117 255 43.3 G_front_sup 596 350 1142 2.676 1.051 0.109 0.091 11 1.3 G_Ins_lg_and_S_cent_ins 733 447 1728 3.103 1.332 0.097 0.098 19 3.3 G_insular_short 2206 1286 4552 2.807 0.553 0.175 0.121 100 10.3 G_occipital_middle 1612 947 2900 2.480 0.514 0.177 0.093 55 6.2 G_occipital_sup 1318 916 3219 2.698 0.622 0.182 0.187 59 15.2 G_oc-temp_lat-fusifor 2372 1699 4682 2.219 0.774 0.223 0.197 152 18.3 G_oc-temp_med-Lingual 1388 860 2581 2.384 0.819 0.185 0.207 97 7.5 G_oc-temp_med-Parahip 2680 1647 6928 3.145 0.936 0.205 0.258 184 21.4 G_orbital 3588 2110 8068 2.979 0.750 0.196 1.375 1728 48.4 G_pariet_inf-Angular 4294 2569 8367 2.804 0.762 0.188 0.865 2859 36.8 G_pariet_inf-Supramar 3311 1871 6310 2.734 0.640 0.199 0.273 354 40.4 G_parietal_sup 3179 1853 4699 2.154 0.667 0.184 0.188 229 29.5 G_postcentral 3342 2096 6722 2.561 0.985 0.188 0.185 246 33.0 G_precentral 2601 1659 6255 2.925 0.706 0.187 0.128 121 14.2 G_precuneus 774 516 2598 3.454 1.025 0.206 0.110 36 3.3 G_rectus 502 259 542 1.983 1.147 0.142 0.130 22 2.4 G_subcallosal 561 353 1054 2.515 0.663 0.165 0.090 12 2.1 G_temp_sup-G_T_transv 2301 1325 5993 3.166 0.729 0.173 0.234 258 15.8 G_temp_sup-Lateral 602 399 1256 2.786 0.603 0.120 0.123 17 4.9 G_temp_sup-Plan_polar 804 557 1549 2.625 0.620 0.143 0.061 11 2.1 G_temp_sup-Plan_tempo 2994 2041 9012 3.350 0.927 0.203 0.137 108 16.8 G_temporal_inf 3430 2221 10650 3.482 0.760 0.180 0.097 91 13.7 G_temporal_middle 527 360 1028 2.896 0.588 0.134 0.053 5 1.2 Lat_Fis-ant-Horizont 393 240 653 3.073 0.976 0.168 0.140 23 2.8 Lat_Fis-ant-Vertical 951 618 1302 2.639 0.517 0.148 0.062 13 2.4 Lat_Fis-post 2691 1644 3232 1.913 0.593 0.188 0.101 71 11.5 Pole_occipital 2102 1390 5587 2.964 0.889 0.208 0.124 84 11.1 Pole_temporal 2149 1430 2560 1.993 0.769 0.168 0.072 45 6.4 S_calcarine 3027 2143 3074 1.798 0.599 0.212 0.238 890 21.0 S_central 1033 736 1763 2.596 0.464 0.113 0.030 8 1.4 S_cingul-Marginalis 446 309 758 3.046 0.546 0.111 0.035 4 0.7 S_circular_insula_ant 1700 1089 2923 3.052 0.579 0.091 0.028 10 1.8 S_circular_insula_inf 1718 1113 3227 3.225 0.681 0.148 0.179 71 6.3 S_circular_insula_sup 582 364 1040 2.831 0.646 0.128 0.059 7 1.5 S_collat_transv_ant 294 220 480 2.384 0.420 0.145 0.046 3 0.6 S_collat_transv_post 2860 1857 5622 3.012 0.635 0.156 0.432 296 36.5 S_front_inf 1712 1085 3292 2.939 0.656 0.161 0.255 168 24.3 S_front_middle 3112 2041 6255 3.390 0.602 0.164 0.284 328 44.3 S_front_sup 349 227 526 2.635 0.664 0.146 0.083 5 1.0 S_interm_prim-Jensen 3098 2072 4796 2.709 0.507 0.143 0.061 42 8.3 S_intrapariet_and_P_trans 1439 885 1990 2.455 0.653 0.158 0.069 25 4.3 S_oc_middle_and_Lunatus 1292 876 1981 2.501 0.469 0.135 0.053 16 2.7 S_oc_sup_and_transversal 751 521 1352 2.991 0.634 0.145 0.062 9 1.8 S_occipital_ant 1240 819 2217 2.857 0.545 0.143 0.061 19 3.3 S_oc-temp_lat 1936 1416 3072 2.527 0.633 0.178 0.103 106 8.8 S_oc-temp_med_and_Lingual 547 350 865 2.875 0.631 0.131 0.051 6 1.3 S_orbital_lateral 827 514 1629 2.609 1.570 0.110 0.066 15 1.5 S_orbital_med-olfact 1244 822 2448 3.425 0.984 0.161 0.091 30 4.2 S_orbital-H_Shaped 1839 1224 3210 2.585 0.567 0.147 0.068 61 5.4 S_parieto_occipital 2438 1380 2661 2.054 1.074 0.175 0.237 726 20.6 S_pericallosal 3323 2254 5140 2.728 0.605 0.159 0.101 113 13.1 S_postcentral 1912 1343 3494 3.238 0.587 0.203 0.540 236 13.5 S_precentral-inf-part 1755 1195 2810 3.181 0.675 0.161 0.102 35 7.6 S_precentral-sup-part 745 508 1410 2.902 1.106 0.141 0.054 11 1.9 S_suborbital 959 650 1860 2.861 0.640 0.119 0.191 62 2.2 S_subparietal 1773 1178 3159 3.272 0.652 0.139 0.071 22 5.5 S_temporal_inf 6132 4006 11203 3.124 0.655 0.146 0.083 1115 21.5 S_temporal_sup 405 261 465 2.207 0.488 0.142 0.047 4 0.8 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fri Jan 3 15:26:59 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 lh ../surf/lh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 278 labels changed using aseg relabeling using gibbs priors... 000: 3047 changed, 150168 examined... 001: 730 changed, 12957 examined... 002: 200 changed, 3969 examined... 003: 78 changed, 1156 examined... 004: 37 changed, 445 examined... 005: 15 changed, 210 examined... 006: 6 changed, 88 examined... 007: 5 changed, 32 examined... 008: 4 changed, 22 examined... 009: 3 changed, 18 examined... 010: 4 changed, 14 examined... 011: 1 changed, 8 examined... 012: 0 changed, 10 examined... 140 labels changed using aseg 000: 94 total segments, 58 labels (408 vertices) changed 001: 36 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 67 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2187 vertices marked for relabeling... 2187 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 38 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Jan 3 15:27:37 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 2301 1710 4148 2.618 1.072 0.252 0.232 356 20.4 caudalanteriorcingulate 4571 2926 10679 3.392 0.656 0.195 0.354 616 90.4 caudalmiddlefrontal 2921 1932 4846 2.293 0.613 0.166 0.065 58 7.6 cuneus 535 349 1236 2.803 0.804 0.251 0.382 75 5.1 entorhinal 3333 2274 6817 2.762 0.606 0.161 0.119 148 21.5 fusiform 7238 4493 14529 2.990 0.670 0.171 0.723 1801 59.1 inferiorparietal 5467 3653 13778 3.226 0.856 0.185 0.111 164 24.7 inferiortemporal 3052 1725 3236 1.822 0.847 0.154 1.724 269 18.6 isthmuscingulate 8550 5319 13628 2.407 0.690 0.178 0.098 264 34.8 lateraloccipital 3700 2413 9480 3.340 1.078 0.160 0.093 105 12.5 lateralorbitofrontal 3556 2569 6563 2.302 0.729 0.201 0.152 170 21.6 lingual 2488 1593 5552 2.827 1.160 0.171 0.128 100 10.9 medialorbitofrontal 6892 4514 17164 3.329 0.752 0.164 0.089 1150 27.1 middletemporal 1093 744 1587 1.952 0.557 0.159 0.095 32 4.4 parahippocampal 2474 1621 4994 2.797 0.674 0.154 0.180 250 9.4 paracentral 1974 1201 4075 3.095 0.703 0.164 0.232 221 15.5 parsopercularis 1060 671 2444 3.106 0.646 0.162 0.079 27 3.9 parsorbitalis 3151 1940 5848 2.768 0.786 0.175 0.328 247 17.8 parstriangularis 1786 1158 1745 1.702 0.614 0.197 0.108 54 8.3 pericalcarine 7717 4856 11933 2.384 0.798 0.174 0.153 1062 53.3 postcentral 2342 1551 3561 2.242 0.847 0.160 0.140 487 8.8 posteriorcingulate 8534 5564 14152 2.576 0.923 0.190 0.265 659 62.7 precentral 4830 3203 10438 2.840 0.664 0.159 0.117 225 18.3 precuneus 1509 1035 3337 2.660 1.294 0.206 0.278 176 11.1 rostralanteriorcingulate 8243 5030 16910 2.974 0.805 0.191 0.623 740 122.6 rostralmiddlefrontal 12832 8668 33098 3.305 0.982 0.196 0.467 2004 92.5 superiorfrontal 6717 4137 11673 2.690 0.574 0.171 0.165 404 49.1 superiorparietal 8538 5379 18221 2.940 0.697 0.151 0.119 375 37.4 superiortemporal 6987 4378 13168 2.783 0.724 0.176 0.568 2915 47.8 supramarginal 664 422 1105 2.434 0.687 0.169 0.083 13 2.4 transversetemporal 2861 1827 5858 3.087 0.981 0.103 0.073 55 8.1 insula #-------------------------------------------- #@# Tessellate rh Fri Jan 3 15:27:50 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 9 found - 9 modified | TOTAL: 9 pass 2 (xy+): 0 found - 9 modified | TOTAL: 9 pass 1 (xy-): 1 found - 1 modified | TOTAL: 10 pass 2 (xy-): 0 found - 1 modified | TOTAL: 10 pass 1 (yz+): 8 found - 8 modified | TOTAL: 18 pass 2 (yz+): 0 found - 8 modified | TOTAL: 18 pass 1 (yz-): 6 found - 6 modified | TOTAL: 24 pass 2 (yz-): 0 found - 6 modified | TOTAL: 24 pass 1 (xz+): 9 found - 9 modified | TOTAL: 33 pass 2 (xz+): 0 found - 9 modified | TOTAL: 33 pass 1 (xz-): 4 found - 4 modified | TOTAL: 37 pass 2 (xz-): 0 found - 4 modified | TOTAL: 37 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 0 found - 0 modified | TOTAL: 8 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 3 found - 3 modified | TOTAL: 4 pass 2 (+-): 0 found - 3 modified | TOTAL: 4 pass 1 (--): 6 found - 6 modified | TOTAL: 10 pass 2 (--): 0 found - 6 modified | TOTAL: 10 pass 1 (-+): 5 found - 5 modified | TOTAL: 15 pass 2 (-+): 0 found - 5 modified | TOTAL: 15 Iteration Number : 2 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+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 2 found - 2 modified | TOTAL: 5 pass 2 (xz-): 0 found - 2 modified | TOTAL: 5 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 3 found - 3 modified | TOTAL: 4 pass 2 (-+): 0 found - 3 modified | TOTAL: 4 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 = 69 (out of 323413: 0.021335) 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 50: 25 vertices, 34 faces slice 60: 2737 vertices, 2870 faces slice 70: 7809 vertices, 8022 faces slice 80: 14956 vertices, 15299 faces slice 90: 24377 vertices, 24823 faces slice 100: 35319 vertices, 35828 faces slice 110: 47923 vertices, 48511 faces slice 120: 61688 vertices, 62307 faces slice 130: 74074 vertices, 74691 faces slice 140: 86664 vertices, 87294 faces slice 150: 98767 vertices, 99392 faces slice 160: 110013 vertices, 110635 faces slice 170: 119513 vertices, 120077 faces slice 180: 125769 vertices, 126270 faces slice 190: 132435 vertices, 133001 faces slice 200: 139962 vertices, 140492 faces slice 210: 146633 vertices, 147134 faces slice 220: 153418 vertices, 153916 faces slice 230: 156945 vertices, 157302 faces slice 240: 157176 vertices, 157486 faces slice 250: 157176 vertices, 157486 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... 157168 voxel in cpt #1: X=-312 [v=157168,e=472440,f=314960] located at (33.342014, 8.070707, 44.216011) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (1.000000, 62.000000, 30.000000) For the whole surface: X=-310 [v=157176,e=472458,f=314972] 2 components have been found keeping component #1 with 157168 vertices done #-------------------------------------------- #@# Smooth1 rh Fri Jan 3 15:27:56 CST 2014 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Fri Jan 3 15:28:00 CST 2014 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts avg radius = 50.9 mm, total surface area = 79058 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.124 (target=0.015) step 005: RMS=0.095 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.073 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.063 (target=0.015) step 030: RMS=0.061 (target=0.015) step 035: RMS=0.060 (target=0.015) step 040: RMS=0.059 (target=0.015) step 045: RMS=0.058 (target=0.015) step 050: RMS=0.058 (target=0.015) step 055: RMS=0.058 (target=0.015) step 060: RMS=0.058 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Fri Jan 3 15:28:25 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.93 +- 0.63 (0.00-->11.97) (max @ vno 66129 --> 66149) face area 0.02 +- 0.03 (-0.36-->1.00) scaling brain by 0.291... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.672, avgs=0 005/300: dt: 0.9000, rms radial error=177.415, avgs=0 010/300: dt: 0.9000, rms radial error=176.864, avgs=0 015/300: dt: 0.9000, rms radial error=176.138, avgs=0 020/300: dt: 0.9000, rms radial error=175.311, avgs=0 025/300: dt: 0.9000, rms radial error=174.425, avgs=0 030/300: dt: 0.9000, rms radial error=173.505, avgs=0 035/300: dt: 0.9000, rms radial error=172.567, avgs=0 040/300: dt: 0.9000, rms radial error=171.621, avgs=0 045/300: dt: 0.9000, rms radial error=170.672, avgs=0 050/300: dt: 0.9000, rms radial error=169.726, avgs=0 055/300: dt: 0.9000, rms radial error=168.784, avgs=0 060/300: dt: 0.9000, rms radial error=167.844, avgs=0 065/300: dt: 0.9000, rms radial error=166.908, avgs=0 070/300: dt: 0.9000, rms radial error=165.977, avgs=0 075/300: dt: 0.9000, rms radial error=165.051, avgs=0 080/300: dt: 0.9000, rms radial error=164.129, avgs=0 085/300: dt: 0.9000, rms radial error=163.213, avgs=0 090/300: dt: 0.9000, rms radial error=162.301, avgs=0 095/300: dt: 0.9000, rms radial error=161.394, avgs=0 100/300: dt: 0.9000, rms radial error=160.492, avgs=0 105/300: dt: 0.9000, rms radial error=159.595, avgs=0 110/300: dt: 0.9000, rms radial error=158.702, avgs=0 115/300: dt: 0.9000, rms radial error=157.814, avgs=0 120/300: dt: 0.9000, rms radial error=156.931, avgs=0 125/300: dt: 0.9000, rms radial error=156.053, avgs=0 130/300: dt: 0.9000, rms radial error=155.179, avgs=0 135/300: dt: 0.9000, rms radial error=154.310, avgs=0 140/300: dt: 0.9000, rms radial error=153.446, avgs=0 145/300: dt: 0.9000, rms radial error=152.587, avgs=0 150/300: dt: 0.9000, rms radial error=151.732, avgs=0 155/300: dt: 0.9000, rms radial error=150.882, avgs=0 160/300: dt: 0.9000, rms radial error=150.036, avgs=0 165/300: dt: 0.9000, rms radial error=149.195, avgs=0 170/300: dt: 0.9000, rms radial error=148.358, avgs=0 175/300: dt: 0.9000, rms radial error=147.526, avgs=0 180/300: dt: 0.9000, rms radial error=146.699, avgs=0 185/300: dt: 0.9000, rms radial error=145.876, avgs=0 190/300: dt: 0.9000, rms radial error=145.057, avgs=0 195/300: dt: 0.9000, rms radial error=144.243, avgs=0 200/300: dt: 0.9000, rms radial error=143.434, avgs=0 205/300: dt: 0.9000, rms radial error=142.629, avgs=0 210/300: dt: 0.9000, rms radial error=141.828, avgs=0 215/300: dt: 0.9000, rms radial error=141.032, avgs=0 220/300: dt: 0.9000, rms radial error=140.241, avgs=0 225/300: dt: 0.9000, rms radial error=139.453, avgs=0 230/300: dt: 0.9000, rms radial error=138.670, avgs=0 235/300: dt: 0.9000, rms radial error=137.892, avgs=0 240/300: dt: 0.9000, rms radial error=137.117, avgs=0 245/300: dt: 0.9000, rms radial error=136.347, avgs=0 250/300: dt: 0.9000, rms radial error=135.581, avgs=0 255/300: dt: 0.9000, rms radial error=134.820, avgs=0 260/300: dt: 0.9000, rms radial error=134.062, avgs=0 265/300: dt: 0.9000, rms radial error=133.309, avgs=0 270/300: dt: 0.9000, rms radial error=132.560, avgs=0 275/300: dt: 0.9000, rms radial error=131.816, avgs=0 280/300: dt: 0.9000, rms radial error=131.075, avgs=0 285/300: dt: 0.9000, rms radial error=130.339, avgs=0 290/300: dt: 0.9000, rms radial error=129.606, avgs=0 295/300: dt: 0.9000, rms radial error=128.878, avgs=0 300/300: dt: 0.9000, rms radial error=128.154, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 19012.88 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 2 (K=40.0), pass 1, starting sse = 3509.47 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00009 epoch 3 (K=160.0), pass 1, starting sse = 507.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00292 epoch 4 (K=640.0), pass 1, starting sse = 89.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/12 = 0.00896 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Fri Jan 3 15:32:26 CST 2014 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 MPS1036-1 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=-312 (nv=157168, nf=314960, ne=472440, g=157) 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... 44718 ambiguous faces found in tessellation segmenting defects... 132 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 4 into 0 -merging segment 46 into 0 -merging segment 5 into 3 -merging segment 0 into 19 -merging segment 53 into 35 -merging segment 44 into 43 -merging segment 50 into 49 -merging segment 58 into 55 -merging segment 94 into 87 -merging segment 96 into 88 -merging segment 98 into 91 121 defects to be corrected 0 vertices coincident reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1237 (-4.5618) -vertex loglikelihood: -6.4722 (-3.2361) -normal dot loglikelihood: -3.5530 (-3.5530) -quad curv loglikelihood: -6.0720 (-3.0360) Total Loglikelihood : -25.2208 CORRECTING DEFECT 0 (vertices=27, convex hull=75) After retessellation of defect 0, euler #=-114 (132136,390760,258510) : difference with theory (-118) = -4 CORRECTING DEFECT 1 (vertices=79, convex hull=51) After retessellation of defect 1, euler #=-113 (132150,390820,258557) : difference with theory (-117) = -4 CORRECTING DEFECT 2 (vertices=2401, convex hull=998) After retessellation of defect 2, euler #=-111 (132893,393547,260543) : difference with theory (-116) = -5 CORRECTING DEFECT 3 (vertices=48, convex hull=104) After retessellation of defect 3, euler #=-110 (132913,393652,260629) : difference with theory (-115) = -5 CORRECTING DEFECT 4 (vertices=25, convex hull=56) After retessellation of defect 4, euler #=-109 (132929,393719,260681) : difference with theory (-114) = -5 CORRECTING DEFECT 5 (vertices=32, convex hull=64) After retessellation of defect 5, euler #=-108 (132949,393800,260743) : difference with theory (-113) = -5 CORRECTING DEFECT 6 (vertices=22, convex hull=42) After retessellation of defect 6, euler #=-107 (132955,393831,260769) : difference with theory (-112) = -5 CORRECTING DEFECT 7 (vertices=12, convex hull=24) After retessellation of defect 7, euler #=-106 (132956,393844,260782) : difference with theory (-111) = -5 CORRECTING DEFECT 8 (vertices=75, convex hull=124) After retessellation of defect 8, euler #=-105 (132998,394029,260926) : difference with theory (-110) = -5 CORRECTING DEFECT 9 (vertices=64, convex hull=103) After retessellation of defect 9, euler #=-104 (133034,394179,261041) : difference with theory (-109) = -5 CORRECTING DEFECT 10 (vertices=54, convex hull=25) After retessellation of defect 10, euler #=-103 (133037,394196,261056) : difference with theory (-108) = -5 CORRECTING DEFECT 11 (vertices=40, convex hull=70) After retessellation of defect 11, euler #=-102 (133059,394289,261128) : difference with theory (-107) = -5 CORRECTING DEFECT 12 (vertices=115, convex hull=138) After retessellation of defect 12, euler #=-101 (133122,394536,261313) : difference with theory (-106) = -5 CORRECTING DEFECT 13 (vertices=46, convex hull=86) After retessellation of defect 13, euler #=-100 (133145,394644,261399) : difference with theory (-105) = -5 CORRECTING DEFECT 14 (vertices=14, convex hull=26) Warning - incorrect dp selected!!!!(-112.092566 >= -112.092572 ) After retessellation of defect 14, euler #=-99 (133146,394654,261409) : difference with theory (-104) = -5 CORRECTING DEFECT 15 (vertices=191, convex hull=98) After retessellation of defect 15, euler #=-98 (133172,394777,261507) : difference with theory (-103) = -5 CORRECTING DEFECT 16 (vertices=11902, convex hull=2284) After retessellation of defect 16, euler #=-106 (136581,406367,269680) : difference with theory (-102) = 4 CORRECTING DEFECT 17 (vertices=33, convex hull=59) After retessellation of defect 17, euler #=-105 (136601,406450,269744) : difference with theory (-101) = 4 CORRECTING DEFECT 18 (vertices=85, convex hull=64) After retessellation of defect 18, euler #=-104 (136617,406524,269803) : difference with theory (-100) = 4 CORRECTING DEFECT 19 (vertices=13, convex hull=21) After retessellation of defect 19, euler #=-103 (136617,406528,269808) : difference with theory (-99) = 4 CORRECTING DEFECT 20 (vertices=46, convex hull=78) After retessellation of defect 20, euler #=-102 (136647,406654,269905) : difference with theory (-98) = 4 CORRECTING DEFECT 21 (vertices=69, convex hull=111) After retessellation of defect 21, euler #=-101 (136685,406819,270033) : difference with theory (-97) = 4 CORRECTING DEFECT 22 (vertices=16, convex hull=16) After retessellation of defect 22, euler #=-100 (136687,406829,270042) : difference with theory (-96) = 4 CORRECTING DEFECT 23 (vertices=1544, convex hull=701) After retessellation of defect 23, euler #=-99 (137182,408687,271406) : difference with theory (-95) = 4 CORRECTING DEFECT 24 (vertices=35, convex hull=58) After retessellation of defect 24, euler #=-98 (137191,408736,271447) : difference with theory (-94) = 4 CORRECTING DEFECT 25 (vertices=43, convex hull=44) After retessellation of defect 25, euler #=-97 (137200,408781,271484) : difference with theory (-93) = 4 CORRECTING DEFECT 26 (vertices=32, convex hull=40) After retessellation of defect 26, euler #=-96 (137205,408813,271512) : difference with theory (-92) = 4 CORRECTING DEFECT 27 (vertices=38, convex hull=34) After retessellation of defect 27, euler #=-95 (137208,408836,271533) : difference with theory (-91) = 4 CORRECTING DEFECT 28 (vertices=43, convex hull=70) After retessellation of defect 28, euler #=-94 (137230,408932,271608) : difference with theory (-90) = 4 CORRECTING DEFECT 29 (vertices=28, convex hull=22) After retessellation of defect 29, euler #=-93 (137233,408947,271621) : difference with theory (-89) = 4 CORRECTING DEFECT 30 (vertices=38, convex hull=65) After retessellation of defect 30, euler #=-92 (137242,409001,271667) : difference with theory (-88) = 4 CORRECTING DEFECT 31 (vertices=30, convex hull=40) After retessellation of defect 31, euler #=-91 (137256,409058,271711) : difference with theory (-87) = 4 CORRECTING DEFECT 32 (vertices=162, convex hull=90) After retessellation of defect 32, euler #=-89 (137281,409179,271809) : difference with theory (-86) = 3 CORRECTING DEFECT 33 (vertices=41, convex hull=84) After retessellation of defect 33, euler #=-88 (137290,409240,271862) : difference with theory (-85) = 3 CORRECTING DEFECT 34 (vertices=27, convex hull=25) After retessellation of defect 34, euler #=-87 (137296,409268,271885) : difference with theory (-84) = 3 CORRECTING DEFECT 35 (vertices=347, convex hull=254) After retessellation of defect 35, euler #=-86 (137436,409806,272284) : difference with theory (-83) = 3 CORRECTING DEFECT 36 (vertices=49, convex hull=77) After retessellation of defect 36, euler #=-85 (137475,409956,272396) : difference with theory (-82) = 3 CORRECTING DEFECT 37 (vertices=26, convex hull=58) After retessellation of defect 37, euler #=-84 (137484,410006,272438) : difference with theory (-81) = 3 CORRECTING DEFECT 38 (vertices=256, convex hull=131) After retessellation of defect 38, euler #=-83 (137570,410324,272671) : difference with theory (-80) = 3 CORRECTING DEFECT 39 (vertices=22, convex hull=31) After retessellation of defect 39, euler #=-82 (137572,410342,272688) : difference with theory (-79) = 3 CORRECTING DEFECT 40 (vertices=106, convex hull=71) After retessellation of defect 40, euler #=-80 (137581,410399,272738) : difference with theory (-78) = 2 CORRECTING DEFECT 41 (vertices=579, convex hull=392) After retessellation of defect 41, euler #=-79 (137605,410661,272977) : difference with theory (-77) = 2 CORRECTING DEFECT 42 (vertices=67, convex hull=52) After retessellation of defect 42, euler #=-78 (137613,410707,273016) : difference with theory (-76) = 2 CORRECTING DEFECT 43 (vertices=29, convex hull=36) After retessellation of defect 43, euler #=-77 (137615,410726,273034) : difference with theory (-75) = 2 CORRECTING DEFECT 44 (vertices=52, convex hull=70) After retessellation of defect 44, euler #=-75 (137633,410813,273105) : difference with theory (-74) = 1 CORRECTING DEFECT 45 (vertices=21, convex hull=63) After retessellation of defect 45, euler #=-74 (137642,410862,273146) : difference with theory (-73) = 1 CORRECTING DEFECT 46 (vertices=82, convex hull=68) After retessellation of defect 46, euler #=-73 (137667,410965,273225) : difference with theory (-72) = 1 CORRECTING DEFECT 47 (vertices=38, convex hull=40) After retessellation of defect 47, euler #=-72 (137670,410985,273243) : difference with theory (-71) = 1 CORRECTING DEFECT 48 (vertices=577, convex hull=386) After retessellation of defect 48, euler #=-70 (137844,411693,273779) : difference with theory (-70) = 0 CORRECTING DEFECT 49 (vertices=67, convex hull=127) After retessellation of defect 49, euler #=-69 (137854,411780,273857) : difference with theory (-69) = 0 CORRECTING DEFECT 50 (vertices=39, convex hull=23) After retessellation of defect 50, euler #=-68 (137863,411814,273883) : difference with theory (-68) = 0 CORRECTING DEFECT 51 (vertices=6, convex hull=31) After retessellation of defect 51, euler #=-67 (137865,411829,273897) : difference with theory (-67) = 0 CORRECTING DEFECT 52 (vertices=253, convex hull=54) After retessellation of defect 52, euler #=-66 (137882,411904,273956) : difference with theory (-66) = 0 CORRECTING DEFECT 53 (vertices=150, convex hull=58) After retessellation of defect 53, euler #=-65 (137907,412002,274030) : difference with theory (-65) = 0 CORRECTING DEFECT 54 (vertices=25, convex hull=32) After retessellation of defect 54, euler #=-64 (137910,412019,274045) : difference with theory (-64) = 0 CORRECTING DEFECT 55 (vertices=216, convex hull=32) After retessellation of defect 55, euler #=-63 (137919,412055,274073) : difference with theory (-63) = 0 CORRECTING DEFECT 56 (vertices=50, convex hull=94) After retessellation of defect 56, euler #=-62 (137949,412185,274174) : difference with theory (-62) = 0 CORRECTING DEFECT 57 (vertices=5, convex hull=17) After retessellation of defect 57, euler #=-61 (137950,412191,274180) : difference with theory (-61) = 0 CORRECTING DEFECT 58 (vertices=33, convex hull=54) After retessellation of defect 58, euler #=-60 (137966,412263,274237) : difference with theory (-60) = 0 CORRECTING DEFECT 59 (vertices=72, convex hull=96) After retessellation of defect 59, euler #=-59 (138002,412415,274354) : difference with theory (-59) = 0 CORRECTING DEFECT 60 (vertices=54, convex hull=76) After retessellation of defect 60, euler #=-58 (138013,412479,274408) : difference with theory (-58) = 0 CORRECTING DEFECT 61 (vertices=16, convex hull=18) After retessellation of defect 61, euler #=-57 (138014,412486,274415) : difference with theory (-57) = 0 CORRECTING DEFECT 62 (vertices=32, convex hull=48) After retessellation of defect 62, euler #=-56 (138029,412552,274467) : difference with theory (-56) = 0 CORRECTING DEFECT 63 (vertices=28, convex hull=70) After retessellation of defect 63, euler #=-55 (138045,412625,274525) : difference with theory (-55) = 0 CORRECTING DEFECT 64 (vertices=227, convex hull=97) After retessellation of defect 64, euler #=-54 (138063,412722,274605) : difference with theory (-54) = 0 CORRECTING DEFECT 65 (vertices=15, convex hull=26) After retessellation of defect 65, euler #=-53 (138068,412747,274626) : difference with theory (-53) = 0 CORRECTING DEFECT 66 (vertices=25, convex hull=57) After retessellation of defect 66, euler #=-52 (138081,412803,274670) : difference with theory (-52) = 0 CORRECTING DEFECT 67 (vertices=66, convex hull=79) After retessellation of defect 67, euler #=-51 (138098,412887,274738) : difference with theory (-51) = 0 CORRECTING DEFECT 68 (vertices=5, convex hull=21) After retessellation of defect 68, euler #=-50 (138099,412896,274747) : difference with theory (-50) = 0 CORRECTING DEFECT 69 (vertices=688, convex hull=297) After retessellation of defect 69, euler #=-49 (138221,413398,275128) : difference with theory (-49) = 0 CORRECTING DEFECT 70 (vertices=574, convex hull=187) After retessellation of defect 70, euler #=-48 (138370,413943,275525) : difference with theory (-48) = 0 CORRECTING DEFECT 71 (vertices=512, convex hull=285) After retessellation of defect 71, euler #=-48 (138587,414744,276109) : difference with theory (-47) = 1 CORRECTING DEFECT 72 (vertices=23, convex hull=56) After retessellation of defect 72, euler #=-47 (138600,414803,276156) : difference with theory (-46) = 1 CORRECTING DEFECT 73 (vertices=6, convex hull=25) After retessellation of defect 73, euler #=-46 (138602,414815,276167) : difference with theory (-45) = 1 CORRECTING DEFECT 74 (vertices=5, convex hull=14) After retessellation of defect 74, euler #=-45 (138603,414820,276172) : difference with theory (-44) = 1 CORRECTING DEFECT 75 (vertices=20, convex hull=55) After retessellation of defect 75, euler #=-44 (138612,414867,276211) : difference with theory (-43) = 1 CORRECTING DEFECT 76 (vertices=25, convex hull=19) Warning - incorrect dp selected!!!!(-78.091505 >= -78.091506 ) After retessellation of defect 76, euler #=-43 (138614,414881,276224) : difference with theory (-42) = 1 CORRECTING DEFECT 77 (vertices=58, convex hull=40) After retessellation of defect 77, euler #=-42 (138621,414917,276254) : difference with theory (-41) = 1 CORRECTING DEFECT 78 (vertices=167, convex hull=138) After retessellation of defect 78, euler #=-42 (138651,415083,276390) : difference with theory (-40) = 2 CORRECTING DEFECT 79 (vertices=128, convex hull=120) After retessellation of defect 79, euler #=-40 (138708,415313,276565) : difference with theory (-39) = 1 CORRECTING DEFECT 80 (vertices=125, convex hull=134) After retessellation of defect 80, euler #=-38 (138762,415539,276739) : difference with theory (-38) = 0 CORRECTING DEFECT 81 (vertices=23, convex hull=49) After retessellation of defect 81, euler #=-37 (138774,415592,276781) : difference with theory (-37) = 0 CORRECTING DEFECT 82 (vertices=9, convex hull=19) After retessellation of defect 82, euler #=-36 (138777,415606,276793) : difference with theory (-36) = 0 CORRECTING DEFECT 83 (vertices=172, convex hull=120) After retessellation of defect 83, euler #=-34 (138811,415774,276929) : difference with theory (-35) = -1 CORRECTING DEFECT 84 (vertices=6, convex hull=23) After retessellation of defect 84, euler #=-33 (138814,415790,276943) : difference with theory (-34) = -1 CORRECTING DEFECT 85 (vertices=81, convex hull=52) After retessellation of defect 85, euler #=-32 (138829,415857,276996) : difference with theory (-33) = -1 CORRECTING DEFECT 86 (vertices=41, convex hull=61) After retessellation of defect 86, euler #=-32 (138848,415941,277061) : difference with theory (-32) = 0 CORRECTING DEFECT 87 (vertices=49, convex hull=24) After retessellation of defect 87, euler #=-31 (138851,415957,277075) : difference with theory (-31) = 0 CORRECTING DEFECT 88 (vertices=16, convex hull=58) After retessellation of defect 88, euler #=-30 (138862,416014,277122) : difference with theory (-30) = 0 CORRECTING DEFECT 89 (vertices=40, convex hull=88) After retessellation of defect 89, euler #=-29 (138881,416107,277197) : difference with theory (-29) = 0 CORRECTING DEFECT 90 (vertices=52, convex hull=81) After retessellation of defect 90, euler #=-28 (138904,416213,277281) : difference with theory (-28) = 0 CORRECTING DEFECT 91 (vertices=23, convex hull=19) After retessellation of defect 91, euler #=-27 (138904,416219,277288) : difference with theory (-27) = 0 CORRECTING DEFECT 92 (vertices=170, convex hull=40) After retessellation of defect 92, euler #=-26 (138922,416288,277340) : difference with theory (-26) = 0 CORRECTING DEFECT 93 (vertices=24, convex hull=12) After retessellation of defect 93, euler #=-25 (138922,416289,277342) : difference with theory (-25) = 0 CORRECTING DEFECT 94 (vertices=9, convex hull=24) After retessellation of defect 94, euler #=-24 (138924,416303,277355) : difference with theory (-24) = 0 CORRECTING DEFECT 95 (vertices=75, convex hull=72) After retessellation of defect 95, euler #=-23 (138937,416371,277411) : difference with theory (-23) = 0 CORRECTING DEFECT 96 (vertices=33, convex hull=20) After retessellation of defect 96, euler #=-22 (138941,416390,277427) : difference with theory (-22) = 0 CORRECTING DEFECT 97 (vertices=20, convex hull=38) After retessellation of defect 97, euler #=-21 (138946,416417,277450) : difference with theory (-21) = 0 CORRECTING DEFECT 98 (vertices=38, convex hull=74) After retessellation of defect 98, euler #=-20 (138969,416515,277526) : difference with theory (-20) = 0 CORRECTING DEFECT 99 (vertices=54, convex hull=34) Warning - incorrect dp selected!!!!(-90.652627 >= -90.652633 ) After retessellation of defect 99, euler #=-19 (138972,416537,277546) : difference with theory (-19) = 0 CORRECTING DEFECT 100 (vertices=46, convex hull=55) After retessellation of defect 100, euler #=-18 (138989,416613,277606) : difference with theory (-18) = 0 CORRECTING DEFECT 101 (vertices=19, convex hull=81) After retessellation of defect 101, euler #=-17 (138996,416665,277652) : difference with theory (-17) = 0 CORRECTING DEFECT 102 (vertices=48, convex hull=25) After retessellation of defect 102, euler #=-16 (139001,416687,277670) : difference with theory (-16) = 0 CORRECTING DEFECT 103 (vertices=16, convex hull=24) After retessellation of defect 103, euler #=-15 (139002,416698,277681) : difference with theory (-15) = 0 CORRECTING DEFECT 104 (vertices=29, convex hull=63) After retessellation of defect 104, euler #=-14 (139011,416749,277724) : difference with theory (-14) = 0 CORRECTING DEFECT 105 (vertices=23, convex hull=57) Warning - incorrect dp selected!!!!(-80.430921 >= -80.430925 ) After retessellation of defect 105, euler #=-13 (139016,416786,277757) : difference with theory (-13) = 0 CORRECTING DEFECT 106 (vertices=21, convex hull=63) After retessellation of defect 106, euler #=-12 (139026,416839,277801) : difference with theory (-12) = 0 CORRECTING DEFECT 107 (vertices=32, convex hull=59) After retessellation of defect 107, euler #=-11 (139036,416893,277846) : difference with theory (-11) = 0 CORRECTING DEFECT 108 (vertices=35, convex hull=73) After retessellation of defect 108, euler #=-10 (139051,416969,277908) : difference with theory (-10) = 0 CORRECTING DEFECT 109 (vertices=34, convex hull=51) After retessellation of defect 109, euler #=-9 (139068,417040,277963) : difference with theory (-9) = 0 CORRECTING DEFECT 110 (vertices=5, convex hull=19) After retessellation of defect 110, euler #=-8 (139068,417044,277968) : difference with theory (-8) = 0 CORRECTING DEFECT 111 (vertices=42, convex hull=75) After retessellation of defect 111, euler #=-7 (139085,417127,278035) : difference with theory (-7) = 0 CORRECTING DEFECT 112 (vertices=35, convex hull=40) After retessellation of defect 112, euler #=-6 (139088,417150,278056) : difference with theory (-6) = 0 CORRECTING DEFECT 113 (vertices=35, convex hull=49) After retessellation of defect 113, euler #=-5 (139097,417194,278092) : difference with theory (-5) = 0 CORRECTING DEFECT 114 (vertices=22, convex hull=50) After retessellation of defect 114, euler #=-4 (139102,417227,278121) : difference with theory (-4) = 0 CORRECTING DEFECT 115 (vertices=24, convex hull=25) After retessellation of defect 115, euler #=-3 (139104,417244,278137) : difference with theory (-3) = 0 CORRECTING DEFECT 116 (vertices=29, convex hull=17) After retessellation of defect 116, euler #=-2 (139107,417257,278148) : difference with theory (-2) = 0 CORRECTING DEFECT 117 (vertices=36, convex hull=26) After retessellation of defect 117, euler #=-1 (139109,417273,278163) : difference with theory (-1) = 0 CORRECTING DEFECT 118 (vertices=43, convex hull=60) After retessellation of defect 118, euler #=0 (139118,417326,278208) : difference with theory (0) = 0 CORRECTING DEFECT 119 (vertices=29, convex hull=45) After retessellation of defect 119, euler #=1 (139127,417369,278243) : difference with theory (1) = 0 CORRECTING DEFECT 120 (vertices=45, convex hull=22) After retessellation of defect 120, euler #=2 (139129,417381,278254) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.91 +- 0.42 (0.02-->25.06) (max @ vno 21956 --> 136290) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.91 +- 0.42 (0.02-->25.06) (max @ vno 21956 --> 136290) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 408 mutations (33.7%), 801 crossovers (66.3%), 594 vertices were eliminated building final representation... 18039 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=139129, nf=278254, ne=417381, g=0) writing corrected surface to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 92.9 minutes 0 defective edges removing intersecting faces 000: 3536 intersecting 001: 472 intersecting 002: 216 intersecting 003: 157 intersecting 004: 111 intersecting 005: 89 intersecting 006: 82 intersecting 007: 80 intersecting 008: 66 intersecting 009: 61 intersecting 010: 55 intersecting expanding nbhd size to 2 011: 60 intersecting 012: 56 intersecting 013: 45 intersecting 014: 43 intersecting 015: 38 intersecting 016: 32 intersecting 017: 28 intersecting 018: 27 intersecting 019: 23 intersecting 020: 17 intersecting expanding nbhd size to 3 021: 17 intersecting expanding nbhd size to 4 022: 22 intersecting expanding nbhd size to 5 023: 22 intersecting 024: 19 intersecting expanding nbhd size to 6 025: 20 intersecting 026: 4 intersecting expanding nbhd size to 7 027: 5 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 139129 - 417381 + 278254 = 2 --> 0 holes F =2V-4: 278254 = 278258-4 (0) 2E=3F: 834762 = 834762 (0) total defect index = 0 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 2110 intersecting 001: 382 intersecting 002: 222 intersecting 003: 155 intersecting 004: 107 intersecting 005: 93 intersecting 006: 82 intersecting expanding nbhd size to 2 007: 82 intersecting 008: 72 intersecting 009: 65 intersecting 010: 58 intersecting 011: 48 intersecting 012: 44 intersecting 013: 33 intersecting 014: 28 intersecting 015: 23 intersecting 016: 17 intersecting 017: 15 intersecting expanding nbhd size to 3 018: 15 intersecting expanding nbhd size to 4 019: 26 intersecting expanding nbhd size to 5 020: 26 intersecting 021: 22 intersecting 022: 10 intersecting 023: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri Jan 3 17:05:42 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 19849 bright wm thresholded. 1516 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (93.0): 93.9 +- 7.7 [70.0 --> 110.0] GM (82.0) : 78.7 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.3 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.29 (0.01-->9.50) (max @ vno 133438 --> 134264) face area 0.28 +- 0.18 (0.00-->23.16) mean absolute distance = 0.81 +- 1.09 3880 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=100, GM=78 mean inside = 89.9, mean outside = 77.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.3, 3906 (3906) missing vertices, mean dist 0.2 [0.8 (%36.8)->0.8 (%63.2))] %61 local maxima, %26 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 0.91 +- 0.35 (0.05-->12.33) (max @ vno 134470 --> 29425) face area 0.28 +- 0.20 (0.00-->15.83) mean absolute distance = 0.46 +- 0.76 4749 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5247145.0, rms=10.04 001: dt: 0.5000, sse=6259453.5, rms=8.168 (0.000%) 002: dt: 0.5000, sse=6482712.5, rms=7.085 (0.000%) 003: dt: 0.5000, sse=6779956.5, rms=6.452 (0.000%) 004: dt: 0.5000, sse=6914660.0, rms=6.080 (0.000%) 005: dt: 0.5000, sse=7081885.0, rms=5.826 (0.000%) 006: dt: 0.5000, sse=7091013.5, rms=5.645 (0.000%) 007: dt: 0.5000, sse=7162657.5, rms=5.488 (0.000%) 008: dt: 0.5000, sse=7117804.0, rms=5.369 (0.000%) 009: dt: 0.5000, sse=7164841.5, rms=5.261 (0.000%) 010: dt: 0.5000, sse=7122625.5, rms=5.169 (0.000%) 011: dt: 0.5000, sse=7148906.5, rms=5.079 (0.000%) 012: dt: 0.5000, sse=7149645.5, rms=5.016 (0.000%) 013: dt: 0.5000, sse=7137562.5, rms=4.944 (0.000%) 014: dt: 0.5000, sse=7097359.0, rms=4.880 (0.000%) 015: dt: 0.5000, sse=7085315.5, rms=4.807 (0.000%) 016: dt: 0.5000, sse=7040418.0, rms=4.739 (0.000%) 017: dt: 0.5000, sse=7048367.5, rms=4.676 (0.000%) 018: dt: 0.5000, sse=7010542.0, rms=4.610 (0.000%) 019: dt: 0.5000, sse=7035936.0, rms=4.544 (0.000%) 020: dt: 0.5000, sse=6993679.5, rms=4.482 (0.000%) 021: dt: 0.5000, sse=6984102.5, rms=4.420 (0.000%) rms = 4.37, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=6944092.0, rms=4.374 (0.000%) 023: dt: 0.2500, sse=4888712.5, rms=4.033 (0.000%) 024: dt: 0.2500, sse=4695740.0, rms=3.972 (0.000%) rms = 3.95, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4576237.0, rms=3.948 (0.000%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 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 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.6, 3553 (2848) missing vertices, mean dist -0.3 [0.5 (%68.5)->0.3 (%31.5))] %74 local maxima, %13 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 0.89 +- 0.35 (0.03-->13.03) (max @ vno 134470 --> 29425) face area 0.34 +- 0.25 (0.00-->13.89) mean absolute distance = 0.33 +- 0.54 3734 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4953174.0, rms=5.35 026: dt: 0.5000, sse=5373015.0, rms=4.559 (0.000%) 027: dt: 0.5000, sse=5956628.5, rms=4.411 (0.000%) 028: dt: 0.5000, sse=6151772.0, rms=4.342 (0.000%) rms = 4.33, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=6610870.5, rms=4.325 (0.000%) 030: dt: 0.2500, sse=5308005.0, rms=4.031 (0.000%) 031: dt: 0.2500, sse=5129532.5, rms=3.961 (0.000%) rms = 3.94, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=5065990.5, rms=3.938 (0.000%) rms = 3.92, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5000326.0, rms=3.916 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 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=89.1, 3377 (2572) missing vertices, mean dist -0.1 [0.4 (%65.4)->0.3 (%34.6))] %79 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 0.89 +- 0.35 (0.03-->13.03) (max @ vno 134470 --> 29425) face area 0.33 +- 0.25 (0.00-->13.84) mean absolute distance = 0.29 +- 0.45 3091 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5085542.0, rms=4.43 034: dt: 0.5000, sse=5471091.5, rms=4.126 (0.000%) rms = 4.10, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=5994640.0, rms=4.100 (0.000%) 036: dt: 0.2500, sse=5362707.0, rms=3.898 (0.000%) rms = 3.86, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5276956.5, rms=3.859 (0.000%) rms = 3.83, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5184327.0, rms=3.831 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=89.7, 3432 (2467) missing vertices, mean dist -0.1 [0.3 (%55.0)->0.3 (%45.0))] %80 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/MPS1036-1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=5206261.5, rms=3.99 039: dt: 0.5000, sse=6491950.0, rms=3.842 (0.000%) rms = 3.96, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=6016112.0, rms=3.767 (0.000%) rms = 3.76, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=5825465.5, rms=3.757 (0.000%) rms = 3.73, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5812347.5, rms=3.725 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 30 non-cortical segments detected only using segment with 2182 vertices erasing segment 0 (vno[0] = 40544) erasing segment 2 (vno[0] = 55482) erasing segment 3 (vno[0] = 74007) erasing segment 4 (vno[0] = 76235) erasing segment 5 (vno[0] = 78263) erasing segment 6 (vno[0] = 83847) erasing segment 7 (vno[0] = 85684) erasing segment 8 (vno[0] = 85824) erasing segment 9 (vno[0] = 86576) erasing segment 10 (vno[0] = 86594) erasing segment 11 (vno[0] = 86606) erasing segment 12 (vno[0] = 87707) erasing segment 13 (vno[0] = 90595) erasing segment 14 (vno[0] = 91511) erasing segment 15 (vno[0] = 91541) erasing segment 16 (vno[0] = 92317) erasing segment 17 (vno[0] = 92378) erasing segment 18 (vno[0] = 93198) erasing segment 19 (vno[0] = 93981) erasing segment 20 (vno[0] = 95588) erasing segment 21 (vno[0] = 99292) erasing segment 22 (vno[0] = 99311) erasing segment 23 (vno[0] = 99872) erasing segment 24 (vno[0] = 101141) erasing segment 25 (vno[0] = 101148) erasing segment 26 (vno[0] = 102878) erasing segment 27 (vno[0] = 105837) erasing segment 28 (vno[0] = 106583) erasing segment 29 (vno[0] = 107249) writing cortex label to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label... writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.curv writing smoothed area to rh.area writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.area vertex spacing 0.89 +- 0.36 (0.04-->13.07) (max @ vno 134470 --> 29425) face area 0.33 +- 0.24 (0.00-->14.20) refinement took 4.8 minutes #-------------------------------------------- #@# Smooth2 rh Fri Jan 3 17:10:28 CST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Fri Jan 3 17:10:32 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.0 mm, total surface area = 81944 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.126 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.071 (target=0.015) step 015: RMS=0.060 (target=0.015) step 020: RMS=0.051 (target=0.015) step 025: RMS=0.043 (target=0.015) step 030: RMS=0.037 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (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 179 vertices thresholded to be in k1 ~ [-0.31 0.56], k2 ~ [-0.17 0.11] total integrated curvature = 0.385*4pi (4.842) --> 1 handles ICI = 1.3, FI = 10.0, variation=165.929 142 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 134 vertices thresholded to be in [-0.18 0.28] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025 done. #----------------------------------------- #@# Curvature Stats rh Fri Jan 3 17:12:05 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm MPS1036-1 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 [ MPS1036-1/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 [ 298 ] Gb_filter = 0 WARN: S lookup min: -0.083616 WARN: S explicit min: 0.000000 vertex = 15 #-------------------------------------------- #@# Sphere rh Fri Jan 3 17:12:12 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 0.278... 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 %18.98 pass 1: epoch 2 of 3 starting distance error %18.81 unfolding complete - removing small folds... starting distance error %18.52 removing remaining folds... final distance error %18.55 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.89 hours #-------------------------------------------- #@# Surf Reg rh Fri Jan 3 18:05:50 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_register -curv ../surf/rh.sphere /soft/freesurfer/5.3.0_1/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_1/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 = 0.564 curvature mean = 0.030, std = 0.920 curvature mean = 0.025, std = 0.862 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 367268.4, tmin=0.7659 d=32.00 min @ (8.00, 8.00, 0.00) sse = 351237.2, tmin=1.5355 d=16.00 min @ (-4.00, -4.00, 4.00) sse = 327558.5, tmin=2.3123 d=8.00 min @ (2.00, 0.00, 0.00) sse = 320100.8, tmin=3.1551 d=4.00 min @ (0.00, -1.00, 0.00) sse = 319156.0, tmin=4.0159 d=2.00 min @ (-0.50, 0.00, 0.00) sse = 318586.9, tmin=4.8818 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 6.56 min curvature mean = 0.003, std = 0.948 curvature mean = 0.009, std = 0.940 curvature mean = 0.001, std = 0.957 curvature mean = 0.004, std = 0.972 curvature mean = 0.000, std = 0.960 curvature mean = 0.001, std = 0.987 2 Reading smoothwm curvature mean = -0.037, std = 0.379 curvature mean = 0.006, std = 0.069 curvature mean = 0.065, std = 0.263 curvature mean = 0.005, std = 0.083 curvature mean = 0.036, std = 0.407 curvature mean = 0.005, std = 0.089 curvature mean = 0.022, std = 0.528 curvature mean = 0.006, std = 0.092 curvature mean = 0.008, std = 0.646 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Fri Jan 3 18:32:55 CST 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 Fri Jan 3 18:32:57 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mrisp_paint -a 5 /soft/freesurfer/5.3.0_1/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_1/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri Jan 3 18:32:59 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 2654 labels changed using aseg relabeling using gibbs priors... 000: 3144 changed, 139129 examined... 001: 760 changed, 13505 examined... 002: 184 changed, 4093 examined... 003: 73 changed, 1031 examined... 004: 39 changed, 395 examined... 005: 11 changed, 211 examined... 006: 3 changed, 57 examined... 007: 1 changed, 22 examined... 008: 1 changed, 5 examined... 009: 0 changed, 9 examined... 283 labels changed using aseg 000: 200 total segments, 160 labels (1085 vertices) changed 001: 44 total segments, 4 labels (36 vertices) changed 002: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 40 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1927 vertices marked for relabeling... 1927 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 36 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri Jan 3 18:33:35 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs MPS1036-1 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/post_analysis/MPS1036-1/mri/filled.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/brain.finalsurfs.mgz... reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... 19849 bright wm thresholded. 1516 bright non-wm voxels segmented. reading original surface position from /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.orig... computing class statistics... border white: 353572 voxels (2.11%) border gray 398276 voxels (2.37%) WM (93.0): 93.9 +- 7.7 [70.0 --> 110.0] GM (82.0) : 78.7 +- 14.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.3 (was 70) setting MAX_BORDER_WHITE to 107.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 48.7 (was 40) setting MAX_GRAY to 92.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.0 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=100, GM=78 mean inside = 89.9, 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/post_analysis/MPS1036-1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.29 (0.01-->9.50) (max @ vno 133438 --> 134264) face area 0.28 +- 0.18 (0.00-->23.16) mean absolute distance = 0.83 +- 1.11 4053 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 28 points - only 0.00% unknown deleting segment 3 with 89 points - only 0.00% unknown deleting segment 4 with 45 points - only 0.00% unknown deleting segment 8 with 57 points - only 0.00% unknown deleting segment 9 with 180 points - only 0.00% unknown deleting segment 10 with 79 points - only 0.00% unknown deleting segment 12 with 15 points - only 0.00% unknown deleting segment 15 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 3 points - only 0.00% unknown deleting segment 18 with 743 points - only 0.00% unknown deleting segment 19 with 22 points - only 0.00% unknown deleting segment 20 with 46 points - only 0.00% unknown deleting segment 21 with 177 points - only 0.00% unknown deleting segment 22 with 216 points - only 0.00% unknown deleting segment 23 with 46 points - only 0.00% unknown deleting segment 24 with 132 points - only 0.00% unknown deleting segment 25 with 6 points - only 0.00% unknown deleting segment 26 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 27 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 28 with 3 points - only 0.00% unknown deleting segment 29 with 57 points - only 0.00% unknown mean border=85.4, 3914 (3911) missing vertices, mean dist 0.2 [0.9 (%37.2)->0.8 (%62.8))] %62 local maxima, %26 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 0.90 +- 0.35 (0.05-->12.33) (max @ vno 134470 --> 29425) face area 0.28 +- 0.19 (0.00-->15.83) mean absolute distance = 0.46 +- 0.76 4921 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5332609.0, rms=10.06 001: dt: 0.5000, sse=6354687.0, rms=8.197 (0.000%) 002: dt: 0.5000, sse=6576443.5, rms=7.119 (0.000%) 003: dt: 0.5000, sse=6873440.0, rms=6.486 (0.000%) 004: dt: 0.5000, sse=7018464.0, rms=6.109 (0.000%) 005: dt: 0.5000, sse=7183313.5, rms=5.850 (0.000%) 006: dt: 0.5000, sse=7202937.0, rms=5.665 (0.000%) 007: dt: 0.5000, sse=7275325.0, rms=5.503 (0.000%) 008: dt: 0.5000, sse=7220239.5, rms=5.378 (0.000%) 009: dt: 0.5000, sse=7257502.5, rms=5.266 (0.000%) 010: dt: 0.5000, sse=7213987.0, rms=5.171 (0.000%) 011: dt: 0.5000, sse=7236876.5, rms=5.078 (0.000%) 012: dt: 0.5000, sse=7234324.0, rms=5.013 (0.000%) 013: dt: 0.5000, sse=7228608.0, rms=4.939 (0.000%) 014: dt: 0.5000, sse=7179347.0, rms=4.873 (0.000%) 015: dt: 0.5000, sse=7159506.5, rms=4.800 (0.000%) 016: dt: 0.5000, sse=7126886.0, rms=4.731 (0.000%) 017: dt: 0.5000, sse=7139816.5, rms=4.667 (0.000%) 018: dt: 0.5000, sse=7089806.5, rms=4.600 (0.000%) 019: dt: 0.5000, sse=7105219.5, rms=4.534 (0.000%) 020: dt: 0.5000, sse=7075496.5, rms=4.471 (0.000%) 021: dt: 0.5000, sse=7053379.5, rms=4.410 (0.000%) rms = 4.36, time step reduction 1 of 3 to 0.250... 022: dt: 0.5000, sse=7029294.5, rms=4.364 (0.000%) 023: dt: 0.2500, sse=4926184.5, rms=4.020 (0.000%) 024: dt: 0.2500, sse=4730567.5, rms=3.957 (0.000%) rms = 3.93, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4597186.5, rms=3.933 (0.000%) positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 14 points - only 57.14% unknown removing 3 vertex label from ripped group deleting segment 6 with 213 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown deleting segment 8 with 93 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 70 points - only 0.00% unknown deleting segment 13 with 34 points - only 0.00% unknown deleting segment 14 with 231 points - only 0.00% unknown deleting segment 15 with 27 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 10 points - only 0.00% unknown deleting segment 18 with 197 points - only 0.00% unknown deleting segment 19 with 58 points - only 0.00% unknown deleting segment 20 with 120 points - only 0.00% unknown deleting segment 22 with 225 points - only 0.00% unknown deleting segment 24 with 259 points - only 0.00% unknown deleting segment 25 with 10 points - only 0.00% unknown deleting segment 27 with 165 points - only 0.00% unknown deleting segment 28 with 7 points - only 0.00% unknown deleting segment 29 with 5 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 30 with 4 points - only 0.00% unknown deleting segment 31 with 174 points - only 0.00% unknown deleting segment 32 with 18 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 33 with 2 points - only 0.00% unknown deleting segment 34 with 14 points - only 0.00% unknown deleting segment 35 with 57 points - only 0.00% unknown deleting segment 36 with 17 points - only 0.00% unknown deleting segment 37 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 40 with 4 points - only 0.00% unknown deleting segment 41 with 50 points - only 0.00% unknown removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.6, 3573 (2849) missing vertices, mean dist -0.3 [0.5 (%68.5)->0.3 (%31.5))] %76 local maxima, %13 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 0.89 +- 0.34 (0.03-->13.03) (max @ vno 134470 --> 29425) face area 0.34 +- 0.24 (0.00-->13.89) mean absolute distance = 0.34 +- 0.55 3921 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5031482.5, rms=5.32 026: dt: 0.5000, sse=5467506.5, rms=4.539 (0.000%) 027: dt: 0.5000, sse=6072256.5, rms=4.390 (0.000%) 028: dt: 0.5000, sse=6254818.0, rms=4.322 (0.000%) rms = 4.30, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=6728342.0, rms=4.304 (0.000%) 030: dt: 0.2500, sse=5399732.0, rms=4.008 (0.000%) 031: dt: 0.2500, sse=5215533.5, rms=3.939 (0.000%) rms = 3.91, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=5141523.0, rms=3.914 (0.000%) rms = 3.89, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=5070795.5, rms=3.892 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 50.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 195 points - only 0.00% unknown deleting segment 4 with 36 points - only 0.00% unknown deleting segment 5 with 94 points - only 0.00% unknown deleting segment 8 with 7 points - only 42.86% unknown deleting segment 9 with 67 points - only 0.00% unknown deleting segment 10 with 34 points - only 0.00% unknown deleting segment 12 with 229 points - only 0.00% unknown deleting segment 13 with 9 points - only 0.00% unknown deleting segment 14 with 24 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 165 points - only 0.00% unknown deleting segment 18 with 55 points - only 0.00% unknown deleting segment 19 with 121 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 21 with 220 points - only 0.00% unknown deleting segment 22 with 260 points - only 0.00% unknown deleting segment 23 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 24 with 2 points - only 0.00% unknown deleting segment 25 with 134 points - only 0.00% unknown deleting segment 26 with 7 points - only 0.00% unknown deleting segment 27 with 5 points - only 0.00% unknown deleting segment 28 with 18 points - only 0.00% unknown deleting segment 29 with 10 points - only 0.00% unknown deleting segment 30 with 171 points - only 0.00% unknown deleting segment 31 with 22 points - only 0.00% unknown deleting segment 32 with 17 points - only 0.00% unknown deleting segment 33 with 57 points - only 0.00% unknown deleting segment 34 with 19 points - only 0.00% unknown deleting segment 35 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 36 with 3 points - only 0.00% unknown deleting segment 37 with 46 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=89.1, 3435 (2579) missing vertices, mean dist -0.1 [0.4 (%65.4)->0.3 (%34.6))] %81 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 0.89 +- 0.34 (0.03-->13.03) (max @ vno 134470 --> 29425) face area 0.33 +- 0.24 (0.00-->13.84) mean absolute distance = 0.29 +- 0.45 3168 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5172889.5, rms=4.45 034: dt: 0.5000, sse=5563910.5, rms=4.148 (0.000%) rms = 4.12, time step reduction 1 of 3 to 0.250... 035: dt: 0.5000, sse=6113178.0, rms=4.117 (0.000%) 036: dt: 0.2500, sse=5454914.5, rms=3.914 (0.000%) rms = 3.87, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=5363056.0, rms=3.875 (0.000%) rms = 3.85, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=5277370.0, rms=3.845 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 50.00% unknown removing 3 vertex label from ripped group deleting segment 2 with 191 points - only 0.00% unknown deleting segment 3 with 29 points - only 0.00% unknown deleting segment 4 with 94 points - only 0.00% unknown deleting segment 5 with 7 points - only 42.86% unknown deleting segment 7 with 68 points - only 0.00% unknown deleting segment 8 with 30 points - only 0.00% unknown deleting segment 9 with 236 points - only 0.00% unknown deleting segment 10 with 30 points - only 0.00% unknown deleting segment 11 with 29 points - only 0.00% unknown deleting segment 12 with 370 points - only 0.00% unknown deleting segment 13 with 54 points - only 0.00% unknown deleting segment 14 with 111 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 18 with 217 points - only 0.00% unknown deleting segment 19 with 256 points - only 0.00% unknown deleting segment 20 with 12 points - only 0.00% unknown deleting segment 21 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 22 with 3 points - only 0.00% unknown deleting segment 23 with 135 points - only 0.00% unknown deleting segment 24 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 25 with 1 points - only 0.00% unknown deleting segment 26 with 6 points - only 0.00% unknown deleting segment 27 with 172 points - only 0.00% unknown deleting segment 28 with 59 points - only 0.00% unknown deleting segment 29 with 19 points - only 0.00% unknown deleting segment 30 with 17 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 31 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 32 with 4 points - only 0.00% unknown deleting segment 33 with 46 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=89.7, 3502 (2473) missing vertices, mean dist -0.1 [0.3 (%55.0)->0.3 (%45.0))] %82 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=5301023.5, rms=4.01 039: dt: 0.5000, sse=6620296.0, rms=3.856 (0.000%) rms = 3.98, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=6132084.5, rms=3.783 (0.000%) rms = 3.77, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=5934949.0, rms=3.771 (0.000%) rms = 3.74, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=5920614.5, rms=3.741 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=63.7, 2866 (2866) missing vertices, mean dist 1.7 [3.5 (%2.0)->3.6 (%98.0))] %23 local maxima, %20 large gradients and %47 min vals, 4166 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=20241062.0, rms=26.52 001: dt: 0.5000, sse=16790462.0, rms=23.656 (0.000%) 002: dt: 0.5000, sse=14109832.0, rms=21.131 (0.000%) 003: dt: 0.5000, sse=12016829.0, rms=18.973 (0.000%) 004: dt: 0.5000, sse=10511746.0, rms=17.213 (0.000%) 005: dt: 0.5000, sse=9432422.0, rms=15.776 (0.000%) 006: dt: 0.5000, sse=8696863.0, rms=14.576 (0.000%) 007: dt: 0.5000, sse=8190534.0, rms=13.506 (0.000%) 008: dt: 0.5000, sse=7832087.0, rms=12.515 (0.000%) 009: dt: 0.5000, sse=7550252.0, rms=11.566 (0.000%) 010: dt: 0.5000, sse=7359131.5, rms=10.658 (0.000%) 011: dt: 0.5000, sse=7332919.5, rms=9.806 (0.000%) 012: dt: 0.5000, sse=7301302.5, rms=8.995 (0.000%) 013: dt: 0.5000, sse=7313749.0, rms=8.292 (0.000%) 014: dt: 0.5000, sse=7342862.0, rms=7.679 (0.000%) 015: dt: 0.5000, sse=7430902.0, rms=7.204 (0.000%) 016: dt: 0.5000, sse=7490342.0, rms=6.818 (0.000%) 017: dt: 0.5000, sse=7537437.0, rms=6.559 (0.000%) 018: dt: 0.5000, sse=7583882.0, rms=6.345 (0.000%) 019: dt: 0.5000, sse=7617366.0, rms=6.194 (0.000%) 020: dt: 0.5000, sse=7625201.0, rms=6.052 (0.000%) 021: dt: 0.5000, sse=7666440.5, rms=5.968 (0.000%) 022: dt: 0.5000, sse=7627294.0, rms=5.881 (0.000%) rms = 5.84, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=7652614.5, rms=5.837 (0.000%) 024: dt: 0.2500, sse=6000558.0, rms=5.300 (0.000%) 025: dt: 0.2500, sse=5891087.5, rms=5.169 (0.000%) rms = 5.18, time step reduction 2 of 3 to 0.125... 026: dt: 0.1250, sse=5723993.0, rms=5.075 (0.000%) 027: dt: 0.1250, sse=5437575.0, rms=4.949 (0.000%) rms = 4.91, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5355485.0, rms=4.910 (0.000%) positioning took 2.3 minutes mean border=62.1, 4837 (1669) missing vertices, mean dist 0.2 [0.3 (%38.3)->0.8 (%61.7))] %35 local maxima, %15 large gradients and %39 min vals, 2242 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=6034838.0, rms=6.43 029: dt: 0.5000, sse=6532442.0, rms=6.234 (0.000%) 030: dt: 0.5000, sse=7656234.5, rms=5.987 (0.000%) rms = 6.02, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=6716884.5, rms=5.465 (0.000%) 032: dt: 0.2500, sse=6402137.0, rms=5.349 (0.000%) rms = 5.39, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=6259824.5, rms=5.251 (0.000%) 034: dt: 0.1250, sse=6036623.0, rms=5.122 (0.000%) 035: dt: 0.1250, sse=5978798.0, rms=5.066 (0.000%) rms = 5.04, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5968216.0, rms=5.042 (0.000%) positioning took 0.8 minutes mean border=61.7, 5877 (1504) missing vertices, mean dist 0.1 [0.3 (%41.3)->0.6 (%58.7))] %38 local maxima, %11 large gradients and %39 min vals, 2219 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=6037313.0, rms=5.22 rms = 5.64, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=5930653.5, rms=5.072 (0.000%) 038: dt: 0.2500, sse=6073213.5, rms=5.020 (0.000%) rms = 5.05, time step reduction 2 of 3 to 0.125... rms = 4.98, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=6011254.5, rms=4.982 (0.000%) positioning took 0.4 minutes mean border=61.3, 9855 (1466) missing vertices, mean dist 0.1 [0.3 (%44.9)->0.5 (%55.1))] %37 local maxima, %10 large gradients and %37 min vals, 2151 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/MPS1036-1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=6016870.0, rms=5.00 rms = 5.38, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=5983969.0, rms=4.881 (0.000%) 041: dt: 0.2500, sse=6347468.5, rms=4.810 (0.000%) rms = 4.82, time step reduction 2 of 3 to 0.125... rms = 4.77, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=6286418.0, rms=4.771 (0.000%) positioning took 0.4 minutes writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.area.pial vertex spacing 1.01 +- 0.52 (0.02-->15.63) (max @ vno 134470 --> 29425) face area 0.39 +- 0.38 (0.00-->17.72) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 139129 vertices processed 25000 of 139129 vertices processed 50000 of 139129 vertices processed 75000 of 139129 vertices processed 100000 of 139129 vertices processed 125000 of 139129 vertices processed 0 of 139129 vertices processed 25000 of 139129 vertices processed 50000 of 139129 vertices processed 75000 of 139129 vertices processed 100000 of 139129 vertices processed 125000 of 139129 vertices processed thickness calculation complete, 2367:3600 truncations. 21964 vertices at 0 distance 64678 vertices at 1 distance 76597 vertices at 2 distance 50489 vertices at 3 distance 23870 vertices at 4 distance 10071 vertices at 5 distance 4119 vertices at 6 distance 1653 vertices at 7 distance 792 vertices at 8 distance 434 vertices at 9 distance 229 vertices at 10 distance 177 vertices at 11 distance 98 vertices at 12 distance 85 vertices at 13 distance 91 vertices at 14 distance 70 vertices at 15 distance 62 vertices at 16 distance 49 vertices at 17 distance 37 vertices at 18 distance 35 vertices at 19 distance 38 vertices at 20 distance writing curvature file /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.thickness positioning took 9.4 minutes #-------------------------------------------- #@# Surf Volume rh Fri Jan 3 18:42:59 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 Fri Jan 3 18:43:00 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts pctsurfcon --s MPS1036-1 --rh-only Log file is /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts/pctsurfcon.log Fri Jan 3 18:43:00 CST 2014 setenv SUBJECTS_DIR /lustre/kovacv/FS/post_analysis cd /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts /soft/freesurfer/5.3.0_1/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux node1107 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_1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.21806/rh.wm.mgh --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 72741 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.21806/rh.wm.mgh Dim: 139129 1 1 mri_vol2surf --mov /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.21806/rh.gm.mgh --projfrac 0.3 --regheader MPS1036-1 --cortex srcvol = /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/mri/orig.mgz as target reference. Loading label /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Reading surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white Done reading source surface Reading thickness /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 85290 Masking with /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.cortex.label Writing to /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.21806/rh.gm.mgh Dim: 139129 1 1 mri_concat /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.21806/rh.wm.mgh /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/tmp.pctsurfcon.21806/rh.gm.mgh --paired-diff-norm --mul 100 --o /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh mri_segstats --in /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh --annot MPS1036-1 rh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh --annot MPS1036-1 rh aparc --sum /lustre/kovacv/FS/post_analysis/MPS1036-1/stats/rh.w-g.pct.stats --snr sysname Linux hostname node1107 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/post_analysis/MPS1036-1/surf/rh.w-g.pct.mgh Vertex Area is 0.65446 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1568 1058.630 2 2002 caudalanteriorcingulate 1669 1029.129 3 2003 caudalmiddlefrontal 4164 2733.358 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 1737 1188.490 6 2006 entorhinal 611 387.161 7 2007 fusiform 4310 3085.285 8 2008 inferiorparietal 8511 5435.341 9 2009 inferiortemporal 3802 2639.895 10 2010 isthmuscingulate 924 515.971 11 2011 lateraloccipital 5713 3817.309 12 2012 lateralorbitofrontal 3109 2059.578 13 2013 lingual 1805 1641.471 14 2014 medialorbitofrontal 2252 1495.370 15 2015 middletemporal 4722 3165.253 16 2016 parahippocampal 2280 1387.319 17 2017 paracentral 2527 1618.983 18 2018 parsopercularis 1977 1335.873 19 2019 parsorbitalis 1098 750.764 20 2020 parstriangularis 1992 1355.890 21 2021 pericalcarine 1019 724.033 22 2022 postcentral 6219 3834.963 23 2023 posteriorcingulate 1828 1275.385 24 2024 precentral 8303 5311.877 25 2025 precuneus 6006 4406.081 26 2026 rostralanteriorcingulate 960 623.316 27 2027 rostralmiddlefrontal 10716 6910.543 28 2028 superiorfrontal 10902 6992.672 29 2029 superiorparietal 7498 4585.292 30 2030 superiortemporal 5604 3634.623 31 2031 supramarginal 5840 3663.642 32 2032 frontalpole 568 313.985 33 2033 temporalpole 676 426.373 34 2034 transversetemporal 424 252.924 35 2035 insula 3522 2247.050 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Fri Jan 3 18:43:10 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1568 1059 3277 3.336 0.610 0.162 0.106 46 6.6 bankssts 1669 1029 2795 2.715 1.157 0.152 0.090 42 5.2 caudalanteriorcingulate 4164 2733 10526 3.365 0.681 0.186 0.190 526 32.7 caudalmiddlefrontal 1737 1188 3233 2.330 0.604 0.226 0.160 181 10.8 cuneus 611 387 1707 3.003 0.768 0.220 0.207 30 6.5 entorhinal 4310 3085 8802 2.493 0.887 0.238 0.219 396 40.6 fusiform 8511 5435 19113 3.106 0.604 0.177 0.197 562 68.8 inferiorparietal 3802 2640 10762 3.397 0.811 0.180 0.145 1484 26.4 inferiortemporal 924 516 910 1.715 0.743 0.170 0.247 93 10.0 isthmuscingulate 5713 3817 11497 2.677 0.686 0.184 0.107 189 25.3 lateraloccipital 3109 2060 7397 2.997 1.057 0.155 0.064 59 8.6 lateralorbitofrontal 1805 1641 2320 1.404 0.658 0.377 0.896 938 28.4 lingual 2252 1495 5105 2.778 1.091 0.158 0.119 72 9.6 medialorbitofrontal 4722 3165 13234 3.505 0.614 0.160 0.088 117 17.4 middletemporal 2280 1387 3135 1.981 0.736 0.217 0.281 521 23.7 parahippocampal 2527 1619 5251 2.896 0.790 0.153 0.094 55 9.7 paracentral 1977 1336 4789 2.968 0.590 0.138 0.090 46 7.6 parsopercularis 1098 751 3003 2.898 0.771 0.173 0.090 33 4.8 parsorbitalis 1992 1356 4313 2.628 0.642 0.153 0.073 49 6.5 parstriangularis 1019 724 1524 1.793 0.743 0.394 1.141 523 35.7 pericalcarine 6219 3835 10569 2.459 0.802 0.143 0.114 159 21.8 postcentral 1828 1275 3203 2.335 0.704 0.176 0.107 74 6.1 posteriorcingulate 8303 5312 15275 2.667 0.884 0.168 0.143 348 44.2 precentral 6006 4406 11706 2.452 0.939 0.207 0.226 497 57.2 precuneus 960 623 2480 3.317 1.170 0.177 0.164 53 8.1 rostralanteriorcingulate 10716 6911 22109 2.870 0.748 0.179 0.142 419 66.6 rostralmiddlefrontal 10902 6993 26422 3.359 0.781 0.163 0.221 614 57.8 superiorfrontal 7498 4585 13865 2.734 0.573 0.156 0.102 367 34.4 superiorparietal 5604 3635 13535 3.142 0.626 0.145 0.087 142 22.8 superiortemporal 5840 3664 11193 2.881 0.643 0.182 0.261 1119 58.9 supramarginal 568 314 1254 2.693 1.198 0.220 0.272 33 5.6 frontalpole 676 426 2120 3.333 0.800 0.230 0.361 56 6.7 temporalpole 424 253 748 2.722 0.630 0.193 0.137 15 2.0 transversetemporal 3522 2247 7393 3.224 0.930 0.148 0.183 197 17.5 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri Jan 3 18:43:22 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 506 labels changed using aseg relabeling using gibbs priors... 000: 9805 changed, 139129 examined... 001: 2434 changed, 37289 examined... 002: 735 changed, 12610 examined... 003: 314 changed, 4037 examined... 004: 150 changed, 1761 examined... 005: 77 changed, 837 examined... 006: 47 changed, 431 examined... 007: 33 changed, 250 examined... 008: 20 changed, 163 examined... 009: 19 changed, 109 examined... 010: 16 changed, 106 examined... 011: 3 changed, 90 examined... 012: 3 changed, 14 examined... 013: 0 changed, 14 examined... 173 labels changed using aseg 000: 346 total segments, 264 labels (3213 vertices) changed 001: 105 total segments, 24 labels (339 vertices) changed 002: 83 total segments, 2 labels (2 vertices) changed 003: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 128 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1309 vertices marked for relabeling... 1309 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 42 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri Jan 3 18:44:05 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1496 959 3211 3.082 1.042 0.190 0.133 54 7.9 G_and_S_frontomargin 751 548 1726 2.777 0.535 0.195 0.117 28 4.0 G_and_S_occipital_inf 1301 810 2204 2.292 0.706 0.165 0.086 25 4.7 G_and_S_paracentral 940 626 2435 3.199 0.789 0.144 0.061 15 2.3 G_and_S_subcentral 1449 806 2289 2.434 0.754 0.213 0.240 72 15.9 G_and_S_transv_frontopol 2711 1796 6095 3.212 0.805 0.137 0.067 47 8.4 G_and_S_cingul-Ant 1747 1168 3393 2.900 0.785 0.158 0.098 44 7.1 G_and_S_cingul-Mid-Ant 1355 971 2580 2.679 0.625 0.154 0.053 24 2.8 G_and_S_cingul-Mid-Post 407 263 681 2.260 0.660 0.153 0.070 14 0.8 G_cingul-Post-dorsal 162 79 105 1.452 0.588 0.157 0.213 22 2.0 G_cingul-Post-ventral 1752 1193 3254 2.250 0.721 0.295 0.504 396 26.9 G_cuneus 1248 872 3929 3.118 0.579 0.160 0.091 37 4.0 G_front_inf-Opercular 423 290 1438 3.180 0.738 0.184 0.089 16 1.9 G_front_inf-Orbital 1253 823 3053 2.765 0.637 0.175 0.111 54 6.6 G_front_inf-Triangul 5769 3553 14944 3.126 0.757 0.197 0.175 365 41.5 G_front_middle 7694 4792 21416 3.503 0.838 0.179 0.292 531 49.0 G_front_sup 629 361 1369 3.245 0.835 0.184 0.425 56 4.6 G_Ins_lg_and_S_cent_ins 649 403 2059 3.989 0.854 0.137 0.247 33 3.2 G_insular_short 2376 1529 6244 3.136 0.551 0.200 0.121 88 12.6 G_occipital_middle 1627 1081 4257 2.995 0.599 0.188 0.093 44 6.4 G_occipital_sup 1765 1156 4323 2.619 0.868 0.234 0.203 108 16.3 G_oc-temp_lat-fusifor 830 687 1355 1.706 0.811 0.497 1.501 738 16.3 G_oc-temp_med-Lingual 2228 1337 4011 2.493 0.804 0.207 0.207 160 19.1 G_oc-temp_med-Parahip 2526 1656 7419 3.165 1.010 0.181 0.138 84 19.3 G_orbital 3233 1876 7573 3.133 0.721 0.194 0.214 344 30.5 G_pariet_inf-Angular 2947 1796 6906 3.004 0.734 0.197 0.338 781 44.5 G_pariet_inf-Supramar 2366 1358 4168 2.728 0.529 0.151 0.115 176 12.2 G_parietal_sup 2507 1417 4519 2.487 0.745 0.153 0.104 81 12.9 G_postcentral 3284 2063 7277 2.706 1.034 0.179 0.161 149 20.4 G_precentral 3228 2058 7235 2.790 0.695 0.213 0.275 297 37.6 G_precuneus 620 417 1898 2.995 1.155 0.182 0.124 21 2.8 G_rectus 296 172 305 1.554 1.187 0.190 0.229 28 3.5 G_subcallosal 331 200 641 2.618 0.590 0.189 0.137 12 1.7 G_temp_sup-G_T_transv 2112 1246 6552 3.312 0.571 0.162 0.116 83 11.7 G_temp_sup-Lateral 821 534 1805 2.786 0.784 0.150 0.223 30 4.1 G_temp_sup-Plan_polar 804 567 1802 2.976 0.512 0.133 0.059 10 2.3 G_temp_sup-Plan_tempo 2287 1643 7825 3.498 0.788 0.197 0.168 89 15.9 G_temporal_inf 3039 1941 9641 3.591 0.631 0.178 0.106 103 13.5 G_temporal_middle 191 147 323 2.166 0.628 0.117 0.026 1 0.2 Lat_Fis-ant-Horizont 197 137 325 2.529 0.585 0.129 0.043 2 0.3 Lat_Fis-ant-Vertical 1275 853 1954 2.973 0.547 0.150 0.074 19 3.7 Lat_Fis-post 2624 1967 4629 2.161 0.643 0.229 0.185 266 18.3 Pole_occipital 1606 1072 5102 3.478 0.848 0.214 0.184 96 11.2 Pole_temporal 1218 726 878 1.093 0.584 0.257 0.693 555 31.9 S_calcarine 3163 2092 3610 2.048 0.653 0.160 0.134 108 15.7 S_central 1237 890 2315 2.787 0.493 0.138 0.043 16 2.1 S_cingul-Marginalis 619 402 1092 2.906 0.645 0.108 0.037 5 1.0 S_circular_insula_ant 1244 808 2141 3.229 0.726 0.153 0.097 89 6.3 S_circular_insula_inf 1327 896 2113 2.697 0.479 0.102 0.041 10 2.3 S_circular_insula_sup 594 417 1087 2.874 0.494 0.133 0.045 7 1.1 S_collat_transv_ant 511 376 616 1.793 0.556 0.129 0.057 4 1.1 S_collat_transv_post 2217 1523 3914 2.847 0.558 0.158 0.127 89 12.3 S_front_inf 2340 1623 4192 2.915 0.606 0.138 0.047 24 4.2 S_front_middle 2784 1867 5717 3.110 0.571 0.159 0.114 393 6.9 S_front_sup 733 479 1068 2.765 0.432 0.167 0.180 166 3.1 S_interm_prim-Jensen 2810 1827 4766 2.766 0.511 0.155 0.143 194 18.9 S_intrapariet_and_P_trans 588 413 1058 2.941 0.679 0.153 0.063 10 1.5 S_oc_middle_and_Lunatus 1681 1060 2584 2.627 0.594 0.130 0.226 36 13.5 S_oc_sup_and_transversal 477 323 1272 3.256 0.459 0.160 0.088 12 1.7 S_occipital_ant 515 383 1020 2.990 0.772 0.129 0.040 5 0.9 S_oc-temp_lat 2382 1849 2684 1.698 0.660 0.273 0.360 530 35.8 S_oc-temp_med_and_Lingual 403 269 696 2.642 0.884 0.129 0.052 7 0.8 S_orbital_lateral 650 421 1157 2.294 1.265 0.106 0.045 6 1.2 S_orbital_med-olfact 1197 796 2029 2.553 0.846 0.153 0.062 23 3.1 S_orbital-H_Shaped 1872 1730 3011 1.912 0.931 0.226 0.173 106 11.0 S_parieto_occipital 1775 1072 2159 2.414 1.209 0.172 0.182 108 12.5 S_pericallosal 2823 1822 4230 2.656 0.509 0.146 0.201 177 8.1 S_postcentral 1887 1234 3772 3.043 0.701 0.157 0.180 73 18.0 S_precentral-inf-part 1651 1062 2620 3.064 0.783 0.149 0.106 62 7.3 S_precentral-sup-part 281 199 547 2.783 0.866 0.157 0.209 10 0.6 S_suborbital 1055 693 2052 2.766 0.590 0.156 0.074 23 3.3 S_subparietal 1143 796 2165 3.322 0.593 0.162 0.129 1382 9.5 S_temporal_inf 6589 4483 13372 3.220 0.565 0.149 0.096 152 24.1 S_temporal_sup 234 148 356 2.466 0.574 0.184 0.288 25 3.6 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Fri Jan 3 18:44:18 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 MPS1036-1 rh ../surf/rh.sphere.reg /soft/freesurfer/5.3.0_1/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_1/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... 857 labels changed using aseg relabeling using gibbs priors... 000: 2767 changed, 139129 examined... 001: 621 changed, 12198 examined... 002: 177 changed, 3472 examined... 003: 49 changed, 967 examined... 004: 38 changed, 300 examined... 005: 17 changed, 206 examined... 006: 4 changed, 95 examined... 007: 3 changed, 23 examined... 008: 3 changed, 19 examined... 009: 4 changed, 18 examined... 010: 5 changed, 19 examined... 011: 5 changed, 24 examined... 012: 7 changed, 29 examined... 013: 3 changed, 29 examined... 014: 7 changed, 16 examined... 015: 5 changed, 29 examined... 016: 1 changed, 21 examined... 017: 0 changed, 10 examined... 239 labels changed using aseg 000: 139 total segments, 104 labels (672 vertices) changed 001: 41 total segments, 6 labels (19 vertices) changed 002: 35 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 38 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1409 vertices marked for relabeling... 1409 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 36 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Fri Jan 3 18:44:53 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/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 MPS1036-1 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1630 1014 2876 2.802 1.103 0.155 0.092 42 5.2 caudalanteriorcingulate 4265 2774 10716 3.380 0.665 0.183 0.165 559 20.6 caudalmiddlefrontal 2142 1482 3945 2.336 0.669 0.207 0.163 98 10.2 cuneus 658 422 1722 2.861 0.841 0.243 0.241 41 9.0 entorhinal 3863 2800 7856 2.445 0.879 0.232 0.208 318 35.1 fusiform 7894 5033 17662 3.097 0.618 0.179 0.204 545 66.0 inferiorparietal 4215 2930 11781 3.358 0.819 0.187 0.155 1528 29.6 inferiortemporal 1059 571 1010 1.700 0.777 0.205 0.280 150 12.4 isthmuscingulate 6061 4030 12195 2.685 0.697 0.185 0.111 288 28.4 lateraloccipital 3841 2524 9420 3.034 1.136 0.164 0.110 101 21.6 lateralorbitofrontal 1804 1611 2273 1.404 0.647 0.370 0.893 956 27.6 lingual 1714 1128 3947 2.645 1.243 0.167 0.147 66 9.0 medialorbitofrontal 5702 3814 15297 3.485 0.619 0.159 0.087 135 21.6 middletemporal 2130 1329 3059 2.021 0.715 0.203 0.264 458 21.0 parahippocampal 2651 1698 5618 2.959 0.818 0.150 0.092 56 9.8 paracentral 1914 1310 4632 2.951 0.590 0.135 0.067 40 4.2 parsopercularis 1162 804 3125 2.910 0.754 0.169 0.073 30 4.1 parsorbitalis 2414 1611 5129 2.648 0.632 0.162 0.085 72 9.3 parstriangularis 1036 741 1556 1.783 0.748 0.399 1.126 530 35.7 pericalcarine 6766 4166 11496 2.476 0.789 0.146 0.115 192 25.0 postcentral 1873 1306 3247 2.332 0.697 0.175 0.105 74 6.2 posteriorcingulate 8004 5125 14662 2.619 0.865 0.172 0.167 357 56.5 precentral 6117 4468 12230 2.492 0.926 0.207 0.210 498 57.3 precuneus 1170 746 2805 3.169 1.232 0.166 0.142 56 8.4 rostralanteriorcingulate 6919 4490 14908 2.931 0.694 0.174 0.131 245 39.2 rostralmiddlefrontal 14699 9394 33079 3.184 0.826 0.168 0.199 732 80.3 superiorfrontal 6404 3917 11681 2.726 0.555 0.159 0.113 356 31.5 superiorparietal 7385 4795 17852 3.173 0.646 0.154 0.111 217 31.6 superiortemporal 5831 3630 11303 2.908 0.629 0.179 0.255 1096 58.4 supramarginal 457 267 755 2.686 0.617 0.212 0.243 37 5.2 transversetemporal 3076 1972 6730 3.331 0.824 0.143 0.188 182 14.7 insula #-------------------------------------------- #@# Cortical ribbon mask Fri Jan 3 18:45:05 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon MPS1036-1 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 = 144 writing volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Jan 3 18:51:51 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 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_1/ASegStatsLUT.txt --subject MPS1036-1 $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_1/ASegStatsLUT.txt --subject MPS1036-1 sysname Linux hostname node1107 machine x86_64 user kovacv UseRobust 0 atlas_icv (eTIV) = 2135681 mm^3 (det: 0.912171 ) Computing euler number orig.nofix lheno = -348, rheno = -312 orig.nofix lhholes = 175, rhholes = 157 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 256254.776 261368.000 diff=-5113.2 pctdiff=-1.995 rhCtxGM: 249294.421 252059.000 diff=-2764.6 pctdiff=-1.109 lhCtxWM: 266964.889 257877.500 diff= 9087.4 pctdiff= 3.404 rhCtxWM: 224612.591 236366.500 diff=-11753.9 pctdiff=-5.233 SubCortGMVol 71398.000 SupraTentVol 1228596.677 (1211312.000) diff=17284.677 pctdiff=1.407 SupraTentVolNotVent 1096465.677 (1079181.000) diff=17284.677 pctdiff=1.576 BrainSegVol 1416444.000 (1409203.000) diff=7241.000 pctdiff=0.511 BrainSegVolNotVent 1274846.000 (1263842.677) diff=11003.323 pctdiff=0.863 BrainSegVolNotVent 1274846.000 CerebellumVol 195206.000 VentChorVol 132131.000 3rd4th5thCSF 9467.000 CSFVol 2621.000, OptChiasmVol 64.000 MaskVol 2138819.000 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 67010 67009.617 4 5 Left-Inf-Lat-Vent 4716 4716.496 5 7 Left-Cerebellum-White-Matter 19922 19921.951 6 8 Left-Cerebellum-Cortex 72840 72839.742 7 10 Left-Thalamus-Proper 8228 8228.178 8 11 Left-Caudate 4580 4579.769 9 12 Left-Putamen 7302 7302.200 10 13 Left-Pallidum 1585 1584.526 11 14 3rd-Ventricle 4727 4726.834 12 15 4th-Ventricle 2364 2363.641 13 16 Brain-Stem 26137 26137.186 14 17 Left-Hippocampus 2875 2874.504 15 18 Left-Amygdala 1519 1518.600 16 24 CSF 2382 2382.016 17 26 Left-Accumbens-area 419 419.445 18 28 Left-VentralDC 3811 3811.076 19 30 Left-vessel 44 44.070 20 31 Left-choroid-plexus 1937 1936.549 23 43 Right-Lateral-Ventricle 52787 52787.492 24 44 Right-Inf-Lat-Vent 5673 5673.220 25 46 Right-Cerebellum-White-Matter 15961 15961.313 26 47 Right-Cerebellum-Cortex 88079 88078.992 27 49 Right-Thalamus-Proper 10287 10286.824 28 50 Right-Caudate 9351 9351.240 29 51 Right-Putamen 6480 6480.240 30 52 Right-Pallidum 2139 2138.611 31 53 Right-Hippocampus 3228 3228.436 32 54 Right-Amygdala 1528 1527.966 33 58 Right-Accumbens-area 605 605.002 34 60 Right-VentralDC 4858 4858.277 35 62 Right-vessel 74 74.138 36 63 Right-choroid-plexus 1887 1887.219 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 54791 54790.742 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 457 456.611 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 61 60.649 45 251 CC_Posterior 820 819.551 46 252 CC_Mid_Posterior 291 291.015 47 253 CC_Central 216 216.173 48 254 CC_Mid_Anterior 205 205.433 49 255 CC_Anterior 210 209.615 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Jan 3 18:53:48 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --volmask SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 outvol /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/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/MPS1036-1/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 = 510679 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc+aseg.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --volmask --a2009s SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 outvol /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/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/MPS1036-1/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 = 510679 Used brute-force search on 0 voxels Writing output aseg to /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Jan 3 18:55:49 CST 2014 /lustre/kovacv/FS/post_analysis/MPS1036-1 mri_aparc2aseg --s MPS1036-1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /lustre/kovacv/FS/post_analysis subject MPS1036-1 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/MPS1036-1/mri/aparc+aseg.mgz Reading lh white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white Reading lh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial Loading lh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/surf/rh.white Reading rh pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial Loading rh annotations from /lustre/kovacv/FS/post_analysis/MPS1036-1/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/MPS1036-1/mri/ribbon.mgz Loading filled from /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 12252 vertices from left hemi Ripped 14273 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/MPS1036-1/mri/aseg.mgz Loading Ctx Seg File /lustre/kovacv/FS/post_analysis/MPS1036-1/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 = 1004932 Used brute-force search on 949 voxels Fixing Parahip LH WM Found 22 clusters 0 k 2.000000 1 k 1.000000 2 k 4.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 5.000000 7 k 2.000000 8 k 1.000000 9 k 1.000000 10 k 3.000000 11 k 1.000000 12 k 14.000000 13 k 1.000000 14 k 1.000000 15 k 1141.000000 16 k 1.000000 17 k 1.000000 18 k 2.000000 19 k 2.000000 20 k 1.000000 21 k 1.000000 Fixing Parahip RH WM Found 32 clusters 0 k 1.000000 1 k 2.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 1.000000 7 k 2.000000 8 k 23.000000 9 k 2.000000 10 k 1.000000 11 k 1.000000 12 k 2790.000000 13 k 1.000000 14 k 7.000000 15 k 1.000000 16 k 1.000000 17 k 1.000000 18 k 1.000000 19 k 2.000000 20 k 1.000000 21 k 1.000000 22 k 1.000000 23 k 1.000000 24 k 1.000000 25 k 4.000000 26 k 2.000000 27 k 1.000000 28 k 1.000000 29 k 1.000000 30 k 1.000000 31 k 12.000000 Writing output aseg to mri/wmparc.mgz /lustre/kovacv/FS/post_analysis/MPS1036-1 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 MPS1036-1 --surf-wm-vol --ctab /soft/freesurfer/5.3.0_1/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 MPS1036-1 --surf-wm-vol --ctab /soft/freesurfer/5.3.0_1/WMParcStatsLUT.txt --etiv sysname Linux hostname node1107 machine x86_64 user kovacv UseRobust 0 atlas_icv (eTIV) = 2135681 mm^3 (det: 0.912171 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 256254.776 261368.000 diff=-5113.2 pctdiff=-1.995 rhCtxGM: 249294.421 252059.000 diff=-2764.6 pctdiff=-1.109 lhCtxWM: 266964.889 257877.500 diff= 9087.4 pctdiff= 3.404 rhCtxWM: 224612.591 236366.500 diff=-11753.9 pctdiff=-5.233 SubCortGMVol 71398.000 SupraTentVol 1228596.677 (1211312.000) diff=17284.677 pctdiff=1.407 SupraTentVolNotVent 1096465.677 (1079181.000) diff=17284.677 pctdiff=1.576 BrainSegVol 1416444.000 (1409203.000) diff=7241.000 pctdiff=0.511 BrainSegVolNotVent 1274846.000 (1263842.677) diff=11003.323 pctdiff=0.863 BrainSegVolNotVent 1274846.000 CerebellumVol 195206.000 VentChorVol 132131.000 3rd4th5thCSF 9467.000 CSFVol 2621.000, OptChiasmVol 64.000 MaskVol 2138819.000 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 3282 3281.789 2 3002 wm-lh-caudalanteriorcingulate 3564 3563.811 3 3003 wm-lh-caudalmiddlefrontal 8947 8947.027 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2593 2593.445 6 3006 wm-lh-entorhinal 655 654.760 7 3007 wm-lh-fusiform 4608 4607.688 8 3008 wm-lh-inferiorparietal 11380 11380.161 9 3009 wm-lh-inferiortemporal 7398 7397.763 10 3010 wm-lh-isthmuscingulate 6154 6153.518 11 3011 wm-lh-lateraloccipital 9683 9683.283 12 3012 wm-lh-lateralorbitofrontal 6285 6285.384 13 3013 wm-lh-lingual 4283 4282.742 14 3014 wm-lh-medialorbitofrontal 4155 4155.014 15 3015 wm-lh-middletemporal 7199 7198.575 16 3016 wm-lh-parahippocampal 1269 1268.619 17 3017 wm-lh-paracentral 4011 4010.517 18 3018 wm-lh-parsopercularis 3365 3365.262 19 3019 wm-lh-parsorbitalis 954 954.231 20 3020 wm-lh-parstriangularis 3414 3413.703 21 3021 wm-lh-pericalcarine 3000 3000.191 22 3022 wm-lh-postcentral 8082 8082.311 23 3023 wm-lh-posteriorcingulate 5645 5645.079 24 3024 wm-lh-precentral 17983 17982.912 25 3025 wm-lh-precuneus 8433 8433.099 26 3026 wm-lh-rostralanteriorcingulate 2616 2616.332 27 3027 wm-lh-rostralmiddlefrontal 17945 17944.547 28 3028 wm-lh-superiorfrontal 21910 21910.219 29 3029 wm-lh-superiorparietal 11806 11805.667 30 3030 wm-lh-superiortemporal 7014 7014.336 31 3031 wm-lh-supramarginal 10582 10582.073 32 3032 wm-lh-frontalpole 319 319.459 33 3033 wm-lh-temporalpole 828 828.194 34 3034 wm-lh-transversetemporal 701 700.567 35 3035 wm-lh-insula 7614 7614.173 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 2859 2859.242 120 4002 wm-rh-caudalanteriorcingulate 3822 3821.953 121 4003 wm-rh-caudalmiddlefrontal 8117 8116.793 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 1820 1820.050 124 4006 wm-rh-entorhinal 728 728.224 125 4007 wm-rh-fusiform 4663 4662.839 126 4008 wm-rh-inferiorparietal 10946 10946.172 127 4009 wm-rh-inferiortemporal 4703 4702.737 128 4010 wm-rh-isthmuscingulate 1528 1528.261 129 4011 wm-rh-lateraloccipital 5312 5311.938 130 4012 wm-rh-lateralorbitofrontal 6331 6331.444 131 4013 wm-rh-lingual 3069 3068.674 132 4014 wm-rh-medialorbitofrontal 3291 3290.704 133 4015 wm-rh-middletemporal 5438 5437.533 134 4016 wm-rh-parahippocampal 2941 2940.542 135 4017 wm-rh-paracentral 4836 4836.378 136 4018 wm-rh-parsopercularis 3224 3224.115 137 4019 wm-rh-parsorbitalis 989 989.412 138 4020 wm-rh-parstriangularis 2972 2971.586 139 4021 wm-rh-pericalcarine 884 884.300 140 4022 wm-rh-postcentral 7040 7040.164 141 4023 wm-rh-posteriorcingulate 4222 4222.451 142 4024 wm-rh-precentral 15875 15875.232 143 4025 wm-rh-precuneus 11422 11422.398 144 4026 wm-rh-rostralanteriorcingulate 2178 2177.915 145 4027 wm-rh-rostralmiddlefrontal 16540 16539.908 146 4028 wm-rh-superiorfrontal 17679 17678.924 147 4029 wm-rh-superiorparietal 9408 9408.209 148 4030 wm-rh-superiortemporal 7458 7458.024 149 4031 wm-rh-supramarginal 8749 8749.039 150 4032 wm-rh-frontalpole 353 353.228 151 4033 wm-rh-temporalpole 711 711.475 152 4034 wm-rh-transversetemporal 541 541.337 153 4035 wm-rh-insula 8220 8220.333 154 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 52776 52776.473 237 5002 Right-UnsegmentedWhiteMatter 39578 39578.223 238 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/post_analysis/MPS1036-1/label #-------------------------------------------- #@# BA Labels lh Fri Jan 3 19:03:10 CST 2014 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.label --trgsubject MPS1036-1 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 717 Checking for and removing duplicates Writing label file ./lh.BA1.label 4846 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.label --trgsubject MPS1036-1 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1210 Checking for and removing duplicates Writing label file ./lh.BA2.label 9119 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.label --trgsubject MPS1036-1 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 384 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4461 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.label --trgsubject MPS1036-1 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 769 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6752 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.label --trgsubject MPS1036-1 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 619 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.label --trgsubject MPS1036-1 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 523 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4593 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.label --trgsubject MPS1036-1 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 2730 Checking for and removing duplicates Writing label file ./lh.BA6.label 16319 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.label --trgsubject MPS1036-1 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 508 Checking for and removing duplicates Writing label file ./lh.BA44.label 4689 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.label --trgsubject MPS1036-1 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1684 Checking for and removing duplicates Writing label file ./lh.BA45.label 5106 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.label --trgsubject MPS1036-1 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1451 Checking for and removing duplicates Writing label file ./lh.V1.label 6092 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.label --trgsubject MPS1036-1 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 2934 Checking for and removing duplicates Writing label file ./lh.V2.label 11048 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.label --trgsubject MPS1036-1 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 510 Checking for and removing duplicates Writing label file ./lh.MT.label 2528 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.perirhinal.label --trgsubject MPS1036-1 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1199 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 170 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1369 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1014 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 189 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1203 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2092 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 459 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2551 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1504 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 183 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1687 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1996 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2136 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2319 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2530 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1549 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 206 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1755 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 7035 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1254 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 8289 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1912 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2064 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1151 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 660 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1811 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3405 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 992 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4397 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3334 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 1305 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4639 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.thresh.label --trgsubject MPS1036-1 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 513 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/MPS1036-1/surf/lh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 150168 Number of reverse mapping hits = 159 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 672 mri_label2label: Done mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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 node1107 machine x86_64 user kovacv subject MPS1036-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 105118 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.BA.annot mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi lh --ctab /soft/freesurfer/5.3.0_1/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 node1107 machine x86_64 user kovacv subject MPS1036-1 hemi lh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 124691 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab MPS1036-1 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 1338 725 1978 2.184 0.619 0.180 0.170 58 7.3 BA1 4674 2993 7654 2.706 0.642 0.160 0.102 191 19.5 BA2 1041 727 962 1.873 0.533 0.265 0.270 101 9.1 BA3a 2328 1610 3015 1.931 0.737 0.197 0.244 835 29.8 BA3b 1912 1235 3306 2.462 0.825 0.169 0.267 240 7.3 BA4a 1385 994 1602 1.883 0.713 0.191 0.160 109 10.1 BA4p 11498 7268 27664 3.319 0.855 0.171 0.142 587 80.8 BA6 2231 1427 4646 2.962 0.706 0.171 0.230 184 31.5 BA44 4234 2593 7794 2.780 0.768 0.169 0.149 354 28.9 BA45 3296 2086 3449 1.665 0.537 0.196 0.127 110 17.1 V1 8011 5322 13242 2.254 0.653 0.189 0.107 289 35.6 V2 2137 1401 4189 2.871 0.596 0.160 0.090 70 6.5 MT 965 658 1949 2.381 0.798 0.220 0.245 80 6.1 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab MPS1036-1 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 899 480 1254 2.061 0.604 0.178 0.155 33 4.8 BA1 2020 1239 3295 2.554 0.587 0.174 0.141 140 9.6 BA2 868 591 729 1.775 0.458 0.285 0.325 113 9.6 BA3a 1291 983 1601 1.643 0.605 0.162 0.104 686 3.0 BA3b 1693 1118 2840 2.313 0.808 0.162 0.218 230 5.9 BA4a 1156 868 1327 1.807 0.662 0.205 0.174 93 8.8 BA4p 6352 3935 14091 3.128 0.900 0.167 0.142 314 46.2 BA6 1396 876 2983 2.980 0.737 0.157 0.090 31 5.3 BA44 1664 937 3249 2.638 0.781 0.192 0.225 290 17.9 BA45 3514 2228 3776 1.665 0.529 0.198 0.126 117 18.4 V1 4037 2673 6281 2.168 0.669 0.194 0.132 176 21.7 V2 587 391 1154 2.736 0.593 0.182 0.149 44 2.5 MT #-------------------------------------------- #@# BA Labels rh Fri Jan 3 19:06:28 CST 2014 mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.label --trgsubject MPS1036-1 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 443 Checking for and removing duplicates Writing label file ./rh.BA1.label 4405 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.label --trgsubject MPS1036-1 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 693 Checking for and removing duplicates Writing label file ./rh.BA2.label 7380 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.label --trgsubject MPS1036-1 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 268 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4248 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.label --trgsubject MPS1036-1 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 316 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4838 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.label --trgsubject MPS1036-1 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 805 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6552 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.label --trgsubject MPS1036-1 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 470 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4943 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.label --trgsubject MPS1036-1 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1987 Checking for and removing duplicates Writing label file ./rh.BA6.label 14243 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.label --trgsubject MPS1036-1 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1238 Checking for and removing duplicates Writing label file ./rh.BA44.label 8150 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.label --trgsubject MPS1036-1 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1263 Checking for and removing duplicates Writing label file ./rh.BA45.label 6618 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.label --trgsubject MPS1036-1 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1040 Checking for and removing duplicates Writing label file ./rh.V1.label 5767 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.label --trgsubject MPS1036-1 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 2200 Checking for and removing duplicates Writing label file ./rh.V2.label 10216 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.label --trgsubject MPS1036-1 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = MPS1036-1 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/5.3.0_1 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 319 Checking for and removing duplicates Writing label file ./rh.MT.label 2251 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.perirhinal.label --trgsubject MPS1036-1 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 752 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 944 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 876 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 986 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2688 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3038 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1698 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1768 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 2183 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 210 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2393 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1388 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 157 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1545 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1489 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1712 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 6959 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 1178 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 8137 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1012 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 175 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1187 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 1178 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 332 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1510 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3232 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 619 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 3851 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 3437 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 849 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 4286 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.thresh.label --trgsubject MPS1036-1 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /lustre/kovacv/FS/post_analysis/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = MPS1036-1 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/post_analysis FREESURFER_HOME /soft/freesurfer/5.3.0_1 Loading source label. Found 268 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/MPS1036-1/surf/rh.white Reading target registration /lustre/kovacv/FS/post_analysis/MPS1036-1/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 139129 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 335 mri_label2label: Done mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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 node1107 machine x86_64 user kovacv subject MPS1036-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 99805 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.BA.annot mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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_1/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/post_analysis/MPS1036-1/label cmdline mris_label2annot --s MPS1036-1 --hemi rh --ctab /soft/freesurfer/5.3.0_1/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 node1107 machine x86_64 user kovacv subject MPS1036-1 hemi rh SUBJECTS_DIR /lustre/kovacv/FS/post_analysis ColorTable /soft/freesurfer/5.3.0_1/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /lustre/kovacv/FS/post_analysis/MPS1036-1/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 117791 unhit vertices Writing annot to /lustre/kovacv/FS/post_analysis/MPS1036-1/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab MPS1036-1 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 962 519 1914 2.615 0.695 0.150 0.077 23 3.4 BA1 3506 2187 5821 2.650 0.595 0.141 0.155 129 14.0 BA2 1023 660 943 1.934 0.492 0.154 0.070 14 3.0 BA3a 2007 1308 2903 1.966 0.733 0.147 0.064 31 5.8 BA3b 1702 1156 3249 2.538 1.011 0.163 0.150 71 8.3 BA4a 1452 948 1845 2.197 0.754 0.182 0.206 89 11.8 BA4p 9435 5919 22394 3.232 0.860 0.170 0.183 558 66.4 BA6 3630 2441 8909 3.024 0.610 0.149 0.081 94 9.8 BA44 4472 3041 10466 2.803 0.677 0.162 0.089 129 19.4 BA45 2190 1719 3468 1.731 0.923 0.386 1.131 1022 62.7 V1 6453 4629 9167 1.829 1.029 0.211 0.225 837 55.0 V2 1691 1159 3794 3.034 0.473 0.156 0.075 35 5.3 MT 801 534 1827 2.634 0.881 0.209 0.218 35 7.2 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab MPS1036-1 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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_1/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 715 361 1392 2.610 0.532 0.151 0.095 20 3.1 BA1 2170 1319 3679 2.647 0.609 0.142 0.199 104 10.1 BA2 924 588 797 1.975 0.512 0.163 0.111 40 4.8 BA3a 1698 1120 2087 1.777 0.487 0.141 0.064 25 5.1 BA3b 1006 666 2073 2.538 1.017 0.173 0.122 29 5.0 BA4a 1204 785 1379 2.050 0.747 0.186 0.207 58 9.1 BA4p 6176 3818 14251 3.154 0.885 0.170 0.195 470 39.9 BA6 901 636 2447 2.974 0.711 0.149 0.088 25 2.2 BA44 1220 796 2856 2.766 0.609 0.172 0.096 42 5.2 BA45 2044 1595 3195 1.714 0.914 0.389 1.079 927 63.1 V1 2990 2189 4247 1.786 0.933 0.258 0.401 684 33.5 V2 290 184 695 3.223 0.367 0.178 0.102 8 1.1 MT /lustre/kovacv/FS/post_analysis/MPS1036-1/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Jan 3 19:09:33 CST 2014 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS1036-1 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject MPS1036-1. processing subject lh.EC_average... reading output surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 1017 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label MPS1036-1 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/lh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 340 198 869 2.583 0.680 0.214 0.143 19 1.9 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Jan 3 19:09:45 CST 2014 mris_spherical_average -erode 1 -orig white -t 0.4 -o MPS1036-1 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject MPS1036-1. processing subject rh.EC_average... reading output surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 957 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label MPS1036-1 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /lustre/kovacv/FS/post_analysis/MPS1036-1/mri/wm.mgz... reading input surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.white... reading input pial surface /lustre/kovacv/FS/post_analysis/MPS1036-1/surf/rh.pial... reading input white surface /lustre/kovacv/FS/post_analysis/MPS1036-1/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 364 196 811 2.620 0.626 0.153 0.109 17 1.8 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Fri Jan 3 11:38:42 CST 2014 Ended at Fri Jan 3 19:09:55 CST 2014 #@#%# recon-all-run-time-hours 7.520 recon-all -s MPS1036-1 finished without error at Fri Jan 3 19:09:56 CST 2014