Wed Mar 4 17:30:03 EST 2015 /export/data/hippocampus/HMN/data/HMN002 /cell_root/software/freesurfer/current/sys/bin/recon-all -s HMN002 -autorecon1 -autorecon2 -hippo-subfields subjid HMN002 setenv SUBJECTS_DIR /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/5.1.0/Linux-x64 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux hippocampus.umd.edu 2.6.32-504.3.3.el6.x86_64 #1 SMP Fri Dec 12 16:05:43 EST 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 24730048 24329292 400756 17912 262424 4766628 -/+ buffers/cache: 19300240 5429808 Swap: 23999484 81268 23918216 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-22:30:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /cell_root/software/freesurfer/current/sys/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /cell_root/software/freesurfer/current/sys/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed Mar 4 17:30:07 EST 2015 Found 1 runs /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/mri/orig/001.mgz /export/data/hippocampus/HMN/data/HMN002/mri/rawavg.mgz /export/data/hippocampus/HMN/data/HMN002 mri_convert /export/data/hippocampus/HMN/data/HMN002/mri/rawavg.mgz /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz --conform mri_convert /export/data/hippocampus/HMN/data/HMN002/mri/rawavg.mgz /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /export/data/hippocampus/HMN/data/HMN002/mri/rawavg.mgz... TR=1900.00, TE=2.32, TI=900.00, flip angle=9.00 i_ras = (0.0436194, -0.999048, -1.38554e-08) j_ras = (-0.0331236, -0.00144619, -0.99945) k_ras = (-0.998499, -0.0435954, 0.0331552) Original Data has (0.449219, 0.449219, 0.9) mm size and (512, 512, 192) 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 /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz... mri_add_xform_to_header -c /export/data/hippocampus/HMN/data/HMN002/mri/transforms/talairach.xfm /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Mar 4 17:30:42 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Mar 4 17:31:21 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7733, pval=0.6675 >= threshold=0.0050) awk -f /cell_root/software/freesurfer/current/sys/bin/extract_talairach_avi_QA.awk /export/data/hippocampus/HMN/data/HMN002/mri/transforms/talairach_avi.log TalAviQA: 0.97609 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Mar 4 17:31:21 EST 2015 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /export/data/hippocampus/HMN/data/HMN002/mri /cell_root/software/freesurfer/current/sys/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 2011/03/02 20:16:39 nicks Exp $ Linux hippocampus.umd.edu 2.6.32-504.3.3.el6.x86_64 #1 SMP Fri Dec 12 16:05:43 EST 2014 x86_64 x86_64 x86_64 GNU/Linux Wed Mar 4 17:31:21 EST 2015 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.27968 /export/data/hippocampus/HMN/data/HMN002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27968/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.27968/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=1900.00, TE=2.32, TI=900.00, flip angle=9.00 i_ras = (-1, 1.11759e-08, 7.07805e-08) j_ras = (1.2666e-07, 6.40284e-09, -1) k_ras = (3.72529e-08, 1, -2.79397e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.27968/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Mar 4 17:31:25 EST 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.27968/nu0.mnc ./tmp.mri_nu_correct.mni.27968/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.27968/0/ [lmarti@hippocampus.umd.edu:/export/data/hippocampus/HMN/data/HMN002/mri/] [2015-03-04 17:31:25] running: /cell_root/software/freesurfer/current/sys/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.27968/0/ ./tmp.mri_nu_correct.mni.27968/nu0.mnc ./tmp.mri_nu_correct.mni.27968/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 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 42 CV of field change: 0.000958845 [lmarti@hippocampus.umd.edu:/export/data/hippocampus/HMN/data/HMN002/mri/] [2015-03-04 17:31:53] running: /cell_root/software/freesurfer/current/sys/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.27968/nu0.mnc ./tmp.mri_nu_correct.mni.27968/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Mar 4 17:32:08 EST 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.27968/nu1.mnc ./tmp.mri_nu_correct.mni.27968/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.27968/1/ [lmarti@hippocampus.umd.edu:/export/data/hippocampus/HMN/data/HMN002/mri/] [2015-03-04 17:32:08] running: /cell_root/software/freesurfer/current/sys/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.27968/1/ ./tmp.mri_nu_correct.mni.27968/nu1.mnc ./tmp.mri_nu_correct.mni.27968/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 31 CV of field change: 0.000975422 [lmarti@hippocampus.umd.edu:/export/data/hippocampus/HMN/data/HMN002/mri/] [2015-03-04 17:32:30] running: /cell_root/software/freesurfer/current/sys/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.27968/nu1.mnc ./tmp.mri_nu_correct.mni.27968/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.27968/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27968/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /export/data/hippocampus/HMN/data/HMN002/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.27968/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.27968/ones.mgz sysname Linux hostname hippocampus.umd.edu machine x86_64 user lmarti input ./tmp.mri_nu_correct.mni.27968/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.27968/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.27968/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27968/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27968/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27968/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.27968/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27968/input.mean.dat sysname Linux hostname hippocampus.umd.edu machine x86_64 user lmarti Loading ./tmp.mri_nu_correct.mni.27968/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.27968/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27968/ones.mgz --i ./tmp.mri_nu_correct.mni.27968/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27968/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27968/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.27968/ones.mgz --i ./tmp.mri_nu_correct.mni.27968/nu2.mnc --sum ./tmp.mri_nu_correct.mni.27968/sum.junk --avgwf ./tmp.mri_nu_correct.mni.27968/output.mean.dat sysname Linux hostname hippocampus.umd.edu machine x86_64 user lmarti Loading ./tmp.mri_nu_correct.mni.27968/ones.mgz Loading ./tmp.mri_nu_correct.mni.27968/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.27968/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.27968/nu2.mnc ./tmp.mri_nu_correct.mni.27968/nu2.mnc mul .96699101332506972420 Saving result to './tmp.mri_nu_correct.mni.27968/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.27968/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.27968/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.27968/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.11759e-08, 7.07805e-08) j_ras = (1.2666e-07, 6.40284e-09, -1) k_ras = (3.72529e-08, 1, -2.79397e-09) INFO: transform src into the like-volume: orig.mgz Reslicing using trilinear interpolation writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping ( 9, 110) to ( 3, 110) Wed Mar 4 17:33:34 EST 2015 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Wed Mar 4 17:33:34 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 2 minutes and 36 seconds. MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 white matter peak found at 111 white matter peak found at 109 gm peak at 77 (77), valley at 56 (56) csf peak at 39, setting threshold to 64 white matter peak found at 111 white matter peak found at 110 gm peak at 78 (78), valley at 58 (58) csf peak at 39, setting threshold to 65 #-------------------------------------------- #@# Skull Stripping Wed Mar 4 17:36:12 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_em_register -skull nu.mgz /cell_root/software/freesurfer/current/sys/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/cell_root/software/freesurfer/current/sys/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.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=19.0 skull bounding box = (51, 31, 45) --> (202, 237, 216) using (101, 100, 131) as brain centroid... mean wm in atlas = 126, using box (82,75,110) --> (119, 125,152) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 initial log_p = -10413.2 ************************************************ First Search limited to translation only. ************************************************ Found translation: (0.6, 10.8, -13.1): log p = -10344.449 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10328.3, old_max_log_p =-10344.4 (thresh=-10334.1) 1.150 0.000 0.000 -18.211; 0.000 1.150 0.000 1.748; 0.000 0.000 1.150 -30.934; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10328.3, old_max_log_p =-10328.3 (thresh=-10318.0) 1.150 0.000 0.000 -18.211; 0.000 1.150 0.000 1.748; 0.000 0.000 1.150 -30.934; 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=-10323.5, old_max_log_p =-10328.3 (thresh=-10318.0) 1.187 0.115 -0.033 -27.380; -0.109 1.096 0.114 5.292; 0.036 -0.111 1.101 -19.919; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10318.5, old_max_log_p =-10323.5 (thresh=-10313.1) 1.188 0.121 -0.005 -31.513; -0.118 1.094 0.132 4.392; 0.008 -0.132 1.102 -14.024; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.18794 0.12117 -0.00483 -31.51318; -0.11797 1.09405 0.13231 4.39156; 0.00846 -0.13192 1.10186 -14.02414; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.18794 0.12117 -0.00483 -31.51318; -0.11797 1.09405 0.13231 4.39156; 0.00846 -0.13192 1.10186 -14.02414; 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: 006: -log(p) = 10318.5 tol 0.000010 Resulting transform: 1.188 0.121 -0.005 -31.513; -0.118 1.094 0.132 4.392; 0.008 -0.132 1.102 -14.024; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10318.5 (old=-10413.2) transform before final EM align: 1.188 0.121 -0.005 -31.513; -0.118 1.094 0.132 4.392; 0.008 -0.132 1.102 -14.024; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.18794 0.12117 -0.00483 -31.51318; -0.11797 1.09405 0.13231 4.39156; 0.00846 -0.13192 1.10186 -14.02414; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.18794 0.12117 -0.00483 -31.51318; -0.11797 1.09405 0.13231 4.39156; 0.00846 -0.13192 1.10186 -14.02414; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1145538.5 after pass:transform: ( 1.19, 0.12, -0.00, -31.51) ( -0.12, 1.09, 0.13, 4.39) ( 0.01, -0.13, 1.10, -14.02) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1145538.5 tol 0.000000 final transform: 1.188 0.121 -0.005 -31.513; -0.118 1.094 0.132 4.392; 0.008 -0.132 1.102 -14.024; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 25 minutes and 13 seconds. mri_watershed -T1 -brain_atlas /cell_root/software/freesurfer/current/sys/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) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 ********************************************************* 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=121 y=95 z=128 r=81 first estimation of the main basin volume: 2304897 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=103, y=82, z=97, Imax=255 CSF=20, 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=21611142047 voxels, voxel volume =1.000 = 21611142047 mmm3 = 21611141.120 cm3 done. PostAnalyze...Basin Prior 119 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=102, z=122, r=8847 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=90 , nb = 40716 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=57 , nb = 2286 LEFT_CER CSF_MIN=0, CSF_intensity=23, CSF_MAX=39 , nb = 2160 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 16848 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=88 , nb = 19170 OTHER CSF_MIN=3, CSF_intensity=32, CSF_MAX=37 , nb = 252 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 90, 59, 52, 73 after analyzing : 44, 59, 59, 62 RIGHT_CER before analyzing : 57, 59, 60, 87 after analyzing : 57, 59, 60, 66 LEFT_CER before analyzing : 39, 49, 62, 81 after analyzing : 39, 57, 62, 63 RIGHT_BRAIN before analyzing : 5, 11, 54, 74 after analyzing : 5, 39, 54, 47 LEFT_BRAIN before analyzing : 88, 57, 51, 71 after analyzing : 43, 57, 57, 60 OTHER before analyzing : 37, 11, 0, 2 after analyzing : 11, 20, 25, 21 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 70.060, std = 5.592 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.79, sigma = 5.34 after rotation: sse = 3.79, sigma = 5.34 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.41, its var is 5.83 before Erosion-Dilatation 1.58% of inacurate vertices after Erosion-Dilatation 2.44% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...39 iterations mri_strip_skull: done peeling brain Brain Size = 1576674 voxels, voxel volume = 1.000 mm3 = 1576674 mmm3 = 1576.674 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Mar 4 18:01:57 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=27.0 skull bounding box = (56, 40, 51) --> (196, 157, 206) using (103, 79, 129) as brain centroid... mean wm in atlas = 107, using box (86,65,110) --> (120, 93,148) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -7568.3 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-1.7, 11.9, -21.0): log p = -7221.098 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7180.6, old_max_log_p =-7221.1 (thresh=-7213.9) 1.064 0.000 0.000 -9.897; 0.000 1.075 0.000 11.412; 0.000 0.000 1.075 -30.499; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7158.5, old_max_log_p =-7180.6 (thresh=-7173.4) 0.984 0.000 0.000 0.356; 0.000 1.146 0.151 -14.717; 0.000 -0.140 1.066 -7.812; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7158.5, old_max_log_p =-7158.5 (thresh=-7151.3) 0.984 0.000 0.000 0.356; 0.000 1.146 0.151 -14.717; 0.000 -0.140 1.066 -7.812; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7093.7, old_max_log_p =-7158.5 (thresh=-7151.3) 1.040 -0.005 -0.001 -4.525; -0.000 1.141 0.181 -19.828; -0.004 -0.173 1.061 -7.200; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7091.5, old_max_log_p =-7093.7 (thresh=-7086.6) 1.059 -0.043 -0.008 -4.048; 0.033 1.113 0.212 -24.909; -0.004 -0.210 1.055 -2.602; 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=-7080.9, old_max_log_p =-7091.5 (thresh=-7084.4) 1.060 -0.043 -0.008 -4.201; 0.033 1.117 0.212 -25.415; -0.004 -0.210 1.057 -2.855; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7076.7, old_max_log_p =-7080.9 (thresh=-7073.8) 1.060 -0.043 -0.008 -4.201; 0.033 1.114 0.212 -25.076; -0.004 -0.211 1.060 -3.108; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05987 -0.04313 -0.00842 -4.20059; 0.03283 1.11446 0.21182 -25.07637; -0.00440 -0.21076 1.05976 -3.10844; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.05987 -0.04313 -0.00842 -4.20059; 0.03283 1.11446 0.21182 -25.07637; -0.00440 -0.21076 1.05976 -3.10844; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 7076.3 after pass:transform: ( 1.06, -0.04, -0.01, -4.20) ( 0.03, 1.11, 0.21, -25.08) ( -0.00, -0.21, 1.06, -3.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 7076.3 tol 0.000010 Resulting transform: 1.060 -0.043 -0.008 -4.201; 0.033 1.114 0.212 -25.076; -0.004 -0.211 1.060 -3.108; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -7076.7 (old=-7568.3) transform before final EM align: 1.060 -0.043 -0.008 -4.201; 0.033 1.114 0.212 -25.076; -0.004 -0.211 1.060 -3.108; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05987 -0.04313 -0.00842 -4.20059; 0.03283 1.11446 0.21182 -25.07637; -0.00440 -0.21076 1.05976 -3.10844; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.05987 -0.04313 -0.00842 -4.20059; 0.03283 1.11446 0.21182 -25.07637; -0.00440 -0.21076 1.05976 -3.10844; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 011: -log(p) = 843059.6 after pass:transform: ( 1.07, -0.04, 0.00, -4.20) ( 0.04, 1.12, 0.22, -25.08) ( -0.00, -0.21, 1.06, -3.11) dfp_em_step_func: 012: -log(p) = 842703.3 after pass:transform: ( 1.06, -0.04, 0.00, -4.20) ( 0.04, 1.12, 0.22, -25.08) ( -0.00, -0.21, 1.06, -3.11) dfp_em_step_func: 013: -log(p) = 842644.1 after pass:transform: ( 1.06, -0.04, 0.00, -4.20) ( 0.04, 1.12, 0.22, -25.08) ( 0.00, -0.21, 1.06, -3.11) dfp_em_step_func: 014: -log(p) = 842630.0 after pass:transform: ( 1.06, -0.04, 0.00, -4.20) ( 0.04, 1.12, 0.22, -25.08) ( 0.00, -0.21, 1.06, -3.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... dfp_em_step_func: 015: -log(p) = 841855.6 after pass:transform: ( 1.04, -0.03, 0.01, -4.20) ( 0.04, 1.11, 0.20, -25.08) ( 0.00, -0.21, 1.05, -3.11) dfp_em_step_func: 016: -log(p) = 841834.9 after pass:transform: ( 1.06, -0.04, 0.01, -4.20) ( 0.04, 1.11, 0.21, -25.08) ( 0.00, -0.21, 1.06, -3.11) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 018: -log(p) = 841834.9 tol 0.000000 final transform: 1.056 -0.036 0.006 -4.201; 0.039 1.114 0.213 -25.076; 0.000 -0.211 1.057 -3.108; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 32 minutes and 29 seconds. #-------------------------------------- #@# CA Normalize Wed Mar 4 18:34:26 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /cell_root/software/freesurfer/current/sys/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 volumes reading atlas from '/cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=27.0 skull bounding box = (56, 40, 51) --> (196, 157, 206) using (103, 79, 129) as brain centroid... mean wm in atlas = 107, using box (86,65,110) --> (120, 93,148) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 107, scaling input intensities by 1.000 scaling channel 0 by 1 using 244171 sample points... INFO: compute sample coordinates transform 1.056 -0.036 0.006 -4.201; 0.039 1.114 0.213 -25.076; 0.000 -0.211 1.057 -3.108; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 42, 52) --> (189, 142, 205) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 242.0 0 of 260 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 44, 51) --> (126, 144, 205) Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 242.0 0 of 289 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 120, 77) --> (175, 158, 127) Left_Cerebellum_White_Matter: limiting intensities to 90.0 --> 242.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 120, 75) --> (128, 159, 128) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 242.0 0 of 9 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 111, 110) --> (142, 173, 137) Brain_Stem: limiting intensities to 83.0 --> 242.0 0 of 8 (0.0%) samples deleted using 577 total control points for intensity normalization... bias field = 1.038 +- 0.057 0 of 577 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 42, 52) --> (189, 142, 205) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 234.0 0 of 260 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 44, 51) --> (126, 144, 205) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 234.0 0 of 283 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 120, 77) --> (175, 158, 127) Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 234.0 0 of 47 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 120, 75) --> (128, 159, 128) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 234.0 0 of 46 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 111, 110) --> (142, 173, 137) Brain_Stem: limiting intensities to 86.0 --> 234.0 14 of 61 (23.0%) samples deleted using 697 total control points for intensity normalization... bias field = 1.006 +- 0.049 0 of 683 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 42, 52) --> (189, 142, 205) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 229.0 0 of 321 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 44, 51) --> (126, 144, 205) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 229.0 0 of 389 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 120, 77) --> (175, 158, 127) Left_Cerebellum_White_Matter: limiting intensities to 81.0 --> 229.0 0 of 69 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 120, 75) --> (128, 159, 128) Right_Cerebellum_White_Matter: limiting intensities to 77.0 --> 229.0 0 of 82 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (112, 111, 110) --> (142, 173, 137) Brain_Stem: limiting intensities to 70.0 --> 229.0 0 of 148 (0.0%) samples deleted using 1009 total control points for intensity normalization... bias field = 1.004 +- 0.044 2 of 1009 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 15 seconds. #-------------------------------------- #@# CA Reg Wed Mar 4 18:36:41 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.29 (predicted orig area = 6.2) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.795, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38919.883 ms 0001: dt=295.936000, rms=0.723 (9.056%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32682.479 ms 0002: dt=129.472000, rms=0.700 (3.142%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36613.582 ms 0003: dt=129.472000, rms=0.693 (0.954%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36082.473 ms 0004: dt=517.888000, rms=0.678 (2.261%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34971.449 ms 0005: dt=32.368000, rms=0.676 (0.215%), neg=0, invalid=766 0006: dt=32.368000, rms=0.675 (0.119%), neg=0, invalid=766 0007: dt=32.368000, rms=0.675 (0.102%), neg=0, invalid=766 0008: dt=32.368000, rms=0.674 (0.099%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39913.250 ms 0009: dt=295.936000, rms=0.669 (0.817%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37770.941 ms 0010: dt=32.368000, rms=0.668 (0.078%), neg=0, invalid=766 0011: dt=32.368000, rms=0.668 (0.033%), neg=0, invalid=766 0012: dt=32.368000, rms=0.668 (-0.034%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41170.008 ms 0013: dt=221.952000, rms=0.665 (0.396%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40199.797 ms 0014: dt=129.472000, rms=0.663 (0.381%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46075.012 ms 0015: dt=92.480000, rms=0.662 (0.024%), neg=0, invalid=766 0016: dt=92.480000, rms=0.662 (0.103%), neg=0, invalid=766 0017: dt=92.480000, rms=0.661 (0.162%), neg=0, invalid=766 0018: dt=92.480000, rms=0.659 (0.223%), neg=0, invalid=766 0019: dt=92.480000, rms=0.658 (0.241%), neg=0, invalid=766 0020: dt=92.480000, rms=0.656 (0.230%), neg=0, invalid=766 0021: dt=92.480000, rms=0.655 (0.219%), neg=0, invalid=766 0022: dt=92.480000, rms=0.653 (0.265%), neg=0, invalid=766 0023: dt=92.480000, rms=0.651 (0.234%), neg=0, invalid=766 0024: dt=92.480000, rms=0.650 (0.192%), neg=0, invalid=766 0025: dt=92.480000, rms=0.649 (0.157%), neg=0, invalid=766 0026: dt=92.480000, rms=0.648 (0.171%), neg=0, invalid=766 0027: dt=92.480000, rms=0.647 (0.173%), neg=0, invalid=766 0028: dt=92.480000, rms=0.646 (0.157%), neg=0, invalid=766 0029: dt=92.480000, rms=0.645 (0.133%), neg=0, invalid=766 0030: dt=92.480000, rms=0.644 (0.116%), neg=0, invalid=766 0031: dt=92.480000, rms=0.643 (0.126%), neg=0, invalid=766 0032: dt=92.480000, rms=0.643 (0.115%), neg=0, invalid=766 0033: dt=92.480000, rms=0.642 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43849.648 ms 0034: dt=0.000000, rms=0.642 (0.001%), neg=0, invalid=766 0035: dt=0.850000, rms=0.642 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.647, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43267.262 ms 0036: dt=36.288000, rms=0.644 (0.449%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42411.453 ms 0037: dt=145.152000, rms=0.638 (0.950%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38318.645 ms 0038: dt=103.680000, rms=0.633 (0.848%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36291.961 ms 0039: dt=36.288000, rms=0.628 (0.833%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40126.895 ms 0040: dt=15.552000, rms=0.627 (0.094%), neg=0, invalid=766 0041: dt=15.552000, rms=0.627 (0.059%), neg=0, invalid=766 0042: dt=15.552000, rms=0.626 (0.097%), neg=0, invalid=766 0043: dt=15.552000, rms=0.625 (0.171%), neg=0, invalid=766 0044: dt=15.552000, rms=0.623 (0.261%), neg=0, invalid=766 0045: dt=15.552000, rms=0.621 (0.341%), neg=0, invalid=766 0046: dt=15.552000, rms=0.619 (0.358%), neg=0, invalid=766 0047: dt=15.552000, rms=0.617 (0.355%), neg=0, invalid=766 0048: dt=15.552000, rms=0.615 (0.338%), neg=0, invalid=766 0049: dt=15.552000, rms=0.613 (0.327%), neg=0, invalid=766 0050: dt=15.552000, rms=0.611 (0.301%), neg=0, invalid=766 0051: dt=15.552000, rms=0.609 (0.281%), neg=0, invalid=766 0052: dt=15.552000, rms=0.607 (0.263%), neg=0, invalid=766 0053: dt=15.552000, rms=0.606 (0.237%), neg=0, invalid=766 0054: dt=15.552000, rms=0.605 (0.205%), neg=0, invalid=766 0055: dt=15.552000, rms=0.604 (0.203%), neg=0, invalid=766 0056: dt=15.552000, rms=0.602 (0.196%), neg=0, invalid=766 0057: dt=15.552000, rms=0.601 (0.195%), neg=0, invalid=766 0058: dt=15.552000, rms=0.600 (0.197%), neg=0, invalid=766 0059: dt=15.552000, rms=0.599 (0.183%), neg=0, invalid=766 0060: dt=15.552000, rms=0.598 (0.157%), neg=0, invalid=766 0061: dt=15.552000, rms=0.597 (0.129%), neg=0, invalid=766 0062: dt=15.552000, rms=0.597 (0.106%), neg=0, invalid=766 0063: dt=15.552000, rms=0.596 (0.095%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45626.684 ms 0064: dt=145.152000, rms=0.595 (0.199%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42892.730 ms 0065: dt=5.184000, rms=0.595 (-0.012%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.595, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40201.211 ms 0066: dt=31.104000, rms=0.594 (0.182%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41991.754 ms 0067: dt=103.680000, rms=0.592 (0.282%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39463.199 ms 0068: dt=9.072000, rms=0.592 (0.009%), neg=0, invalid=766 0069: dt=9.072000, rms=0.592 (0.026%), neg=0, invalid=766 0070: dt=9.072000, rms=0.592 (-0.003%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.622, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43879.793 ms 0071: dt=12.327869, rms=0.620 (0.350%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39861.969 ms 0072: dt=19.200000, rms=0.618 (0.359%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40306.105 ms 0073: dt=11.200000, rms=0.617 (0.137%), neg=0, invalid=766 0074: dt=11.200000, rms=0.616 (0.208%), neg=0, invalid=766 0075: dt=11.200000, rms=0.614 (0.255%), neg=0, invalid=766 0076: dt=11.200000, rms=0.613 (0.226%), neg=0, invalid=766 0077: dt=11.200000, rms=0.612 (0.205%), neg=0, invalid=766 0078: dt=11.200000, rms=0.610 (0.219%), neg=0, invalid=766 0079: dt=11.200000, rms=0.609 (0.225%), neg=0, invalid=766 0080: dt=11.200000, rms=0.607 (0.248%), neg=0, invalid=766 0081: dt=11.200000, rms=0.606 (0.277%), neg=0, invalid=766 0082: dt=11.200000, rms=0.604 (0.308%), neg=0, invalid=766 0083: dt=11.200000, rms=0.602 (0.246%), neg=0, invalid=766 0084: dt=11.200000, rms=0.602 (0.144%), neg=0, invalid=766 0085: dt=11.200000, rms=0.601 (0.055%), neg=0, invalid=766 0086: dt=11.200000, rms=0.601 (-0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43330.754 ms 0087: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.601, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44015.617 ms 0088: dt=1.600000, rms=0.601 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42439.523 ms 0089: dt=0.000000, rms=0.601 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41986.223 ms 0090: dt=0.000000, rms=0.601 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44985.164 ms 0091: dt=0.777778, rms=0.652 (0.077%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46180.934 ms 0092: dt=0.063000, rms=0.652 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45014.273 ms 0093: dt=0.500000, rms=0.651 (0.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46942.391 ms 0094: dt=0.044665, rms=0.651 (0.001%), neg=0, invalid=766 0095: dt=0.044665, rms=0.651 (0.001%), neg=0, invalid=766 0096: dt=0.044665, rms=0.651 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.732, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44084.570 ms 0097: dt=0.899604, rms=0.713 (2.508%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44856.652 ms 0098: dt=1.024000, rms=0.710 (0.416%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43244.152 ms 0099: dt=0.916667, rms=0.710 (0.119%), neg=0, invalid=766 0100: dt=0.916667, rms=0.709 (0.041%), neg=0, invalid=766 0101: dt=0.916667, rms=0.709 (-0.109%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.709, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42037.926 ms 0102: dt=1.201389, rms=0.708 (0.208%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38760.340 ms 0103: dt=0.000000, rms=0.708 (0.001%), neg=0, invalid=766 0104: dt=0.100000, rms=0.708 (-0.004%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.662, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37893.996 ms 0105: dt=0.133765, rms=0.657 (0.692%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41090.508 ms 0106: dt=0.320000, rms=0.656 (0.189%), neg=0, invalid=766 0107: dt=0.160000, rms=0.653 (0.421%), neg=0, invalid=766 0108: dt=0.160000, rms=0.652 (0.176%), neg=0, invalid=766 0109: dt=0.160000, rms=0.652 (-0.084%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35414.422 ms 0110: dt=0.000000, rms=0.652 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39041.422 ms 0111: dt=0.096000, rms=0.651 (0.084%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41295.164 ms 0112: dt=0.492188, rms=0.651 (0.136%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40437.523 ms 0113: dt=0.028000, rms=0.650 (0.016%), neg=0, invalid=766 0114: dt=0.028000, rms=0.650 (0.005%), neg=0, invalid=766 0115: dt=0.028000, rms=0.650 (-0.006%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.11790 (31) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (848 voxels, overlap=0.490) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (848 voxels, peak = 28), gca=27.6 gca peak = 0.14022 (22) mri peak = 0.12069 (31) Right_Lateral_Ventricle (43): linear fit = 1.35 x + 0.0 (798 voxels, overlap=0.505) Right_Lateral_Ventricle (43): linear fit = 1.35 x + 0.0 (798 voxels, peak = 30), gca=29.7 gca peak = 0.24234 (100) mri peak = 0.12465 (100) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (442 voxels, overlap=0.996) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (442 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.11260 (103) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (373 voxels, overlap=0.826) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (373 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.10781 (75) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (875 voxels, overlap=0.015) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (875 voxels, peak = 76), gca=75.6 gca peak = 0.29892 (64) mri peak = 0.07451 (71) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (645 voxels, overlap=0.072) Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (645 voxels, peak = 70), gca=70.4 gca peak = 0.12541 (104) mri peak = 0.10406 (107) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (68819 voxels, overlap=0.633) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (68819 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.08767 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (70522 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (70522 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.04804 (72) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (38967 voxels, overlap=0.389) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (38967 voxels, peak = 72), gca=72.4 gca peak = 0.13270 (63) mri peak = 0.05073 (72) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (38363 voxels, overlap=0.251) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (38363 voxels, peak = 72), gca=72.4 gca peak = 0.15182 (70) mri peak = 0.10796 (86) Right_Caudate (50): linear fit = 1.20 x + 0.0 (699 voxels, overlap=0.024) Right_Caudate (50): linear fit = 1.20 x + 0.0 (699 voxels, peak = 84), gca=84.0 gca peak = 0.14251 (76) mri peak = 0.11606 (87) Left_Caudate (11): linear fit = 1.08 x + 0.0 (802 voxels, overlap=0.491) Left_Caudate (11): linear fit = 1.08 x + 0.0 (802 voxels, peak = 82), gca=81.7 gca peak = 0.12116 (60) mri peak = 0.05811 (75) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (24402 voxels, overlap=0.003) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (24402 voxels, peak = 74), gca=73.5 gca peak = 0.12723 (61) mri peak = 0.06234 (75) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (29100 voxels, overlap=0.006) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (29100 voxels, peak = 76), gca=76.2 gca peak = 0.22684 (88) mri peak = 0.05632 (96) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8350 voxels, overlap=0.134) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8350 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.06323 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7981 voxels, overlap=0.867) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7981 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.08837 (75) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (334 voxels, overlap=0.124) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (334 voxels, peak = 74), gca=74.4 gca peak = 0.39668 (62) mri peak = 0.10292 (76) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (359 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (359 voxels, peak = 78), gca=77.5 gca peak = 0.10129 (93) mri peak = 0.06474 (100) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5266 voxels, overlap=0.697) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (5266 voxels, peak = 100), gca=100.0 gca peak = 0.12071 (89) mri peak = 0.06431 (97) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4648 voxels, overlap=0.626) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4648 voxels, peak = 96), gca=95.7 gca peak = 0.13716 (82) mri peak = 0.08137 (90) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2721 voxels, overlap=0.592) Left_Putamen (12): linear fit = 1.10 x + 0.0 (2721 voxels, peak = 90), gca=90.2 gca peak = 0.15214 (84) mri peak = 0.09692 (93) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2662 voxels, overlap=0.554) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2662 voxels, peak = 92), gca=92.4 gca peak = 0.08983 (85) mri peak = 0.06895 (88) Brain_Stem (16): linear fit = 1.08 x + 0.0 (10253 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.08 x + 0.0 (10253 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.06181 (100) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (979 voxels, overlap=0.705) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (979 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.06437 (100) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1040 voxels, overlap=0.742) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1040 voxels, peak = 101), gca=101.1 gca peak = 0.21100 (36) mri peak = 1.00000 (43) gca peak = 0.13542 (27) mri peak = 0.15829 (27) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (515 voxels, overlap=0.705) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (515 voxels, peak = 26), gca=26.3 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) not using caudate to estimate GM means estimating mean gm scale to be 1.18 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 1.16 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35438.086 ms 0116: dt=110.976000, rms=0.645 (3.366%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34504.824 ms 0117: dt=221.952000, rms=0.640 (0.788%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36765.578 ms 0118: dt=295.936000, rms=0.633 (1.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37943.344 ms 0119: dt=32.368000, rms=0.631 (0.241%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37115.711 ms 0120: dt=32.368000, rms=0.631 (0.061%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40204.172 ms 0121: dt=32.368000, rms=0.631 (0.027%), neg=0, invalid=766 0122: dt=32.368000, rms=0.631 (0.026%), neg=0, invalid=766 0123: dt=32.368000, rms=0.630 (0.048%), neg=0, invalid=766 0124: dt=32.368000, rms=0.630 (0.089%), neg=0, invalid=766 0125: dt=32.368000, rms=0.629 (0.138%), neg=0, invalid=766 0126: dt=32.368000, rms=0.628 (0.190%), neg=0, invalid=766 0127: dt=32.368000, rms=0.626 (0.214%), neg=0, invalid=766 0128: dt=32.368000, rms=0.625 (0.226%), neg=0, invalid=766 0129: dt=32.368000, rms=0.624 (0.207%), neg=0, invalid=766 0130: dt=32.368000, rms=0.622 (0.186%), neg=0, invalid=766 0131: dt=32.368000, rms=0.621 (0.160%), neg=0, invalid=766 0132: dt=32.368000, rms=0.621 (0.139%), neg=0, invalid=766 0133: dt=32.368000, rms=0.620 (0.141%), neg=0, invalid=766 0134: dt=32.368000, rms=0.619 (0.154%), neg=0, invalid=766 0135: dt=32.368000, rms=0.618 (0.155%), neg=0, invalid=766 0136: dt=32.368000, rms=0.617 (0.136%), neg=0, invalid=766 0137: dt=32.368000, rms=0.616 (0.119%), neg=0, invalid=766 0138: dt=32.368000, rms=0.616 (0.106%), neg=0, invalid=766 0139: dt=32.368000, rms=0.615 (0.093%), neg=0, invalid=766 0140: dt=32.368000, rms=0.614 (0.084%), neg=0, invalid=766 0141: dt=32.368000, rms=0.614 (0.086%), neg=0, invalid=766 0142: dt=32.368000, rms=0.613 (0.093%), neg=0, invalid=766 0143: dt=32.368000, rms=0.613 (0.092%), neg=0, invalid=766 0144: dt=32.368000, rms=0.612 (0.083%), neg=0, invalid=766 0145: dt=32.368000, rms=0.612 (0.070%), neg=0, invalid=766 0146: dt=32.368000, rms=0.611 (0.059%), neg=0, invalid=766 0147: dt=32.368000, rms=0.611 (0.063%), neg=0, invalid=766 0148: dt=32.368000, rms=0.611 (0.056%), neg=0, invalid=766 0149: dt=32.368000, rms=0.610 (0.059%), neg=0, invalid=766 0150: dt=32.368000, rms=0.610 (0.061%), neg=0, invalid=766 0151: dt=32.368000, rms=0.610 (0.062%), neg=0, invalid=766 0152: dt=32.368000, rms=0.609 (0.061%), neg=0, invalid=766 0153: dt=32.368000, rms=0.609 (0.053%), neg=0, invalid=766 0154: dt=32.368000, rms=0.609 (0.047%), neg=0, invalid=766 0155: dt=32.368000, rms=0.608 (0.044%), neg=0, invalid=766 0156: dt=32.368000, rms=0.608 (0.044%), neg=0, invalid=766 0157: dt=32.368000, rms=0.608 (0.048%), neg=0, invalid=766 0158: dt=32.368000, rms=0.608 (0.054%), neg=0, invalid=766 0159: dt=32.368000, rms=0.607 (0.048%), neg=0, invalid=766 0160: dt=32.368000, rms=0.607 (0.049%), neg=0, invalid=766 0161: dt=32.368000, rms=0.607 (0.044%), neg=0, invalid=766 0162: dt=32.368000, rms=0.606 (0.040%), neg=0, invalid=766 0163: dt=32.368000, rms=0.606 (0.038%), neg=0, invalid=766 0164: dt=32.368000, rms=0.606 (0.041%), neg=0, invalid=766 0165: dt=32.368000, rms=0.606 (0.044%), neg=0, invalid=766 0166: dt=32.368000, rms=0.605 (0.047%), neg=0, invalid=766 0167: dt=32.368000, rms=0.605 (0.039%), neg=0, invalid=766 0168: dt=32.368000, rms=0.605 (0.036%), neg=0, invalid=766 0169: dt=32.368000, rms=0.605 (0.036%), neg=0, invalid=766 0170: dt=32.368000, rms=0.604 (0.038%), neg=0, invalid=766 0171: dt=32.368000, rms=0.604 (0.038%), neg=0, invalid=766 0172: dt=32.368000, rms=0.604 (0.033%), neg=0, invalid=766 0173: dt=32.368000, rms=0.604 (0.027%), neg=0, invalid=766 0174: dt=32.368000, rms=0.604 (0.027%), neg=0, invalid=766 0175: dt=32.368000, rms=0.604 (0.028%), neg=0, invalid=766 0176: dt=32.368000, rms=0.603 (0.030%), neg=0, invalid=766 0177: dt=32.368000, rms=0.603 (0.027%), neg=0, invalid=766 0178: dt=32.368000, rms=0.603 (0.027%), neg=0, invalid=766 0179: dt=32.368000, rms=0.603 (0.030%), neg=0, invalid=766 0180: dt=32.368000, rms=0.603 (0.026%), neg=0, invalid=766 0181: dt=32.368000, rms=0.603 (0.028%), neg=0, invalid=766 0182: dt=32.368000, rms=0.602 (0.029%), neg=0, invalid=766 0183: dt=32.368000, rms=0.602 (0.030%), neg=0, invalid=766 0184: dt=32.368000, rms=0.602 (0.029%), neg=0, invalid=766 0185: dt=32.368000, rms=0.602 (0.021%), neg=0, invalid=766 0186: dt=32.368000, rms=0.602 (0.022%), neg=0, invalid=766 0187: dt=32.368000, rms=0.602 (0.025%), neg=0, invalid=766 0188: dt=32.368000, rms=0.601 (0.027%), neg=0, invalid=766 0189: dt=32.368000, rms=0.601 (0.027%), neg=0, invalid=766 0190: dt=32.368000, rms=0.601 (0.021%), neg=0, invalid=766 0191: dt=32.368000, rms=0.601 (0.020%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44351.352 ms 0192: dt=517.888000, rms=0.601 (0.039%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44535.574 ms 0193: dt=73.984000, rms=0.601 (0.006%), neg=0, invalid=766 0194: dt=73.984000, rms=0.601 (0.006%), neg=0, invalid=766 0195: dt=73.984000, rms=0.601 (0.010%), neg=0, invalid=766 0196: dt=73.984000, rms=0.601 (0.013%), neg=0, invalid=766 0197: dt=73.984000, rms=0.601 (0.012%), neg=0, invalid=766 0198: dt=73.984000, rms=0.600 (0.013%), neg=0, invalid=766 0199: dt=73.984000, rms=0.600 (0.020%), neg=0, invalid=766 0200: dt=73.984000, rms=0.600 (0.040%), neg=0, invalid=766 0201: dt=73.984000, rms=0.600 (0.033%), neg=0, invalid=766 0202: dt=73.984000, rms=0.600 (0.019%), neg=0, invalid=766 0203: dt=73.984000, rms=0.600 (0.024%), neg=0, invalid=766 0204: dt=73.984000, rms=0.599 (0.034%), neg=0, invalid=766 0205: dt=73.984000, rms=0.599 (0.039%), neg=0, invalid=766 0206: dt=73.984000, rms=0.599 (0.033%), neg=0, invalid=766 0207: dt=73.984000, rms=0.599 (0.029%), neg=0, invalid=766 0208: dt=73.984000, rms=0.599 (0.037%), neg=0, invalid=766 0209: dt=73.984000, rms=0.598 (0.038%), neg=0, invalid=766 0210: dt=73.984000, rms=0.598 (0.027%), neg=0, invalid=766 0211: dt=73.984000, rms=0.598 (0.026%), neg=0, invalid=766 0212: dt=73.984000, rms=0.598 (0.038%), neg=0, invalid=766 0213: dt=73.984000, rms=0.598 (0.043%), neg=0, invalid=766 0214: dt=73.984000, rms=0.597 (0.041%), neg=0, invalid=766 0215: dt=73.984000, rms=0.597 (0.032%), neg=0, invalid=766 0216: dt=73.984000, rms=0.597 (0.030%), neg=0, invalid=766 0217: dt=73.984000, rms=0.597 (0.034%), neg=0, invalid=766 0218: dt=73.984000, rms=0.597 (0.031%), neg=0, invalid=766 0219: dt=73.984000, rms=0.596 (0.042%), neg=0, invalid=766 0220: dt=73.984000, rms=0.596 (0.027%), neg=0, invalid=766 0221: dt=73.984000, rms=0.596 (0.024%), neg=0, invalid=766 0222: dt=73.984000, rms=0.596 (0.036%), neg=0, invalid=766 0223: dt=73.984000, rms=0.596 (0.037%), neg=0, invalid=766 0224: dt=73.984000, rms=0.595 (0.030%), neg=0, invalid=766 0225: dt=73.984000, rms=0.595 (0.017%), neg=0, invalid=766 0226: dt=73.984000, rms=0.595 (0.026%), neg=0, invalid=766 0227: dt=73.984000, rms=0.595 (0.032%), neg=0, invalid=766 0228: dt=73.984000, rms=0.595 (0.037%), neg=0, invalid=766 0229: dt=73.984000, rms=0.595 (0.035%), neg=0, invalid=766 0230: dt=73.984000, rms=0.594 (0.035%), neg=0, invalid=766 0231: dt=73.984000, rms=0.594 (0.020%), neg=0, invalid=766 0232: dt=73.984000, rms=0.594 (0.027%), neg=0, invalid=766 0233: dt=73.984000, rms=0.594 (0.028%), neg=0, invalid=766 0234: dt=73.984000, rms=0.594 (0.026%), neg=0, invalid=766 0235: dt=73.984000, rms=0.594 (0.019%), neg=0, invalid=766 0236: dt=73.984000, rms=0.593 (0.027%), neg=0, invalid=766 0237: dt=73.984000, rms=0.593 (0.028%), neg=0, invalid=766 0238: dt=73.984000, rms=0.593 (0.031%), neg=0, invalid=766 0239: dt=73.984000, rms=0.593 (0.025%), neg=0, invalid=766 0240: dt=73.984000, rms=0.593 (0.021%), neg=0, invalid=766 0241: dt=73.984000, rms=0.593 (0.014%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49945.605 ms 0242: dt=517.888000, rms=0.593 (0.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65228.754 ms 0243: dt=0.004335, rms=0.593 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.593, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48200.809 ms 0244: dt=92.480000, rms=0.592 (0.044%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48339.938 ms 0245: dt=129.472000, rms=0.592 (0.054%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47683.906 ms 0246: dt=110.976000, rms=0.592 (0.015%), neg=0, invalid=766 0247: dt=110.976000, rms=0.592 (0.026%), neg=0, invalid=766 0248: dt=110.976000, rms=0.591 (0.032%), neg=0, invalid=766 0249: dt=110.976000, rms=0.591 (0.033%), neg=0, invalid=766 0250: dt=110.976000, rms=0.591 (0.035%), neg=0, invalid=766 0251: dt=110.976000, rms=0.591 (0.036%), neg=0, invalid=766 0252: dt=110.976000, rms=0.591 (0.025%), neg=0, invalid=766 0253: dt=110.976000, rms=0.591 (0.012%), neg=0, invalid=766 0254: dt=110.976000, rms=0.591 (0.016%), neg=0, invalid=766 0255: dt=110.976000, rms=0.590 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49366.223 ms 0256: dt=517.888000, rms=0.590 (0.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48449.883 ms 0257: dt=32.368000, rms=0.590 (0.006%), neg=0, invalid=766 0258: dt=32.368000, rms=0.590 (0.002%), neg=0, invalid=766 0259: dt=32.368000, rms=0.590 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.592, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45790.816 ms 0260: dt=62.208000, rms=0.590 (0.374%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44793.848 ms 0261: dt=145.152000, rms=0.585 (0.852%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41853.281 ms 0262: dt=25.920000, rms=0.583 (0.336%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45092.383 ms 0263: dt=82.944000, rms=0.581 (0.286%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41519.152 ms 0264: dt=36.288000, rms=0.580 (0.302%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43713.758 ms 0265: dt=36.288000, rms=0.578 (0.230%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43775.215 ms 0266: dt=103.680000, rms=0.577 (0.286%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41585.234 ms 0267: dt=25.920000, rms=0.575 (0.270%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44850.316 ms 0268: dt=103.680000, rms=0.573 (0.272%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42265.516 ms 0269: dt=31.104000, rms=0.572 (0.241%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44798.812 ms 0270: dt=36.288000, rms=0.571 (0.140%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44132.152 ms 0271: dt=103.680000, rms=0.570 (0.241%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41536.801 ms 0272: dt=20.736000, rms=0.569 (0.161%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43564.520 ms 0273: dt=580.608000, rms=0.563 (1.114%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41947.316 ms 0274: dt=25.920000, rms=0.560 (0.414%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42195.219 ms 0275: dt=31.104000, rms=0.560 (0.095%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46168.492 ms 0276: dt=145.152000, rms=0.558 (0.234%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43478.531 ms 0277: dt=20.736000, rms=0.558 (0.059%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47852.160 ms 0278: dt=580.608000, rms=0.555 (0.602%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42271.016 ms 0279: dt=36.288000, rms=0.553 (0.297%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41868.805 ms 0280: dt=25.920000, rms=0.553 (0.066%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46680.023 ms 0281: dt=414.720000, rms=0.551 (0.317%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41617.246 ms 0282: dt=25.920000, rms=0.550 (0.116%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43804.379 ms 0283: dt=103.680000, rms=0.549 (0.185%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44813.406 ms 0284: dt=20.736000, rms=0.549 (0.027%), neg=0, invalid=766 0285: dt=20.736000, rms=0.549 (0.015%), neg=0, invalid=766 0286: dt=20.736000, rms=0.549 (0.025%), neg=0, invalid=766 0287: dt=20.736000, rms=0.549 (0.044%), neg=0, invalid=766 0288: dt=20.736000, rms=0.548 (0.065%), neg=0, invalid=766 0289: dt=20.736000, rms=0.548 (0.078%), neg=0, invalid=766 0290: dt=20.736000, rms=0.547 (0.090%), neg=0, invalid=766 0291: dt=20.736000, rms=0.547 (0.100%), neg=0, invalid=766 0292: dt=20.736000, rms=0.546 (0.104%), neg=0, invalid=766 0293: dt=20.736000, rms=0.546 (0.092%), neg=0, invalid=766 0294: dt=20.736000, rms=0.545 (0.092%), neg=0, invalid=766 0295: dt=20.736000, rms=0.545 (0.099%), neg=0, invalid=766 0296: dt=20.736000, rms=0.544 (0.112%), neg=0, invalid=766 0297: dt=20.736000, rms=0.544 (0.113%), neg=0, invalid=766 0298: dt=20.736000, rms=0.543 (0.102%), neg=0, invalid=766 0299: dt=20.736000, rms=0.543 (0.094%), neg=0, invalid=766 0300: dt=20.736000, rms=0.542 (0.089%), neg=0, invalid=766 0301: dt=20.736000, rms=0.541 (0.104%), neg=0, invalid=766 0302: dt=20.736000, rms=0.541 (0.111%), neg=0, invalid=766 0303: dt=20.736000, rms=0.540 (0.105%), neg=0, invalid=766 0304: dt=20.736000, rms=0.540 (0.095%), neg=0, invalid=766 0305: dt=20.736000, rms=0.539 (0.087%), neg=0, invalid=766 0306: dt=20.736000, rms=0.539 (0.082%), neg=0, invalid=766 0307: dt=20.736000, rms=0.538 (0.089%), neg=0, invalid=766 0308: dt=20.736000, rms=0.538 (0.091%), neg=0, invalid=766 0309: dt=20.736000, rms=0.537 (0.085%), neg=0, invalid=766 0310: dt=20.736000, rms=0.537 (0.074%), neg=0, invalid=766 0311: dt=20.736000, rms=0.537 (0.067%), neg=0, invalid=766 0312: dt=20.736000, rms=0.536 (0.062%), neg=0, invalid=766 0313: dt=20.736000, rms=0.536 (0.071%), neg=0, invalid=766 0314: dt=20.736000, rms=0.536 (0.075%), neg=0, invalid=766 0315: dt=20.736000, rms=0.535 (0.072%), neg=0, invalid=766 0316: dt=20.736000, rms=0.535 (0.067%), neg=0, invalid=766 0317: dt=20.736000, rms=0.535 (0.057%), neg=0, invalid=766 0318: dt=20.736000, rms=0.534 (0.056%), neg=0, invalid=766 0319: dt=20.736000, rms=0.534 (0.059%), neg=0, invalid=766 0320: dt=20.736000, rms=0.534 (0.059%), neg=0, invalid=766 0321: dt=20.736000, rms=0.533 (0.059%), neg=0, invalid=766 0322: dt=20.736000, rms=0.533 (0.052%), neg=0, invalid=766 0323: dt=20.736000, rms=0.533 (0.047%), neg=0, invalid=766 0324: dt=20.736000, rms=0.532 (0.050%), neg=0, invalid=766 0325: dt=20.736000, rms=0.532 (0.055%), neg=0, invalid=766 0326: dt=20.736000, rms=0.532 (0.053%), neg=0, invalid=766 0327: dt=20.736000, rms=0.532 (0.044%), neg=0, invalid=766 0328: dt=20.736000, rms=0.531 (0.041%), neg=0, invalid=766 0329: dt=20.736000, rms=0.531 (0.038%), neg=0, invalid=766 0330: dt=20.736000, rms=0.531 (0.045%), neg=0, invalid=766 0331: dt=20.736000, rms=0.531 (0.049%), neg=0, invalid=766 0332: dt=20.736000, rms=0.531 (0.044%), neg=0, invalid=766 0333: dt=20.736000, rms=0.530 (0.041%), neg=0, invalid=766 0334: dt=20.736000, rms=0.530 (0.033%), neg=0, invalid=766 0335: dt=20.736000, rms=0.530 (0.031%), neg=0, invalid=766 0336: dt=20.736000, rms=0.530 (0.035%), neg=0, invalid=766 0337: dt=20.736000, rms=0.530 (0.040%), neg=0, invalid=766 0338: dt=20.736000, rms=0.529 (0.034%), neg=0, invalid=766 0339: dt=20.736000, rms=0.529 (0.034%), neg=0, invalid=766 0340: dt=20.736000, rms=0.529 (0.036%), neg=0, invalid=766 0341: dt=20.736000, rms=0.529 (0.033%), neg=0, invalid=766 0342: dt=20.736000, rms=0.529 (0.031%), neg=0, invalid=766 0343: dt=20.736000, rms=0.529 (0.035%), neg=0, invalid=766 0344: dt=20.736000, rms=0.528 (0.032%), neg=0, invalid=766 0345: dt=20.736000, rms=0.528 (0.028%), neg=0, invalid=766 0346: dt=20.736000, rms=0.528 (0.030%), neg=0, invalid=766 0347: dt=20.736000, rms=0.528 (0.033%), neg=0, invalid=766 0348: dt=20.736000, rms=0.528 (0.032%), neg=0, invalid=766 0349: dt=20.736000, rms=0.528 (0.029%), neg=0, invalid=766 0350: dt=20.736000, rms=0.527 (0.026%), neg=0, invalid=766 0351: dt=20.736000, rms=0.527 (0.026%), neg=0, invalid=766 0352: dt=20.736000, rms=0.527 (0.026%), neg=0, invalid=766 0353: dt=20.736000, rms=0.527 (0.025%), neg=0, invalid=766 0354: dt=20.736000, rms=0.527 (0.023%), neg=0, invalid=766 0355: dt=20.736000, rms=0.527 (0.026%), neg=0, invalid=766 0356: dt=20.736000, rms=0.527 (0.024%), neg=0, invalid=766 0357: dt=20.736000, rms=0.526 (0.026%), neg=0, invalid=766 0358: dt=20.736000, rms=0.526 (0.026%), neg=0, invalid=766 0359: dt=20.736000, rms=0.526 (0.025%), neg=0, invalid=766 0360: dt=20.736000, rms=0.526 (0.029%), neg=0, invalid=766 0361: dt=20.736000, rms=0.526 (0.027%), neg=0, invalid=766 0362: dt=20.736000, rms=0.526 (0.025%), neg=0, invalid=766 0363: dt=20.736000, rms=0.526 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50023.914 ms 0364: dt=331.776000, rms=0.526 (0.019%), neg=0, invalid=766 0365: dt=331.776000, rms=0.526 (-1.333%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.526, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47550.523 ms 0366: dt=36.288000, rms=0.525 (0.200%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46682.492 ms 0367: dt=145.152000, rms=0.523 (0.227%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47805.148 ms 0368: dt=25.920000, rms=0.523 (0.021%), neg=0, invalid=766 0369: dt=25.920000, rms=0.523 (0.029%), neg=0, invalid=766 0370: dt=25.920000, rms=0.523 (0.029%), neg=0, invalid=766 0371: dt=25.920000, rms=0.523 (0.040%), neg=0, invalid=766 0372: dt=25.920000, rms=0.522 (0.042%), neg=0, invalid=766 0373: dt=25.920000, rms=0.522 (0.043%), neg=0, invalid=766 0374: dt=25.920000, rms=0.522 (0.041%), neg=0, invalid=766 0375: dt=25.920000, rms=0.522 (0.045%), neg=0, invalid=766 0376: dt=25.920000, rms=0.522 (0.043%), neg=0, invalid=766 0377: dt=25.920000, rms=0.521 (0.039%), neg=0, invalid=766 0378: dt=25.920000, rms=0.521 (0.036%), neg=0, invalid=766 0379: dt=25.920000, rms=0.521 (0.035%), neg=0, invalid=766 0380: dt=25.920000, rms=0.521 (0.036%), neg=0, invalid=766 0381: dt=25.920000, rms=0.521 (0.037%), neg=0, invalid=766 0382: dt=25.920000, rms=0.520 (0.040%), neg=0, invalid=766 0383: dt=25.920000, rms=0.520 (0.031%), neg=0, invalid=766 0384: dt=25.920000, rms=0.520 (0.038%), neg=0, invalid=766 0385: dt=25.920000, rms=0.520 (0.039%), neg=0, invalid=766 0386: dt=25.920000, rms=0.520 (0.045%), neg=0, invalid=766 0387: dt=25.920000, rms=0.519 (0.039%), neg=0, invalid=766 0388: dt=25.920000, rms=0.519 (0.032%), neg=0, invalid=766 0389: dt=25.920000, rms=0.519 (0.034%), neg=0, invalid=766 0390: dt=25.920000, rms=0.519 (0.044%), neg=0, invalid=766 0391: dt=25.920000, rms=0.519 (0.043%), neg=0, invalid=766 0392: dt=25.920000, rms=0.518 (0.034%), neg=0, invalid=766 0393: dt=25.920000, rms=0.518 (0.031%), neg=0, invalid=766 0394: dt=25.920000, rms=0.518 (0.029%), neg=0, invalid=766 0395: dt=25.920000, rms=0.518 (0.034%), neg=0, invalid=766 0396: dt=25.920000, rms=0.518 (0.036%), neg=0, invalid=766 0397: dt=25.920000, rms=0.518 (0.024%), neg=0, invalid=766 0398: dt=25.920000, rms=0.518 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48742.195 ms 0399: dt=124.416000, rms=0.517 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45625.965 ms 0400: dt=9.072000, rms=0.517 (0.003%), neg=0, invalid=766 0401: dt=9.072000, rms=0.517 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.530, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42737.090 ms 0402: dt=11.200000, rms=0.529 (0.158%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45906.363 ms 0403: dt=44.800000, rms=0.527 (0.402%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42408.016 ms 0404: dt=38.400000, rms=0.524 (0.498%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43105.637 ms 0405: dt=7.886040, rms=0.522 (0.334%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43071.973 ms 0406: dt=19.200000, rms=0.521 (0.205%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43008.258 ms 0407: dt=19.200000, rms=0.520 (0.258%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43386.246 ms 0408: dt=7.080460, rms=0.519 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43670.465 ms 0409: dt=32.000000, rms=0.517 (0.388%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43248.477 ms 0410: dt=32.000000, rms=0.517 (0.139%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43294.105 ms 0411: dt=9.492537, rms=0.516 (0.206%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43825.410 ms 0412: dt=11.200000, rms=0.515 (0.119%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43325.727 ms 0413: dt=44.800000, rms=0.514 (0.285%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44890.664 ms 0414: dt=5.624242, rms=0.513 (0.098%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47902.742 ms 0415: dt=128.000000, rms=0.511 (0.432%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41446.602 ms 0416: dt=2.800000, rms=0.510 (0.114%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43875.500 ms 0417: dt=9.600000, rms=0.509 (0.325%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43055.996 ms 0418: dt=11.200000, rms=0.508 (0.159%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43676.594 ms 0419: dt=44.800000, rms=0.507 (0.170%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43995.668 ms 0420: dt=6.720000, rms=0.507 (0.063%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43288.566 ms 0421: dt=38.400000, rms=0.506 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44595.699 ms 0422: dt=25.600000, rms=0.505 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43736.816 ms 0423: dt=11.200000, rms=0.505 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45062.145 ms 0424: dt=38.400000, rms=0.504 (0.110%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41658.062 ms 0425: dt=8.000000, rms=0.504 (0.050%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43984.340 ms 0426: dt=44.800000, rms=0.503 (0.170%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41191.352 ms 0427: dt=9.600000, rms=0.503 (0.038%), neg=0, invalid=766 0428: dt=9.600000, rms=0.503 (0.055%), neg=0, invalid=766 0429: dt=9.600000, rms=0.502 (0.060%), neg=0, invalid=766 0430: dt=9.600000, rms=0.502 (0.073%), neg=0, invalid=766 0431: dt=9.600000, rms=0.502 (0.098%), neg=0, invalid=766 0432: dt=9.600000, rms=0.501 (0.119%), neg=0, invalid=766 0433: dt=9.600000, rms=0.500 (0.128%), neg=0, invalid=766 0434: dt=9.600000, rms=0.500 (0.132%), neg=0, invalid=766 0435: dt=9.600000, rms=0.499 (0.133%), neg=0, invalid=766 0436: dt=9.600000, rms=0.498 (0.141%), neg=0, invalid=766 0437: dt=9.600000, rms=0.498 (0.140%), neg=0, invalid=766 0438: dt=9.600000, rms=0.497 (0.136%), neg=0, invalid=766 0439: dt=9.600000, rms=0.496 (0.134%), neg=0, invalid=766 0440: dt=9.600000, rms=0.496 (0.123%), neg=0, invalid=766 0441: dt=9.600000, rms=0.495 (0.124%), neg=0, invalid=766 0442: dt=9.600000, rms=0.494 (0.123%), neg=0, invalid=766 0443: dt=9.600000, rms=0.494 (0.110%), neg=0, invalid=766 0444: dt=9.600000, rms=0.493 (0.099%), neg=0, invalid=766 0445: dt=9.600000, rms=0.493 (0.098%), neg=0, invalid=766 0446: dt=9.600000, rms=0.492 (0.096%), neg=0, invalid=766 0447: dt=9.600000, rms=0.492 (0.091%), neg=0, invalid=766 0448: dt=9.600000, rms=0.492 (0.080%), neg=0, invalid=766 0449: dt=9.600000, rms=0.491 (0.076%), neg=0, invalid=766 0450: dt=9.600000, rms=0.491 (0.073%), neg=0, invalid=766 0451: dt=9.600000, rms=0.490 (0.075%), neg=0, invalid=766 0452: dt=9.600000, rms=0.490 (0.066%), neg=0, invalid=766 0453: dt=9.600000, rms=0.490 (0.064%), neg=0, invalid=766 0454: dt=9.600000, rms=0.490 (0.057%), neg=0, invalid=766 0455: dt=9.600000, rms=0.489 (0.058%), neg=0, invalid=766 0456: dt=9.600000, rms=0.489 (0.048%), neg=0, invalid=766 0457: dt=9.600000, rms=0.489 (0.041%), neg=0, invalid=766 0458: dt=9.600000, rms=0.489 (0.040%), neg=0, invalid=766 0459: dt=9.600000, rms=0.488 (0.037%), neg=0, invalid=766 0460: dt=9.600000, rms=0.488 (0.038%), neg=0, invalid=766 0461: dt=9.600000, rms=0.488 (0.034%), neg=0, invalid=766 0462: dt=9.600000, rms=0.488 (0.033%), neg=0, invalid=766 0463: dt=9.600000, rms=0.488 (0.034%), neg=0, invalid=766 0464: dt=9.600000, rms=0.488 (0.031%), neg=0, invalid=766 0465: dt=9.600000, rms=0.487 (0.032%), neg=0, invalid=766 0466: dt=9.600000, rms=0.487 (0.034%), neg=0, invalid=766 0467: dt=9.600000, rms=0.487 (0.028%), neg=0, invalid=766 0468: dt=9.600000, rms=0.487 (0.029%), neg=0, invalid=766 0469: dt=9.600000, rms=0.487 (0.025%), neg=0, invalid=766 0470: dt=9.600000, rms=0.487 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46626.379 ms 0471: dt=44.800000, rms=0.487 (0.014%), neg=0, invalid=766 0472: dt=44.800000, rms=0.487 (-0.109%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.487, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43847.082 ms 0473: dt=25.600000, rms=0.486 (0.230%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41194.695 ms 0474: dt=11.200000, rms=0.485 (0.091%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43840.777 ms 0475: dt=8.000000, rms=0.485 (0.005%), neg=0, invalid=766 0476: dt=8.000000, rms=0.485 (0.021%), neg=0, invalid=766 0477: dt=8.000000, rms=0.485 (0.020%), neg=0, invalid=766 0478: dt=8.000000, rms=0.485 (0.011%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43563.305 ms 0479: dt=9.600000, rms=0.485 (0.004%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.517, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41561.246 ms 0480: dt=0.000000, rms=0.517 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43644.410 ms 0481: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.578, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42046.844 ms 0482: dt=2.237458, rms=0.567 (2.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42083.121 ms 0483: dt=1.792000, rms=0.565 (0.307%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42678.715 ms 0484: dt=1.024000, rms=0.565 (0.041%), neg=0, invalid=766 0485: dt=1.024000, rms=0.565 (-0.008%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.565, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42095.332 ms 0486: dt=3.069767, rms=0.561 (0.565%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43275.656 ms 0487: dt=1.280000, rms=0.561 (0.035%), neg=0, invalid=766 0488: dt=1.280000, rms=0.561 (0.031%), neg=0, invalid=766 0489: dt=1.280000, rms=0.561 (0.007%), neg=0, invalid=766 0490: dt=1.280000, rms=0.561 (-0.134%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42547.895 ms 0491: dt=0.384000, rms=0.561 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43085.516 ms 0492: dt=1.536000, rms=0.561 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44467.652 ms 0493: dt=1.536000, rms=0.561 (0.005%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.534, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39711.148 ms 0494: dt=0.146354, rms=0.530 (0.840%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40722.012 ms 0495: dt=0.127033, rms=0.527 (0.544%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39574.457 ms 0496: dt=0.096000, rms=0.525 (0.328%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39403.934 ms 0497: dt=0.112000, rms=0.523 (0.327%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35468.898 ms 0498: dt=0.028000, rms=0.523 (0.069%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38167.793 ms 0499: dt=0.112000, rms=0.522 (0.266%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40528.734 ms 0500: dt=0.112000, rms=0.520 (0.228%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42734.809 ms 0501: dt=0.384000, rms=0.517 (0.668%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37300.781 ms 0502: dt=0.028000, rms=0.517 (0.031%), neg=0, invalid=766 0503: dt=0.028000, rms=0.517 (0.028%), neg=0, invalid=766 0504: dt=0.028000, rms=0.516 (0.051%), neg=0, invalid=766 0505: dt=0.028000, rms=0.516 (0.072%), neg=0, invalid=766 0506: dt=0.028000, rms=0.515 (0.090%), neg=0, invalid=766 0507: dt=0.028000, rms=0.515 (0.103%), neg=0, invalid=766 0508: dt=0.028000, rms=0.514 (0.113%), neg=0, invalid=766 0509: dt=0.028000, rms=0.514 (0.118%), neg=0, invalid=766 0510: dt=0.028000, rms=0.513 (0.123%), neg=0, invalid=766 0511: dt=0.028000, rms=0.513 (0.013%), neg=0, invalid=766 0512: dt=0.028000, rms=0.513 (0.029%), neg=0, invalid=766 0513: dt=0.028000, rms=0.513 (0.038%), neg=0, invalid=766 0514: dt=0.028000, rms=0.512 (0.048%), neg=0, invalid=766 0515: dt=0.028000, rms=0.512 (0.055%), neg=0, invalid=766 0516: dt=0.028000, rms=0.512 (0.013%), neg=0, invalid=766 0517: dt=0.028000, rms=0.512 (0.022%), neg=0, invalid=766 0518: dt=0.028000, rms=0.512 (0.034%), neg=0, invalid=766 0519: dt=0.028000, rms=0.512 (0.041%), neg=0, invalid=766 0520: dt=0.028000, rms=0.511 (0.045%), neg=0, invalid=766 0521: dt=0.028000, rms=0.511 (0.053%), neg=0, invalid=766 0522: dt=0.028000, rms=0.511 (0.057%), neg=0, invalid=766 0523: dt=0.028000, rms=0.511 (0.059%), neg=0, invalid=766 0524: dt=0.028000, rms=0.510 (0.063%), neg=0, invalid=766 0525: dt=0.028000, rms=0.510 (0.063%), neg=0, invalid=766 0526: dt=0.028000, rms=0.510 (0.064%), neg=0, invalid=766 0527: dt=0.028000, rms=0.510 (0.005%), neg=0, invalid=766 0528: dt=0.028000, rms=0.509 (0.014%), neg=0, invalid=766 0529: dt=0.028000, rms=0.509 (0.019%), neg=0, invalid=766 0530: dt=0.028000, rms=0.509 (0.020%), neg=0, invalid=766 0531: dt=0.028000, rms=0.509 (0.026%), neg=0, invalid=766 0532: dt=0.028000, rms=0.509 (0.027%), neg=0, invalid=766 0533: dt=0.028000, rms=0.509 (0.032%), neg=0, invalid=766 0534: dt=0.028000, rms=0.509 (0.032%), neg=0, invalid=766 0535: dt=0.028000, rms=0.508 (0.036%), neg=0, invalid=766 0536: dt=0.028000, rms=0.508 (0.033%), neg=0, invalid=766 0537: dt=0.028000, rms=0.508 (0.039%), neg=0, invalid=766 0538: dt=0.028000, rms=0.508 (0.036%), neg=0, invalid=766 0539: dt=0.028000, rms=0.508 (0.037%), neg=0, invalid=766 0540: dt=0.028000, rms=0.508 (0.037%), neg=0, invalid=766 0541: dt=0.028000, rms=0.507 (0.037%), neg=0, invalid=766 0542: dt=0.028000, rms=0.507 (0.034%), neg=0, invalid=766 0543: dt=0.028000, rms=0.507 (0.032%), neg=0, invalid=766 0544: dt=0.028000, rms=0.507 (0.033%), neg=0, invalid=766 0545: dt=0.028000, rms=0.507 (0.032%), neg=0, invalid=766 0546: dt=0.028000, rms=0.507 (0.030%), neg=0, invalid=766 0547: dt=0.028000, rms=0.506 (0.031%), neg=0, invalid=766 0548: dt=0.028000, rms=0.506 (0.027%), neg=0, invalid=766 0549: dt=0.028000, rms=0.506 (0.026%), neg=0, invalid=766 0550: dt=0.028000, rms=0.506 (0.026%), neg=0, invalid=766 0551: dt=0.028000, rms=0.506 (0.024%), neg=0, invalid=766 0552: dt=0.028000, rms=0.506 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39388.219 ms 0553: dt=0.112000, rms=0.506 (0.005%), neg=0, invalid=766 0554: dt=0.112000, rms=0.506 (0.006%), neg=0, invalid=766 0555: dt=0.112000, rms=0.506 (0.008%), neg=0, invalid=766 0556: dt=0.112000, rms=0.506 (0.003%), neg=0, invalid=766 0557: dt=0.112000, rms=0.506 (0.010%), neg=0, invalid=766 0558: dt=0.028000, rms=0.506 (0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42255.047 ms 0559: dt=0.384000, rms=0.501 (0.813%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42682.000 ms 0560: dt=0.448000, rms=0.501 (0.171%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37311.273 ms 0561: dt=0.028000, rms=0.501 (0.003%), neg=0, invalid=766 0562: dt=0.028000, rms=0.501 (0.002%), neg=0, invalid=766 0563: dt=0.028000, rms=0.501 (0.004%), neg=0, invalid=766 0564: dt=0.028000, rms=0.501 (0.004%), neg=0, invalid=766 0565: dt=0.028000, rms=0.501 (0.005%), neg=0, invalid=766 0566: dt=0.028000, rms=0.500 (0.006%), neg=0, invalid=766 0567: dt=0.028000, rms=0.500 (0.009%), neg=0, invalid=766 0568: dt=0.028000, rms=0.500 (-0.001%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.498, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49372.496 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0569: dt=44.800000, rms=0.484 (2.815%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50136.102 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0570: dt=32.000000, rms=0.476 (1.646%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51289.816 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0571: dt=10.245614, rms=0.474 (0.292%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47680.609 ms iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0572: dt=19.200000, rms=0.473 (0.267%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48176.590 ms iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0573: dt=11.200000, rms=0.472 (0.187%), neg=0, invalid=766 0574: dt=11.200000, rms=0.471 (0.172%), neg=0, invalid=766 0575: dt=11.200000, rms=0.470 (0.318%), neg=0, invalid=766 0576: dt=11.200000, rms=0.468 (0.366%), neg=0, invalid=766 0577: dt=11.200000, rms=0.466 (0.375%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 16 iterations, nbhd size=2, neg = 0 0578: dt=11.200000, rms=0.464 (0.402%), neg=0, invalid=766 0579: dt=11.200000, rms=0.463 (0.326%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0580: dt=11.200000, rms=0.462 (0.280%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0581: dt=11.200000, rms=0.460 (0.243%), neg=0, invalid=766 0582: dt=11.200000, rms=0.459 (0.238%), neg=0, invalid=766 0583: dt=11.200000, rms=0.458 (0.202%), neg=0, invalid=766 0584: dt=11.200000, rms=0.457 (0.222%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0585: dt=11.200000, rms=0.457 (0.163%), neg=0, invalid=766 0586: dt=11.200000, rms=0.456 (0.157%), neg=0, invalid=766 0587: dt=11.200000, rms=0.455 (0.133%), neg=0, invalid=766 0588: dt=11.200000, rms=0.455 (0.126%), neg=0, invalid=766 0589: dt=11.200000, rms=0.454 (0.100%), neg=0, invalid=766 0590: dt=11.200000, rms=0.454 (0.126%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0591: dt=11.200000, rms=0.453 (0.103%), neg=0, invalid=766 0592: dt=11.200000, rms=0.453 (0.093%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50836.930 ms 0593: dt=11.200000, rms=0.453 (0.024%), neg=0, invalid=766 0594: dt=11.200000, rms=0.453 (0.024%), neg=0, invalid=766 0595: dt=11.200000, rms=0.452 (0.035%), neg=0, invalid=766 0596: dt=11.200000, rms=0.452 (0.034%), neg=0, invalid=766 0597: dt=11.200000, rms=0.452 (0.030%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.452, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47588.395 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0598: dt=32.000000, rms=0.449 (0.600%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50368.340 ms 0599: dt=9.600000, rms=0.449 (0.151%), neg=0, invalid=766 0600: dt=9.600000, rms=0.448 (0.088%), neg=0, invalid=766 0601: dt=9.600000, rms=0.448 (0.094%), neg=0, invalid=766 0602: dt=9.600000, rms=0.447 (0.116%), neg=0, invalid=766 0603: dt=9.600000, rms=0.447 (0.093%), neg=0, invalid=766 0604: dt=9.600000, rms=0.447 (0.099%), neg=0, invalid=766 0605: dt=9.600000, rms=0.446 (0.046%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46972.367 ms 0606: dt=8.000000, rms=0.446 (0.024%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53152.035 ms 0607: dt=1.777778, rms=0.459 (0.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49245.555 ms 0608: dt=0.720000, rms=0.459 (0.004%), neg=0, invalid=766 0609: dt=0.720000, rms=0.459 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52434.027 ms 0610: dt=4.387097, rms=0.459 (0.128%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50815.324 ms 0611: dt=2.304000, rms=0.459 (0.023%), neg=0, invalid=766 0612: dt=2.304000, rms=0.459 (0.013%), neg=0, invalid=766 0613: dt=2.304000, rms=0.459 (-0.039%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.476, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50985.773 ms 0614: dt=0.479167, rms=0.476 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50605.281 ms 0615: dt=0.320000, rms=0.476 (0.012%), neg=0, invalid=766 0616: dt=0.320000, rms=0.476 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53212.973 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0617: dt=1.536000, rms=0.475 (0.265%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53960.125 ms iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0618: dt=0.320000, rms=0.475 (0.009%), neg=0, invalid=766 0619: dt=0.320000, rms=0.475 (0.017%), neg=0, invalid=766 0620: dt=0.320000, rms=0.475 (0.011%), neg=0, invalid=766 0621: dt=0.320000, rms=0.475 (-0.026%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.458, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54333.578 ms iter 0, gcam->neg = 405 after 10 iterations, nbhd size=1, neg = 0 0622: dt=1.975793, rms=0.430 (5.965%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54126.754 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0623: dt=0.001500, rms=0.430 (0.006%), neg=0, invalid=766 0624: dt=0.001500, rms=0.430 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.430, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53638.207 ms iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0625: dt=0.020000, rms=0.430 (0.026%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53199.738 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0626: dt=0.024000, rms=0.430 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0627: dt=0.024000, rms=0.430 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 0 iterations, nbhd size=0, neg = 0 0628: dt=0.024000, rms=0.430 (-0.029%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.418, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53087.828 ms iter 0, gcam->neg = 502 after 11 iterations, nbhd size=1, neg = 0 0629: dt=1.208419, rms=0.404 (3.272%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53763.762 ms 0630: dt=0.000438, rms=0.404 (-0.016%), neg=0, invalid=766 0631: dt=0.000438, rms=0.404 (0.004%), neg=0, invalid=766 0632: dt=0.000438, rms=0.404 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.404, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53628.328 ms 0633: dt=0.001500, rms=0.404 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53699.684 ms 0634: dt=0.001000, rms=0.404 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.399, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52589.730 ms iter 0, gcam->neg = 200 after 40 iterations, nbhd size=4, neg = 0 0635: dt=0.320000, rms=0.396 (0.936%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52687.418 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0636: dt=0.004000, rms=0.396 (-0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0637: dt=0.004000, rms=0.396 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0638: dt=0.004000, rms=0.396 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0639: dt=0.004000, rms=0.396 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0640: dt=0.004000, rms=0.396 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0641: dt=0.004000, rms=0.395 (0.018%), neg=0, invalid=766 0642: dt=0.004000, rms=0.395 (0.021%), neg=0, invalid=766 0643: dt=0.004000, rms=0.395 (0.023%), neg=0, invalid=766 0644: dt=0.004000, rms=0.395 (0.021%), neg=0, invalid=766 0645: dt=0.004000, rms=0.395 (0.028%), neg=0, invalid=766 0646: dt=0.004000, rms=0.395 (0.030%), neg=0, invalid=766 0647: dt=0.004000, rms=0.395 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0648: dt=0.004000, rms=0.395 (0.033%), neg=0, invalid=766 0649: dt=0.004000, rms=0.395 (0.030%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54570.781 ms iter 0, gcam->neg = 216 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 26051.180 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0650: dt=0.384000, rms=0.395 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50077.984 ms iter 0, gcam->neg = 216 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 26576.986 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0651: dt=0.384000, rms=0.395 (0.000%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.394, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47996.164 ms iter 0, gcam->neg = 70 after 200 iterations, nbhd size=4, neg = 3 starting rms=0.012, neg=3, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 26763.301 ms iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.012 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0652: dt=11.200000, rms=0.395 (-0.114%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49279.328 ms iter 0, gcam->neg = 139 after 200 iterations, nbhd size=3, neg = 4 starting rms=0.013, neg=4, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 26114.711 ms iter 1, dt=0.000000: new neg 4, old_neg 4, delta 0, rms=0.013 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0653: dt=25.600000, rms=0.395 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51280.395 ms iter 0, gcam->neg = 198 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.010, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 26256.379 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.010 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0654: dt=3.777778, rms=0.395 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51661.117 ms iter 0, gcam->neg = 333 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.010, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 24637.432 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.010 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0655: dt=6.912000, rms=0.395 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48309.586 ms iter 0, gcam->neg = 238 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.008, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23680.672 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.008 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0656: dt=1.436364, rms=0.395 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49256.719 ms iter 0, gcam->neg = 495 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.008, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 22075.498 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.008 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0657: dt=2.606061, rms=0.395 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44610.504 ms iter 0, gcam->neg = 70 after 14 iterations, nbhd size=2, neg = 0 0658: dt=0.112000, rms=0.393 (0.335%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50160.250 ms iter 0, gcam->neg = 33 after 9 iterations, nbhd size=1, neg = 0 0659: dt=0.064000, rms=0.393 (0.146%), neg=0, invalid=766 iter 0, gcam->neg = 33 after 14 iterations, nbhd size=2, neg = 0 0660: dt=0.064000, rms=0.392 (0.123%), neg=0, invalid=766 iter 0, gcam->neg = 65 after 26 iterations, nbhd size=3, neg = 0 0661: dt=0.064000, rms=0.391 (0.214%), neg=0, invalid=766 iter 0, gcam->neg = 136 after 18 iterations, nbhd size=2, neg = 0 0662: dt=0.064000, rms=0.390 (0.257%), neg=0, invalid=766 iter 0, gcam->neg = 217 after 17 iterations, nbhd size=2, neg = 0 0663: dt=0.064000, rms=0.389 (0.269%), neg=0, invalid=766 iter 0, gcam->neg = 315 after 18 iterations, nbhd size=2, neg = 0 0664: dt=0.064000, rms=0.388 (0.241%), neg=0, invalid=766 iter 0, gcam->neg = 424 after 26 iterations, nbhd size=3, neg = 0 0665: dt=0.064000, rms=0.388 (0.186%), neg=0, invalid=766 iter 0, gcam->neg = 617 after 36 iterations, nbhd size=3, neg = 0 0666: dt=0.064000, rms=0.387 (0.113%), neg=0, invalid=766 iter 0, gcam->neg = 776 after 29 iterations, nbhd size=3, neg = 0 0667: dt=0.064000, rms=0.387 (0.069%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49754.746 ms 0668: dt=0.000438, rms=0.387 (0.002%), neg=0, invalid=766 0669: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0670: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0671: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0672: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0673: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0674: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0675: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0676: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0677: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0678: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 0679: dt=0.000438, rms=0.387 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.387, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50506.195 ms iter 0, gcam->neg = 39 after 30 iterations, nbhd size=4, neg = 0 0680: dt=0.112000, rms=0.386 (0.219%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50434.129 ms 0681: dt=0.000438, rms=0.386 (0.002%), neg=0, invalid=766 0682: dt=0.000438, rms=0.386 (0.001%), neg=0, invalid=766 0683: dt=0.000438, rms=0.386 (0.001%), neg=0, invalid=766 0684: dt=0.000438, rms=0.386 (0.002%), neg=0, invalid=766 0685: dt=0.000438, rms=0.386 (0.002%), neg=0, invalid=766 0686: dt=0.000438, rms=0.386 (0.003%), neg=0, invalid=766 0687: dt=0.000438, rms=0.386 (0.003%), neg=0, invalid=766 0688: dt=0.000438, rms=0.386 (0.003%), neg=0, invalid=766 0689: dt=0.000438, rms=0.386 (0.004%), neg=0, invalid=766 0690: dt=0.000438, rms=0.386 (0.004%), neg=0, invalid=766 0691: dt=0.000438, rms=0.386 (0.004%), neg=0, invalid=766 0692: dt=0.000438, rms=0.386 (0.004%), neg=0, invalid=766 0693: dt=0.000438, rms=0.386 (0.005%), neg=0, invalid=766 0694: dt=0.000438, rms=0.386 (0.005%), neg=0, invalid=766 0695: dt=0.000438, rms=0.386 (0.005%), neg=0, invalid=766 0696: dt=0.000438, rms=0.386 (0.005%), neg=0, invalid=766 0697: dt=0.000438, rms=0.386 (0.005%), neg=0, invalid=766 0698: dt=0.000438, rms=0.386 (0.005%), neg=0, invalid=766 0699: dt=0.000438, rms=0.386 (0.005%), neg=0, invalid=766 0700: dt=0.000438, rms=0.386 (0.005%), neg=0, invalid=766 0701: dt=0.000438, rms=0.386 (0.006%), neg=0, invalid=766 0702: dt=0.000438, rms=0.386 (0.006%), neg=0, invalid=766 0703: dt=0.000438, rms=0.386 (0.006%), neg=0, invalid=766 0704: dt=0.000438, rms=0.386 (0.006%), neg=0, invalid=766 0705: dt=0.000438, rms=0.386 (0.006%), neg=0, invalid=766 0706: dt=0.000438, rms=0.386 (0.006%), neg=0, invalid=766 0707: dt=0.000438, rms=0.386 (0.006%), neg=0, invalid=766 0708: dt=0.000438, rms=0.386 (0.006%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.384, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48959.801 ms iter 0, gcam->neg = 9 after 6 iterations, nbhd size=1, neg = 0 0709: dt=0.028000, rms=0.384 (0.079%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 48791.000 ms iter 0, gcam->neg = 13 after 7 iterations, nbhd size=1, neg = 0 0710: dt=0.028000, rms=0.384 (0.072%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 6 iterations, nbhd size=1, neg = 0 0711: dt=0.028000, rms=0.383 (0.067%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 22 iterations, nbhd size=3, neg = 0 0712: dt=0.028000, rms=0.383 (0.122%), neg=0, invalid=766 iter 0, gcam->neg = 35 after 17 iterations, nbhd size=2, neg = 0 0713: dt=0.028000, rms=0.382 (0.158%), neg=0, invalid=766 iter 0, gcam->neg = 47 after 9 iterations, nbhd size=1, neg = 0 0714: dt=0.028000, rms=0.382 (0.180%), neg=0, invalid=766 iter 0, gcam->neg = 58 after 28 iterations, nbhd size=3, neg = 0 0715: dt=0.028000, rms=0.381 (0.187%), neg=0, invalid=766 iter 0, gcam->neg = 72 after 24 iterations, nbhd size=2, neg = 0 0716: dt=0.028000, rms=0.380 (0.183%), neg=0, invalid=766 iter 0, gcam->neg = 100 after 28 iterations, nbhd size=3, neg = 0 0717: dt=0.028000, rms=0.380 (0.166%), neg=0, invalid=766 iter 0, gcam->neg = 127 after 35 iterations, nbhd size=3, neg = 0 0718: dt=0.028000, rms=0.379 (0.138%), neg=0, invalid=766 iter 0, gcam->neg = 135 after 29 iterations, nbhd size=3, neg = 0 0719: dt=0.028000, rms=0.379 (0.129%), neg=0, invalid=766 iter 0, gcam->neg = 154 after 34 iterations, nbhd size=3, neg = 0 0720: dt=0.028000, rms=0.378 (0.084%), neg=0, invalid=766 iter 0, gcam->neg = 183 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 23118.398 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0721: dt=0.028000, rms=0.378 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47161.867 ms 0722: dt=0.000438, rms=0.378 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47464.461 ms 0723: dt=0.000250, rms=0.378 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.378, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47977.348 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0724: dt=0.001500, rms=0.378 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46805.586 ms iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0725: dt=0.016000, rms=0.378 (0.033%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46155.297 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0726: dt=0.000750, rms=0.378 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0727: dt=0.000750, rms=0.378 (0.001%), neg=0, invalid=766 0728: dt=0.000750, rms=0.378 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0729: dt=0.000750, rms=0.378 (0.004%), neg=0, invalid=766 0730: dt=0.000750, rms=0.378 (0.005%), neg=0, invalid=766 0731: dt=0.000750, rms=0.378 (0.006%), neg=0, invalid=766 0732: dt=0.000750, rms=0.378 (0.007%), neg=0, invalid=766 0733: dt=0.000750, rms=0.378 (0.008%), neg=0, invalid=766 0734: dt=0.000750, rms=0.378 (0.008%), neg=0, invalid=766 0735: dt=0.000750, rms=0.378 (0.009%), neg=0, invalid=766 0736: dt=0.000750, rms=0.378 (0.009%), neg=0, invalid=766 0737: dt=0.000750, rms=0.378 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0738: dt=0.000750, rms=0.378 (0.010%), neg=0, invalid=766 0739: dt=0.000750, rms=0.378 (0.010%), neg=0, invalid=766 0740: dt=0.000750, rms=0.378 (0.011%), neg=0, invalid=766 0741: dt=0.000750, rms=0.378 (0.011%), neg=0, invalid=766 0742: dt=0.000750, rms=0.378 (0.011%), neg=0, invalid=766 0743: dt=0.000750, rms=0.378 (0.011%), neg=0, invalid=766 0744: dt=0.000750, rms=0.378 (0.011%), neg=0, invalid=766 0745: dt=0.000750, rms=0.378 (0.011%), neg=0, invalid=766 0746: dt=0.000750, rms=0.378 (0.011%), neg=0, invalid=766 0747: dt=0.000750, rms=0.378 (0.011%), neg=0, invalid=766 0748: dt=0.000750, rms=0.377 (0.011%), neg=0, invalid=766 0749: dt=0.000750, rms=0.377 (0.011%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.376, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49101.184 ms iter 0, gcam->neg = 12 after 13 iterations, nbhd size=2, neg = 0 0750: dt=0.020000, rms=0.376 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47609.410 ms iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0751: dt=0.007000, rms=0.376 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0752: dt=0.007000, rms=0.376 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0753: dt=0.007000, rms=0.376 (0.033%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 18 iterations, nbhd size=2, neg = 0 0754: dt=0.007000, rms=0.376 (0.045%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0755: dt=0.007000, rms=0.376 (0.057%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 15 iterations, nbhd size=2, neg = 0 0756: dt=0.007000, rms=0.375 (0.064%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0757: dt=0.007000, rms=0.375 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 19 iterations, nbhd size=2, neg = 0 0758: dt=0.007000, rms=0.375 (0.075%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 19 iterations, nbhd size=2, neg = 0 0759: dt=0.007000, rms=0.375 (0.078%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 17 iterations, nbhd size=2, neg = 0 0760: dt=0.007000, rms=0.374 (0.080%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 20 iterations, nbhd size=2, neg = 0 0761: dt=0.007000, rms=0.374 (0.076%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 27 iterations, nbhd size=3, neg = 0 0762: dt=0.007000, rms=0.374 (0.077%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 22 iterations, nbhd size=2, neg = 0 0763: dt=0.007000, rms=0.373 (0.076%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.373, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43149.105 ms iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0764: dt=0.001750, rms=0.373 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42329.199 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0765: dt=0.007000, rms=0.373 (0.019%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42068.660 ms iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0766: dt=0.007000, rms=0.373 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 14 iterations, nbhd size=2, neg = 0 0767: dt=0.007000, rms=0.373 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 17 iterations, nbhd size=2, neg = 0 0768: dt=0.007000, rms=0.373 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0769: dt=0.007000, rms=0.373 (0.049%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 30 iterations, nbhd size=3, neg = 0 0770: dt=0.007000, rms=0.373 (0.053%), neg=0, invalid=766 iter 0, gcam->neg = 19 after 16 iterations, nbhd size=2, neg = 0 0771: dt=0.007000, rms=0.372 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 19 after 18 iterations, nbhd size=2, neg = 0 0772: dt=0.007000, rms=0.372 (0.075%), neg=0, invalid=766 iter 0, gcam->neg = 19 after 17 iterations, nbhd size=2, neg = 0 0773: dt=0.007000, rms=0.372 (0.078%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 29 iterations, nbhd size=3, neg = 0 0774: dt=0.007000, rms=0.371 (0.081%), neg=0, invalid=766 iter 0, gcam->neg = 30 after 18 iterations, nbhd size=2, neg = 0 0775: dt=0.007000, rms=0.371 (0.087%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 21 iterations, nbhd size=2, neg = 0 0776: dt=0.007000, rms=0.371 (0.087%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 19 iterations, nbhd size=2, neg = 0 0777: dt=0.007000, rms=0.371 (0.088%), neg=0, invalid=766 iter 0, gcam->neg = 30 after 19 iterations, nbhd size=2, neg = 0 0778: dt=0.007000, rms=0.370 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 26 after 17 iterations, nbhd size=2, neg = 0 0779: dt=0.007000, rms=0.370 (0.083%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 6 hours, 50 minutes and 26 seconds. #-------------------------------------- #@# CA Reg Inv Thu Mar 5 01:27:07 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Thu Mar 5 01:28:28 EST 2015 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11333897 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 30 seconds. #-------------------------------------- #@# SkullLTA Thu Mar 5 01:29:58 EST 2015 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /cell_root/software/freesurfer/current/sys/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/cell_root/software/freesurfer/current/sys/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=20.0 skull bounding box = (48, 31, 43) --> (204, 200, 220) using (100, 87, 132) as brain centroid... mean wm in atlas = 126, using box (81,66,110) --> (119, 107,153) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10325.5, old_max_log_p =-10351.9 (thresh=-10341.5) 1.124 -0.038 0.006 -12.486; 0.048 1.398 0.067 -37.440; 0.005 -0.085 1.077 -19.044; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10323.0, old_max_log_p =-10325.5 (thresh=-10315.2) 1.039 -0.035 0.006 -2.117; 0.048 1.398 0.067 -37.440; 0.005 -0.085 1.077 -19.044; 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=-10316.7, old_max_log_p =-10323.0 (thresh=-10312.7) 1.059 -0.038 0.043 -10.545; 0.045 1.320 0.069 -29.043; -0.028 -0.079 1.096 -14.180; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10313.2, old_max_log_p =-10316.7 (thresh=-10306.4) 1.054 -0.058 0.015 -3.716; 0.063 1.325 0.051 -29.173; -0.001 -0.058 1.100 -21.698; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05437 -0.05775 0.01500 -3.71647; 0.06282 1.32533 0.05102 -29.17267; -0.00122 -0.05839 1.10023 -21.69822; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.05437 -0.05775 0.01500 -3.71647; 0.06282 1.32533 0.05102 -29.17267; -0.00122 -0.05839 1.10023 -21.69822; 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: 005: -log(p) = 10313.2 tol 0.000010 Resulting transform: 1.054 -0.058 0.015 -3.716; 0.063 1.325 0.051 -29.173; -0.001 -0.058 1.100 -21.698; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10313.2 (old=-10351.9) transform before final EM align: 1.054 -0.058 0.015 -3.716; 0.063 1.325 0.051 -29.173; -0.001 -0.058 1.100 -21.698; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05437 -0.05775 0.01500 -3.71647; 0.06282 1.32533 0.05102 -29.17267; -0.00122 -0.05839 1.10023 -21.69822; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.05437 -0.05775 0.01500 -3.71647; 0.06282 1.32533 0.05102 -29.17267; -0.00122 -0.05839 1.10023 -21.69822; 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: 007: -log(p) = 1145442.8 tol 0.000000 final transform: 1.054 -0.058 0.015 -3.716; 0.063 1.325 0.051 -29.173; -0.001 -0.058 1.100 -21.698; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 24 minutes and 20 seconds. #-------------------------------------- #@# SubCort Seg Thu Mar 5 01:54:19 EST 2015 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /cell_root/software/freesurfer/current/sys/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /cell_root/software/freesurfer/current/sys/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 = 0.13822 (31) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (128 voxels, overlap=0.525) Left_Lateral_Ventricle (4): linear fit = 1.15 x + 0.0 (128 voxels, peak = 31), gca=31.0 gca peak = 0.14982 (20) mri peak = 0.13115 (31) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (156 voxels, overlap=0.402) Right_Lateral_Ventricle (43): linear fit = 1.42 x + 0.0 (156 voxels, peak = 28), gca=28.5 gca peak = 0.28003 (97) mri peak = 0.14661 (100) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (549 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (549 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.11883 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (541 voxels, overlap=0.820) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (541 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.10723 (76) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1013 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1013 voxels, peak = 74), gca=74.4 gca peak = 0.32745 (63) mri peak = 0.06541 (74) Left_Hippocampus (17): linear fit = 1.15 x + 0.0 (991 voxels, overlap=0.232) Left_Hippocampus (17): linear fit = 1.15 x + 0.0 (991 voxels, peak = 72), gca=72.4 gca peak = 0.08597 (105) mri peak = 0.11051 (108) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (37793 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (37793 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.09929 (109) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (37503 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (37503 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.05639 (72) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (64315 voxels, overlap=0.477) Left_Cerebral_Cortex (3): linear fit = 1.15 x + 0.0 (64315 voxels, peak = 72), gca=72.4 gca peak = 0.08598 (64) mri peak = 0.05976 (72) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (64632 voxels, overlap=0.405) Right_Cerebral_Cortex (42): linear fit = 1.15 x + 0.0 (64632 voxels, peak = 74), gca=73.6 gca peak = 0.24164 (71) mri peak = 0.12520 (88) Right_Caudate (50): linear fit = 1.23 x + 0.0 (627 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.23 x + 0.0 (627 voxels, peak = 87), gca=87.0 gca peak = 0.18227 (75) mri peak = 0.14870 (87) Left_Caudate (11): linear fit = 1.10 x + 0.0 (669 voxels, overlap=0.414) Left_Caudate (11): linear fit = 1.10 x + 0.0 (669 voxels, peak = 82), gca=82.5 gca peak = 0.10629 (62) mri peak = 0.06820 (75) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (29778 voxels, overlap=0.073) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (29778 voxels, peak = 76), gca=76.0 gca peak = 0.11668 (59) mri peak = 0.07394 (75) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (31354 voxels, overlap=0.041) Right_Cerebellum_Cortex (47): linear fit = 1.23 x + 0.0 (31354 voxels, peak = 72), gca=72.3 gca peak = 0.17849 (88) mri peak = 0.10399 (96) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5517 voxels, overlap=0.251) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5517 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.09126 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4253 voxels, overlap=0.826) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (4253 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.09800 (75) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (489 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (489 voxels, peak = 74), gca=73.6 gca peak = 0.42394 (62) mri peak = 0.10262 (76) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (495 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (495 voxels, peak = 78), gca=77.5 gca peak = 0.10041 (96) mri peak = 0.07571 (98) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (4128 voxels, overlap=0.820) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (4128 voxels, peak = 101), gca=100.8 gca peak = 0.13978 (88) mri peak = 0.07576 (97) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4118 voxels, overlap=0.582) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (4118 voxels, peak = 97), gca=96.8 gca peak = 0.08514 (81) mri peak = 0.09683 (92) Left_Putamen (12): linear fit = 1.08 x + 0.0 (2715 voxels, overlap=0.545) Left_Putamen (12): linear fit = 1.08 x + 0.0 (2715 voxels, peak = 87), gca=87.1 gca peak = 0.09624 (82) mri peak = 0.09850 (93) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2802 voxels, overlap=0.435) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2802 voxels, peak = 90), gca=90.2 gca peak = 0.07543 (88) mri peak = 0.06763 (84) Brain_Stem (16): linear fit = 1.02 x + 0.0 (10811 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.02 x + 0.0 (10811 voxels, peak = 90), gca=90.2 gca peak = 0.12757 (95) mri peak = 0.06754 (100) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1343 voxels, overlap=0.782) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1343 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.06447 (100) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1331 voxels, overlap=0.844) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1331 voxels, peak = 97), gca=96.6 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.15625 (27) Fourth_Ventricle (15): linear fit = 1.15 x + 0.0 (190 voxels, overlap=0.829) Fourth_Ventricle (15): linear fit = 1.15 x + 0.0 (190 voxels, peak = 26), gca=26.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.18 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 1.24 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11680 (31) mri peak = 0.13822 (31) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (128 voxels, overlap=0.640) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (128 voxels, peak = 31), gca=31.0 gca peak = 0.13471 (29) mri peak = 0.13115 (31) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (156 voxels, overlap=0.721) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (156 voxels, peak = 30), gca=29.7 gca peak = 0.30362 (100) mri peak = 0.14661 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (549 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (549 voxels, peak = 100), gca=100.0 gca peak = 0.18507 (101) mri peak = 0.11883 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (541 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (541 voxels, peak = 101), gca=101.0 gca peak = 0.21056 (75) mri peak = 0.10723 (76) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1013 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1013 voxels, peak = 75), gca=75.0 gca peak = 0.26159 (72) mri peak = 0.06541 (74) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (991 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (991 voxels, peak = 72), gca=72.0 gca peak = 0.08345 (108) mri peak = 0.11051 (108) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37793 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37793 voxels, peak = 108), gca=108.0 gca peak = 0.08551 (108) mri peak = 0.09929 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37503 voxels, overlap=0.649) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (37503 voxels, peak = 108), gca=108.0 gca peak = 0.06942 (72) mri peak = 0.05639 (72) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (64315 voxels, overlap=0.879) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (64315 voxels, peak = 72), gca=72.0 gca peak = 0.07675 (73) mri peak = 0.05976 (72) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (64632 voxels, overlap=0.908) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (64632 voxels, peak = 73), gca=73.0 gca peak = 0.22036 (90) mri peak = 0.12520 (88) Right_Caudate (50): linear fit = 1.00 x + 0.0 (627 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (627 voxels, peak = 90), gca=90.0 gca peak = 0.13745 (82) mri peak = 0.14870 (87) Left_Caudate (11): linear fit = 0.98 x + 0.0 (669 voxels, overlap=0.911) Left_Caudate (11): linear fit = 0.98 x + 0.0 (669 voxels, peak = 80), gca=80.0 gca peak = 0.09020 (76) mri peak = 0.06820 (75) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (29778 voxels, overlap=0.968) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (29778 voxels, peak = 76), gca=76.0 gca peak = 0.10431 (73) mri peak = 0.07394 (75) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (31354 voxels, overlap=0.958) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (31354 voxels, peak = 73), gca=73.0 gca peak = 0.17137 (94) mri peak = 0.10399 (96) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5517 voxels, overlap=0.927) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (5517 voxels, peak = 96), gca=96.3 gca peak = 0.15715 (93) mri peak = 0.09126 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4253 voxels, overlap=0.997) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4253 voxels, peak = 93), gca=93.0 gca peak = 0.32863 (73) mri peak = 0.09800 (75) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (489 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (489 voxels, peak = 73), gca=73.0 gca peak = 0.32891 (78) mri peak = 0.10262 (76) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (495 voxels, overlap=0.998) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (495 voxels, peak = 78), gca=78.0 gca peak = 0.10141 (99) mri peak = 0.07571 (98) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4128 voxels, overlap=0.981) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4128 voxels, peak = 99), gca=99.0 gca peak = 0.09775 (97) mri peak = 0.07576 (97) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4118 voxels, overlap=0.910) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4118 voxels, peak = 97), gca=97.0 gca peak = 0.08622 (87) mri peak = 0.09683 (92) Left_Putamen (12): linear fit = 1.02 x + 0.0 (2715 voxels, overlap=0.855) Left_Putamen (12): linear fit = 1.02 x + 0.0 (2715 voxels, peak = 89), gca=89.2 gca peak = 0.08544 (85) mri peak = 0.09850 (93) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2802 voxels, overlap=0.855) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2802 voxels, peak = 85), gca=85.0 gca peak = 0.07235 (87) mri peak = 0.06763 (84) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10811 voxels, overlap=0.811) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10811 voxels, peak = 87), gca=87.0 gca peak = 0.13825 (104) mri peak = 0.06754 (100) Right_VentralDC (60): linear fit = 0.95 x + 0.0 (1343 voxels, overlap=0.898) Right_VentralDC (60): linear fit = 0.95 x + 0.0 (1343 voxels, peak = 99), gca=98.8 gca peak = 0.14568 (97) mri peak = 0.06447 (100) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1331 voxels, overlap=0.900) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1331 voxels, peak = 97), gca=97.0 gca peak = 0.19676 (45) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.20195 (27) mri peak = 0.15625 (27) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (190 voxels, overlap=0.640) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (190 voxels, peak = 26), gca=26.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.18244 (40) gca peak Third_Ventricle = 0.19676 (45) gca peak CSF = 0.25447 (48) gca peak Left_Accumbens_area = 0.51612 (77) gca peak Left_undetermined = 0.95107 (36) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.08601 (47) gca peak Right_Inf_Lat_Vent = 0.28322 (38) gca peak Right_Accumbens_area = 0.27484 (88) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.12959 (48) gca peak Fifth_Ventricle = 0.45827 (52) gca peak WM_hypointensities = 0.15229 (84) gca peak non_WM_hypointensities = 0.11940 (54) gca peak Optic_Chiasm = 0.34474 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.00 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 22886 gm and wm labels changed (%34 to gray, %66 to white out of all changed labels) 284 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 74705 changed. image ll: -2.164, PF=1.000 pass 2: 12030 changed. image ll: -2.161, PF=1.000 pass 3: 4156 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 22 minutes and 26 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /export/data/hippocampus/HMN/data/HMN002/mri/transforms/cc_up.lta HMN002 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /export/data/hippocampus/HMN/data/HMN002/mri/transforms/cc_up.lta reading aseg from /export/data/hippocampus/HMN/data/HMN002/mri/aseg.auto_noCCseg.mgz reading norm from /export/data/hippocampus/HMN/data/HMN002/mri/norm.mgz 35596 voxels in left wm, 52745 in right wm, xrange [121, 130] searching rotation angles z=[-5 9], y=[-8 6] searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.7 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.2 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.7 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.2 global minimum found at slice 125.8, rotations (-0.67, 2.42) final transformation (x=125.8, yr=-0.669, zr=2.417): 0.999 -0.042 -0.012 7.234; 0.042 0.999 -0.000 41.830; 0.012 0.000 1.000 2.539; 0.000 0.000 0.000 1.000; updating x range to be [125, 129] in xformed coordinates best xformed slice 128 cc center is found at 128 153 113 eigenvectors: -0.001 -0.003 1.000; -0.007 -1.000 -0.003; 1.000 -0.007 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /export/data/hippocampus/HMN/data/HMN002/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.0 minutes #-------------------------------------- #@# Merge ASeg Thu Mar 5 02:17:47 EST 2015 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Mar 5 02:17:47 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 873 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 4 minutes and 38 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 110 gm peak at 80 (80), valley at 0 (-1) csf peak at 40, setting threshold to 66 white matter peak found at 111 white matter peak found at 110 gm peak at 79 (79), valley at 0 (-1) csf peak at 39, setting threshold to 65 #-------------------------------------------- #@# Mask BFS Thu Mar 5 02:22:28 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1559617 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Mar 5 02:22:31 EST 2015 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.4 +- 6.2 [80.0 --> 125.0] GM (78.0) : 77.2 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 86.8 setting top of gray matter range to 96.4 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... 8095 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4800 filled 1901 bright non-wm voxels segmented. 4277 diagonally connected voxels added... white matter segmentation took 2.3 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.68 minutes reading wm segmentation from wm.seg.mgz... 365 voxels added to wm to prevent paths from MTL structures to cortex 3141 additional wm voxels added 0 additional wm voxels added SEG EDIT: 34637 voxels turned on, 39657 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 100 new 100 115,126,128 old 100 new 100 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 36 found - 36 modified | TOTAL: 36 pass 2 (xy+): 0 found - 36 modified | TOTAL: 36 pass 1 (xy-): 26 found - 26 modified | TOTAL: 62 pass 2 (xy-): 0 found - 26 modified | TOTAL: 62 pass 1 (yz+): 40 found - 40 modified | TOTAL: 102 pass 2 (yz+): 0 found - 40 modified | TOTAL: 102 pass 1 (yz-): 41 found - 41 modified | TOTAL: 143 pass 2 (yz-): 0 found - 41 modified | TOTAL: 143 pass 1 (xz+): 32 found - 32 modified | TOTAL: 175 pass 2 (xz+): 0 found - 32 modified | TOTAL: 175 pass 1 (xz-): 39 found - 39 modified | TOTAL: 214 pass 2 (xz-): 0 found - 39 modified | TOTAL: 214 Iteration Number : 1 pass 1 (+++): 22 found - 22 modified | TOTAL: 22 pass 2 (+++): 0 found - 22 modified | TOTAL: 22 pass 1 (+++): 18 found - 18 modified | TOTAL: 40 pass 2 (+++): 0 found - 18 modified | TOTAL: 40 pass 1 (+++): 18 found - 18 modified | TOTAL: 58 pass 2 (+++): 0 found - 18 modified | TOTAL: 58 pass 1 (+++): 23 found - 23 modified | TOTAL: 81 pass 2 (+++): 0 found - 23 modified | TOTAL: 81 Iteration Number : 1 pass 1 (++): 243 found - 243 modified | TOTAL: 243 pass 2 (++): 0 found - 243 modified | TOTAL: 243 pass 1 (+-): 192 found - 192 modified | TOTAL: 435 pass 2 (+-): 0 found - 192 modified | TOTAL: 435 pass 1 (--): 178 found - 178 modified | TOTAL: 613 pass 2 (--): 1 found - 179 modified | TOTAL: 614 pass 3 (--): 0 found - 179 modified | TOTAL: 614 pass 1 (-+): 199 found - 199 modified | TOTAL: 813 pass 2 (-+): 0 found - 199 modified | TOTAL: 813 Iteration Number : 2 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 3 found - 3 modified | TOTAL: 13 pass 2 (xy-): 0 found - 3 modified | TOTAL: 13 pass 1 (yz+): 12 found - 12 modified | TOTAL: 25 pass 2 (yz+): 0 found - 12 modified | TOTAL: 25 pass 1 (yz-): 9 found - 9 modified | TOTAL: 34 pass 2 (yz-): 0 found - 9 modified | TOTAL: 34 pass 1 (xz+): 12 found - 12 modified | TOTAL: 46 pass 2 (xz+): 0 found - 12 modified | TOTAL: 46 pass 1 (xz-): 9 found - 9 modified | TOTAL: 55 pass 2 (xz-): 0 found - 9 modified | TOTAL: 55 Iteration Number : 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 3 pass 2 (+++): 0 found - 2 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 4 found - 4 modified | TOTAL: 8 pass 2 (+-): 0 found - 4 modified | TOTAL: 8 pass 1 (--): 5 found - 5 modified | TOTAL: 13 pass 2 (--): 0 found - 5 modified | TOTAL: 13 pass 1 (-+): 4 found - 4 modified | TOTAL: 17 pass 2 (-+): 0 found - 4 modified | TOTAL: 17 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 2 found - 2 modified | TOTAL: 4 pass 2 (xz+): 0 found - 2 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 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 = 1190 (out of 458729: 0.259412) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Mar 5 02:25:37 EST 2015 /export/data/hippocampus/HMN/data/HMN002/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.056 -0.036 0.006 -4.201; 0.039 1.114 0.213 -25.076; 0.000 -0.211 1.057 -3.108; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.056 -0.036 0.006 -4.201; 0.039 1.114 0.213 -25.076; 0.000 -0.211 1.057 -3.108; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2165 (min = 350, max = 1400), aspect = 1.19 (min = 0.10, max = 0.75) need search nearby using seed (127, 124, 146), TAL = (1.0, 18.0, 4.0) talairach voxel to voxel transform 0.946 0.028 -0.011 4.646; -0.032 0.864 -0.173 20.983; -0.007 0.172 0.911 7.118; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 124, 146) --> (1.0, 18.0, 4.0) done. writing output to filled.mgz... filling took 1.1 minutes talairach cc position changed to (1.00, 18.00, 4.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 18.00, 4.00) SRC: (109.63, 99.25, 160.76) search lh wm seed point around talairach space (-17.00, 18.00, 4.00), SRC: (143.67, 98.09, 160.52) 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 Mar 5 02:26:41 EST 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 4 found - 4 modified | TOTAL: 6 pass 2 (yz+): 0 found - 4 modified | TOTAL: 6 pass 1 (yz-): 0 found - 0 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 0 found - 0 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 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 : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 8 (out of 220107: 0.003635) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 60: 2812 vertices, 3006 faces slice 70: 11007 vertices, 11346 faces slice 80: 21461 vertices, 21855 faces slice 90: 33376 vertices, 33792 faces slice 100: 45338 vertices, 45757 faces slice 110: 58140 vertices, 58612 faces slice 120: 71026 vertices, 71502 faces slice 130: 83383 vertices, 83827 faces slice 140: 94972 vertices, 95451 faces slice 150: 105510 vertices, 105906 faces slice 160: 114252 vertices, 114668 faces slice 170: 123584 vertices, 123938 faces slice 180: 130598 vertices, 130936 faces slice 190: 135887 vertices, 136169 faces slice 200: 138892 vertices, 139043 faces slice 210: 139026 vertices, 139142 faces slice 220: 139026 vertices, 139142 faces slice 230: 139026 vertices, 139142 faces slice 240: 139026 vertices, 139142 faces slice 250: 139026 vertices, 139142 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... 139026 voxel in cpt #1: X=-116 [v=139026,e=417426,f=278284] located at (-26.700523, -8.207112, 33.916355) For the whole surface: X=-116 [v=139026,e=417426,f=278284] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Mar 5 02:26:51 EST 2015 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /export/data/hippocampus/HMN/data/HMN002/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 Mar 5 02:26:56 EST 2015 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /export/data/hippocampus/HMN/data/HMN002/scripts avg radius = 44.6 mm, total surface area = 73612 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes Not saving sulc step 000: RMS=0.104 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.061 (target=0.015) step 015: RMS=0.055 (target=0.015) step 020: RMS=0.049 (target=0.015) step 025: RMS=0.045 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.037 (target=0.015) step 045: RMS=0.036 (target=0.015) step 050: RMS=0.036 (target=0.015) step 055: RMS=0.035 (target=0.015) step 060: RMS=0.035 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Mar 5 02:27:40 EST 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.97 +- 0.57 (0.00-->7.59) (max @ vno 50055 --> 51345) face area 0.03 +- 0.03 (-0.12-->0.80) scaling brain by 0.316... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.098, avgs=0 005/300: dt: 0.9000, rms radial error=175.840, avgs=0 010/300: dt: 0.9000, rms radial error=175.285, avgs=0 015/300: dt: 0.9000, rms radial error=174.557, avgs=0 020/300: dt: 0.9000, rms radial error=173.727, avgs=0 025/300: dt: 0.9000, rms radial error=172.842, avgs=0 030/300: dt: 0.9000, rms radial error=171.926, avgs=0 035/300: dt: 0.9000, rms radial error=170.994, avgs=0 040/300: dt: 0.9000, rms radial error=170.053, avgs=0 045/300: dt: 0.9000, rms radial error=169.110, avgs=0 050/300: dt: 0.9000, rms radial error=168.166, avgs=0 055/300: dt: 0.9000, rms radial error=167.225, avgs=0 060/300: dt: 0.9000, rms radial error=166.287, avgs=0 065/300: dt: 0.9000, rms radial error=165.353, avgs=0 070/300: dt: 0.9000, rms radial error=164.424, avgs=0 075/300: dt: 0.9000, rms radial error=163.499, avgs=0 080/300: dt: 0.9000, rms radial error=162.580, avgs=0 085/300: dt: 0.9000, rms radial error=161.669, avgs=0 090/300: dt: 0.9000, rms radial error=160.762, avgs=0 095/300: dt: 0.9000, rms radial error=159.859, avgs=0 100/300: dt: 0.9000, rms radial error=158.961, avgs=0 105/300: dt: 0.9000, rms radial error=158.068, avgs=0 110/300: dt: 0.9000, rms radial error=157.180, avgs=0 115/300: dt: 0.9000, rms radial error=156.297, avgs=0 120/300: dt: 0.9000, rms radial error=155.418, avgs=0 125/300: dt: 0.9000, rms radial error=154.543, avgs=0 130/300: dt: 0.9000, rms radial error=153.673, avgs=0 135/300: dt: 0.9000, rms radial error=152.808, avgs=0 140/300: dt: 0.9000, rms radial error=151.946, avgs=0 145/300: dt: 0.9000, rms radial error=151.087, avgs=0 150/300: dt: 0.9000, rms radial error=150.233, avgs=0 155/300: dt: 0.9000, rms radial error=149.383, avgs=0 160/300: dt: 0.9000, rms radial error=148.539, avgs=0 165/300: dt: 0.9000, rms radial error=147.699, avgs=0 170/300: dt: 0.9000, rms radial error=146.864, avgs=0 175/300: dt: 0.9000, rms radial error=146.033, avgs=0 180/300: dt: 0.9000, rms radial error=145.207, avgs=0 185/300: dt: 0.9000, rms radial error=144.387, avgs=0 190/300: dt: 0.9000, rms radial error=143.570, avgs=0 195/300: dt: 0.9000, rms radial error=142.759, avgs=0 200/300: dt: 0.9000, rms radial error=141.952, avgs=0 205/300: dt: 0.9000, rms radial error=141.149, avgs=0 210/300: dt: 0.9000, rms radial error=140.351, avgs=0 215/300: dt: 0.9000, rms radial error=139.558, avgs=0 220/300: dt: 0.9000, rms radial error=138.769, avgs=0 225/300: dt: 0.9000, rms radial error=137.985, avgs=0 230/300: dt: 0.9000, rms radial error=137.205, avgs=0 235/300: dt: 0.9000, rms radial error=136.429, avgs=0 240/300: dt: 0.9000, rms radial error=135.658, avgs=0 245/300: dt: 0.9000, rms radial error=134.891, avgs=0 250/300: dt: 0.9000, rms radial error=134.129, avgs=0 255/300: dt: 0.9000, rms radial error=133.370, avgs=0 260/300: dt: 0.9000, rms radial error=132.616, avgs=0 265/300: dt: 0.9000, rms radial error=131.867, avgs=0 270/300: dt: 0.9000, rms radial error=131.121, avgs=0 275/300: dt: 0.9000, rms radial error=130.380, avgs=0 280/300: dt: 0.9000, rms radial error=129.642, avgs=0 285/300: dt: 0.9000, rms radial error=128.909, avgs=0 290/300: dt: 0.9000, rms radial error=128.180, avgs=0 295/300: dt: 0.9000, rms radial error=127.456, avgs=0 300/300: dt: 0.9000, rms radial error=126.735, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16188.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 2693.79 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 = 278.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00724 epoch 4 (K=640.0), pass 1, starting sse = 23.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00711 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Mar 5 02:32:58 EST 2015 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /export/data/hippocampus/HMN/data/HMN002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 HMN002 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-116 (nv=139026, nf=278284, ne=417426, g=59) 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... 11981 ambiguous faces found in tessellation segmenting defects... 54 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 32 into 31 -merging segment 48 into 47 52 defects to be corrected 0 vertices coincident reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2063 (-4.6032) -vertex loglikelihood: -5.8106 (-2.9053) -normal dot loglikelihood: -3.5744 (-3.5744) -quad curv loglikelihood: -6.2798 (-3.1399) Total Loglikelihood : -24.8711 CORRECTING DEFECT 0 (vertices=700, convex hull=235) After retessellation of defect 0, euler #=-48 (132295,395010,262667) : difference with theory (-49) = -1 CORRECTING DEFECT 1 (vertices=218, convex hull=120) After retessellation of defect 1, euler #=-47 (132316,395128,262765) : difference with theory (-48) = -1 CORRECTING DEFECT 2 (vertices=42, convex hull=84) After retessellation of defect 2, euler #=-46 (132325,395189,262818) : difference with theory (-47) = -1 CORRECTING DEFECT 3 (vertices=204, convex hull=177) After retessellation of defect 3, euler #=-45 (132355,395370,262970) : difference with theory (-46) = -1 CORRECTING DEFECT 4 (vertices=66, convex hull=98) After retessellation of defect 4, euler #=-44 (132369,395459,263046) : difference with theory (-45) = -1 CORRECTING DEFECT 5 (vertices=160, convex hull=120) After retessellation of defect 5, euler #=-43 (132380,395550,263127) : difference with theory (-44) = -1 CORRECTING DEFECT 6 (vertices=142, convex hull=133) After retessellation of defect 6, euler #=-42 (132440,395793,263311) : difference with theory (-43) = -1 CORRECTING DEFECT 7 (vertices=26, convex hull=23) After retessellation of defect 7, euler #=-41 (132440,395805,263324) : difference with theory (-42) = -1 CORRECTING DEFECT 8 (vertices=32, convex hull=76) After retessellation of defect 8, euler #=-40 (132454,395876,263382) : difference with theory (-41) = -1 CORRECTING DEFECT 9 (vertices=1275, convex hull=133) After retessellation of defect 9, euler #=-39 (132481,396017,263497) : difference with theory (-40) = -1 CORRECTING DEFECT 10 (vertices=27, convex hull=84) After retessellation of defect 10, euler #=-38 (132490,396078,263550) : difference with theory (-39) = -1 CORRECTING DEFECT 11 (vertices=40, convex hull=65) After retessellation of defect 11, euler #=-37 (132513,396174,263624) : difference with theory (-38) = -1 CORRECTING DEFECT 12 (vertices=44, convex hull=97) After retessellation of defect 12, euler #=-36 (132544,396305,263725) : difference with theory (-37) = -1 CORRECTING DEFECT 13 (vertices=82, convex hull=147) After retessellation of defect 13, euler #=-35 (132585,396497,263877) : difference with theory (-36) = -1 CORRECTING DEFECT 14 (vertices=47, convex hull=78) After retessellation of defect 14, euler #=-34 (132618,396633,263981) : difference with theory (-35) = -1 CORRECTING DEFECT 15 (vertices=7, convex hull=30) After retessellation of defect 15, euler #=-33 (132620,396647,263994) : difference with theory (-34) = -1 CORRECTING DEFECT 16 (vertices=16, convex hull=28) After retessellation of defect 16, euler #=-32 (132622,396663,264009) : difference with theory (-33) = -1 CORRECTING DEFECT 17 (vertices=36, convex hull=93) After retessellation of defect 17, euler #=-31 (132648,396776,264097) : difference with theory (-32) = -1 CORRECTING DEFECT 18 (vertices=26, convex hull=64) After retessellation of defect 18, euler #=-30 (132660,396840,264150) : difference with theory (-31) = -1 CORRECTING DEFECT 19 (vertices=32, convex hull=60) After retessellation of defect 19, euler #=-29 (132671,396901,264201) : difference with theory (-30) = -1 CORRECTING DEFECT 20 (vertices=730, convex hull=307) After retessellation of defect 20, euler #=-29 (132790,397414,264595) : difference with theory (-29) = 0 CORRECTING DEFECT 21 (vertices=23, convex hull=72) After retessellation of defect 21, euler #=-28 (132804,397480,264648) : difference with theory (-28) = 0 CORRECTING DEFECT 22 (vertices=229, convex hull=69) After retessellation of defect 22, euler #=-27 (132814,397544,264703) : difference with theory (-27) = 0 CORRECTING DEFECT 23 (vertices=31, convex hull=67) After retessellation of defect 23, euler #=-26 (132833,397627,264768) : difference with theory (-26) = 0 CORRECTING DEFECT 24 (vertices=192, convex hull=53) After retessellation of defect 24, euler #=-25 (132854,397715,264836) : difference with theory (-25) = 0 CORRECTING DEFECT 25 (vertices=278, convex hull=45) After retessellation of defect 25, euler #=-24 (132866,397767,264877) : difference with theory (-24) = 0 CORRECTING DEFECT 26 (vertices=62, convex hull=75) After retessellation of defect 26, euler #=-23 (132893,397880,264964) : difference with theory (-23) = 0 CORRECTING DEFECT 27 (vertices=37, convex hull=71) After retessellation of defect 27, euler #=-22 (132913,397970,265035) : difference with theory (-22) = 0 CORRECTING DEFECT 28 (vertices=11, convex hull=13) After retessellation of defect 28, euler #=-21 (132914,397976,265041) : difference with theory (-21) = 0 CORRECTING DEFECT 29 (vertices=26, convex hull=74) After retessellation of defect 29, euler #=-20 (132926,398039,265093) : difference with theory (-20) = 0 CORRECTING DEFECT 30 (vertices=35, convex hull=27) After retessellation of defect 30, euler #=-19 (132929,398056,265108) : difference with theory (-19) = 0 CORRECTING DEFECT 31 (vertices=62, convex hull=66) After retessellation of defect 31, euler #=-17 (132945,398137,265175) : difference with theory (-18) = -1 CORRECTING DEFECT 32 (vertices=19, convex hull=52) After retessellation of defect 32, euler #=-16 (132956,398190,265218) : difference with theory (-17) = -1 CORRECTING DEFECT 33 (vertices=17, convex hull=58) After retessellation of defect 33, euler #=-15 (132965,398238,265258) : difference with theory (-16) = -1 CORRECTING DEFECT 34 (vertices=67, convex hull=89) After retessellation of defect 34, euler #=-14 (132980,398320,265326) : difference with theory (-15) = -1 CORRECTING DEFECT 35 (vertices=35, convex hull=22) After retessellation of defect 35, euler #=-13 (132988,398352,265351) : difference with theory (-14) = -1 CORRECTING DEFECT 36 (vertices=830, convex hull=239) After retessellation of defect 36, euler #=-12 (133098,398797,265687) : difference with theory (-13) = -1 CORRECTING DEFECT 37 (vertices=20, convex hull=21) After retessellation of defect 37, euler #=-11 (133104,398819,265704) : difference with theory (-12) = -1 CORRECTING DEFECT 38 (vertices=31, convex hull=50) After retessellation of defect 38, euler #=-10 (133113,398863,265740) : difference with theory (-11) = -1 CORRECTING DEFECT 39 (vertices=35, convex hull=74) After retessellation of defect 39, euler #=-9 (133123,398924,265792) : difference with theory (-10) = -1 CORRECTING DEFECT 40 (vertices=83, convex hull=84) After retessellation of defect 40, euler #=-8 (133158,399065,265899) : difference with theory (-9) = -1 CORRECTING DEFECT 41 (vertices=26, convex hull=65) After retessellation of defect 41, euler #=-7 (133167,399115,265941) : difference with theory (-8) = -1 CORRECTING DEFECT 42 (vertices=32, convex hull=58) After retessellation of defect 42, euler #=-6 (133182,399179,265991) : difference with theory (-7) = -1 CORRECTING DEFECT 43 (vertices=17, convex hull=59) After retessellation of defect 43, euler #=-5 (133192,399231,266034) : difference with theory (-6) = -1 CORRECTING DEFECT 44 (vertices=52, convex hull=91) After retessellation of defect 44, euler #=-4 (133222,399358,266132) : difference with theory (-5) = -1 CORRECTING DEFECT 45 (vertices=34, convex hull=71) After retessellation of defect 45, euler #=-3 (133241,399445,266201) : difference with theory (-4) = -1 CORRECTING DEFECT 46 (vertices=165, convex hull=155) After retessellation of defect 46, euler #=-2 (133289,399669,266378) : difference with theory (-3) = -1 CORRECTING DEFECT 47 (vertices=82, convex hull=83) After retessellation of defect 47, euler #=-1 (133313,399781,266467) : difference with theory (-2) = -1 CORRECTING DEFECT 48 (vertices=141, convex hull=66) After retessellation of defect 48, euler #=-1 (133331,399871,266539) : difference with theory (-1) = 0 CORRECTING DEFECT 49 (vertices=133, convex hull=118) After retessellation of defect 49, euler #=0 (133371,400050,266679) : difference with theory (0) = 0 CORRECTING DEFECT 50 (vertices=33, convex hull=71) After retessellation of defect 50, euler #=1 (133389,400131,266743) : difference with theory (1) = 0 CORRECTING DEFECT 51 (vertices=40, convex hull=69) After retessellation of defect 51, euler #=2 (133401,400197,266798) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.08-->12.25) (max @ vno 59820 --> 70555) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.08-->12.25) (max @ vno 59820 --> 70555) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 219 mutations (34.5%), 416 crossovers (65.5%), 633 vertices were eliminated building final representation... 5625 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133401, nf=266798, ne=400197, g=0) writing corrected surface to /export/data/hippocampus/HMN/data/HMN002/surf/lh.orig... defective orientation at vertex 130350(130352) with faces 258935 and 266533 defective orientation at vertex 130350(130666) with faces 258935 and 266534 defective orientation at vertex 130351(130352) with faces 258937 and 266535 defective orientation at vertex 130351(130667) with faces 258937 and 266478 defective orientation at vertex 130352(130350) with faces 258935 and 266533 defective orientation at vertex 130352(130351) with faces 258937 and 266535 defective orientation at vertex 130666(130350) with faces 258935 and 266534 defective orientation at vertex 130666(130667) with faces 266534 and 258936 defective orientation at vertex 130667(130666) with faces 258936 and 266534 defective orientation at vertex 130667(130351) with faces 258937 and 266478 0.007 % of the vertices (10 vertices) exhibit an orientation change topology fixing took 58.3 minutes 0 defective edges removing intersecting faces 000: 539 intersecting 001: 22 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 133401 - 400197 + 266798 = 2 --> 0 holes F =2V-4: 266798 = 266802-4 (0) 2E=3F: 800394 = 800394 (0) total defect index = 0 /export/data/hippocampus/HMN/data/HMN002/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 181 intersecting 001: 7 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Mar 5 03:31:24 EST 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs HMN002 lh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /export/data/hippocampus/HMN/data/HMN002/mri/filled.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/brain.finalsurfs.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... 11882 bright wm thresholded. 2069 bright non-wm voxels segmented. reading original surface position from /export/data/hippocampus/HMN/data/HMN002/surf/lh.orig... computing class statistics... border white: 252636 voxels (1.51%) border gray 299430 voxels (1.78%) WM (97.0): 98.1 +- 6.7 [70.0 --> 110.0] GM (87.0) : 85.7 +- 10.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.6 (was 70) setting MAX_BORDER_WHITE to 112.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 57.1 (was 40) setting MAX_GRAY to 99.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /export/data/hippocampus/HMN/data/HMN002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.02-->5.61) (max @ vno 7330 --> 132208) face area 0.28 +- 0.13 (0.00-->6.52) mean absolute distance = 0.70 +- 0.80 5608 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=106, GM=78 using class modes intead of means.... mean inside = 98.2, mean outside = 83.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=86.3, 91 (91) missing vertices, mean dist 0.4 [0.4 (%29.5)->0.8 (%70.5))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.07-->5.36) (max @ vno 7330 --> 132208) face area 0.28 +- 0.14 (0.00-->6.04) mean absolute distance = 0.39 +- 0.50 4459 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4102983.0, rms=8.09 001: dt: 0.5000, sse=4764169.5, rms=5.71 002: dt: 0.5000, sse=5043544.0, rms=4.35 003: dt: 0.5000, sse=5282367.0, rms=3.56 004: dt: 0.5000, sse=5399216.0, rms=3.10 005: dt: 0.5000, sse=5517713.5, rms=2.83 006: dt: 0.5000, sse=5555745.5, rms=2.67 007: dt: 0.5000, sse=5604113.5, rms=2.57 008: dt: 0.5000, sse=5615588.0, rms=2.51 rms = 2.47, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5648258.5, rms=2.47 010: dt: 0.2500, sse=3554015.2, rms=1.82 011: dt: 0.2500, sse=3390192.5, rms=1.70 rms = 1.68, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3320624.5, rms=1.68 rms = 1.66, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3282680.0, rms=1.66 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=89.7, 66 (6) missing vertices, mean dist -0.3 [0.4 (%81.2)->0.3 (%18.8))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.26 (0.04-->6.95) (max @ vno 132744 --> 70479) face area 0.35 +- 0.17 (0.00-->7.22) mean absolute distance = 0.25 +- 0.35 3457 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3853939.8, rms=4.51 014: dt: 0.5000, sse=4076507.2, rms=2.72 015: dt: 0.5000, sse=4313818.5, rms=2.31 016: dt: 0.5000, sse=4634719.5, rms=2.11 rms = 2.21, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=3986382.0, rms=1.70 018: dt: 0.2500, sse=3774716.5, rms=1.48 019: dt: 0.2500, sse=3690509.2, rms=1.41 rms = 1.39, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3660396.0, rms=1.39 rms = 1.38, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3627605.5, rms=1.38 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... mean border=91.6, 59 (3) missing vertices, mean dist -0.1 [0.3 (%72.6)->0.2 (%27.4))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->7.59) (max @ vno 132744 --> 70479) face area 0.34 +- 0.17 (0.00-->7.01) mean absolute distance = 0.21 +- 0.31 3924 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3725827.5, rms=2.68 022: dt: 0.5000, sse=4052589.0, rms=1.83 rms = 1.90, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3862198.5, rms=1.46 024: dt: 0.2500, sse=3797763.0, rms=1.28 rms = 1.24, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3751965.0, rms=1.24 rms = 1.23, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3714811.8, rms=1.23 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... mean border=92.1, 91 (3) missing vertices, mean dist -0.0 [0.2 (%56.5)->0.2 (%43.5))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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 /export/data/hippocampus/HMN/data/HMN002/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3718891.2, rms=1.40 027: dt: 0.5000, sse=4614643.5, rms=1.17 rms = 1.51, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4291444.0, rms=1.03 rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.02, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4264585.5, rms=1.02 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 19 non-cortical segments detected only using segment with 1887 vertices erasing segment 1 (vno[0] = 60884) erasing segment 2 (vno[0] = 66774) erasing segment 3 (vno[0] = 73134) erasing segment 4 (vno[0] = 83864) erasing segment 5 (vno[0] = 87249) erasing segment 6 (vno[0] = 92045) erasing segment 7 (vno[0] = 92138) erasing segment 8 (vno[0] = 96316) erasing segment 9 (vno[0] = 97214) erasing segment 10 (vno[0] = 97259) erasing segment 11 (vno[0] = 100034) erasing segment 12 (vno[0] = 100055) erasing segment 13 (vno[0] = 100076) erasing segment 14 (vno[0] = 101029) erasing segment 15 (vno[0] = 101936) erasing segment 16 (vno[0] = 101959) erasing segment 17 (vno[0] = 132983) erasing segment 18 (vno[0] = 133099) writing cortex label to /export/data/hippocampus/HMN/data/HMN002/label/lh.cortex.label... LabelWrite: saving to /export/data/hippocampus/HMN/data/HMN002/label/lh.cortex.label writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.curv writing smoothed area to lh.area writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.area vertex spacing 0.89 +- 0.26 (0.07-->7.60) (max @ vno 132744 --> 70479) face area 0.33 +- 0.16 (0.00-->7.27) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=69.1, 123 (123) missing vertices, mean dist 1.8 [1.3 (%0.0)->3.0 (%100.0))] %17 local maxima, %40 large gradients and %39 min vals, 2606 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, 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=16554955.0, rms=23.35 001: dt: 0.5000, sse=13096917.0, rms=20.24 002: dt: 0.5000, sse=10607992.0, rms=17.69 003: dt: 0.5000, sse=8823639.0, rms=15.62 004: dt: 0.5000, sse=7589602.0, rms=13.93 005: dt: 0.5000, sse=6761959.0, rms=12.60 006: dt: 0.5000, sse=6277445.0, rms=11.58 007: dt: 0.5000, sse=6000964.0, rms=10.76 008: dt: 0.5000, sse=5854822.0, rms=10.04 009: dt: 0.5000, sse=5772577.0, rms=9.40 010: dt: 0.5000, sse=5728740.5, rms=8.79 011: dt: 0.5000, sse=5711670.0, rms=8.17 012: dt: 0.5000, sse=5674914.5, rms=7.53 013: dt: 0.5000, sse=5654315.0, rms=6.87 014: dt: 0.5000, sse=5646178.0, rms=6.19 015: dt: 0.5000, sse=5615815.0, rms=5.53 016: dt: 0.5000, sse=5664740.5, rms=4.92 017: dt: 0.5000, sse=5664847.0, rms=4.45 018: dt: 0.5000, sse=5759560.5, rms=4.09 019: dt: 0.5000, sse=5778381.5, rms=3.86 020: dt: 0.5000, sse=5885265.5, rms=3.69 021: dt: 0.5000, sse=5934685.5, rms=3.61 022: dt: 0.5000, sse=5970940.0, rms=3.53 rms = 3.49, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=5967367.0, rms=3.49 024: dt: 0.2500, sse=4511610.0, rms=3.03 025: dt: 0.2500, sse=4418108.5, rms=2.92 rms = 2.92, time step reduction 2 of 3 to 0.125... rms = 2.87, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4346607.0, rms=2.87 positioning took 3.5 minutes mean border=67.3, 1494 (19) missing vertices, mean dist 0.2 [0.2 (%41.5)->0.6 (%58.5))] %41 local maxima, %22 large gradients and %32 min vals, 1229 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, 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=4912577.5, rms=4.32 027: dt: 0.5000, sse=5141480.5, rms=3.75 028: dt: 0.5000, sse=6063369.5, rms=3.49 rms = 3.60, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5255423.5, rms=3.08 030: dt: 0.2500, sse=4913391.5, rms=2.94 rms = 2.95, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=4849792.5, rms=2.89 032: dt: 0.1250, sse=4744173.5, rms=2.82 rms = 2.80, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4719243.5, rms=2.80 positioning took 1.2 minutes mean border=66.3, 2085 (16) missing vertices, mean dist 0.1 [0.2 (%36.9)->0.4 (%63.1))] %53 local maxima, %10 large gradients and %32 min vals, 1299 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, 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=4798855.5, rms=3.22 rms = 3.33, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4678051.5, rms=2.97 035: dt: 0.2500, sse=4744783.5, rms=2.82 rms = 2.81, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=4878649.0, rms=2.81 037: dt: 0.1250, sse=4776298.5, rms=2.71 rms = 2.70, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4802865.5, rms=2.70 positioning took 0.8 minutes mean border=65.7, 4408 (12) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.3 (%56.3))] %53 local maxima, % 9 large gradients and %31 min vals, 1112 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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 /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4812541.0, rms=2.78 rms = 3.00, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=4778070.0, rms=2.68 040: dt: 0.2500, sse=4982242.5, rms=2.63 rms = 2.63, time step reduction 2 of 3 to 0.125... rms = 2.61, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4947610.5, rms=2.61 positioning took 0.6 minutes writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.area.pial vertex spacing 1.05 +- 0.48 (0.05-->8.46) (max @ vno 132744 --> 70479) face area 0.43 +- 0.35 (0.00-->7.80) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133401 vertices processed 25000 of 133401 vertices processed 50000 of 133401 vertices processed 75000 of 133401 vertices processed 100000 of 133401 vertices processed 125000 of 133401 vertices processed 0 of 133401 vertices processed 25000 of 133401 vertices processed 50000 of 133401 vertices processed 75000 of 133401 vertices processed 100000 of 133401 vertices processed 125000 of 133401 vertices processed thickness calculation complete, 3406:4972 truncations. 45236 vertices at 0 distance 68893 vertices at 1 distance 69898 vertices at 2 distance 40805 vertices at 3 distance 18762 vertices at 4 distance 7454 vertices at 5 distance 2987 vertices at 6 distance 1343 vertices at 7 distance 721 vertices at 8 distance 416 vertices at 9 distance 261 vertices at 10 distance 186 vertices at 11 distance 135 vertices at 12 distance 100 vertices at 13 distance 69 vertices at 14 distance 54 vertices at 15 distance 57 vertices at 16 distance 45 vertices at 17 distance 29 vertices at 18 distance 43 vertices at 19 distance 38 vertices at 20 distance writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.thickness positioning took 14.2 minutes #-------------------------------------------- #@# Smooth2 lh Thu Mar 5 03:45:33 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /export/data/hippocampus/HMN/data/HMN002/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 Mar 5 03:45:38 EST 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 44.3 mm, total surface area = 81276 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.113 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.049 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.018 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 0.7 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 292 vertices thresholded to be in k1 ~ [-0.27 0.25], k2 ~ [-0.10 0.04] total integrated curvature = 0.457*4pi (5.746) --> 1 handles ICI = 1.5, FI = 8.9, variation=155.405 155 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 146 vertices thresholded to be in [-0.15 0.12] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.022 done. #-------------------------------------------- #@# Tessellate rh Thu Mar 5 03:48:04 EST 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 2 found - 2 modified | TOTAL: 4 pass 2 (xz+): 0 found - 2 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4 (out of 222306: 0.001799) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 60: 1055 vertices, 1157 faces slice 70: 6761 vertices, 6992 faces slice 80: 14986 vertices, 15364 faces slice 90: 26361 vertices, 26764 faces slice 100: 38540 vertices, 38946 faces slice 110: 50260 vertices, 50724 faces slice 120: 63727 vertices, 64177 faces slice 130: 77117 vertices, 77571 faces slice 140: 89381 vertices, 89849 faces slice 150: 101494 vertices, 101963 faces slice 160: 112460 vertices, 112871 faces slice 170: 121745 vertices, 122105 faces slice 180: 130243 vertices, 130560 faces slice 190: 136529 vertices, 136797 faces slice 200: 140367 vertices, 140572 faces slice 210: 140958 vertices, 141060 faces slice 220: 140958 vertices, 141060 faces slice 230: 140958 vertices, 141060 faces slice 240: 140958 vertices, 141060 faces slice 250: 140958 vertices, 141060 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... 140958 voxel in cpt #1: X=-102 [v=140958,e=423180,f=282120] located at (30.163332, -2.783496, 32.737370) For the whole surface: X=-102 [v=140958,e=423180,f=282120] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Mar 5 03:48:14 EST 2015 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /export/data/hippocampus/HMN/data/HMN002/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 Mar 5 03:48:20 EST 2015 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /export/data/hippocampus/HMN/data/HMN002/scripts avg radius = 44.3 mm, total surface area = 74407 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes Not saving sulc step 000: RMS=0.105 (target=0.015) step 005: RMS=0.079 (target=0.015) step 010: RMS=0.062 (target=0.015) step 015: RMS=0.055 (target=0.015) step 020: RMS=0.049 (target=0.015) step 025: RMS=0.045 (target=0.015) step 030: RMS=0.043 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.039 (target=0.015) step 045: RMS=0.039 (target=0.015) step 050: RMS=0.038 (target=0.015) step 055: RMS=0.037 (target=0.015) step 060: RMS=0.037 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Mar 5 03:49:05 EST 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.56 (0.00-->7.22) (max @ vno 102383 --> 103651) face area 0.03 +- 0.03 (-0.31-->0.87) scaling brain by 0.328... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.487, avgs=0 005/300: dt: 0.9000, rms radial error=175.232, avgs=0 010/300: dt: 0.9000, rms radial error=174.685, avgs=0 015/300: dt: 0.9000, rms radial error=173.966, avgs=0 020/300: dt: 0.9000, rms radial error=173.146, avgs=0 025/300: dt: 0.9000, rms radial error=172.271, avgs=0 030/300: dt: 0.9000, rms radial error=171.363, avgs=0 035/300: dt: 0.9000, rms radial error=170.437, avgs=0 040/300: dt: 0.9000, rms radial error=169.502, avgs=0 045/300: dt: 0.9000, rms radial error=168.565, avgs=0 050/300: dt: 0.9000, rms radial error=167.628, avgs=0 055/300: dt: 0.9000, rms radial error=166.692, avgs=0 060/300: dt: 0.9000, rms radial error=165.760, avgs=0 065/300: dt: 0.9000, rms radial error=164.832, avgs=0 070/300: dt: 0.9000, rms radial error=163.908, avgs=0 075/300: dt: 0.9000, rms radial error=162.988, avgs=0 080/300: dt: 0.9000, rms radial error=162.073, avgs=0 085/300: dt: 0.9000, rms radial error=161.163, avgs=0 090/300: dt: 0.9000, rms radial error=160.257, avgs=0 095/300: dt: 0.9000, rms radial error=159.355, avgs=0 100/300: dt: 0.9000, rms radial error=158.459, avgs=0 105/300: dt: 0.9000, rms radial error=157.568, avgs=0 110/300: dt: 0.9000, rms radial error=156.682, avgs=0 115/300: dt: 0.9000, rms radial error=155.799, avgs=0 120/300: dt: 0.9000, rms radial error=154.922, avgs=0 125/300: dt: 0.9000, rms radial error=154.049, avgs=0 130/300: dt: 0.9000, rms radial error=153.181, avgs=0 135/300: dt: 0.9000, rms radial error=152.317, avgs=0 140/300: dt: 0.9000, rms radial error=151.458, avgs=0 145/300: dt: 0.9000, rms radial error=150.603, avgs=0 150/300: dt: 0.9000, rms radial error=149.753, avgs=0 155/300: dt: 0.9000, rms radial error=148.907, avgs=0 160/300: dt: 0.9000, rms radial error=148.066, avgs=0 165/300: dt: 0.9000, rms radial error=147.228, avgs=0 170/300: dt: 0.9000, rms radial error=146.398, avgs=0 175/300: dt: 0.9000, rms radial error=145.571, avgs=0 180/300: dt: 0.9000, rms radial error=144.748, avgs=0 185/300: dt: 0.9000, rms radial error=143.930, avgs=0 190/300: dt: 0.9000, rms radial error=143.117, avgs=0 195/300: dt: 0.9000, rms radial error=142.304, avgs=0 200/300: dt: 0.9000, rms radial error=141.503, avgs=0 205/300: dt: 0.9000, rms radial error=140.704, avgs=0 210/300: dt: 0.9000, rms radial error=139.906, avgs=0 215/300: dt: 0.9000, rms radial error=139.113, avgs=0 220/300: dt: 0.9000, rms radial error=138.324, avgs=0 225/300: dt: 0.9000, rms radial error=137.548, avgs=0 230/300: dt: 0.9000, rms radial error=136.770, avgs=0 235/300: dt: 0.9000, rms radial error=135.996, avgs=0 240/300: dt: 0.9000, rms radial error=135.227, avgs=0 245/300: dt: 0.9000, rms radial error=134.463, avgs=0 250/300: dt: 0.9000, rms radial error=133.702, avgs=0 255/300: dt: 0.9000, rms radial error=132.946, avgs=0 260/300: dt: 0.9000, rms radial error=132.194, avgs=0 265/300: dt: 0.9000, rms radial error=131.447, avgs=0 270/300: dt: 0.9000, rms radial error=130.704, avgs=0 275/300: dt: 0.9000, rms radial error=129.965, avgs=0 280/300: dt: 0.9000, rms radial error=129.230, avgs=0 285/300: dt: 0.9000, rms radial error=128.500, avgs=0 290/300: dt: 0.9000, rms radial error=127.773, avgs=0 295/300: dt: 0.9000, rms radial error=127.051, avgs=0 300/300: dt: 0.9000, rms radial error=126.333, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16189.88 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 = 2593.22 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 247.68 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00538 epoch 4 (K=640.0), pass 1, starting sse = 20.48 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/12 = 0.00580 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Mar 5 03:55:00 EST 2015 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /export/data/hippocampus/HMN/data/HMN002/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 HMN002 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-102 (nv=140958, nf=282120, ne=423180, g=52) 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... 8986 ambiguous faces found in tessellation segmenting defects... 58 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 4 57 defects to be corrected 0 vertices coincident reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2850 (-4.6425) -vertex loglikelihood: -5.7730 (-2.8865) -normal dot loglikelihood: -3.4516 (-3.4516) -quad curv loglikelihood: -6.2498 (-3.1249) Total Loglikelihood : -24.7593 CORRECTING DEFECT 0 (vertices=675, convex hull=246) After retessellation of defect 0, euler #=-52 (135720,405717,269945) : difference with theory (-54) = -2 CORRECTING DEFECT 1 (vertices=70, convex hull=34) After retessellation of defect 1, euler #=-51 (135723,405742,269968) : difference with theory (-53) = -2 CORRECTING DEFECT 2 (vertices=108, convex hull=88) After retessellation of defect 2, euler #=-50 (135742,405846,270054) : difference with theory (-52) = -2 CORRECTING DEFECT 3 (vertices=22, convex hull=43) After retessellation of defect 3, euler #=-49 (135750,405886,270087) : difference with theory (-51) = -2 CORRECTING DEFECT 4 (vertices=54, convex hull=63) After retessellation of defect 4, euler #=-47 (135765,405951,270139) : difference with theory (-50) = -3 CORRECTING DEFECT 5 (vertices=30, convex hull=62) After retessellation of defect 5, euler #=-46 (135774,406008,270188) : difference with theory (-49) = -3 CORRECTING DEFECT 6 (vertices=28, convex hull=65) After retessellation of defect 6, euler #=-45 (135789,406077,270243) : difference with theory (-48) = -3 CORRECTING DEFECT 7 (vertices=917, convex hull=97) After retessellation of defect 7, euler #=-45 (135821,406215,270349) : difference with theory (-47) = -2 CORRECTING DEFECT 8 (vertices=37, convex hull=37) After retessellation of defect 8, euler #=-44 (135824,406239,270371) : difference with theory (-46) = -2 CORRECTING DEFECT 9 (vertices=25, convex hull=64) After retessellation of defect 9, euler #=-43 (135839,406308,270426) : difference with theory (-45) = -2 CORRECTING DEFECT 10 (vertices=23, convex hull=60) After retessellation of defect 10, euler #=-42 (135850,406364,270472) : difference with theory (-44) = -2 CORRECTING DEFECT 11 (vertices=34, convex hull=88) After retessellation of defect 11, euler #=-41 (135866,406448,270541) : difference with theory (-43) = -2 CORRECTING DEFECT 12 (vertices=39, convex hull=62) After retessellation of defect 12, euler #=-40 (135883,406526,270603) : difference with theory (-42) = -2 CORRECTING DEFECT 13 (vertices=38, convex hull=67) After retessellation of defect 13, euler #=-39 (135901,406608,270668) : difference with theory (-41) = -2 CORRECTING DEFECT 14 (vertices=27, convex hull=59) After retessellation of defect 14, euler #=-38 (135920,406687,270729) : difference with theory (-40) = -2 CORRECTING DEFECT 15 (vertices=61, convex hull=82) After retessellation of defect 15, euler #=-37 (135960,406841,270844) : difference with theory (-39) = -2 CORRECTING DEFECT 16 (vertices=462, convex hull=222) After retessellation of defect 16, euler #=-36 (136091,407339,271212) : difference with theory (-38) = -2 CORRECTING DEFECT 17 (vertices=18, convex hull=35) After retessellation of defect 17, euler #=-35 (136100,407378,271243) : difference with theory (-37) = -2 CORRECTING DEFECT 18 (vertices=38, convex hull=34) After retessellation of defect 18, euler #=-34 (136103,407400,271263) : difference with theory (-36) = -2 CORRECTING DEFECT 19 (vertices=80, convex hull=39) After retessellation of defect 19, euler #=-33 (136112,407446,271301) : difference with theory (-35) = -2 CORRECTING DEFECT 20 (vertices=54, convex hull=64) After retessellation of defect 20, euler #=-32 (136139,407559,271388) : difference with theory (-34) = -2 CORRECTING DEFECT 21 (vertices=31, convex hull=45) After retessellation of defect 21, euler #=-31 (136154,407618,271433) : difference with theory (-33) = -2 CORRECTING DEFECT 22 (vertices=6, convex hull=27) After retessellation of defect 22, euler #=-30 (136155,407627,271442) : difference with theory (-32) = -2 CORRECTING DEFECT 23 (vertices=215, convex hull=48) After retessellation of defect 23, euler #=-29 (136167,407684,271488) : difference with theory (-31) = -2 CORRECTING DEFECT 24 (vertices=42, convex hull=72) After retessellation of defect 24, euler #=-28 (136191,407785,271566) : difference with theory (-30) = -2 CORRECTING DEFECT 25 (vertices=33, convex hull=67) After retessellation of defect 25, euler #=-27 (136202,407847,271618) : difference with theory (-29) = -2 CORRECTING DEFECT 26 (vertices=73, convex hull=111) After retessellation of defect 26, euler #=-26 (136248,408033,271759) : difference with theory (-28) = -2 CORRECTING DEFECT 27 (vertices=110, convex hull=66) After retessellation of defect 27, euler #=-25 (136262,408103,271816) : difference with theory (-27) = -2 CORRECTING DEFECT 28 (vertices=23, convex hull=57) After retessellation of defect 28, euler #=-24 (136274,408162,271864) : difference with theory (-26) = -2 CORRECTING DEFECT 29 (vertices=33, convex hull=52) After retessellation of defect 29, euler #=-23 (136288,408222,271911) : difference with theory (-25) = -2 CORRECTING DEFECT 30 (vertices=9, convex hull=18) After retessellation of defect 30, euler #=-22 (136289,408230,271919) : difference with theory (-24) = -2 CORRECTING DEFECT 31 (vertices=21, convex hull=22) After retessellation of defect 31, euler #=-21 (136292,408246,271933) : difference with theory (-23) = -2 CORRECTING DEFECT 32 (vertices=72, convex hull=23) After retessellation of defect 32, euler #=-20 (136296,408263,271947) : difference with theory (-22) = -2 CORRECTING DEFECT 33 (vertices=28, convex hull=41) After retessellation of defect 33, euler #=-20 (136305,408307,271982) : difference with theory (-21) = -1 CORRECTING DEFECT 34 (vertices=56, convex hull=24) After retessellation of defect 34, euler #=-19 (136310,408329,272000) : difference with theory (-20) = -1 CORRECTING DEFECT 35 (vertices=36, convex hull=88) After retessellation of defect 35, euler #=-18 (136327,408414,272069) : difference with theory (-19) = -1 CORRECTING DEFECT 36 (vertices=6, convex hull=24) After retessellation of defect 36, euler #=-17 (136327,408421,272077) : difference with theory (-18) = -1 CORRECTING DEFECT 37 (vertices=156, convex hull=47) After retessellation of defect 37, euler #=-16 (136337,408471,272118) : difference with theory (-17) = -1 CORRECTING DEFECT 38 (vertices=7, convex hull=15) After retessellation of defect 38, euler #=-15 (136339,408479,272125) : difference with theory (-16) = -1 CORRECTING DEFECT 39 (vertices=33, convex hull=70) After retessellation of defect 39, euler #=-14 (136351,408542,272177) : difference with theory (-15) = -1 CORRECTING DEFECT 40 (vertices=24, convex hull=47) After retessellation of defect 40, euler #=-13 (136363,408594,272218) : difference with theory (-14) = -1 CORRECTING DEFECT 41 (vertices=17, convex hull=18) After retessellation of defect 41, euler #=-12 (136368,408612,272232) : difference with theory (-13) = -1 CORRECTING DEFECT 42 (vertices=38, convex hull=23) After retessellation of defect 42, euler #=-11 (136369,408621,272241) : difference with theory (-12) = -1 CORRECTING DEFECT 43 (vertices=52, convex hull=67) After retessellation of defect 43, euler #=-10 (136391,408718,272317) : difference with theory (-11) = -1 CORRECTING DEFECT 44 (vertices=6, convex hull=21) After retessellation of defect 44, euler #=-9 (136391,408723,272323) : difference with theory (-10) = -1 CORRECTING DEFECT 45 (vertices=261, convex hull=143) After retessellation of defect 45, euler #=-9 (136447,408970,272514) : difference with theory (-9) = 0 CORRECTING DEFECT 46 (vertices=44, convex hull=62) After retessellation of defect 46, euler #=-8 (136463,409050,272579) : difference with theory (-8) = 0 CORRECTING DEFECT 47 (vertices=27, convex hull=59) After retessellation of defect 47, euler #=-7 (136476,409114,272631) : difference with theory (-7) = 0 CORRECTING DEFECT 48 (vertices=27, convex hull=60) After retessellation of defect 48, euler #=-6 (136491,409183,272686) : difference with theory (-6) = 0 CORRECTING DEFECT 49 (vertices=79, convex hull=109) After retessellation of defect 49, euler #=-5 (136520,409321,272796) : difference with theory (-5) = 0 CORRECTING DEFECT 50 (vertices=198, convex hull=50) After retessellation of defect 50, euler #=-4 (136542,409407,272861) : difference with theory (-4) = 0 CORRECTING DEFECT 51 (vertices=36, convex hull=82) After retessellation of defect 51, euler #=-3 (136555,409477,272919) : difference with theory (-3) = 0 CORRECTING DEFECT 52 (vertices=351, convex hull=103) After retessellation of defect 52, euler #=-2 (136613,409695,273080) : difference with theory (-2) = 0 CORRECTING DEFECT 53 (vertices=50, convex hull=85) After retessellation of defect 53, euler #=-1 (136640,409809,273168) : difference with theory (-1) = 0 CORRECTING DEFECT 54 (vertices=57, convex hull=51) After retessellation of defect 54, euler #=0 (136653,409866,273213) : difference with theory (0) = 0 CORRECTING DEFECT 55 (vertices=84, convex hull=99) After retessellation of defect 55, euler #=1 (136684,410007,273324) : difference with theory (1) = 0 CORRECTING DEFECT 56 (vertices=73, convex hull=99) After retessellation of defect 56, euler #=2 (136699,410091,273394) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.06-->11.98) (max @ vno 306 --> 4911) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.06-->11.98) (max @ vno 306 --> 4911) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 207 mutations (33.8%), 406 crossovers (66.2%), 263 vertices were eliminated building final representation... 4259 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=136699, nf=273394, ne=410091, g=0) writing corrected surface to /export/data/hippocampus/HMN/data/HMN002/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 50.9 minutes 0 defective edges removing intersecting faces 000: 498 intersecting 001: 20 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 136699 - 410091 + 273394 = 2 --> 0 holes F =2V-4: 273394 = 273398-4 (0) 2E=3F: 820182 = 820182 (0) total defect index = 0 /export/data/hippocampus/HMN/data/HMN002/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 92 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Mar 5 04:46:02 EST 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs HMN002 rh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /export/data/hippocampus/HMN/data/HMN002/mri/filled.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/brain.finalsurfs.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... 12100 bright wm thresholded. 2080 bright non-wm voxels segmented. reading original surface position from /export/data/hippocampus/HMN/data/HMN002/surf/rh.orig... computing class statistics... border white: 252636 voxels (1.51%) border gray 299430 voxels (1.78%) WM (97.0): 98.0 +- 6.9 [70.0 --> 110.0] GM (87.0) : 85.8 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.9 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 79.0 (was 85) setting MAX_CSF to 58.8 (was 40) setting MAX_GRAY to 99.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 74.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.7 (was 40) repositioning cortical surface to gray/white boundary reading volume /export/data/hippocampus/HMN/data/HMN002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.04-->5.78) (max @ vno 111201 --> 136449) face area 0.28 +- 0.13 (0.00-->7.65) mean absolute distance = 0.70 +- 0.81 5544 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=106, GM=79 using class modes intead of means.... mean inside = 98.4, mean outside = 84.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=86.8, 72 (72) missing vertices, mean dist 0.4 [0.5 (%30.2)->0.8 (%69.8))] %73 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.07-->5.79) (max @ vno 51773 --> 51772) face area 0.28 +- 0.14 (0.00-->6.23) mean absolute distance = 0.39 +- 0.50 4214 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4075391.5, rms=7.73 001: dt: 0.5000, sse=4791392.5, rms=5.38 002: dt: 0.5000, sse=5051756.5, rms=4.12 003: dt: 0.5000, sse=5299804.5, rms=3.43 004: dt: 0.5000, sse=5437011.5, rms=3.03 005: dt: 0.5000, sse=5501947.0, rms=2.79 006: dt: 0.5000, sse=5566222.5, rms=2.62 007: dt: 0.5000, sse=5585892.5, rms=2.53 008: dt: 0.5000, sse=5608480.5, rms=2.46 rms = 2.42, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5620829.0, rms=2.42 010: dt: 0.2500, sse=3628310.5, rms=1.80 011: dt: 0.2500, sse=3454340.5, rms=1.69 rms = 1.67, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3386250.5, rms=1.67 rms = 1.65, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3346055.8, rms=1.65 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.2, 54 (12) missing vertices, mean dist -0.3 [0.4 (%80.9)->0.3 (%19.1))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.06-->6.00) (max @ vno 51773 --> 51772) face area 0.34 +- 0.17 (0.00-->7.44) mean absolute distance = 0.25 +- 0.34 4068 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3901785.2, rms=4.43 014: dt: 0.5000, sse=4111815.5, rms=2.68 015: dt: 0.5000, sse=4316380.5, rms=2.23 016: dt: 0.5000, sse=4595734.0, rms=2.02 rms = 2.12, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=3988335.8, rms=1.65 018: dt: 0.2500, sse=3779467.8, rms=1.44 019: dt: 0.2500, sse=3708121.8, rms=1.38 rms = 1.35, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3670302.5, rms=1.35 rms = 1.33, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3642201.8, rms=1.33 positioning took 1.1 minutes 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 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=92.1, 56 (5) missing vertices, mean dist -0.1 [0.2 (%72.8)->0.2 (%27.2))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->6.15) (max @ vno 51773 --> 51772) face area 0.33 +- 0.16 (0.00-->7.01) mean absolute distance = 0.20 +- 0.30 3541 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3760879.8, rms=2.69 022: dt: 0.5000, sse=4062065.2, rms=1.78 rms = 1.80, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3871960.0, rms=1.42 024: dt: 0.2500, sse=3806172.8, rms=1.22 rms = 1.18, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3760796.0, rms=1.18 rms = 1.17, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3731153.2, rms=1.17 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=92.6, 99 (3) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))] %94 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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 /export/data/hippocampus/HMN/data/HMN002/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3736304.5, rms=1.35 027: dt: 0.5000, sse=4564150.0, rms=1.10 rms = 1.42, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4260731.5, rms=0.97 rms = 0.97, time step reduction 2 of 3 to 0.125... rms = 0.96, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4234940.5, rms=0.96 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 11 non-cortical segments detected only using segment with 1928 vertices erasing segment 0 (vno[0] = 46589) erasing segment 2 (vno[0] = 90201) erasing segment 3 (vno[0] = 92382) erasing segment 4 (vno[0] = 93494) erasing segment 5 (vno[0] = 93618) erasing segment 6 (vno[0] = 95948) erasing segment 7 (vno[0] = 96026) erasing segment 8 (vno[0] = 98574) erasing segment 9 (vno[0] = 104205) erasing segment 10 (vno[0] = 104270) writing cortex label to /export/data/hippocampus/HMN/data/HMN002/label/rh.cortex.label... LabelWrite: saving to /export/data/hippocampus/HMN/data/HMN002/label/rh.cortex.label writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.curv writing smoothed area to rh.area writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.area vertex spacing 0.89 +- 0.25 (0.08-->6.24) (max @ vno 51773 --> 51772) face area 0.33 +- 0.16 (0.00-->7.00) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=70.3, 82 (82) missing vertices, mean dist 1.8 [0.9 (%0.0)->2.9 (%100.0))] %18 local maxima, %42 large gradients and %36 min vals, 2688 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, 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=16092127.0, rms=22.64 001: dt: 0.5000, sse=12701618.0, rms=19.55 002: dt: 0.5000, sse=10280120.0, rms=17.04 003: dt: 0.5000, sse=8568176.0, rms=15.03 004: dt: 0.5000, sse=7410803.0, rms=13.44 005: dt: 0.5000, sse=6653103.5, rms=12.20 006: dt: 0.5000, sse=6179308.5, rms=11.23 007: dt: 0.5000, sse=5935779.0, rms=10.42 008: dt: 0.5000, sse=5782097.5, rms=9.70 009: dt: 0.5000, sse=5722526.5, rms=9.06 010: dt: 0.5000, sse=5671540.5, rms=8.44 011: dt: 0.5000, sse=5657262.5, rms=7.85 012: dt: 0.5000, sse=5620930.5, rms=7.22 013: dt: 0.5000, sse=5625775.0, rms=6.58 014: dt: 0.5000, sse=5634167.5, rms=5.94 015: dt: 0.5000, sse=5648099.5, rms=5.36 016: dt: 0.5000, sse=5722630.0, rms=4.84 017: dt: 0.5000, sse=5777541.5, rms=4.46 018: dt: 0.5000, sse=5883496.0, rms=4.14 019: dt: 0.5000, sse=5924531.5, rms=3.95 020: dt: 0.5000, sse=5972378.5, rms=3.78 021: dt: 0.5000, sse=6025382.5, rms=3.69 022: dt: 0.5000, sse=6011741.5, rms=3.60 rms = 3.56, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=6076673.0, rms=3.56 024: dt: 0.2500, sse=4529025.0, rms=3.05 025: dt: 0.2500, sse=4418403.5, rms=2.93 rms = 2.92, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4370254.0, rms=2.92 027: dt: 0.1250, sse=4180393.5, rms=2.79 rms = 2.77, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4156441.2, rms=2.77 positioning took 3.7 minutes mean border=68.3, 1445 (17) missing vertices, mean dist 0.2 [0.2 (%40.3)->0.6 (%59.7))] %43 local maxima, %23 large gradients and %30 min vals, 1074 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, 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=4776384.0, rms=4.47 029: dt: 0.5000, sse=4947324.5, rms=3.89 030: dt: 0.5000, sse=5997894.0, rms=3.66 rms = 3.75, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=5204625.5, rms=3.21 032: dt: 0.2500, sse=4875986.5, rms=3.05 rms = 3.05, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=4908868.0, rms=3.05 034: dt: 0.1250, sse=4723997.5, rms=2.89 rms = 2.86, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4710372.5, rms=2.86 positioning took 1.1 minutes mean border=67.0, 1823 (15) missing vertices, mean dist 0.1 [0.2 (%34.6)->0.4 (%65.4))] %56 local maxima, %10 large gradients and %30 min vals, 1209 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, 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=4809860.0, rms=3.34 rms = 3.48, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=4677156.0, rms=3.06 037: dt: 0.2500, sse=4727441.0, rms=2.89 rms = 2.87, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4890182.5, rms=2.87 039: dt: 0.1250, sse=4784689.5, rms=2.77 rms = 2.74, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4815907.0, rms=2.74 positioning took 0.8 minutes mean border=66.5, 4108 (13) missing vertices, mean dist 0.1 [0.2 (%42.8)->0.3 (%57.2))] %56 local maxima, % 9 large gradients and %29 min vals, 1010 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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 /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4824547.5, rms=2.81 rms = 3.08, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4789053.0, rms=2.71 rms = 2.66, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=4997433.5, rms=2.66 043: dt: 0.1250, sse=4919479.5, rms=2.61 rms = 2.59, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4963043.5, rms=2.59 positioning took 0.7 minutes writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.area.pial vertex spacing 1.04 +- 0.48 (0.04-->8.48) (max @ vno 51773 --> 51772) face area 0.42 +- 0.35 (0.00-->7.91) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136699 vertices processed 25000 of 136699 vertices processed 50000 of 136699 vertices processed 75000 of 136699 vertices processed 100000 of 136699 vertices processed 125000 of 136699 vertices processed 0 of 136699 vertices processed 25000 of 136699 vertices processed 50000 of 136699 vertices processed 75000 of 136699 vertices processed 100000 of 136699 vertices processed 125000 of 136699 vertices processed thickness calculation complete, 3234:4951 truncations. 49120 vertices at 0 distance 65969 vertices at 1 distance 70607 vertices at 2 distance 43069 vertices at 3 distance 20030 vertices at 4 distance 8278 vertices at 5 distance 3235 vertices at 6 distance 1458 vertices at 7 distance 713 vertices at 8 distance 365 vertices at 9 distance 247 vertices at 10 distance 175 vertices at 11 distance 123 vertices at 12 distance 105 vertices at 13 distance 96 vertices at 14 distance 93 vertices at 15 distance 77 vertices at 16 distance 80 vertices at 17 distance 62 vertices at 18 distance 35 vertices at 19 distance 55 vertices at 20 distance writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.thickness positioning took 14.4 minutes #-------------------------------------------- #@# Smooth2 rh Thu Mar 5 05:00:29 EST 2015 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /export/data/hippocampus/HMN/data/HMN002/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Thu Mar 5 05:00:34 EST 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 44.0 mm, total surface area = 82570 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.050 (target=0.015) step 020: RMS=0.043 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.030 (target=0.015) step 035: RMS=0.027 (target=0.015) step 040: RMS=0.024 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.018 (target=0.015) step 055: RMS=0.017 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 0.8 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 290 vertices thresholded to be in k1 ~ [-0.29 0.42], k2 ~ [-0.11 0.07] total integrated curvature = 0.442*4pi (5.560) --> 1 handles ICI = 1.5, FI = 10.7, variation=178.534 167 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 153 vertices thresholded to be in [-0.17 0.21] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025 done. #-------------------------------------------- #@# ASeg Stats Thu Mar 5 05:03:06 EST 2015 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /export/data/hippocampus/HMN/data/HMN002 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /cell_root/software/freesurfer/current/sys/ASegStatsLUT.txt --subject HMN002 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /cell_root/software/freesurfer/current/sys/ASegStatsLUT.txt --subject HMN002 sysname Linux hostname hippocampus.umd.edu machine x86_64 user lmarti atlas_icv (eTIV) = 1309444 mm^3 (det: 1.487735 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 200673 rh white matter volume 202202 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 213437.531791, pTot = 514187.959097 c = 300750.427305 rh surface-based volumes (mm3): wTot = 214221.708716, pTot = 518408.319389 c = 304186.610673 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 1822 1822 4 5 Left-Inf-Lat-Vent 584 584 5 7 Left-Cerebellum-White-Matter 11333 11333 6 8 Left-Cerebellum-Cortex 58691 58691 7 10 Left-Thalamus-Proper 6704 6704 8 11 Left-Caudate 3471 3471 9 12 Left-Putamen 6150 6150 10 13 Left-Pallidum 1735 1735 11 14 3rd-Ventricle 605 605 12 15 4th-Ventricle 1330 1330 13 16 Brain-Stem 18262 18262 14 17 Left-Hippocampus 3705 3705 15 18 Left-Amygdala 1563 1563 16 24 CSF 998 998 17 26 Left-Accumbens-area 525 525 18 28 Left-VentralDC 3657 3657 19 30 Left-vessel 50 50 20 31 Left-choroid-plexus 700 700 23 43 Right-Lateral-Ventricle 1930 1930 24 44 Right-Inf-Lat-Vent 106 106 25 46 Right-Cerebellum-White-Matter 11397 11397 26 47 Right-Cerebellum-Cortex 57882 57882 27 49 Right-Thalamus-Proper 6772 6772 28 50 Right-Caudate 3547 3547 29 51 Right-Putamen 6127 6127 30 52 Right-Pallidum 1708 1708 31 53 Right-Hippocampus 4056 4056 32 54 Right-Amygdala 1696 1696 33 58 Right-Accumbens-area 653 653 34 60 Right-VentralDC 3678 3678 35 62 Right-vessel 40 40 36 63 Right-choroid-plexus 762 762 37 72 5th-Ventricle 3 3 38 77 WM-hypointensities 2163 2163 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 2 2 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 191 191 45 251 CC_Posterior 787 787 46 252 CC_Mid_Posterior 391 391 47 253 CC_Central 529 529 48 254 CC_Mid_Anterior 417 417 49 255 CC_Anterior 821 821 Reporting on 45 segmentations SubCortGrayVol = 190582 #-------------------------------------------- #@# Hippocampal Subfields processing Thu Mar 5 05:13:08 EST 2015 mkdir -p /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh HMN002 left /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh HMN002 right /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults cp /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults/HMN002/left/segmentationWithoutPartialVolumingLog/posterior_left* /export/data/hippocampus/HMN/data/HMN002/mri cp /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults/HMN002/left/segmentationWithoutPartialVolumingLog/posterior_Left* /export/data/hippocampus/HMN/data/HMN002/mri cp /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults/HMN002/right/segmentationWithoutPartialVolumingLog/posterior_right* /export/data/hippocampus/HMN/data/HMN002/mri cp /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults/HMN002/right/segmentationWithoutPartialVolumingLog/posterior_Right* /export/data/hippocampus/HMN/data/HMN002/mri rm -rf /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults #------------------------------------------ recon-all -s HMN002 finished without error at Thu Mar 5 07:37:14 EST 2015 New invocation of recon-all Thu Apr 2 13:57:35 EDT 2015 /export/data/hippocampus/HMN/data/HMN002 /cell_root/software/freesurfer/current/sys/bin/recon-all -s HMN002 -autorecon3 -hippo-subfields subjid HMN002 setenv SUBJECTS_DIR /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/5.1.0/Linux-x64 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux hippocampus.umd.edu 2.6.32-504.3.3.el6.x86_64 #1 SMP Fri Dec 12 16:05:43 EST 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 24730048 19927144 4802904 5712 261404 2418616 -/+ buffers/cache: 17247124 7482924 Swap: 23999484 522592 23476892 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:37-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/04/02-17:57:38-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: lmarti Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.3.3.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /cell_root/software/freesurfer/current/sys/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /cell_root/software/freesurfer/current/sys/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Sphere lh Thu Apr 2 13:57:38 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.95 hours scaling brain by 0.305... pass 1: epoch 1 of 3 starting distance error %20.33 pass 1: epoch 2 of 3 starting distance error %20.28 unfolding complete - removing small folds... starting distance error %20.22 removing remaining folds... final distance error %20.23 expanding nbhd size to 1 1176: 3 negative triangles #-------------------------------------------- #@# Surf Reg lh Thu Apr 2 15:54:51 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_register -curv ../surf/lh.sphere /cell_root/software/freesurfer/current/sys/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /cell_root/software/freesurfer/current/sys/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.644 curvature mean = 0.025, std = 0.929 curvature mean = 0.024, std = 0.869 curvature mean = 0.016, std = 0.951 curvature mean = 0.011, std = 0.944 curvature mean = 0.015, std = 0.964 curvature mean = 0.005, std = 0.975 curvature mean = 0.014, std = 0.967 curvature mean = 0.001, std = 0.989 curvature mean = -0.030, std = 0.303 curvature mean = 0.003, std = 0.066 curvature mean = 0.075, std = 0.335 curvature mean = 0.003, std = 0.079 curvature mean = 0.033, std = 0.525 curvature mean = 0.003, std = 0.085 curvature mean = 0.017, std = 0.664 curvature mean = 0.003, std = 0.089 curvature mean = 0.006, std = 0.776 expanding nbhd size to 1 1110: 3 negative triangles #-------------------------------------------- #@# Jacobian white lh Thu Apr 2 16:45:15 EDT 2015 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Apr 2 16:45:17 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mrisp_paint -a 5 /cell_root/software/freesurfer/current/sys/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 /cell_root/software/freesurfer/current/sys/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Apr 2 16:45:19 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 HMN002 lh ../surf/lh.sphere.reg /cell_root/software/freesurfer/current/sys/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /cell_root/software/freesurfer/current/sys/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... 1312 labels changed using aseg relabeling using gibbs priors... 000: 3050 changed, 133401 examined... 001: 677 changed, 12985 examined... 002: 160 changed, 3794 examined... 003: 54 changed, 943 examined... 004: 17 changed, 322 examined... 005: 4 changed, 115 examined... 006: 3 changed, 26 examined... 007: 1 changed, 16 examined... 008: 0 changed, 7 examined... 197 labels changed using aseg 000: 115 total segments, 71 labels (251 vertices) changed 001: 43 total segments, 4 labels (10 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 59 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1663 vertices marked for relabeling... 1663 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 4 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Apr 2 16:46:24 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs HMN002 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /export/data/hippocampus/HMN/data/HMN002/mri/filled.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/brain.finalsurfs.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... 11882 bright wm thresholded. 2069 bright non-wm voxels segmented. reading original surface position from /export/data/hippocampus/HMN/data/HMN002/surf/lh.orig... computing class statistics... border white: 252636 voxels (1.51%) border gray 299430 voxels (1.78%) WM (97.0): 98.1 +- 6.7 [70.0 --> 110.0] GM (87.0) : 85.7 +- 10.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 67.6 (was 70) setting MAX_BORDER_WHITE to 112.7 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 57.1 (was 40) setting MAX_GRAY to 99.3 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 72.8 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 46.7 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=106, GM=78 using class modes intead of means.... mean inside = 98.2, mean outside = 83.8 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 /export/data/hippocampus/HMN/data/HMN002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.02-->5.61) (max @ vno 7330 --> 132208) face area 0.28 +- 0.13 (0.00-->6.52) mean absolute distance = 0.70 +- 0.81 5691 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 426 points - only 0.00% unknown deleting segment 4 with 38 points - only 0.00% unknown mean border=86.3, 92 (92) missing vertices, mean dist 0.4 [0.5 (%29.5)->0.8 (%70.5))] %76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.07-->5.36) (max @ vno 7330 --> 132208) face area 0.28 +- 0.14 (0.00-->6.03) mean absolute distance = 0.39 +- 0.51 4528 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4113369.2, rms=8.08 001: dt: 0.5000, sse=4780825.0, rms=5.70 002: dt: 0.5000, sse=5062608.0, rms=4.34 003: dt: 0.5000, sse=5303088.5, rms=3.56 004: dt: 0.5000, sse=5418975.5, rms=3.09 005: dt: 0.5000, sse=5539090.0, rms=2.83 006: dt: 0.5000, sse=5577033.5, rms=2.67 007: dt: 0.5000, sse=5627134.0, rms=2.57 008: dt: 0.5000, sse=5637868.0, rms=2.50 rms = 2.47, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5670191.0, rms=2.47 010: dt: 0.2500, sse=3570591.0, rms=1.82 011: dt: 0.2500, sse=3405685.5, rms=1.71 rms = 1.68, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3337603.8, rms=1.68 rms = 1.66, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3299633.8, rms=1.66 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 349 points - only 0.00% unknown deleting segment 3 with 36 points - only 0.00% unknown deleting segment 4 with 82 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=89.7, 103 (28) missing vertices, mean dist -0.3 [0.4 (%81.1)->0.3 (%18.9))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.04-->6.95) (max @ vno 132744 --> 70479) face area 0.35 +- 0.17 (0.00-->7.22) mean absolute distance = 0.25 +- 0.36 3538 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3878371.0, rms=4.50 014: dt: 0.5000, sse=4100456.8, rms=2.72 015: dt: 0.5000, sse=4341677.0, rms=2.31 016: dt: 0.5000, sse=4662870.0, rms=2.11 rms = 2.22, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4012240.0, rms=1.70 018: dt: 0.2500, sse=3800202.5, rms=1.49 019: dt: 0.2500, sse=3715522.5, rms=1.42 rms = 1.40, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3684964.8, rms=1.40 rms = 1.38, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3651553.0, rms=1.38 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 394 points - only 0.00% unknown deleting segment 2 with 37 points - only 0.00% unknown deleting segment 3 with 9 points - only 55.56% unknown deleting segment 5 with 146 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown mean border=91.6, 130 (21) missing vertices, mean dist -0.1 [0.3 (%72.5)->0.2 (%27.5))] %93 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.09-->7.59) (max @ vno 132744 --> 70479) face area 0.34 +- 0.16 (0.00-->7.01) mean absolute distance = 0.21 +- 0.32 3988 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3756717.8, rms=2.68 022: dt: 0.5000, sse=4085795.5, rms=1.83 rms = 1.91, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3895057.8, rms=1.46 024: dt: 0.2500, sse=3830763.2, rms=1.28 rms = 1.25, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3785432.2, rms=1.25 rms = 1.24, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3748261.2, rms=1.24 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 405 points - only 0.00% unknown deleting segment 2 with 41 points - only 0.00% unknown deleting segment 3 with 12 points - only 58.33% unknown deleting segment 4 with 146 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown mean border=92.1, 187 (20) missing vertices, mean dist -0.0 [0.2 (%56.5)->0.2 (%43.5))] %94 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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=3752366.5, rms=1.40 027: dt: 0.5000, sse=4661970.0, rms=1.18 rms = 1.51, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4333788.5, rms=1.04 rms = 1.04, time step reduction 2 of 3 to 0.125... rms = 1.03, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4306502.5, rms=1.03 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 4 with 7 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=69.1, 124 (124) missing vertices, mean dist 1.8 [1.3 (%0.0)->3.0 (%100.0))] %17 local maxima, %40 large gradients and %39 min vals, 2613 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, 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=16553420.0, rms=23.35 001: dt: 0.5000, sse=13094515.0, rms=20.24 002: dt: 0.5000, sse=10601742.0, rms=17.68 003: dt: 0.5000, sse=8817933.0, rms=15.61 004: dt: 0.5000, sse=7592022.0, rms=13.92 005: dt: 0.5000, sse=6766282.5, rms=12.59 006: dt: 0.5000, sse=6282531.0, rms=11.57 007: dt: 0.5000, sse=6004235.0, rms=10.75 008: dt: 0.5000, sse=5858950.5, rms=10.03 009: dt: 0.5000, sse=5775425.5, rms=9.39 010: dt: 0.5000, sse=5729838.0, rms=8.78 011: dt: 0.5000, sse=5714690.0, rms=8.17 012: dt: 0.5000, sse=5675796.0, rms=7.52 013: dt: 0.5000, sse=5656562.0, rms=6.87 014: dt: 0.5000, sse=5648564.5, rms=6.18 015: dt: 0.5000, sse=5626982.0, rms=5.52 016: dt: 0.5000, sse=5665012.0, rms=4.91 017: dt: 0.5000, sse=5681236.5, rms=4.44 018: dt: 0.5000, sse=5761048.0, rms=4.08 019: dt: 0.5000, sse=5782855.5, rms=3.86 020: dt: 0.5000, sse=5875633.5, rms=3.69 021: dt: 0.5000, sse=5923645.5, rms=3.60 022: dt: 0.5000, sse=5963998.5, rms=3.53 rms = 3.49, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=5957652.5, rms=3.49 024: dt: 0.2500, sse=4509955.0, rms=3.03 025: dt: 0.2500, sse=4409960.0, rms=2.91 rms = 2.91, time step reduction 2 of 3 to 0.125... rms = 2.87, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4337490.5, rms=2.87 positioning took 3.6 minutes mean border=67.3, 1464 (27) missing vertices, mean dist 0.2 [0.2 (%41.5)->0.6 (%58.5))] %41 local maxima, %22 large gradients and %32 min vals, 1232 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, 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=4905192.0, rms=4.33 027: dt: 0.5000, sse=5132793.5, rms=3.76 028: dt: 0.5000, sse=6046915.0, rms=3.49 rms = 3.60, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=5240977.0, rms=3.09 030: dt: 0.2500, sse=4909362.0, rms=2.95 rms = 2.95, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=4846057.0, rms=2.90 032: dt: 0.1250, sse=4743504.0, rms=2.83 rms = 2.80, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4720147.5, rms=2.80 positioning took 1.2 minutes mean border=66.3, 2048 (21) missing vertices, mean dist 0.1 [0.2 (%36.9)->0.4 (%63.1))] %53 local maxima, %10 large gradients and %32 min vals, 1315 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, 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=4798872.5, rms=3.22 rms = 3.33, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=4677751.0, rms=2.97 035: dt: 0.2500, sse=4745447.0, rms=2.82 rms = 2.81, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=4884905.0, rms=2.81 037: dt: 0.1250, sse=4779935.5, rms=2.71 rms = 2.69, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4807072.5, rms=2.69 positioning took 0.8 minutes mean border=65.7, 4413 (18) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.3 (%56.3))] %53 local maxima, % 9 large gradients and %31 min vals, 1114 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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 /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4817174.0, rms=2.78 rms = 3.00, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=4782410.5, rms=2.68 040: dt: 0.2500, sse=4986016.5, rms=2.63 rms = 2.63, time step reduction 2 of 3 to 0.125... rms = 2.61, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4950554.0, rms=2.61 positioning took 0.6 minutes writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.area.pial vertex spacing 1.05 +- 0.48 (0.05-->8.46) (max @ vno 132744 --> 70479) face area 0.43 +- 0.35 (0.00-->7.83) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133401 vertices processed 25000 of 133401 vertices processed 50000 of 133401 vertices processed 75000 of 133401 vertices processed 100000 of 133401 vertices processed 125000 of 133401 vertices processed 0 of 133401 vertices processed 25000 of 133401 vertices processed 50000 of 133401 vertices processed 75000 of 133401 vertices processed 100000 of 133401 vertices processed 125000 of 133401 vertices processed thickness calculation complete, 3422:4893 truncations. 45197 vertices at 0 distance 68904 vertices at 1 distance 69888 vertices at 2 distance 40918 vertices at 3 distance 18749 vertices at 4 distance 7440 vertices at 5 distance 2984 vertices at 6 distance 1333 vertices at 7 distance 702 vertices at 8 distance 396 vertices at 9 distance 253 vertices at 10 distance 183 vertices at 11 distance 131 vertices at 12 distance 102 vertices at 13 distance 73 vertices at 14 distance 54 vertices at 15 distance 56 vertices at 16 distance 44 vertices at 17 distance 28 vertices at 18 distance 38 vertices at 19 distance 33 vertices at 20 distance writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.thickness positioning took 13.9 minutes #-------------------------------------------- #@# Surf Volume lh Thu Apr 2 17:00:20 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Thu Apr 2 17:00:20 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/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 HMN002 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white... reading input pial surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial... reading input white surface /export/data/hippocampus/HMN/data/HMN002/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 1400 975 2963 3.047 0.522 0.114 0.028 12 1.5 bankssts 947 623 2823 4.002 0.668 0.180 0.137 36 5.8 caudalanteriorcingulate 3356 2296 8861 3.278 0.721 0.132 0.044 45 6.2 caudalmiddlefrontal 1805 1229 2745 2.086 0.624 0.160 0.058 31 4.4 cuneus 596 407 2101 3.602 0.801 0.158 0.080 9 1.8 entorhinal 4370 2945 11491 3.276 0.699 0.154 0.074 112 13.3 fusiform 6742 4384 16197 3.156 0.769 0.147 0.135 293 29.1 inferiorparietal 4876 3233 13418 3.310 0.815 0.149 0.093 283 15.7 inferiortemporal 1351 856 3034 3.159 0.971 0.153 0.149 54 3.6 isthmuscingulate 7859 5002 13693 2.540 0.750 0.160 0.088 218 24.7 lateraloccipital 3737 2541 10020 3.388 0.717 0.158 0.079 83 11.1 lateralorbitofrontal 4465 3000 7728 2.358 0.726 0.158 0.082 102 11.8 lingual 2881 1923 7163 3.095 0.922 0.164 0.171 141 15.8 medialorbitofrontal 4752 3162 14992 3.545 0.787 0.146 0.053 107 10.3 middletemporal 1137 704 2779 3.086 0.773 0.109 0.036 10 1.6 parahippocampal 2004 1319 3960 2.759 0.593 0.111 0.033 16 2.8 paracentral 2109 1461 5106 2.974 0.538 0.122 0.042 34 3.8 parsopercularis 942 633 3162 3.477 0.750 0.171 0.075 24 2.8 parsorbitalis 1732 1198 4613 3.197 0.603 0.113 0.029 19 2.1 parstriangularis 1482 1036 1539 1.676 0.554 0.169 0.157 66 5.0 pericalcarine 6482 4210 12873 2.504 0.952 0.130 0.078 159 19.3 postcentral 1713 1150 4256 3.188 0.799 0.159 0.070 41 4.4 posteriorcingulate 7685 4973 17638 3.097 0.653 0.117 0.043 120 14.5 precentral 5897 4007 14242 3.040 0.730 0.148 0.075 148 14.2 precuneus 1293 875 3792 3.581 0.703 0.165 0.072 34 3.9 rostralanteriorcingulate 9049 6067 22086 2.866 0.808 0.146 0.065 190 21.4 rostralmiddlefrontal 10503 7051 29674 3.455 0.829 0.143 0.060 193 24.6 superiorfrontal 9366 6104 21149 2.810 0.843 0.134 0.051 156 20.2 superiorparietal 6046 3985 16293 3.481 0.696 0.125 0.045 97 11.4 superiortemporal 5596 3730 14453 3.192 0.777 0.134 0.048 202 10.8 supramarginal 273 180 1062 4.022 0.541 0.228 0.150 17 1.8 frontalpole 631 427 2881 4.351 0.473 0.188 0.252 41 3.5 temporalpole 681 436 1343 2.857 0.520 0.145 0.059 11 1.4 transversetemporal 2942 1885 7266 3.658 0.823 0.132 0.067 50 7.7 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Apr 2 17:00:39 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 HMN002 lh ../surf/lh.sphere.reg /cell_root/software/freesurfer/current/sys/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /cell_root/software/freesurfer/current/sys/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 9 labels changed using aseg relabeling using gibbs priors... 000: 9229 changed, 133401 examined... 001: 2170 changed, 34999 examined... 002: 692 changed, 11193 examined... 003: 301 changed, 3827 examined... 004: 153 changed, 1681 examined... 005: 81 changed, 831 examined... 006: 40 changed, 457 examined... 007: 25 changed, 232 examined... 008: 18 changed, 143 examined... 009: 8 changed, 102 examined... 010: 4 changed, 40 examined... 011: 4 changed, 27 examined... 012: 6 changed, 21 examined... 013: 3 changed, 32 examined... 014: 0 changed, 16 examined... 4 labels changed using aseg 000: 308 total segments, 224 labels (2894 vertices) changed 001: 114 total segments, 31 labels (64 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 126 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1008 vertices marked for relabeling... 1008 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 4 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Apr 2 17:01:43 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/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 HMN002 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white... reading input pial surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial... reading input white surface /export/data/hippocampus/HMN/data/HMN002/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 1597 1140 3696 2.693 0.867 0.167 0.089 47 4.5 G_and_S_frontomargin 1742 1128 3601 2.824 0.552 0.151 0.074 48 4.8 G_and_S_occipital_inf 1767 1078 3498 2.635 0.597 0.139 0.065 28 5.0 G_and_S_paracentral 1415 958 3982 3.241 0.751 0.141 0.051 28 2.8 G_and_S_subcentral 742 497 2380 3.445 0.890 0.175 0.093 25 2.8 G_and_S_transv_frontopol 1874 1280 4757 3.371 0.596 0.154 0.059 36 4.4 G_and_S_cingul-Ant 1071 736 2846 3.608 0.721 0.163 0.121 33 5.8 G_and_S_cingul-Mid-Ant 1192 824 2869 3.303 0.604 0.154 0.071 26 3.0 G_and_S_cingul-Mid-Post 497 328 1700 3.700 0.665 0.196 0.328 42 1.9 G_cingul-Post-dorsal 222 138 537 2.992 1.083 0.140 0.060 4 0.4 G_cingul-Post-ventral 1669 1149 2576 1.947 0.736 0.172 0.068 32 4.7 G_cuneus 1299 866 3918 3.263 0.524 0.146 0.062 32 3.6 G_front_inf-Opercular 262 172 983 3.788 0.428 0.180 0.086 7 0.9 G_front_inf-Orbital 960 655 3120 3.406 0.595 0.137 0.042 18 1.6 G_front_inf-Triangul 4767 3127 14685 3.271 0.830 0.161 0.075 121 13.5 G_front_middle 7098 4722 23219 3.649 0.805 0.155 0.073 165 19.8 G_front_sup 409 254 1300 4.134 0.776 0.127 0.081 7 1.3 G_Ins_lg_and_S_cent_ins 560 350 2217 4.312 0.544 0.173 0.110 18 2.2 G_insular_short 3056 1715 6924 3.048 0.721 0.186 0.295 282 26.6 G_occipital_middle 1430 849 2749 2.593 0.681 0.147 0.104 59 7.7 G_occipital_sup 1420 910 4851 3.558 0.625 0.172 0.082 42 4.7 G_oc-temp_lat-fusifor 2668 1767 4510 2.210 0.765 0.170 0.075 52 8.3 G_oc-temp_med-Lingual 1338 862 4104 3.409 0.838 0.138 0.062 19 3.0 G_oc-temp_med-Parahip 2612 1759 9357 3.651 0.656 0.188 0.107 87 10.6 G_orbital 2537 1675 8242 3.559 0.876 0.157 0.066 179 7.3 G_pariet_inf-Angular 3167 2070 9817 3.408 0.773 0.143 0.089 75 6.3 G_pariet_inf-Supramar 4097 2673 11819 3.133 0.941 0.143 0.050 71 8.5 G_parietal_sup 2424 1483 5510 2.723 0.946 0.139 0.091 96 12.2 G_postcentral 2917 1834 9000 3.418 0.630 0.125 0.049 54 6.6 G_precentral 2827 1920 9032 3.360 0.764 0.173 0.112 99 10.1 G_precuneus 1041 735 3705 3.459 0.774 0.217 0.117 52 5.1 G_rectus 553 321 1077 2.929 1.188 0.201 0.330 62 9.3 G_subcallosal 506 314 1179 3.042 0.557 0.144 0.072 9 1.2 G_temp_sup-G_T_transv 2126 1355 8148 3.888 0.613 0.143 0.061 56 5.6 G_temp_sup-Lateral 648 432 2005 3.796 0.487 0.100 0.029 4 0.8 G_temp_sup-Plan_polar 1163 848 2898 3.041 0.641 0.126 0.039 17 2.0 G_temp_sup-Plan_tempo 2244 1470 7967 3.590 0.942 0.178 0.157 253 11.6 G_temporal_inf 3171 2076 11717 3.789 0.733 0.158 0.057 78 7.6 G_temporal_middle 401 277 818 3.038 0.426 0.076 0.013 1 0.2 Lat_Fis-ant-Horizont 310 219 492 2.809 0.472 0.098 0.016 1 0.2 Lat_Fis-ant-Vertical 1203 804 1952 3.005 0.594 0.125 0.042 12 1.9 Lat_Fis-post 2049 1421 2702 1.859 0.515 0.203 0.164 95 8.0 Pole_occipital 1608 1121 6439 3.972 0.714 0.191 0.169 69 7.8 Pole_temporal 2012 1383 2680 2.215 0.873 0.134 0.045 22 3.9 S_calcarine 3377 2272 4393 2.167 0.714 0.110 0.033 43 5.0 S_central 1267 842 2400 2.826 0.627 0.111 0.033 12 1.8 S_cingul-Marginalis 561 374 1083 3.398 0.609 0.100 0.025 3 0.6 S_circular_insula_ant 1467 953 2825 3.342 0.711 0.092 0.035 13 2.3 S_circular_insula_inf 1551 1043 2800 3.165 0.695 0.124 0.038 15 2.3 S_circular_insula_sup 1116 754 2241 3.065 0.658 0.109 0.047 9 1.5 S_collat_transv_ant 334 226 504 2.602 0.458 0.124 0.036 3 0.5 S_collat_transv_post 1769 1215 3312 2.661 0.626 0.095 0.022 10 1.7 S_front_inf 1816 1226 3301 2.563 0.651 0.120 0.034 19 2.6 S_front_middle 2995 2075 6226 2.951 0.576 0.114 0.034 27 4.1 S_front_sup 160 114 268 2.859 0.699 0.112 0.022 1 0.1 S_interm_prim-Jensen 3603 2379 6499 2.669 0.623 0.120 0.037 39 5.1 S_intrapariet_and_P_trans 1093 720 1562 2.456 0.556 0.133 0.054 16 2.0 S_oc_middle_and_Lunatus 1533 1002 2452 2.663 0.599 0.119 0.029 14 1.9 S_oc_sup_and_transversal 667 462 1028 2.710 0.423 0.118 0.028 5 0.9 S_occipital_ant 1128 764 2104 2.953 0.473 0.123 0.038 13 1.8 S_oc-temp_lat 2594 1745 4721 2.779 0.557 0.140 0.086 77 6.5 S_oc-temp_med_and_Lingual 409 281 676 2.481 0.467 0.108 0.023 2 0.5 S_orbital_lateral 892 595 1812 3.159 0.894 0.136 0.217 31 1.9 S_orbital_med-olfact 1295 890 2786 3.153 0.737 0.145 0.062 19 2.8 S_orbital-H_Shaped 1812 1248 2995 2.568 0.593 0.144 0.065 50 3.6 S_parieto_occipital 1434 883 2313 3.139 1.187 0.134 0.044 24 2.7 S_pericallosal 2842 1905 4817 2.607 0.696 0.123 0.039 33 4.6 S_postcentral 1459 1007 2553 2.822 0.385 0.083 0.017 4 1.0 S_precentral-inf-part 1671 1121 2890 2.925 0.688 0.114 0.033 13 2.4 S_precentral-sup-part 626 437 1183 2.774 0.827 0.100 0.025 3 0.6 S_suborbital 1399 932 2575 2.887 0.609 0.118 0.031 13 1.8 S_subparietal 1473 991 2557 3.021 0.530 0.124 0.033 13 2.0 S_temporal_inf 5256 3560 10052 3.033 0.576 0.112 0.030 58 6.4 S_temporal_sup 430 295 888 3.131 0.792 0.166 0.057 8 0.9 S_temporal_transverse #-------------------------------------------- #@# Sphere rh Thu Apr 2 17:02:15 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.26 hours scaling brain by 0.312... pass 1: epoch 1 of 3 starting distance error %19.59 pass 1: epoch 2 of 3 starting distance error %19.56 unfolding complete - removing small folds... starting distance error %19.46 removing remaining folds... final distance error %19.48 #-------------------------------------------- #@# Surf Reg rh Thu Apr 2 18:18:06 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_register -curv ../surf/rh.sphere /cell_root/software/freesurfer/current/sys/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /cell_root/software/freesurfer/current/sys/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = -0.000, std = 0.635 curvature mean = 0.020, std = 0.929 curvature mean = 0.026, std = 0.868 curvature mean = 0.005, std = 0.948 curvature mean = 0.012, std = 0.945 curvature mean = 0.002, std = 0.959 curvature mean = 0.005, std = 0.975 curvature mean = 0.000, std = 0.960 curvature mean = 0.001, std = 0.989 curvature mean = -0.035, std = 0.319 curvature mean = 0.004, std = 0.070 curvature mean = 0.081, std = 0.319 curvature mean = 0.004, std = 0.084 curvature mean = 0.042, std = 0.499 curvature mean = 0.004, std = 0.090 curvature mean = 0.024, std = 0.633 curvature mean = 0.004, std = 0.093 curvature mean = 0.009, std = 0.746 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Thu Apr 2 18:54:56 EDT 2015 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu Apr 2 18:54:59 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mrisp_paint -a 5 /cell_root/software/freesurfer/current/sys/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 /cell_root/software/freesurfer/current/sys/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Apr 2 18:55:01 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 HMN002 rh ../surf/rh.sphere.reg /cell_root/software/freesurfer/current/sys/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /cell_root/software/freesurfer/current/sys/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... 1100 labels changed using aseg relabeling using gibbs priors... 000: 3007 changed, 136699 examined... 001: 684 changed, 12940 examined... 002: 170 changed, 3785 examined... 003: 73 changed, 1019 examined... 004: 33 changed, 446 examined... 005: 7 changed, 180 examined... 006: 8 changed, 44 examined... 007: 4 changed, 34 examined... 008: 1 changed, 25 examined... 009: 2 changed, 7 examined... 010: 0 changed, 15 examined... 145 labels changed using aseg 000: 105 total segments, 67 labels (538 vertices) changed 001: 41 total segments, 3 labels (24 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 27 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1074 vertices marked for relabeling... 1074 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 52 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Apr 2 18:55:53 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs HMN002 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /export/data/hippocampus/HMN/data/HMN002/mri/filled.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/brain.finalsurfs.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... 12100 bright wm thresholded. 2080 bright non-wm voxels segmented. reading original surface position from /export/data/hippocampus/HMN/data/HMN002/surf/rh.orig... computing class statistics... border white: 252636 voxels (1.51%) border gray 299430 voxels (1.78%) WM (97.0): 98.0 +- 6.9 [70.0 --> 110.0] GM (87.0) : 85.8 +- 10.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 68.9 (was 70) setting MAX_BORDER_WHITE to 112.9 (was 105) setting MIN_BORDER_WHITE to 79.0 (was 85) setting MAX_CSF to 58.8 (was 40) setting MAX_GRAY to 99.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 74.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 48.7 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=106, GM=79 using class modes intead of means.... mean inside = 98.4, mean outside = 84.2 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 /export/data/hippocampus/HMN/data/HMN002/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.04-->5.78) (max @ vno 111201 --> 136449) face area 0.28 +- 0.13 (0.00-->7.65) mean absolute distance = 0.71 +- 0.81 5602 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 41 points - only 0.00% unknown deleting segment 2 with 187 points - only 0.00% unknown mean border=86.8, 72 (72) missing vertices, mean dist 0.4 [0.5 (%30.2)->0.8 (%69.8))] %73 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.07-->5.79) (max @ vno 51773 --> 51772) face area 0.28 +- 0.14 (0.00-->6.23) mean absolute distance = 0.39 +- 0.50 4231 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4078195.2, rms=7.73 001: dt: 0.5000, sse=4796023.5, rms=5.38 002: dt: 0.5000, sse=5057737.0, rms=4.12 003: dt: 0.5000, sse=5307322.5, rms=3.43 004: dt: 0.5000, sse=5444313.5, rms=3.03 005: dt: 0.5000, sse=5509832.0, rms=2.79 006: dt: 0.5000, sse=5574401.5, rms=2.62 007: dt: 0.5000, sse=5593694.0, rms=2.53 008: dt: 0.5000, sse=5616345.0, rms=2.46 rms = 2.42, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5628707.5, rms=2.42 010: dt: 0.2500, sse=3633689.8, rms=1.80 011: dt: 0.2500, sse=3459456.0, rms=1.69 rms = 1.67, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3391353.5, rms=1.67 rms = 1.65, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3350903.5, rms=1.65 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 1 with 35 points - only 0.00% unknown deleting segment 2 with 166 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=90.2, 57 (12) missing vertices, mean dist -0.3 [0.4 (%80.9)->0.3 (%19.1))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.06-->6.00) (max @ vno 51773 --> 51772) face area 0.34 +- 0.17 (0.00-->7.43) mean absolute distance = 0.25 +- 0.34 4099 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3907003.2, rms=4.42 014: dt: 0.5000, sse=4116639.2, rms=2.68 015: dt: 0.5000, sse=4321639.5, rms=2.23 016: dt: 0.5000, sse=4600473.0, rms=2.02 rms = 2.12, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=3992796.8, rms=1.65 018: dt: 0.2500, sse=3783666.2, rms=1.44 019: dt: 0.2500, sse=3712304.0, rms=1.38 rms = 1.35, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3674381.0, rms=1.35 rms = 1.33, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3646235.5, rms=1.33 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 50 points - only 0.00% unknown deleting segment 1 with 159 points - only 0.00% unknown removing 3 vertex label from ripped group removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown mean border=92.1, 60 (5) missing vertices, mean dist -0.1 [0.2 (%72.8)->0.2 (%27.2))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.05-->6.15) (max @ vno 51773 --> 51772) face area 0.33 +- 0.16 (0.00-->7.01) mean absolute distance = 0.20 +- 0.30 3566 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3765016.5, rms=2.69 022: dt: 0.5000, sse=4067165.2, rms=1.78 rms = 1.80, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3876562.5, rms=1.42 024: dt: 0.2500, sse=3810416.2, rms=1.22 rms = 1.18, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=3765041.8, rms=1.18 rms = 1.17, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3735364.0, rms=1.17 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 55 points - only 0.00% unknown deleting segment 1 with 170 points - only 0.00% unknown removing 3 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown mean border=92.6, 99 (3) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))] %94 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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=3740466.5, rms=1.35 027: dt: 0.5000, sse=4569845.0, rms=1.10 rms = 1.42, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4266167.0, rms=0.97 rms = 0.97, time step reduction 2 of 3 to 0.125... rms = 0.96, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=4240360.0, rms=0.96 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=70.3, 85 (85) missing vertices, mean dist 1.8 [0.9 (%0.0)->2.9 (%100.0))] %18 local maxima, %42 large gradients and %36 min vals, 2701 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, 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=16086005.0, rms=22.63 001: dt: 0.5000, sse=12696436.0, rms=19.55 002: dt: 0.5000, sse=10275199.0, rms=17.03 003: dt: 0.5000, sse=8563766.0, rms=15.02 004: dt: 0.5000, sse=7406525.5, rms=13.43 005: dt: 0.5000, sse=6649129.0, rms=12.19 006: dt: 0.5000, sse=6175275.0, rms=11.22 007: dt: 0.5000, sse=5932694.5, rms=10.41 008: dt: 0.5000, sse=5779208.0, rms=9.69 009: dt: 0.5000, sse=5726261.0, rms=9.05 010: dt: 0.5000, sse=5669933.5, rms=8.44 011: dt: 0.5000, sse=5658164.0, rms=7.84 012: dt: 0.5000, sse=5621068.0, rms=7.21 013: dt: 0.5000, sse=5623200.0, rms=6.58 014: dt: 0.5000, sse=5635005.0, rms=5.93 015: dt: 0.5000, sse=5646232.0, rms=5.36 016: dt: 0.5000, sse=5726227.5, rms=4.84 017: dt: 0.5000, sse=5778322.5, rms=4.45 018: dt: 0.5000, sse=5884207.0, rms=4.14 019: dt: 0.5000, sse=5926059.5, rms=3.95 020: dt: 0.5000, sse=5977622.0, rms=3.78 021: dt: 0.5000, sse=6028858.5, rms=3.68 022: dt: 0.5000, sse=6016614.0, rms=3.59 rms = 3.55, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=6079856.0, rms=3.55 024: dt: 0.2500, sse=4527683.0, rms=3.04 025: dt: 0.2500, sse=4419813.0, rms=2.93 rms = 2.92, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4370120.5, rms=2.92 027: dt: 0.1250, sse=4178314.0, rms=2.79 rms = 2.77, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4150110.8, rms=2.77 positioning took 3.6 minutes mean border=68.3, 1447 (15) missing vertices, mean dist 0.2 [0.2 (%40.3)->0.6 (%59.7))] %43 local maxima, %23 large gradients and %30 min vals, 1077 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, 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=4771126.0, rms=4.48 029: dt: 0.5000, sse=4942175.0, rms=3.89 030: dt: 0.5000, sse=6003020.5, rms=3.66 rms = 3.76, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=5208684.0, rms=3.21 032: dt: 0.2500, sse=4873559.5, rms=3.05 rms = 3.05, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=4912286.5, rms=3.05 034: dt: 0.1250, sse=4718412.0, rms=2.89 rms = 2.86, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=4709719.0, rms=2.86 positioning took 1.1 minutes mean border=67.0, 1830 (14) missing vertices, mean dist 0.1 [0.2 (%34.6)->0.4 (%65.4))] %56 local maxima, %10 large gradients and %30 min vals, 1217 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, 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=4808841.0, rms=3.34 rms = 3.48, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=4674941.5, rms=3.06 037: dt: 0.2500, sse=4725474.5, rms=2.89 rms = 2.87, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4889946.5, rms=2.87 039: dt: 0.1250, sse=4793560.0, rms=2.77 rms = 2.75, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4821719.5, rms=2.75 positioning took 0.8 minutes mean border=66.5, 4109 (13) missing vertices, mean dist 0.1 [0.2 (%42.9)->0.3 (%57.1))] %56 local maxima, % 9 large gradients and %29 min vals, 996 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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 /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4829876.0, rms=2.81 rms = 3.08, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4796498.5, rms=2.71 rms = 2.66, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=5007179.5, rms=2.66 043: dt: 0.1250, sse=4930215.0, rms=2.61 rms = 2.58, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=4967374.0, rms=2.58 positioning took 0.7 minutes writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.area.pial vertex spacing 1.04 +- 0.48 (0.04-->8.48) (max @ vno 51773 --> 51772) face area 0.42 +- 0.35 (0.00-->7.93) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 136699 vertices processed 25000 of 136699 vertices processed 50000 of 136699 vertices processed 75000 of 136699 vertices processed 100000 of 136699 vertices processed 125000 of 136699 vertices processed 0 of 136699 vertices processed 25000 of 136699 vertices processed 50000 of 136699 vertices processed 75000 of 136699 vertices processed 100000 of 136699 vertices processed 125000 of 136699 vertices processed thickness calculation complete, 3254:4954 truncations. 49106 vertices at 0 distance 65991 vertices at 1 distance 70576 vertices at 2 distance 43187 vertices at 3 distance 20001 vertices at 4 distance 8254 vertices at 5 distance 3200 vertices at 6 distance 1457 vertices at 7 distance 716 vertices at 8 distance 360 vertices at 9 distance 237 vertices at 10 distance 178 vertices at 11 distance 124 vertices at 12 distance 105 vertices at 13 distance 104 vertices at 14 distance 92 vertices at 15 distance 81 vertices at 16 distance 79 vertices at 17 distance 64 vertices at 18 distance 32 vertices at 19 distance 48 vertices at 20 distance writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.thickness positioning took 13.6 minutes #-------------------------------------------- #@# Surf Volume rh Thu Apr 2 19:09:28 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Thu Apr 2 19:09:28 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/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 HMN002 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white... reading input pial surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial... reading input white surface /export/data/hippocampus/HMN/data/HMN002/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 1615 1119 3721 3.252 0.528 0.115 0.030 17 2.1 bankssts 891 590 2182 2.988 1.018 0.133 0.040 12 1.5 caudalanteriorcingulate 3577 2422 9507 3.188 0.696 0.129 0.427 162 9.0 caudalmiddlefrontal 2080 1324 3318 2.182 0.652 0.152 0.072 42 7.0 cuneus 590 392 2044 3.721 0.741 0.163 0.085 10 2.2 entorhinal 5041 3352 12565 3.155 0.746 0.153 0.078 251 14.1 fusiform 7780 5120 19344 3.180 0.717 0.131 0.053 129 16.9 inferiorparietal 4809 3170 14593 3.509 0.757 0.147 0.090 112 13.3 inferiortemporal 1285 851 3028 3.132 0.938 0.153 0.067 30 3.0 isthmuscingulate 7135 4400 12970 2.708 0.764 0.154 0.081 215 21.9 lateraloccipital 4188 2852 10631 3.218 0.767 0.165 0.114 255 20.6 lateralorbitofrontal 3775 2551 6141 2.307 0.682 0.161 0.085 145 13.2 lingual 2349 1648 5866 2.926 0.746 0.156 0.079 86 7.4 medialorbitofrontal 5366 3583 16514 3.583 0.790 0.141 0.054 102 13.1 middletemporal 1182 752 2894 3.523 0.791 0.124 0.044 14 2.2 parahippocampal 2562 1578 5163 2.907 0.588 0.142 0.308 102 28.1 paracentral 1780 1201 4151 3.020 0.528 0.129 0.174 400 4.6 parsopercularis 1190 815 4071 3.444 0.729 0.167 0.078 33 3.6 parsorbitalis 1909 1274 5070 3.224 0.796 0.125 0.040 27 3.1 parstriangularis 1767 1234 1878 1.700 0.566 0.158 0.100 44 8.3 pericalcarine 7351 4549 13297 2.504 0.884 0.112 0.057 125 12.3 postcentral 1652 1082 3908 2.940 0.948 0.152 0.058 30 4.0 posteriorcingulate 7783 4992 17178 3.006 0.641 0.113 0.046 139 12.5 precentral 5923 3934 14617 3.149 0.789 0.142 0.058 112 13.9 precuneus 911 582 2477 3.438 0.770 0.139 0.055 15 1.8 rostralanteriorcingulate 8104 5395 19934 2.926 0.819 0.158 0.074 223 23.6 rostralmiddlefrontal 11581 7757 31830 3.375 0.796 0.141 0.061 220 31.8 superiorfrontal 9428 6052 20111 2.788 0.776 0.129 0.187 351 17.9 superiorparietal 5865 3791 16131 3.559 0.726 0.114 0.051 122 8.9 superiortemporal 5587 3628 13453 3.187 0.716 0.142 0.399 482 29.2 supramarginal 499 335 1903 3.377 0.948 0.253 0.173 28 3.3 frontalpole 599 401 2509 3.932 0.752 0.188 0.514 286 2.7 temporalpole 550 334 1014 2.846 0.398 0.143 0.070 10 1.8 transversetemporal 2933 1911 6908 3.434 0.770 0.134 0.058 40 6.7 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Apr 2 19:09:47 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 HMN002 rh ../surf/rh.sphere.reg /cell_root/software/freesurfer/current/sys/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /cell_root/software/freesurfer/current/sys/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... 4 labels changed using aseg relabeling using gibbs priors... 000: 9574 changed, 136699 examined... 001: 2233 changed, 36466 examined... 002: 665 changed, 11402 examined... 003: 278 changed, 3637 examined... 004: 153 changed, 1582 examined... 005: 86 changed, 869 examined... 006: 40 changed, 445 examined... 007: 26 changed, 225 examined... 008: 13 changed, 128 examined... 009: 10 changed, 68 examined... 010: 3 changed, 52 examined... 011: 3 changed, 20 examined... 012: 3 changed, 20 examined... 013: 3 changed, 12 examined... 014: 1 changed, 16 examined... 015: 1 changed, 8 examined... 016: 2 changed, 6 examined... 017: 2 changed, 10 examined... 018: 2 changed, 10 examined... 019: 2 changed, 9 examined... 020: 2 changed, 11 examined... 021: 0 changed, 9 examined... 6 labels changed using aseg 000: 320 total segments, 236 labels (2905 vertices) changed 001: 112 total segments, 28 labels (194 vertices) changed 002: 85 total segments, 1 labels (1 vertices) changed 003: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 142 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 642 vertices marked for relabeling... 642 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 0 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Apr 2 19:10:48 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/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 HMN002 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white... reading input pial surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial... reading input white surface /export/data/hippocampus/HMN/data/HMN002/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 1154 801 3859 3.404 0.877 0.208 0.116 49 4.9 G_and_S_frontomargin 1424 895 3255 3.204 0.588 0.149 0.075 36 4.5 G_and_S_occipital_inf 1759 969 3496 2.877 0.607 0.153 0.311 147 27.3 G_and_S_paracentral 1549 999 3882 3.343 0.712 0.146 0.081 29 3.2 G_and_S_subcentral 973 658 2819 3.039 0.931 0.166 0.085 30 2.9 G_and_S_transv_frontopol 2177 1473 5458 3.351 0.677 0.125 0.045 24 4.0 G_and_S_cingul-Ant 1048 745 2737 3.215 0.587 0.124 0.034 10 1.5 G_and_S_cingul-Mid-Ant 1257 858 3068 3.240 0.656 0.161 0.063 24 3.2 G_and_S_cingul-Mid-Post 568 365 1926 3.592 0.815 0.188 0.083 16 2.1 G_cingul-Post-dorsal 205 133 638 3.792 0.725 0.183 0.109 6 0.6 G_cingul-Post-ventral 1846 1176 2745 1.989 0.721 0.152 0.064 34 5.2 G_cuneus 1077 726 3197 3.128 0.556 0.154 0.276 397 4.2 G_front_inf-Opercular 304 194 973 3.561 0.668 0.153 0.059 6 0.8 G_front_inf-Orbital 883 576 3010 3.471 0.756 0.138 0.048 18 1.7 G_front_inf-Triangul 4270 2767 13307 3.252 0.781 0.171 0.400 251 16.3 G_front_middle 8281 5428 25415 3.536 0.813 0.159 0.126 224 31.2 G_front_sup 459 301 1309 3.922 0.631 0.131 0.057 7 0.9 G_Ins_lg_and_S_cent_ins 569 350 2057 3.860 0.676 0.168 0.093 14 2.2 G_insular_short 2082 1230 5847 3.366 0.694 0.155 0.117 116 6.9 G_occipital_middle 2446 1413 4805 2.784 0.566 0.146 0.117 147 8.1 G_occipital_sup 1937 1252 5762 3.389 0.721 0.158 0.076 45 5.6 G_oc-temp_lat-fusifor 2423 1549 4182 2.281 0.782 0.174 0.089 56 8.7 G_oc-temp_med-Lingual 1560 990 4673 3.560 0.979 0.171 0.115 181 6.2 G_oc-temp_med-Parahip 3028 2062 10517 3.521 0.676 0.202 0.166 270 20.9 G_orbital 2962 1816 9887 3.624 0.775 0.159 0.087 87 10.4 G_pariet_inf-Angular 3039 1868 8462 3.441 0.673 0.164 0.730 502 25.3 G_pariet_inf-Supramar 2792 1776 7390 3.074 0.933 0.139 0.484 166 5.4 G_parietal_sup 2663 1512 5499 2.663 0.773 0.120 0.053 72 5.9 G_postcentral 2997 1855 8749 3.334 0.587 0.122 0.048 43 5.9 G_precentral 2769 1783 8711 3.446 0.790 0.165 0.084 80 9.5 G_precuneus 627 472 2078 2.989 0.629 0.228 0.146 59 3.5 G_rectus 279 182 561 2.968 0.763 0.083 0.039 2 0.3 G_subcallosal 434 259 923 2.914 0.375 0.135 0.073 9 1.5 G_temp_sup-G_T_transv 2155 1341 8279 4.113 0.590 0.152 0.057 46 5.0 G_temp_sup-Lateral 884 578 2397 3.548 0.536 0.090 0.025 4 0.9 G_temp_sup-Plan_polar 624 443 1636 3.200 0.474 0.091 0.028 4 0.8 G_temp_sup-Plan_tempo 2446 1602 9823 3.833 0.782 0.176 0.141 90 9.7 G_temporal_inf 3224 2129 12100 3.868 0.732 0.160 0.072 86 10.4 G_temporal_middle 443 306 941 3.224 0.625 0.095 0.020 2 0.4 Lat_Fis-ant-Horizont 222 160 334 2.233 0.347 0.102 0.019 1 0.2 Lat_Fis-ant-Vertical 1316 894 2194 2.908 0.558 0.118 0.033 11 1.8 Lat_Fis-post 2650 1759 3567 2.007 0.630 0.189 0.105 76 12.4 Pole_occipital 1683 1125 6524 3.838 0.750 0.187 0.251 319 7.4 Pole_temporal 2110 1440 2949 2.299 0.872 0.148 0.101 120 10.4 S_calcarine 3441 2294 4343 2.086 0.672 0.090 0.021 14 3.1 S_central 1379 929 2445 2.652 0.510 0.108 0.032 11 1.8 S_cingul-Marginalis 630 428 1416 3.539 0.652 0.106 0.028 3 0.7 S_circular_insula_ant 1201 771 1980 2.876 0.594 0.088 0.023 5 1.2 S_circular_insula_inf 1148 781 1983 3.060 0.556 0.122 0.036 10 1.8 S_circular_insula_sup 1189 809 2081 2.853 0.396 0.092 0.021 4 1.1 S_collat_transv_ant 381 240 708 2.936 0.631 0.160 0.049 6 0.8 S_collat_transv_post 1673 1133 3342 2.686 0.649 0.108 0.034 19 2.3 S_front_inf 1974 1326 3725 2.581 0.758 0.151 0.068 40 5.3 S_front_middle 3270 2215 6343 2.925 0.558 0.111 0.033 28 4.7 S_front_sup 614 446 1063 2.594 0.524 0.100 0.018 3 0.5 S_interm_prim-Jensen 3545 2356 6483 2.681 0.650 0.118 0.042 42 5.5 S_intrapariet_and_P_trans 880 596 1456 2.779 0.506 0.127 0.036 9 1.3 S_oc_middle_and_Lunatus 2002 1373 3604 2.749 0.462 0.118 0.029 17 2.4 S_oc_sup_and_transversal 699 450 1065 2.774 0.402 0.116 0.035 6 0.9 S_occipital_ant 1010 697 2038 3.116 0.457 0.141 0.045 14 2.0 S_oc-temp_lat 2388 1627 4012 2.851 0.639 0.114 0.032 19 3.2 S_oc-temp_med_and_Lingual 370 257 699 2.956 0.601 0.132 0.039 3 0.6 S_orbital_lateral 612 422 1043 2.493 0.836 0.109 0.029 4 0.7 S_orbital_med-olfact 1671 1147 3580 3.030 0.787 0.131 0.048 21 3.1 S_orbital-H_Shaped 2259 1525 4113 2.822 0.765 0.119 0.033 22 3.0 S_parieto_occipital 1388 868 1687 2.304 0.874 0.132 0.044 25 2.2 S_pericallosal 2949 1963 4375 2.465 0.523 0.100 0.026 21 3.0 S_postcentral 2036 1372 3580 2.876 0.549 0.102 0.026 17 2.0 S_precentral-inf-part 1354 923 2295 2.828 0.564 0.098 0.022 7 1.3 S_precentral-sup-part 397 273 751 2.735 0.813 0.122 0.029 3 0.6 S_suborbital 1323 895 2681 2.812 0.610 0.114 0.030 11 1.6 S_subparietal 1486 1016 2585 3.025 0.503 0.111 0.024 8 1.7 S_temporal_inf 6485 4425 12963 3.084 0.596 0.107 0.026 55 6.9 S_temporal_sup 285 208 543 3.088 0.469 0.111 0.024 2 0.3 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Thu Apr 2 19:11:07 EDT 2015 /export/data/hippocampus/HMN/data/HMN002/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon HMN002 SUBJECTS_DIR is /export/data/hippocampus/HMN/data 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 = 107 writing volume /export/data/hippocampus/HMN/data/HMN002/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Apr 2 19:30:33 EDT 2015 /export/data/hippocampus/HMN/data/HMN002 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /cell_root/software/freesurfer/current/sys/ASegStatsLUT.txt --subject HMN002 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /cell_root/software/freesurfer/current/sys/ASegStatsLUT.txt --subject HMN002 sysname Linux hostname hippocampus.umd.edu machine x86_64 user lmarti atlas_icv (eTIV) = 1309444 mm^3 (det: 1.487735 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 200673 rh white matter volume 202202 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 213437.531791, pTot = 514186.236133 c = 300748.704341 rh surface-based volumes (mm3): wTot = 214221.708716, pTot = 518409.897137 c = 304188.188421 Computing SupraTentVolCor SupraTentVolCor = 58396.000 SupraTentVol = 1090992.133 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 1822 1822 4 5 Left-Inf-Lat-Vent 584 584 5 7 Left-Cerebellum-White-Matter 11333 11333 6 8 Left-Cerebellum-Cortex 58691 58691 7 10 Left-Thalamus-Proper 6704 6704 8 11 Left-Caudate 3471 3471 9 12 Left-Putamen 6150 6150 10 13 Left-Pallidum 1735 1735 11 14 3rd-Ventricle 605 605 12 15 4th-Ventricle 1330 1330 13 16 Brain-Stem 18262 18262 14 17 Left-Hippocampus 3705 3705 15 18 Left-Amygdala 1563 1563 16 24 CSF 998 998 17 26 Left-Accumbens-area 525 525 18 28 Left-VentralDC 3657 3657 19 30 Left-vessel 50 50 20 31 Left-choroid-plexus 700 700 23 43 Right-Lateral-Ventricle 1930 1930 24 44 Right-Inf-Lat-Vent 106 106 25 46 Right-Cerebellum-White-Matter 11397 11397 26 47 Right-Cerebellum-Cortex 57882 57882 27 49 Right-Thalamus-Proper 6772 6772 28 50 Right-Caudate 3547 3547 29 51 Right-Putamen 6127 6127 30 52 Right-Pallidum 1708 1708 31 53 Right-Hippocampus 4056 4056 32 54 Right-Amygdala 1696 1696 33 58 Right-Accumbens-area 653 653 34 60 Right-VentralDC 3678 3678 35 62 Right-vessel 40 40 36 63 Right-choroid-plexus 762 762 37 72 5th-Ventricle 3 3 38 77 WM-hypointensities 2163 2163 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 2 2 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 191 191 45 251 CC_Posterior 787 787 46 252 CC_Mid_Posterior 391 391 47 253 CC_Central 529 529 48 254 CC_Mid_Anterior 417 417 49 255 CC_Anterior 821 821 Reporting on 45 segmentations SubCortGrayVol = 190582 #----------------------------------------- #@# AParc-to-ASeg Thu Apr 2 19:40:01 EDT 2015 /export/data/hippocampus/HMN/data/HMN002 mri_aparc2aseg --s HMN002 --volmask SUBJECTS_DIR /export/data/hippocampus/HMN/data subject HMN002 outvol /export/data/hippocampus/HMN/data/HMN002/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading lh pial surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial Loading lh annotations from /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading rh pial surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial Loading rh annotations from /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/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 = 596533 Used brute-force search on 0 voxels Writing output aseg to /export/data/hippocampus/HMN/data/HMN002/mri/aparc+aseg.mgz /export/data/hippocampus/HMN/data/HMN002 mri_aparc2aseg --s HMN002 --volmask --a2009s SUBJECTS_DIR /export/data/hippocampus/HMN/data subject HMN002 outvol /export/data/hippocampus/HMN/data/HMN002/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading lh pial surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial Loading lh annotations from /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading rh pial surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial Loading rh annotations from /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/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 = 596533 Used brute-force search on 0 voxels Writing output aseg to /export/data/hippocampus/HMN/data/HMN002/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu Apr 2 19:45:25 EDT 2015 /export/data/hippocampus/HMN/data/HMN002 mri_aparc2aseg --s HMN002 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /export/data/hippocampus/HMN/data subject HMN002 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /export/data/hippocampus/HMN/data/HMN002/mri/aparc+aseg.mgz Reading lh white surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading lh pial surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial Loading lh annotations from /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading rh pial surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial Loading rh annotations from /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/mri/ribbon.mgz Loading filled from /export/data/hippocampus/HMN/data/HMN002/mri/filled.mgz Ripping vertices labeled as unkown Ripped 6701 vertices from left hemi Ripped 7062 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 /export/data/hippocampus/HMN/data/HMN002/mri/aseg.mgz Loading Ctx Seg File /export/data/hippocampus/HMN/data/HMN002/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 = 970254 Used brute-force search on 392 voxels Fixing Parahip LH WM Found 18 clusters 0 k 1.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 3.000000 5 k 1.000000 6 k 2.000000 7 k 3.000000 8 k 1.000000 9 k 1.000000 10 k 1.000000 11 k 2.000000 12 k 4.000000 13 k 5.000000 14 k 3.000000 15 k 3.000000 16 k 16.000000 17 k 1262.000000 Fixing Parahip RH WM Found 7 clusters 0 k 1.000000 1 k 1608.000000 2 k 2.000000 3 k 1.000000 4 k 1.000000 5 k 5.000000 6 k 22.000000 Writing output aseg to mri/wmparc.mgz /export/data/hippocampus/HMN/data/HMN002 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject HMN002 --surf-wm-vol --ctab /cell_root/software/freesurfer/current/sys/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject HMN002 --surf-wm-vol --ctab /cell_root/software/freesurfer/current/sys/WMParcStatsLUT.txt --etiv sysname Linux hostname hippocampus.umd.edu machine x86_64 user lmarti atlas_icv (eTIV) = 1309444 mm^3 (det: 1.487735 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 200673 rh white matter volume 202202 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1560412 # brainmaskvolume 1560412.0 # nbrainsegvoxels 221781 # brainsegvolume 221781.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 1 3001 wm-lh-bankssts 2211 2211 2 3002 wm-lh-caudalanteriorcingulate 2244 2244 3 3003 wm-lh-caudalmiddlefrontal 6432 6432 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 1616 1616 6 3006 wm-lh-entorhinal 706 706 7 3007 wm-lh-fusiform 5851 5851 8 3008 wm-lh-inferiorparietal 8630 8630 9 3009 wm-lh-inferiortemporal 5383 5383 10 3010 wm-lh-isthmuscingulate 3133 3133 11 3011 wm-lh-lateraloccipital 8403 8403 12 3012 wm-lh-lateralorbitofrontal 5831 5831 13 3013 wm-lh-lingual 4923 4923 14 3014 wm-lh-medialorbitofrontal 3536 3536 15 3015 wm-lh-middletemporal 4861 4861 16 3016 wm-lh-parahippocampal 1424 1424 17 3017 wm-lh-paracentral 3393 3393 18 3018 wm-lh-parsopercularis 2331 2331 19 3019 wm-lh-parsorbitalis 793 793 20 3020 wm-lh-parstriangularis 2187 2187 21 3021 wm-lh-pericalcarine 2256 2256 22 3022 wm-lh-postcentral 6389 6389 23 3023 wm-lh-posteriorcingulate 3947 3947 24 3024 wm-lh-precentral 10368 10368 25 3025 wm-lh-precuneus 7441 7441 26 3026 wm-lh-rostralanteriorcingulate 2091 2091 27 3027 wm-lh-rostralmiddlefrontal 10805 10805 28 3028 wm-lh-superiorfrontal 15121 15121 29 3029 wm-lh-superiorparietal 11180 11180 30 3030 wm-lh-superiortemporal 6975 6975 31 3031 wm-lh-supramarginal 7223 7223 32 3032 wm-lh-frontalpole 206 206 33 3033 wm-lh-temporalpole 522 522 34 3034 wm-lh-transversetemporal 668 668 35 3035 wm-lh-insula 7461 7461 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 3000 3000 120 4002 wm-rh-caudalanteriorcingulate 2490 2490 121 4003 wm-rh-caudalmiddlefrontal 5774 5774 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1712 1712 124 4006 wm-rh-entorhinal 686 686 125 4007 wm-rh-fusiform 6007 6007 126 4008 wm-rh-inferiorparietal 9273 9273 127 4009 wm-rh-inferiortemporal 5035 5035 128 4010 wm-rh-isthmuscingulate 2738 2738 129 4011 wm-rh-lateraloccipital 7941 7941 130 4012 wm-rh-lateralorbitofrontal 6359 6359 131 4013 wm-rh-lingual 4509 4509 132 4014 wm-rh-medialorbitofrontal 2746 2746 133 4015 wm-rh-middletemporal 5750 5750 134 4016 wm-rh-parahippocampal 1789 1789 135 4017 wm-rh-paracentral 4124 4124 136 4018 wm-rh-parsopercularis 2354 2354 137 4019 wm-rh-parsorbitalis 1039 1039 138 4020 wm-rh-parstriangularis 2192 2192 139 4021 wm-rh-pericalcarine 2302 2302 140 4022 wm-rh-postcentral 6651 6651 141 4023 wm-rh-posteriorcingulate 3440 3440 142 4024 wm-rh-precentral 10802 10802 143 4025 wm-rh-precuneus 7352 7352 144 4026 wm-rh-rostralanteriorcingulate 2067 2067 145 4027 wm-rh-rostralmiddlefrontal 10175 10175 146 4028 wm-rh-superiorfrontal 16559 16559 147 4029 wm-rh-superiorparietal 10394 10394 148 4030 wm-rh-superiortemporal 5699 5699 149 4031 wm-rh-supramarginal 7139 7139 150 4032 wm-rh-frontalpole 372 372 151 4033 wm-rh-temporalpole 568 568 152 4034 wm-rh-transversetemporal 614 614 153 4035 wm-rh-insula 7391 7391 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 22941 22941 237 5002 Right-UnsegmentedWhiteMatter 23339 23339 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /export/data/hippocampus/HMN/data/HMN002/label #-------------------------------------------- #@# BA Labels lh Thu Apr 2 20:03:52 EDT 2015 mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA1.label --trgsubject HMN002 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 304 Checking for and removing duplicates Writing label file ./lh.BA1.label 4433 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label --trgsubject HMN002 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 469 Checking for and removing duplicates Writing label file ./lh.BA2.label 8378 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA3a.label --trgsubject HMN002 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 171 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4248 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA3b.label --trgsubject HMN002 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 347 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6330 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA4a.label --trgsubject HMN002 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 373 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6157 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA4p.label --trgsubject HMN002 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 223 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4293 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA6.label --trgsubject HMN002 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 1479 Checking for and removing duplicates Writing label file ./lh.BA6.label 15068 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA44.label --trgsubject HMN002 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 300 Checking for and removing duplicates Writing label file ./lh.BA44.label 4481 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA45.label --trgsubject HMN002 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 333 Checking for and removing duplicates Writing label file ./lh.BA45.label 3755 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.V1.label --trgsubject HMN002 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 774 Checking for and removing duplicates Writing label file ./lh.V1.label 5415 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.V2.label --trgsubject HMN002 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 2673 Checking for and removing duplicates Writing label file ./lh.V2.label 10787 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.MT.label --trgsubject HMN002 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 482 Checking for and removing duplicates Writing label file ./lh.MT.label 2500 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s HMN002 --hemi lh --ctab /cell_root/software/freesurfer/current/sys/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose Reading ctab /cell_root/software/freesurfer/current/sys/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /export/data/hippocampus/HMN/data/HMN002/label cmdline mris_label2annot --s HMN002 --hemi lh --ctab /cell_root/software/freesurfer/current/sys/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --a BA --maxstatwinner --noverbose sysname Linux hostname hippocampus.umd.edu machine x86_64 user lmarti subject HMN002 hemi lh SUBJECTS_DIR /export/data/hippocampus/HMN/data ColorTable /cell_root/software/freesurfer/current/sys/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /export/data/hippocampus/HMN/data/HMN002/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 94616 unhit vertices Writing annot to /export/data/hippocampus/HMN/data/HMN002/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab HMN002 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white... reading input pial surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial... reading input white surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /cell_root/software/freesurfer/current/sys/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 1114 615 2886 3.067 0.896 0.176 0.165 85 10.7 BA1 3884 2575 7774 2.732 0.773 0.121 0.068 60 5.9 BA2 1037 683 1033 2.078 0.536 0.128 0.041 9 1.8 BA3a 2464 1641 4125 2.096 0.967 0.121 0.041 27 4.3 BA3b 1682 1044 3850 3.003 0.527 0.123 0.046 18 3.6 BA4a 1302 866 2492 2.912 0.409 0.106 0.051 42 3.4 BA4p 9843 6507 28531 3.435 0.792 0.137 0.056 167 22.2 BA6 2134 1482 5354 3.000 0.548 0.119 0.042 36 3.5 BA44 2516 1715 6611 3.088 0.682 0.123 0.041 36 4.2 BA45 2593 1953 3085 1.626 0.554 0.181 0.138 94 8.8 V1 8180 5230 12957 2.321 0.701 0.161 0.070 174 24.4 V2 2036 1291 4015 2.935 0.603 0.125 0.081 53 4.1 MT #-------------------------------------------- #@# BA Labels rh Thu Apr 2 20:06:18 EDT 2015 mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA1.label --trgsubject HMN002 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 518 Checking for and removing duplicates Writing label file ./rh.BA1.label 4480 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA2.label --trgsubject HMN002 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 705 Checking for and removing duplicates Writing label file ./rh.BA2.label 7392 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA3a.label --trgsubject HMN002 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4191 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA3b.label --trgsubject HMN002 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 555 Checking for and removing duplicates Writing label file ./rh.BA3b.label 5077 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA4a.label --trgsubject HMN002 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 440 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6187 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA4p.label --trgsubject HMN002 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4684 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA6.label --trgsubject HMN002 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 1415 Checking for and removing duplicates Writing label file ./rh.BA6.label 13671 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA44.label --trgsubject HMN002 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 848 Checking for and removing duplicates Writing label file ./rh.BA44.label 7760 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA45.label --trgsubject HMN002 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 695 Checking for and removing duplicates Writing label file ./rh.BA45.label 6050 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.V1.label --trgsubject HMN002 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 992 Checking for and removing duplicates Writing label file ./rh.V1.label 5719 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.V2.label --trgsubject HMN002 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 2481 Checking for and removing duplicates Writing label file ./rh.V2.label 10497 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/rh.MT.label --trgsubject HMN002 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = HMN002 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 /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /export/data/hippocampus/HMN/data/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white Reading target registration /export/data/hippocampus/HMN/data/HMN002/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 300 Checking for and removing duplicates Writing label file ./rh.MT.label 2232 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s HMN002 --hemi rh --ctab /cell_root/software/freesurfer/current/sys/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose Reading ctab /cell_root/software/freesurfer/current/sys/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /export/data/hippocampus/HMN/data/HMN002/label cmdline mris_label2annot --s HMN002 --hemi rh --ctab /cell_root/software/freesurfer/current/sys/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --a BA --maxstatwinner --noverbose sysname Linux hostname hippocampus.umd.edu machine x86_64 user lmarti subject HMN002 hemi rh SUBJECTS_DIR /export/data/hippocampus/HMN/data ColorTable /cell_root/software/freesurfer/current/sys/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /export/data/hippocampus/HMN/data/HMN002/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 95850 unhit vertices Writing annot to /export/data/hippocampus/HMN/data/HMN002/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab HMN002 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white... reading input pial surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial... reading input white surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /cell_root/software/freesurfer/current/sys/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 1106 534 2561 3.010 0.618 0.143 0.150 45 3.7 BA1 3902 2560 6604 2.517 0.563 0.096 0.025 27 3.8 BA2 1068 708 1073 1.959 0.463 0.122 0.038 8 1.6 BA3a 2449 1554 3693 1.963 0.805 0.102 0.035 41 3.9 BA3b 1720 1005 3608 3.038 0.514 0.128 0.253 129 25.7 BA4a 1241 814 2325 2.839 0.427 0.088 0.027 8 1.4 BA4p 8909 5802 24046 3.290 0.763 0.132 0.101 153 23.6 BA6 3916 2610 8458 2.962 0.599 0.120 0.043 71 7.3 BA44 3745 2507 10469 3.186 0.773 0.138 0.105 426 7.3 BA45 3087 2234 3791 1.718 0.592 0.174 0.099 74 13.3 V1 7922 4819 12331 2.403 0.676 0.163 0.101 358 31.0 V2 1784 1154 3558 3.016 0.610 0.135 0.079 75 3.0 MT /export/data/hippocampus/HMN/data/HMN002/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Thu Apr 2 20:08:48 EDT 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o HMN002 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject HMN002. processing subject lh.EC_average... reading output surface /export/data/hippocampus/HMN/data/HMN002/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 995 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label HMN002 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.white... reading input pial surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.pial... reading input white surface /export/data/hippocampus/HMN/data/HMN002/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 372 226 1465 3.598 0.744 0.183 0.307 5 6.3 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Thu Apr 2 20:09:05 EDT 2015 mris_spherical_average -erode 1 -orig white -t 0.4 -o HMN002 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject HMN002. processing subject rh.EC_average... reading output surface /export/data/hippocampus/HMN/data/HMN002/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 876 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label HMN002 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.white... reading input pial surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.pial... reading input white surface /export/data/hippocampus/HMN/data/HMN002/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 287 184 1112 3.696 0.734 0.114 0.043 2 0.5 ./rh.entorhinal_exvivo.label #-------------------------------------------- #@# Hippocampal Subfields processing Thu Apr 2 20:09:23 EDT 2015 mkdir -p /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh HMN002 left /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh HMN002 right /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults cp /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults/HMN002/left/segmentationWithoutPartialVolumingLog/posterior_left* /export/data/hippocampus/HMN/data/HMN002/mri cp /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults/HMN002/left/segmentationWithoutPartialVolumingLog/posterior_Left* /export/data/hippocampus/HMN/data/HMN002/mri cp /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults/HMN002/right/segmentationWithoutPartialVolumingLog/posterior_right* /export/data/hippocampus/HMN/data/HMN002/mri cp /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults/HMN002/right/segmentationWithoutPartialVolumingLog/posterior_Right* /export/data/hippocampus/HMN/data/HMN002/mri rm -rf /export/data/hippocampus/HMN/data/HMN002/tmp/subfieldResults #------------------------------------------ recon-all -s HMN002 finished without error at Thu Apr 2 22:25:31 EDT 2015 New invocation of recon-all Tue Dec 15 23:37:48 EST 2015 /export/data/hippocampus/HMN/data/HMN002 /cell_root/software/freesurfer/dev/sys/bin/recon-all -s HMN002 -hippocampal-subfields-T1T2 HMN002/T2/T2_HMN002.mgz T1T2 subjid HMN002 setenv SUBJECTS_DIR /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/dev/sys Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/6.0.0b/Linux-x64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151006 Linux hippocampus.umd.edu 2.6.32-504.23.4.el6.x86_64 #1 SMP Fri May 29 10:16:43 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 37140912 28771524 8369388 5388 279516 1561736 -/+ buffers/cache: 26930272 10210640 Swap: 23999484 0 23999484 ######################################## program versions used $Id: recon-all,v 1.547 2015/10/01 21:20:26 greve 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: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_convert.c,v 1.223 2015/09/24 21:25:48 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_em_register.c,v 1.103 2015/08/26 16:51:09 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_ca_normalize.c,v 1.64 2015/08/26 16:50:50 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_ca_register.c,v 1.93 2015/06/24 16:03:22 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_ca_label.c,v 1.109 2015/08/26 16:46:38 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_concatenate_lta.c,v 1.15 2015/08/19 16:35:05 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_sphere.c,v 1.59 2014/11/06 01:38:58 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_make_surfaces.c,v 1.159 2015/09/15 19:01:19 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mris_calc.c,v 1.53 2015/06/04 20:50:50 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.51 2015/09/22 20:57:47 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_robust_template.cpp,v 1.51 2015/09/22 20:57:47 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:48-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:49-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_segstats.c,v 1.118 2015/10/05 23:59:50 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/16-04:37:49-GMT BuildTimeStamp: Oct 6 2015 06:03:00 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /cell_root/software/freesurfer/dev/sys/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /cell_root/software/freesurfer/dev/sys/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cell_root/software/freesurfer/dev/sys Previous: /cell_root/software/freesurfer/current/sys #-------------------------------------------- #@# Hippocampal Subfields processing (T1 + T2 volume) left Tue Dec 15 23:37:50 EST 2015 /cell_root/software/freesurfer/dev/sys/bin/segmentSF_T1T2.sh /cell_root/software/freesurfer/dev/sys/MCRv80 /cell_root/software/freesurfer/dev/sys HMN002 /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/T2/T2_HMN002.mgz left T1T2 See log file: /export/data/hippocampus/HMN/data/HMN002/scripts/hippocampal-subfields-T1T2.log #-------------------------------------------- #@# Hippocampal Subfields processing (T1 + T2 volume) right Wed Dec 16 00:12:27 EST 2015 /cell_root/software/freesurfer/dev/sys/bin/segmentSF_T1T2.sh /cell_root/software/freesurfer/dev/sys/MCRv80 /cell_root/software/freesurfer/dev/sys HMN002 /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/T2/T2_HMN002.mgz right T1T2 See log file: /export/data/hippocampus/HMN/data/HMN002/scripts/hippocampal-subfields-T1T2.log #------------------------------------------ Started at Tue Dec 15 23:37:48 EST 2015 Ended at Wed Dec 16 00:43:53 EST 2015 #@#%# recon-all-run-time-hours 1.101 recon-all -s HMN002 finished without error at Wed Dec 16 00:43:53 EST 2015 New invocation of recon-all Tue Dec 22 16:40:08 EST 2015 /export/data/hippocampus/HMN/data/HMN002 /cell_root/software/freesurfer/dev/sys/bin/recon-all -s HMN002 -hippocampal-subfields-T1T2 HMN002/T2/T2_HMN002.mgz T1T2 subjid HMN002 setenv SUBJECTS_DIR /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/dev/sys Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/6-2015-12-15/Linux-x64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151215 Linux hippocampus.umd.edu 2.6.32-504.23.4.el6.x86_64 #1 SMP Fri May 29 10:16:43 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 37140912 33642384 3498528 23864 9300 3413416 -/+ buffers/cache: 30219668 6921244 Swap: 23999484 1338384 22661100 ######################################## program versions used $Id: recon-all,v 1.557 2015/12/09 20:02:53 zkaufman 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: $ TimeStamp: 2015/12/22-21:40:08-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:08-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:10-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:10-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:10-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:10-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:10-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:10-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:11-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_em_register.c,v 1.103 2015/08/26 16:51:09 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:11-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_normalize.c,v 1.65 2015/10/10 17:28:19 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:11-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_register.c,v 1.94 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:12-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_label.c,v 1.109 2015/08/26 16:46:38 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:12-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:12-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:13-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:13-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:13-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:13-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:13-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:13-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:13-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:15-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_fix_topology.c,v 1.49 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:15-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:15-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:15-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:15-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:15-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:17-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:17-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:17-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:17-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:17-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:17-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:19-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:19-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:19-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:19-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:19-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/22-21:40:19-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /cell_root/software/freesurfer/dev/sys/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /cell_root/software/freesurfer/dev/sys/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cell_root/software/freesurfer/dev/sys Previous: /cell_root/software/freesurfer/current/sys #-------------------------------------------- #@# Hippocampal Subfields processing (T1 + T2 volume) left Tue Dec 22 16:40:27 EST 2015 /cell_root/software/freesurfer/dev/sys/bin/segmentSF_T1T2.sh /cell_root/software/freesurfer/dev/sys/MCRv80 /cell_root/software/freesurfer/dev/sys HMN002 /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/T2/T2_HMN002.mgz left T1T2 See log file: /export/data/hippocampus/HMN/data/HMN002/scripts/hippocampal-subfields-T1T2.log #-------------------------------------------- #@# Hippocampal Subfields processing (T1 + T2 volume) right Tue Dec 22 17:23:44 EST 2015 /cell_root/software/freesurfer/dev/sys/bin/segmentSF_T1T2.sh /cell_root/software/freesurfer/dev/sys/MCRv80 /cell_root/software/freesurfer/dev/sys HMN002 /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/T2/T2_HMN002.mgz right T1T2 See log file: /export/data/hippocampus/HMN/data/HMN002/scripts/hippocampal-subfields-T1T2.log #------------------------------------------ Started at Tue Dec 22 16:40:02 EST 2015 Ended at Tue Dec 22 18:01:04 EST 2015 #@#%# recon-all-run-time-hours 1.351 recon-all -s HMN002 finished without error at Tue Dec 22 18:01:04 EST 2015 New invocation of recon-all Sat Dec 26 16:07:44 EST 2015 /export/data/hippocampus/HMN/data/HMN002 /cell_root/software/freesurfer/dev/sys/bin/recon-all -s HMN002 -hippocampal-subfields-T1T2 HMN002/T2/T2_HMN002.mgz T1T2 subjid HMN002 setenv SUBJECTS_DIR /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/dev/sys Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/6-2015-12-15/Linux-x64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151215 Linux hippocampus.umd.edu 2.6.32-504.23.4.el6.x86_64 #1 SMP Fri May 29 10:16:43 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 37140912 30409880 6731032 4692 143372 545544 -/+ buffers/cache: 29720964 7419948 Swap: 23999484 77836 23921648 ######################################## program versions used $Id: recon-all,v 1.557 2015/12/09 20:02:53 zkaufman 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: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_em_register.c,v 1.103 2015/08/26 16:51:09 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_normalize.c,v 1.65 2015/10/10 17:28:19 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_register.c,v 1.94 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_label.c,v 1.109 2015/08/26 16:46:38 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_fix_topology.c,v 1.49 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/26-21:07:44-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-504.23.4.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /cell_root/software/freesurfer/dev/sys/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /cell_root/software/freesurfer/dev/sys/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cell_root/software/freesurfer/dev/sys Previous: /cell_root/software/freesurfer/current/sys #-------------------------------------------- #@# Hippocampal Subfields processing (T1 + T2 volume) left Sat Dec 26 16:07:45 EST 2015 /cell_root/software/freesurfer/dev/sys/bin/segmentSF_T1T2.sh /cell_root/software/freesurfer/dev/sys/MCRv80 /cell_root/software/freesurfer/dev/sys HMN002 /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/T2/T2_HMN002.mgz left T1T2 See log file: /export/data/hippocampus/HMN/data/HMN002/scripts/hippocampal-subfields-T1T2.log #-------------------------------------------- #@# Hippocampal Subfields processing (T1 + T2 volume) right Sat Dec 26 16:42:07 EST 2015 /cell_root/software/freesurfer/dev/sys/bin/segmentSF_T1T2.sh /cell_root/software/freesurfer/dev/sys/MCRv80 /cell_root/software/freesurfer/dev/sys HMN002 /export/data/hippocampus/HMN/data /export/data/hippocampus/HMN/data/HMN002/T2/T2_HMN002.mgz right T1T2 See log file: /export/data/hippocampus/HMN/data/HMN002/scripts/hippocampal-subfields-T1T2.log #------------------------------------------ Started at Sat Dec 26 16:07:43 EST 2015 Ended at Sat Dec 26 17:14:26 EST 2015 #@#%# recon-all-run-time-hours 1.112 recon-all -s HMN002 finished without error at Sat Dec 26 17:14:26 EST 2015 New invocation of recon-all Mon Jan 25 13:14:40 EST 2016 /export/data/hippocampus/HMN/data/HMN002 /cell_root/software/freesurfer/dev/sys/bin/recon-all -all -s HMN002 -hippocampal-subfields-T1T2 HMN002/T2/T2_HMN002.mgz T1T2 subjid HMN002 setenv SUBJECTS_DIR /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/dev/sys Actual FREESURFER_HOME /afs/glue.umd.edu/software/freesurfer/6-2015-12-15/Linux-x64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151215 Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 37140792 24186564 12954228 12272 404376 4921732 -/+ buffers/cache: 18860456 18280336 Swap: 23999484 0 23999484 ######################################## program versions used $Id: recon-all,v 1.557 2015/12/09 20:02:53 zkaufman 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: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_em_register.c,v 1.103 2015/08/26 16:51:09 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_normalize.c,v 1.65 2015/10/10 17:28:19 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_register.c,v 1.94 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_ca_label.c,v 1.109 2015/08/26 16:46:38 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_fix_topology.c,v 1.49 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_make_surfaces.c,v 1.162 2015/12/10 21:15:02 fischl Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mris_calc.c,v 1.54 2015/12/14 23:18:58 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_robust_template.cpp,v 1.52 2015/12/15 21:20:46 mreuter Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/01/25-18:14:40-GMT BuildTimeStamp: Dec 15 2015 21:05:51 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: gengf Machine: hippocampus.umd.edu Platform: Linux PlatformVersion: 2.6.32-573.12.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /cell_root/software/freesurfer/dev/sys/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /cell_root/software/freesurfer/dev/sys/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /cell_root/software/freesurfer/dev/sys Previous: /cell_root/software/freesurfer/current/sys #-------------------------------------------- #@# MotionCor Mon Jan 25 13:14:42 EST 2016 Found 1 runs /export/data/hippocampus/HMN/data/HMN002/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 /export/data/hippocampus/HMN/data/HMN002/mri/orig/001.mgz /export/data/hippocampus/HMN/data/HMN002/mri/rawavg.mgz /export/data/hippocampus/HMN/data/HMN002 mri_convert /export/data/hippocampus/HMN/data/HMN002/mri/rawavg.mgz /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz --conform mri_convert /export/data/hippocampus/HMN/data/HMN002/mri/rawavg.mgz /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz --conform $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /export/data/hippocampus/HMN/data/HMN002/mri/rawavg.mgz... TR=1900.00, TE=2.32, TI=900.00, flip angle=9.00 i_ras = (0.0436194, -0.999048, -1.38554e-08) j_ras = (-0.0331236, -0.00144619, -0.99945) k_ras = (-0.998499, -0.0435954, 0.0331552) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz... mri_add_xform_to_header -c /export/data/hippocampus/HMN/data/HMN002/mri/transforms/talairach.xfm /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz /export/data/hippocampus/HMN/data/HMN002/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jan 25 13:15:09 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 4 /export/data/hippocampus/HMN/data/HMN002/mri /cell_root/software/freesurfer/dev/sys/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 4 nIters 1 $Id: mri_nu_correct.mni,v 1.25 2015/12/09 20:02:53 zkaufman Exp $ Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux Mon Jan 25 13:15:09 EST 2016 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 tmpdir is ./tmp.mri_nu_correct.mni.25457 /export/data/hippocampus/HMN/data/HMN002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25457/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25457/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from orig.mgz... TR=1900.00, TE=2.32, TI=900.00, flip angle=9.00 i_ras = (-1, 3.72529e-09, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (3.72529e-09, 1, 1.16415e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.25457/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jan 25 13:15:11 EST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.25457/nu0.mnc ./tmp.mri_nu_correct.mni.25457/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25457/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 4 [gengf@hippocampus.umd.edu:/export/data/hippocampus/HMN/data/HMN002/mri/] [2016-01-25 13:15:11] running: /cell_root/software/freesurfer/dev/sys/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 1e-4 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.25457/0/ ./tmp.mri_nu_correct.mni.25457/nu0.mnc ./tmp.mri_nu_correct.mni.25457/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 76 CV of field change: 9.91031e-05 mri_convert ./tmp.mri_nu_correct.mni.25457/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.25457/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from ./tmp.mri_nu_correct.mni.25457/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (3.72529e-09, 1, 1.16415e-10) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Jan 25 13:16:20 EST 2016 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jan 25 13:16:59 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7733, pval=0.6675 >= threshold=0.0050) awk -f /cell_root/software/freesurfer/dev/sys/bin/extract_talairach_avi_QA.awk /export/data/hippocampus/HMN/data/HMN002/mri/transforms/talairach_avi.log tal_QC_AZS /export/data/hippocampus/HMN/data/HMN002/mri/transforms/talairach_avi.log TalAviQA: 0.97859 z-score: 0 #-------------------------------------------- #@# Intensity Normalization Mon Jan 25 13:16:59 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_normalize -g 1 orig_nu.mgz T1.mgz using max gradient = 1.000 reading from orig_nu.mgz... normalizing image... talairach transform 1.08530 0.00450 -0.05216 -1.30782; -0.10379 1.18402 0.18375 -27.79831; 0.06503 -0.15230 1.13118 -30.08842; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 81 (81), valley at 57 (57) csf peak at 40, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 81 (81), valley at 58 (58) csf peak at 40, setting threshold to 67 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 16 seconds. #-------------------------------------------- #@# Skull Stripping Mon Jan 25 13:19:15 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /cell_root/software/freesurfer/dev/sys/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=97 z=128 r=81 first estimation of the main basin volume: 2254769 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=149, y=90, z=97, Imax=255 CSF=19, 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=19081965532 voxels, voxel volume =1.000 = 19081965532 mmm3 = 19081965.568 cm3 done. PostAnalyze...Basin Prior 12 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=102, z=123, r=8751 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=23, CSF_MAX=63 , nb = 40527 RIGHT_CER CSF_MIN=0, CSF_intensity=13, CSF_MAX=58 , nb = -1042206666 LEFT_CER CSF_MIN=0, CSF_intensity=10, CSF_MAX=47 , nb = 1069292531 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=23, CSF_MAX=64 , nb = 1076270606 LEFT_BRAIN CSF_MIN=1, CSF_intensity=23, CSF_MAX=65 , nb = 1079519490 OTHER CSF_MIN=0, CSF_intensity=26, CSF_MAX=44 , nb = 1065723577 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 63, 60, 59, 75 after analyzing : 50, 60, 60, 63 RIGHT_CER before analyzing : 58, 58, 59, 76 after analyzing : 46, 58, 59, 62 LEFT_CER before analyzing : 47, 55, 59, 75 after analyzing : 47, 57, 59, 61 RIGHT_BRAIN before analyzing : 64, 59, 57, 75 after analyzing : 49, 59, 59, 63 LEFT_BRAIN before analyzing : 65, 60, 59, 75 after analyzing : 50, 60, 60, 63 OTHER before analyzing : 44, 62, 74, 86 after analyzing : 44, 70, 74, 74 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.010 curvature mean = 67.998, std = 6.318 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.01, sigma = 5.06 after rotation: sse = 4.01, sigma = 5.06 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 4.52, its var is 5.73 before Erosion-Dilatation 1.31% of inacurate vertices after Erosion-Dilatation 2.67% 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...37 iterations mri_strip_skull: done peeling brain Brain Size = 1537109 voxels, voxel volume = 1.000 mm3 = 1537109 mmm3 = 1537.109 cm3 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #-------------------------------------------- #@# Nu Intensity Correction Mon Jan 25 13:19:43 EST 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 4 /export/data/hippocampus/HMN/data/HMN002/mri /cell_root/software/freesurfer/dev/sys/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 4 nIters 1 $Id: mri_nu_correct.mni,v 1.25 2015/12/09 20:02:53 zkaufman Exp $ Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux Mon Jan 25 13:19:43 EST 2016 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 tmpdir is ./tmp.mri_nu_correct.mni.26691 /export/data/hippocampus/HMN/data/HMN002/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26691/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.26691/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from orig.mgz... TR=1900.00, TE=2.32, TI=900.00, flip angle=9.00 i_ras = (-1, 3.72529e-09, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (3.72529e-09, 1, 1.16415e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.26691/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jan 25 13:19:46 EST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.26691/nu0.mnc ./tmp.mri_nu_correct.mni.26691/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.26691/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 4 [gengf@hippocampus.umd.edu:/export/data/hippocampus/HMN/data/HMN002/mri/] [2016-01-25 13:19:46] running: /cell_root/software/freesurfer/dev/sys/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 1e-4 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.26691/0/ ./tmp.mri_nu_correct.mni.26691/nu0.mnc ./tmp.mri_nu_correct.mni.26691/nu1.imp 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 76 CV of field change: 9.91031e-05 mri_binarize --i ./tmp.mri_nu_correct.mni.26691/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.26691/ones.mgz $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /export/data/hippocampus/HMN/data/HMN002/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.26691/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.26691/ones.mgz sysname Linux hostname hippocampus.umd.edu machine x86_64 user gengf input ./tmp.mri_nu_correct.mni.26691/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.26691/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.26691/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.26691/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26691/input.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.26691/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.26691/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26691/input.mean.dat sysname Linux hostname hippocampus.umd.edu machine x86_64 user gengf UseRobust 0 Loading ./tmp.mri_nu_correct.mni.26691/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.26691/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.26691/ones.mgz --i ./tmp.mri_nu_correct.mni.26691/nu1.mnc --sum ./tmp.mri_nu_correct.mni.26691/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26691/output.mean.dat $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.26691/ones.mgz --i ./tmp.mri_nu_correct.mni.26691/nu1.mnc --sum ./tmp.mri_nu_correct.mni.26691/sum.junk --avgwf ./tmp.mri_nu_correct.mni.26691/output.mean.dat sysname Linux hostname hippocampus.umd.edu machine x86_64 user gengf UseRobust 0 Loading ./tmp.mri_nu_correct.mni.26691/ones.mgz Loading ./tmp.mri_nu_correct.mni.26691/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.26691/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.26691/nu1.mnc ./tmp.mri_nu_correct.mni.26691/nu1.mnc mul .94131487830820623985 Saving result to './tmp.mri_nu_correct.mni.26691/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.26691/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.26691/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from ./tmp.mri_nu_correct.mni.26691/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-09, -3.72529e-09) j_ras = (0, 0, -1) k_ras = (3.72529e-09, 1, 1.16415e-10) 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 9 seconds. mapping (10, 108) to ( 3, 110) Mon Jan 25 13:21:23 EST 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /export/data/hippocampus/HMN/data/HMN002/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #------------------------------------- #@# EM Registration Mon Jan 25 13:21:24 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca'... average std = 7.4 using min determinant for regularization = 5.4 0 singular and 937 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.2 or > 452.2 total sample mean = 78.8 (1019 zeros) ************************************************ spacing=8, using 2854 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2854, passno 0, spacing 8 resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=29.1 skull bounding box = (56, 40, 55) --> (196, 156, 205) using (103, 79, 130) as brain centroid... mean wm in atlas = 105, using box (86,65,112) --> (120, 93,148) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 0.1 after smoothing, mri peak at 107, scaling input intensities by 0.981 scaling channel 0 by 0.981308 initial log_p = -4.429 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.041172 @ (-9.091, 9.091, -27.273) max log p = -3.818430 @ (13.636, 4.545, 13.636) max log p = -3.694221 @ (-6.818, 6.818, -6.818) max log p = -3.652837 @ (1.136, -3.409, -1.136) max log p = -3.640543 @ (1.705, 0.568, 2.841) max log p = -3.640543 @ (0.000, 0.000, 0.000) Found translation: (0.6, 17.6, -18.8): log p = -3.641 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.478, old_max_log_p =-3.641 (thresh=-3.6) 1.00000 0.00000 0.00000 0.56818; 0.00000 1.14016 0.13053 -13.13393; 0.00000 -0.16136 1.06580 -10.38215; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.478, old_max_log_p =-3.478 (thresh=-3.5) 1.00000 0.00000 0.00000 0.56818; 0.00000 1.14016 0.13053 -13.13393; 0.00000 -0.16136 1.06580 -10.38215; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.372, old_max_log_p =-3.478 (thresh=-3.5) 1.01596 -0.07175 -0.04434 9.59143; 0.06292 1.09975 0.09042 -11.95994; 0.03471 -0.12782 1.06848 -18.58121; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.372, old_max_log_p =-3.372 (thresh=-3.4) 1.01596 -0.07175 -0.04434 9.59143; 0.06292 1.09975 0.09042 -11.95994; 0.03471 -0.12782 1.06848 -18.58121; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.347, old_max_log_p =-3.372 (thresh=-3.4) 1.01535 -0.05267 -0.05124 9.04034; 0.04645 1.10464 0.09150 -10.00444; 0.04271 -0.12805 1.06686 -19.37934; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.346, old_max_log_p =-3.347 (thresh=-3.3) 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2854 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; nsamples 2854 Quasinewton: input matrix 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.346 (old=-4.429) transform before final EM align: 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 314792 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; nsamples 314792 Quasinewton: input matrix 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = 3.9 tol 0.000000 final transform: 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... registration took 14 minutes and 40 seconds. #-------------------------------------- #@# CA Normalize Mon Jan 25 13:36:04 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.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 '/cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 97 --> 105 resetting gm mean[0]: 60 --> 60 input volume #1 is the most T1-like using real data threshold=29.1 skull bounding box = (56, 40, 55) --> (196, 156, 205) using (103, 79, 130) as brain centroid... mean wm in atlas = 105, using box (86,65,112) --> (120, 93,148) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 107 +- 0.1 after smoothing, mri peak at 107, scaling input intensities by 0.981 scaling channel 0 by 0.981308 using 245868 sample points... INFO: compute sample coordinates transform 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (124, 42, 51) --> (193, 144, 207) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 243.0 0 of 3418 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (64, 42, 53) --> (130, 149, 208) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 243.0 6 of 4212 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (128, 119, 76) --> (177, 157, 125) Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 243.0 0 of 17 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (85, 121, 76) --> (128, 159, 128) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 243.0 2 of 44 (4.5%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (112, 111, 109) --> (147, 173, 137) Brain_Stem: limiting intensities to 81.0 --> 243.0 0 of 95 (0.0%) samples deleted using 7786 total control points for intensity normalization... bias field = 0.991 +- 0.038 38 of 7778 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (124, 42, 51) --> (193, 144, 207) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 228.0 0 of 3658 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (64, 42, 53) --> (130, 149, 208) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 228.0 3 of 4596 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (128, 119, 76) --> (177, 157, 125) Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 228.0 0 of 98 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (85, 121, 76) --> (128, 159, 128) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 228.0 0 of 62 (0.0%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (112, 111, 109) --> (147, 173, 137) Brain_Stem: limiting intensities to 73.0 --> 228.0 0 of 142 (0.0%) samples deleted using 8556 total control points for intensity normalization... bias field = 1.023 +- 0.037 27 of 8484 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39361 control points for structure... bounding box (124, 42, 51) --> (193, 144, 207) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 225.0 13 of 3615 (0.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39033 control points for structure... bounding box (64, 42, 53) --> (130, 149, 208) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 225.0 34 of 4548 (0.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 2873 control points for structure... bounding box (128, 119, 76) --> (177, 157, 125) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 225.0 11 of 111 (9.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2551 control points for structure... bounding box (85, 121, 76) --> (128, 159, 128) Right_Cerebellum_White_Matter: limiting intensities to 72.0 --> 225.0 1 of 119 (0.8%) samples deleted finding control points in Brain_Stem.... found 3424 control points for structure... bounding box (112, 111, 109) --> (147, 173, 137) forcing use of sample 3 @ (134, 160, 122) Brain_Stem: limiting intensities to 72.0 --> 225.0 1 of 185 (0.5%) samples deleted using 8578 total control points for intensity normalization... bias field = 1.020 +- 0.036 31 of 8404 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 46 seconds. #-------------------------------------- #@# CA Reg Mon Jan 25 13:37:50 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.21 (predicted orig area = 6.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** 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=0.828, neg=0, invalid=3294 0001: dt=326.295680, rms=0.726 (12.248%), neg=0, invalid=3294 0002: dt=192.191045, rms=0.704 (3.077%), neg=0, invalid=3294 0003: dt=221.952000, rms=0.694 (1.470%), neg=0, invalid=3294 0004: dt=164.288660, rms=0.688 (0.779%), neg=0, invalid=3294 0005: dt=295.936000, rms=0.684 (0.549%), neg=0, invalid=3294 0006: dt=133.818182, rms=0.682 (0.429%), neg=0, invalid=3294 0007: dt=517.888000, rms=0.678 (0.507%), neg=0, invalid=3294 0008: dt=129.472000, rms=0.676 (0.266%), neg=0, invalid=3294 0009: dt=517.888000, rms=0.674 (0.269%), neg=0, invalid=3294 0010: dt=129.472000, rms=0.673 (0.229%), neg=0, invalid=3294 0011: dt=129.472000, rms=0.672 (0.081%), neg=0, invalid=3294 0012: dt=129.472000, rms=0.671 (0.140%), neg=0, invalid=3294 0013: dt=129.472000, rms=0.670 (0.180%), neg=0, invalid=3294 0014: dt=129.472000, rms=0.669 (0.195%), neg=0, invalid=3294 0015: dt=129.472000, rms=0.667 (0.219%), neg=0, invalid=3294 0016: dt=129.472000, rms=0.666 (0.224%), neg=0, invalid=3294 0017: dt=129.472000, rms=0.664 (0.226%), neg=0, invalid=3294 0018: dt=129.472000, rms=0.663 (0.198%), neg=0, invalid=3294 0019: dt=129.472000, rms=0.662 (0.202%), neg=0, invalid=3294 0020: dt=129.472000, rms=0.661 (0.189%), neg=0, invalid=3294 0021: dt=129.472000, rms=0.659 (0.177%), neg=0, invalid=3294 0022: dt=129.472000, rms=0.658 (0.158%), neg=0, invalid=3294 0023: dt=129.472000, rms=0.658 (0.110%), neg=0, invalid=3294 0024: dt=129.472000, rms=0.657 (0.101%), neg=0, invalid=3294 0025: dt=1479.680000, rms=0.656 (0.193%), neg=0, invalid=3294 0026: dt=73.984000, rms=0.655 (0.042%), neg=0, invalid=3294 0027: dt=73.984000, rms=0.655 (0.010%), neg=0, invalid=3294 0028: dt=73.984000, rms=0.655 (0.009%), neg=0, invalid=3294 0029: dt=73.984000, rms=0.655 (0.007%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=3294 0030: dt=221.952000, rms=0.652 (0.570%), neg=0, invalid=3294 0031: dt=92.480000, rms=0.652 (0.023%), neg=0, invalid=3294 0032: dt=92.480000, rms=0.652 (0.019%), neg=0, invalid=3294 0033: dt=92.480000, rms=0.652 (0.034%), neg=0, invalid=3294 0034: dt=92.480000, rms=0.651 (0.052%), neg=0, invalid=3294 0035: dt=92.480000, rms=0.651 (0.085%), neg=0, invalid=3294 0036: dt=92.480000, rms=0.650 (0.105%), neg=0, invalid=3294 0037: dt=92.480000, rms=0.649 (0.098%), neg=0, invalid=3294 0038: dt=92.480000, rms=0.649 (0.090%), neg=0, invalid=3294 0039: dt=129.472000, rms=0.649 (0.007%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.655, neg=0, invalid=3294 0040: dt=36.288000, rms=0.653 (0.371%), neg=0, invalid=3294 0041: dt=145.152000, rms=0.649 (0.666%), neg=0, invalid=3294 0042: dt=276.148148, rms=0.634 (2.163%), neg=0, invalid=3294 0043: dt=27.882353, rms=0.631 (0.507%), neg=0, invalid=3294 0044: dt=6.480000, rms=0.631 (0.007%), neg=0, invalid=3294 0045: dt=6.480000, rms=0.631 (-0.010%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.632, neg=0, invalid=3294 0046: dt=145.152000, rms=0.629 (0.498%), neg=0, invalid=3294 0047: dt=145.152000, rms=0.624 (0.691%), neg=0, invalid=3294 0048: dt=36.288000, rms=0.624 (0.039%), neg=0, invalid=3294 0049: dt=36.288000, rms=0.624 (0.043%), neg=0, invalid=3294 0050: dt=36.288000, rms=0.623 (0.096%), neg=0, invalid=3294 0051: dt=36.288000, rms=0.622 (0.158%), neg=0, invalid=3294 0052: dt=36.288000, rms=0.621 (0.247%), neg=0, invalid=3294 0053: dt=36.288000, rms=0.619 (0.292%), neg=0, invalid=3294 0054: dt=36.288000, rms=0.617 (0.293%), neg=0, invalid=3294 0055: dt=36.288000, rms=0.616 (0.254%), neg=0, invalid=3294 0056: dt=36.288000, rms=0.614 (0.224%), neg=0, invalid=3294 0057: dt=36.288000, rms=0.613 (0.219%), neg=0, invalid=3294 0058: dt=36.288000, rms=0.611 (0.210%), neg=0, invalid=3294 0059: dt=36.288000, rms=0.610 (0.219%), neg=0, invalid=3294 0060: dt=36.288000, rms=0.609 (0.226%), neg=0, invalid=3294 0061: dt=36.288000, rms=0.609 (0.022%), neg=0, invalid=3294 0062: dt=36.288000, rms=0.608 (0.042%), neg=0, invalid=3294 0063: dt=36.288000, rms=0.608 (0.019%), neg=0, invalid=3294 0064: dt=9.072000, rms=0.608 (0.013%), neg=0, invalid=3294 0065: dt=4.536000, rms=0.608 (0.001%), neg=0, invalid=3294 0066: dt=1.134000, rms=0.608 (-0.001%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.630, neg=0, invalid=3294 0067: dt=11.200000, rms=0.627 (0.335%), neg=0, invalid=3294 0068: dt=11.200000, rms=0.627 (0.123%), neg=0, invalid=3294 0069: dt=11.200000, rms=0.626 (0.118%), neg=0, invalid=3294 0070: dt=11.200000, rms=0.625 (0.110%), neg=0, invalid=3294 0071: dt=11.200000, rms=0.625 (0.112%), neg=0, invalid=3294 0072: dt=11.200000, rms=0.624 (0.151%), neg=0, invalid=3294 0073: dt=11.200000, rms=0.622 (0.287%), neg=0, invalid=3294 0074: dt=11.200000, rms=0.619 (0.415%), neg=0, invalid=3294 0075: dt=11.200000, rms=0.616 (0.502%), neg=0, invalid=3294 0076: dt=11.200000, rms=0.613 (0.465%), neg=0, invalid=3294 0077: dt=5.600000, rms=0.613 (0.000%), neg=0, invalid=3294 0078: dt=2.800000, rms=0.613 (-0.001%), neg=0, invalid=3294 0079: dt=0.700000, rms=0.613 (0.000%), neg=0, invalid=3294 0080: dt=2.000000, rms=0.613 (0.001%), neg=0, invalid=3294 0081: dt=2.400000, rms=0.613 (0.003%), neg=0, invalid=3294 0082: dt=0.010937, rms=0.613 (-0.001%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=3294 0083: dt=0.010937, rms=0.613 (0.096%), neg=0, invalid=3294 0084: dt=0.010937, rms=0.613 (0.000%), neg=0, invalid=3294 0085: dt=0.000684, rms=0.613 (0.000%), neg=0, invalid=3294 0086: dt=0.000043, rms=0.613 (0.000%), neg=0, invalid=3294 0087: dt=0.000003, rms=0.613 (0.000%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.664, neg=0, invalid=3294 0088: dt=1.479167, rms=0.662 (0.333%), neg=0, invalid=3294 0089: dt=0.252000, rms=0.662 (0.006%), neg=0, invalid=3294 0090: dt=0.252000, rms=0.662 (0.002%), neg=0, invalid=3294 0091: dt=0.252000, rms=0.662 (-0.017%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.662, neg=0, invalid=3294 0092: dt=0.432000, rms=0.662 (0.097%), neg=0, invalid=3294 0093: dt=0.063000, rms=0.662 (0.002%), neg=0, invalid=3294 0094: dt=0.063000, rms=0.662 (0.001%), neg=0, invalid=3294 0095: dt=0.063000, rms=0.662 (-0.002%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.734, neg=0, invalid=3294 0096: dt=1.297136, rms=0.722 (1.626%), neg=0, invalid=3294 0097: dt=1.280000, rms=0.719 (0.501%), neg=0, invalid=3294 0098: dt=1.024000, rms=0.718 (0.113%), neg=0, invalid=3294 0099: dt=1.024000, rms=0.718 (0.027%), neg=0, invalid=3294 0100: dt=1.024000, rms=0.718 (-0.169%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.718, neg=0, invalid=3294 0101: dt=1.280000, rms=0.717 (0.219%), neg=0, invalid=3294 0102: dt=0.000000, rms=0.717 (-0.000%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.668, neg=0, invalid=3294 0103: dt=0.728378, rms=0.654 (2.074%), neg=0, invalid=3294 0104: dt=0.064000, rms=0.654 (0.098%), neg=0, invalid=3294 0105: dt=0.064000, rms=0.654 (-0.041%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.654, neg=0, invalid=3294 0106: dt=0.028000, rms=0.653 (0.106%), neg=0, invalid=3294 0107: dt=0.007000, rms=0.653 (0.001%), neg=0, invalid=3294 0108: dt=0.007000, rms=0.653 (0.002%), neg=0, invalid=3294 0109: dt=0.007000, rms=0.653 (-0.005%), neg=0, invalid=3294 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12974 (17) mri peak = 0.06475 (28) Left_Lateral_Ventricle (4): linear fit = 1.62 x + 0.0 (1635 voxels, overlap=0.359) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1635 voxels, peak = 27), gca=25.5 gca peak = 0.13808 (16) mri peak = 0.08101 (51) Right_Lateral_Ventricle (43): linear fit = 1.89 x + 0.0 (771 voxels, overlap=0.146) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (771 voxels, peak = 30), gca=24.0 gca peak = 0.25042 (96) mri peak = 0.08288 (99) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (918 voxels, overlap=0.978) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (918 voxels, peak = 99), gca=99.4 gca peak = 0.22986 (96) mri peak = 0.10553 (91) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (782 voxels, overlap=0.634) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (782 voxels, peak = 90), gca=89.8 gca peak = 0.21624 (56) mri peak = 0.10542 (74) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1037 voxels, overlap=0.012) Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1037 voxels, peak = 71), gca=70.8 gca peak = 0.29672 (58) mri peak = 0.09214 (74) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (589 voxels, overlap=0.020) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (589 voxels, peak = 72), gca=72.2 gca peak = 0.11066 (101) mri peak = 0.11864 (102) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (65530 voxels, overlap=0.618) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (65530 voxels, peak = 105), gca=104.5 gca peak = 0.10944 (101) mri peak = 0.13152 (103) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (63717 voxels, overlap=0.538) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (63717 voxels, peak = 106), gca=105.5 gca peak = 0.14864 (59) mri peak = 0.05242 (75) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (47337 voxels, overlap=0.004) Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (47337 voxels, peak = 75), gca=74.6 gca peak = 0.16234 (58) mri peak = 0.05707 (72) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (49203 voxels, overlap=0.010) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (49203 voxels, peak = 71), gca=71.1 gca peak = 0.14764 (67) mri peak = 0.14984 (83) Right_Caudate (50): linear fit = 1.25 x + 0.0 (772 voxels, overlap=0.013) Right_Caudate (50): linear fit = 1.25 x + 0.0 (772 voxels, peak = 84), gca=84.1 gca peak = 0.15152 (71) mri peak = 0.11271 (85) Left_Caudate (11): linear fit = 1.15 x + 0.0 (1010 voxels, overlap=0.035) Left_Caudate (11): linear fit = 1.15 x + 0.0 (1010 voxels, peak = 82), gca=82.0 gca peak = 0.12476 (59) mri peak = 0.05877 (72) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (28414 voxels, overlap=0.016) Left_Cerebellum_Cortex (8): linear fit = 1.25 x + 0.0 (28414 voxels, peak = 73), gca=73.5 gca peak = 0.13886 (58) mri peak = 0.06452 (72) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (32297 voxels, overlap=0.011) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (32297 voxels, peak = 73), gca=73.4 gca peak = 0.19332 (88) mri peak = 0.07886 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8596 voxels, overlap=0.198) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8596 voxels, peak = 95), gca=95.5 gca peak = 0.19182 (87) mri peak = 0.07364 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7779 voxels, overlap=0.788) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7779 voxels, peak = 94), gca=93.5 gca peak = 0.19349 (58) mri peak = 0.08588 (76) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (446 voxels, overlap=0.070) Left_Amygdala (18): linear fit = 1.28 x + 0.0 (446 voxels, peak = 75), gca=74.5 gca peak = 0.32581 (57) mri peak = 0.10097 (74) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (513 voxels, overlap=0.045) Right_Amygdala (54): linear fit = 1.30 x + 0.0 (513 voxels, peak = 74), gca=74.4 gca peak = 0.09144 (86) mri peak = 0.08154 (101) Left_Thalamus_Proper (10): linear fit = 1.14 x + 0.0 (5223 voxels, overlap=0.144) Left_Thalamus_Proper (10): linear fit = 1.14 x + 0.0 (5223 voxels, peak = 98), gca=98.5 gca peak = 0.10273 (84) mri peak = 0.05927 (94) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4324 voxels, overlap=0.537) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4324 voxels, peak = 94), gca=94.5 gca peak = 0.13860 (78) mri peak = 0.06161 (87) Left_Putamen (12): linear fit = 1.18 x + 0.0 (2541 voxels, overlap=0.107) Left_Putamen (12): linear fit = 1.18 x + 0.0 (2541 voxels, peak = 92), gca=92.4 gca peak = 0.12691 (78) mri peak = 0.08568 (87) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2488 voxels, overlap=0.284) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2488 voxels, peak = 87), gca=87.0 gca peak = 0.11764 (82) mri peak = 0.08759 (88) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10048 voxels, overlap=0.629) Brain_Stem (16): linear fit = 1.10 x + 0.0 (10048 voxels, peak = 90), gca=89.8 gca peak = 0.10015 (86) mri peak = 0.07824 (99) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1060 voxels, overlap=0.628) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1060 voxels, peak = 95), gca=95.0 gca peak = 0.11151 (90) mri peak = 0.08632 (99) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1325 voxels, overlap=0.441) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1325 voxels, peak = 99), gca=99.5 gca peak = 0.19608 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13512 (19) mri peak = 0.16595 (27) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (445 voxels, overlap=0.473) Fourth_Ventricle (15): linear fit = 1.38 x + 0.0 (445 voxels, peak = 26), gca=26.3 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.12743 (29) gca peak Left_Thalamus = 0.71074 (95) gca peak Third_Ventricle = 0.19608 (23) gca peak CSF = 0.17789 (37) gca peak Left_Accumbens_area = 0.50032 (62) gca peak Left_undetermined = 0.97690 (28) gca peak Left_vessel = 0.36001 (53) gca peak Left_choroid_plexus = 0.12300 (45) gca peak Right_Inf_Lat_Vent = 0.21149 (25) gca peak Right_Accumbens_area = 0.31737 (65) gca peak Right_vessel = 0.50186 (52) gca peak Right_choroid_plexus = 0.10991 (44) gca peak Fifth_Ventricle = 0.55462 (35) gca peak WM_hypointensities = 0.10555 (76) gca peak non_WM_hypointensities = 0.08508 (48) gca peak Optic_Chiasm = 0.30852 (73) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 1.26 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.46 x + 0.0 saving intensity scales to talairach.label_intensities.txt ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** 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=0.648, neg=0, invalid=3294 0110: dt=117.664596, rms=0.619 (4.591%), neg=0, invalid=3294 0111: dt=295.936000, rms=0.612 (1.107%), neg=0, invalid=3294 0112: dt=369.920000, rms=0.606 (1.023%), neg=0, invalid=3294 0113: dt=73.984000, rms=0.604 (0.218%), neg=0, invalid=3294 0114: dt=73.984000, rms=0.604 (0.084%), neg=0, invalid=3294 0115: dt=73.984000, rms=0.603 (0.098%), neg=0, invalid=3294 0116: dt=73.984000, rms=0.602 (0.161%), neg=0, invalid=3294 0117: dt=73.984000, rms=0.601 (0.279%), neg=0, invalid=3294 0118: dt=73.984000, rms=0.598 (0.337%), neg=0, invalid=3294 0119: dt=73.984000, rms=0.597 (0.298%), neg=0, invalid=3294 0120: dt=73.984000, rms=0.595 (0.236%), neg=0, invalid=3294 0121: dt=73.984000, rms=0.594 (0.175%), neg=0, invalid=3294 0122: dt=73.984000, rms=0.593 (0.153%), neg=0, invalid=3294 0123: dt=73.984000, rms=0.592 (0.168%), neg=0, invalid=3294 0124: dt=73.984000, rms=0.591 (0.179%), neg=0, invalid=3294 0125: dt=73.984000, rms=0.590 (0.150%), neg=0, invalid=3294 0126: dt=73.984000, rms=0.590 (0.119%), neg=0, invalid=3294 0127: dt=73.984000, rms=0.589 (0.094%), neg=0, invalid=3294 0128: dt=295.936000, rms=0.589 (0.044%), neg=0, invalid=3294 0129: dt=295.936000, rms=0.588 (0.103%), neg=0, invalid=3294 0130: dt=295.936000, rms=0.588 (-0.027%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.589, neg=0, invalid=3294 0131: dt=129.472000, rms=0.587 (0.244%), neg=0, invalid=3294 0132: dt=517.888000, rms=0.586 (0.239%), neg=0, invalid=3294 0133: dt=517.888000, rms=0.586 (-0.433%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.588, neg=0, invalid=3294 0134: dt=65.163636, rms=0.584 (0.584%), neg=0, invalid=3294 0135: dt=227.183246, rms=0.576 (1.503%), neg=0, invalid=3294 0136: dt=49.745455, rms=0.572 (0.692%), neg=0, invalid=3294 0137: dt=580.608000, rms=0.560 (2.078%), neg=0, invalid=3294 0138: dt=36.288000, rms=0.558 (0.247%), neg=0, invalid=3294 0139: dt=36.288000, rms=0.558 (0.061%), neg=0, invalid=3294 0140: dt=36.288000, rms=0.558 (0.028%), neg=0, invalid=3294 0141: dt=36.288000, rms=0.558 (-0.004%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.558, neg=0, invalid=3294 0142: dt=92.673835, rms=0.556 (0.483%), neg=0, invalid=3294 0143: dt=36.288000, rms=0.555 (0.119%), neg=0, invalid=3294 0144: dt=36.288000, rms=0.555 (0.048%), neg=0, invalid=3294 0145: dt=36.288000, rms=0.554 (0.079%), neg=0, invalid=3294 0146: dt=36.288000, rms=0.554 (0.088%), neg=0, invalid=3294 0147: dt=36.288000, rms=0.553 (0.085%), neg=0, invalid=3294 0148: dt=36.288000, rms=0.553 (0.068%), neg=0, invalid=3294 0149: dt=414.720000, rms=0.552 (0.128%), neg=0, invalid=3294 0150: dt=36.288000, rms=0.552 (0.108%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.562, neg=0, invalid=3294 0151: dt=11.200000, rms=0.560 (0.223%), neg=0, invalid=3294 0152: dt=25.600000, rms=0.559 (0.203%), neg=0, invalid=3294 0153: dt=25.600000, rms=0.557 (0.417%), neg=0, invalid=3294 0154: dt=25.600000, rms=0.554 (0.482%), neg=0, invalid=3294 0155: dt=25.600000, rms=0.552 (0.427%), neg=0, invalid=3294 0156: dt=25.600000, rms=0.549 (0.438%), neg=0, invalid=3294 0157: dt=25.600000, rms=0.547 (0.456%), neg=0, invalid=3294 0158: dt=25.600000, rms=0.545 (0.339%), neg=0, invalid=3294 0159: dt=25.600000, rms=0.544 (0.146%), neg=0, invalid=3294 0160: dt=25.600000, rms=0.544 (-0.003%), neg=0, invalid=3294 0161: dt=0.000000, rms=0.544 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.545, neg=0, invalid=3294 0162: dt=11.200000, rms=0.544 (0.126%), neg=0, invalid=3294 0163: dt=0.000000, rms=0.544 (-0.001%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.570, neg=0, invalid=3294 0164: dt=0.144000, rms=0.570 (0.055%), neg=0, invalid=3294 0165: dt=0.011250, rms=0.570 (0.000%), neg=0, invalid=3294 0166: dt=0.011250, rms=0.570 (-0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.570, neg=0, invalid=3294 0167: dt=0.252000, rms=0.570 (0.065%), neg=0, invalid=3294 0168: dt=0.144000, rms=0.570 (0.001%), neg=0, invalid=3294 0169: dt=0.144000, rms=0.570 (-0.001%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.617, neg=0, invalid=3294 0170: dt=1.091783, rms=0.606 (1.808%), neg=0, invalid=3294 0171: dt=0.448000, rms=0.605 (0.184%), neg=0, invalid=3294 0172: dt=0.448000, rms=0.605 (0.044%), neg=0, invalid=3294 0173: dt=0.448000, rms=0.605 (-0.211%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.605, neg=0, invalid=3294 0174: dt=0.448000, rms=0.604 (0.112%), neg=0, invalid=3294 0175: dt=0.112000, rms=0.604 (0.005%), neg=0, invalid=3294 0176: dt=0.112000, rms=0.604 (0.003%), neg=0, invalid=3294 0177: dt=0.112000, rms=0.604 (-0.006%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.575, neg=0, invalid=3294 0178: dt=0.695652, rms=0.563 (2.125%), neg=0, invalid=3294 0179: dt=0.064000, rms=0.563 (0.081%), neg=0, invalid=3294 0180: dt=0.064000, rms=0.563 (-0.084%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.563, neg=0, invalid=3294 0181: dt=0.016000, rms=0.563 (0.059%), neg=0, invalid=3294 0182: dt=0.000000, rms=0.563 (-0.000%), neg=0, invalid=3294 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 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.556, neg=0, invalid=3294 0183: dt=32.368000, rms=0.556 (0.055%), neg=0, invalid=3294 0184: dt=32.368000, rms=0.556 (0.029%), neg=0, invalid=3294 0185: dt=32.368000, rms=0.556 (0.024%), neg=0, invalid=3294 0186: dt=32.368000, rms=0.556 (0.025%), neg=0, invalid=3294 0187: dt=32.368000, rms=0.555 (0.015%), neg=0, invalid=3294 0188: dt=32.368000, rms=0.555 (0.030%), neg=0, invalid=3294 0189: dt=32.368000, rms=0.555 (0.075%), neg=0, invalid=3294 0190: dt=32.368000, rms=0.554 (0.134%), neg=0, invalid=3294 0191: dt=32.368000, rms=0.553 (0.179%), neg=0, invalid=3294 0192: dt=32.368000, rms=0.552 (0.187%), neg=0, invalid=3294 0193: dt=32.368000, rms=0.551 (0.162%), neg=0, invalid=3294 0194: dt=32.368000, rms=0.551 (0.119%), neg=0, invalid=3294 0195: dt=32.368000, rms=0.550 (0.075%), neg=0, invalid=3294 0196: dt=0.000000, rms=0.550 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.550, neg=0, invalid=3294 0197: dt=221.952000, rms=0.548 (0.335%), neg=0, invalid=3294 0198: dt=92.480000, rms=0.548 (0.052%), neg=0, invalid=3294 0199: dt=92.480000, rms=0.548 (0.029%), neg=0, invalid=3294 0200: dt=92.480000, rms=0.548 (0.050%), neg=0, invalid=3294 0201: dt=92.480000, rms=0.547 (0.064%), neg=0, invalid=3294 0202: dt=92.480000, rms=0.547 (0.071%), neg=0, invalid=3294 0203: dt=92.480000, rms=0.546 (0.065%), neg=0, invalid=3294 0204: dt=92.480000, rms=0.546 (0.055%), neg=0, invalid=3294 0205: dt=517.888000, rms=0.546 (0.020%), neg=0, invalid=3294 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.546, neg=0, invalid=3294 0206: dt=36.288000, rms=0.545 (0.196%), neg=0, invalid=3294 0207: dt=145.152000, rms=0.542 (0.608%), neg=0, invalid=3294 0208: dt=414.720000, rms=0.533 (1.702%), neg=0, invalid=3294 0209: dt=29.357798, rms=0.531 (0.283%), neg=0, invalid=3294 0210: dt=9.072000, rms=0.531 (0.006%), neg=0, invalid=3294 0211: dt=9.072000, rms=0.531 (0.000%), neg=0, invalid=3294 0212: dt=9.072000, rms=0.531 (-0.015%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=3294 0213: dt=124.416000, rms=0.529 (0.383%), neg=0, invalid=3294 0214: dt=36.288000, rms=0.528 (0.139%), neg=0, invalid=3294 0215: dt=36.288000, rms=0.528 (0.059%), neg=0, invalid=3294 0216: dt=36.288000, rms=0.528 (0.099%), neg=0, invalid=3294 0217: dt=36.288000, rms=0.527 (0.123%), neg=0, invalid=3294 0218: dt=36.288000, rms=0.526 (0.132%), neg=0, invalid=3294 0219: dt=36.288000, rms=0.526 (0.129%), neg=0, invalid=3294 0220: dt=36.288000, rms=0.525 (0.116%), neg=0, invalid=3294 0221: dt=36.288000, rms=0.524 (0.111%), neg=0, invalid=3294 0222: dt=497.664000, rms=0.523 (0.217%), neg=0, invalid=3294 0223: dt=82.944000, rms=0.523 (0.113%), neg=0, invalid=3294 0224: dt=82.944000, rms=0.522 (0.035%), neg=0, invalid=3294 0225: dt=82.944000, rms=0.522 (0.064%), neg=0, invalid=3294 0226: dt=82.944000, rms=0.522 (0.107%), neg=0, invalid=3294 0227: dt=82.944000, rms=0.521 (0.097%), neg=0, invalid=3294 0228: dt=82.944000, rms=0.520 (0.126%), neg=0, invalid=3294 0229: dt=82.944000, rms=0.520 (0.129%), neg=0, invalid=3294 0230: dt=82.944000, rms=0.519 (0.142%), neg=0, invalid=3294 0231: dt=82.944000, rms=0.518 (0.128%), neg=0, invalid=3294 0232: dt=82.944000, rms=0.518 (0.133%), neg=0, invalid=3294 0233: dt=82.944000, rms=0.517 (0.122%), neg=0, invalid=3294 0234: dt=82.944000, rms=0.516 (0.120%), neg=0, invalid=3294 0235: dt=103.680000, rms=0.516 (0.014%), neg=0, invalid=3294 0236: dt=103.680000, rms=0.516 (0.010%), neg=0, invalid=3294 0237: dt=103.680000, rms=0.516 (0.018%), neg=0, invalid=3294 0238: dt=103.680000, rms=0.516 (0.023%), neg=0, invalid=3294 0239: dt=103.680000, rms=0.516 (0.034%), neg=0, invalid=3294 0240: dt=103.680000, rms=0.516 (0.037%), neg=0, invalid=3294 0241: dt=103.680000, rms=0.515 (0.043%), neg=0, invalid=3294 0242: dt=103.680000, rms=0.515 (0.047%), neg=0, invalid=3294 0243: dt=103.680000, rms=0.515 (0.054%), neg=0, invalid=3294 0244: dt=103.680000, rms=0.515 (0.056%), neg=0, invalid=3294 0245: dt=103.680000, rms=0.514 (0.059%), neg=0, invalid=3294 0246: dt=103.680000, rms=0.514 (0.060%), neg=0, invalid=3294 0247: dt=103.680000, rms=0.514 (0.060%), neg=0, invalid=3294 0248: dt=103.680000, rms=0.513 (0.060%), neg=0, invalid=3294 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0249: dt=103.680000, rms=0.513 (0.059%), neg=0, invalid=3294 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.520, neg=0, invalid=3294 0250: dt=1.600000, rms=0.520 (0.002%), neg=0, invalid=3294 0251: dt=0.175000, rms=0.520 (0.000%), neg=0, invalid=3294 0252: dt=0.175000, rms=0.520 (-0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.520, neg=0, invalid=3294 0253: dt=2.000000, rms=0.520 (0.002%), neg=0, invalid=3294 0254: dt=0.600000, rms=0.520 (0.000%), neg=0, invalid=3294 0255: dt=0.600000, rms=0.520 (-0.000%), neg=0, invalid=3294 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.539, neg=0, invalid=3294 0256: dt=3.826087, rms=0.535 (0.815%), neg=0, invalid=3294 0257: dt=1.166667, rms=0.535 (0.021%), neg=0, invalid=3294 0258: dt=1.166667, rms=0.535 (-0.008%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.535, neg=0, invalid=3294 0259: dt=1.008000, rms=0.535 (0.019%), neg=0, invalid=3294 0260: dt=0.252000, rms=0.535 (0.001%), neg=0, invalid=3294 0261: dt=0.252000, rms=0.535 (0.000%), neg=0, invalid=3294 0262: dt=0.252000, rms=0.535 (-0.002%), neg=0, invalid=3294 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.553, neg=0, invalid=3294 0263: dt=0.000000, rms=0.553 (0.000%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=3294 0264: dt=0.112000, rms=0.553 (0.009%), neg=0, invalid=3294 0265: dt=0.080000, rms=0.553 (0.003%), neg=0, invalid=3294 0266: dt=0.080000, rms=0.553 (0.000%), neg=0, invalid=3294 0267: dt=0.080000, rms=0.553 (-0.010%), neg=0, invalid=3294 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.525, neg=0, invalid=3294 0268: dt=0.648571, rms=0.515 (1.868%), neg=0, invalid=3294 0269: dt=0.028000, rms=0.515 (0.043%), neg=0, invalid=3294 0270: dt=0.028000, rms=0.515 (0.001%), neg=0, invalid=3294 0271: dt=0.028000, rms=0.515 (-0.088%), neg=0, invalid=3294 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.515, neg=0, invalid=3294 0272: dt=0.006000, rms=0.515 (0.001%), neg=0, invalid=3294 0273: dt=0.000013, rms=0.515 (0.000%), neg=0, invalid=3294 0274: dt=0.000013, rms=0.515 (-0.000%), neg=0, invalid=3294 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 47 minutes and 20 seconds. FSRUNTIME@ mri_ca_register 1.7890 hours 1 threads #-------------------------------------- #@# Remove Neck Mon Jan 25 15:25:11 EST 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... setting orig areas to linear transform determinant scaled 6.61 removing structures at least 25 mm from brain... 11255673 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 8 seconds. #-------------------------------------- #@# SkullLTA Mon Jan 25 15:26:19 EST 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /cell_root/software/freesurfer/dev/sys/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull_2.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/cell_root/software/freesurfer/dev/sys/average/RB_all_withskull_2014-08-21.gca'... average std = 23.5 using min determinant for regularization = 55.2 0 singular and 5018 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 15.9 or > 1063.6 total sample mean = 86.3 (1445 zeros) ************************************************ spacing=8, using 3388 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3388, passno 0, spacing 8 resetting wm mean[0]: 110 --> 118 resetting gm mean[0]: 70 --> 70 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (48, 31, 43) --> (204, 199, 220) using (100, 87, 132) as brain centroid... mean wm in atlas = 118, using box (81,66,110) --> (119, 107,153) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 0.1 after smoothing, mri peak at 108, scaling input intensities by 1.093 scaling channel 0 by 1.09259 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.930, old_max_log_p =-4.143 (thresh=-4.1) 1.09150 -0.05662 -0.05509 0.21018; 0.05336 1.26885 0.10510 -30.45313; 0.04537 -0.13605 1.13354 -27.38407; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.930, old_max_log_p =-3.930 (thresh=-3.9) 1.09150 -0.05662 -0.05509 0.21018; 0.05336 1.26885 0.10510 -30.45313; 0.04537 -0.13605 1.13354 -27.38407; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.896, old_max_log_p =-3.930 (thresh=-3.9) 1.07223 -0.01496 -0.04942 -0.69168; 0.01877 1.24102 0.14252 -27.79085; 0.04615 -0.18602 1.19396 -29.78955; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.896, old_max_log_p =-3.896 (thresh=-3.9) 1.07223 -0.01496 -0.04942 -0.69168; 0.01877 1.24102 0.14252 -27.79085; 0.04615 -0.18602 1.19396 -29.78955; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.876, old_max_log_p =-3.896 (thresh=-3.9) 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03751 -0.16498 1.19229 -30.76015; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.875, old_max_log_p =-3.876 (thresh=-3.9) 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03742 -0.16459 1.18950 -30.43341; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3388 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03742 -0.16459 1.18950 -30.43341; 0.00000 0.00000 0.00000 1.00000; nsamples 3388 Quasinewton: input matrix 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03742 -0.16459 1.18950 -30.43341; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03742 -0.16459 1.18950 -30.43341; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.875 (old=-4.143) transform before final EM align: 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03742 -0.16459 1.18950 -30.43341; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 380366 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03742 -0.16459 1.18950 -30.43341; 0.00000 0.00000 0.00000 1.00000; nsamples 380366 Quasinewton: input matrix 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03742 -0.16459 1.18950 -30.43341; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 4.3 after pass:transform: ( 1.08, -0.01, -0.04, -3.86) ( 0.01, 1.25, 0.12, -24.62) ( 0.04, -0.16, 1.19, -30.43) dfp_em_step_func: 009: -log(p) = 4.3 after pass:transform: ( 1.08, -0.01, -0.04, -3.86) ( 0.01, 1.25, 0.12, -24.62) ( 0.04, -0.16, 1.19, -30.43) dfp_em_step_func: 010: -log(p) = 4.3 after pass:transform: ( 1.08, -0.01, -0.04, -3.86) ( 0.01, 1.25, 0.12, -24.62) ( 0.04, -0.16, 1.19, -30.43) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000 final transform: 1.07519 -0.00615 -0.03876 -3.85564; 0.00925 1.24544 0.12343 -24.61773; 0.03742 -0.16459 1.18950 -30.43341; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 17 minutes and 39 seconds. #-------------------------------------- #@# SubCort Seg Mon Jan 25 15:43:58 EST 2016 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca aseg.auto_noCCseg.mgz sysname Linux hostname hippocampus.umd.edu machine x86_64 setenv SUBJECTS_DIR /export/data/hippocampus/HMN/data cd /export/data/hippocampus/HMN/data/HMN002/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca... reading input volume from norm.mgz... average std[0] = 7.4 reading transform from transforms/talairach.m3z... setting orig areas to linear transform determinant scaled 6.61 Atlas used for the 3D morph was /cell_root/software/freesurfer/dev/sys/average/RB_all_2015-08-04.gca average std = 7.4 using min determinant for regularization = 5.4 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16337 (20) mri peak = 0.12222 (28) Left_Lateral_Ventricle (4): linear fit = 1.49 x + 0.0 (214 voxels, overlap=0.203) Left_Lateral_Ventricle (4): linear fit = 1.49 x + 0.0 (214 voxels, peak = 30), gca=29.7 gca peak = 0.19190 (13) mri peak = 0.12315 (28) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (227 voxels, overlap=0.140) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (227 voxels, peak = 27), gca=19.5 gca peak = 0.24200 (96) mri peak = 0.15990 (100) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (793 voxels, overlap=0.951) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (793 voxels, peak = 99), gca=99.4 gca peak = 0.14904 (91) mri peak = 0.24369 (101) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (665 voxels, overlap=0.464) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (665 voxels, peak = 96), gca=96.0 gca peak = 0.25211 (57) mri peak = 0.11008 (75) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (865 voxels, overlap=0.016) Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (865 voxels, peak = 73), gca=72.7 gca peak = 0.31987 (57) mri peak = 0.08267 (76) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (896 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.25 x + 0.0 (896 voxels, peak = 72), gca=71.5 gca peak = 0.08094 (102) mri peak = 0.11447 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47934 voxels, overlap=0.649) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47934 voxels, peak = 103), gca=102.5 gca peak = 0.08600 (104) mri peak = 0.12675 (105) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (45694 voxels, overlap=0.534) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (45694 voxels, peak = 106), gca=105.6 gca peak = 0.09612 (57) mri peak = 0.05816 (72) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (68821 voxels, overlap=0.096) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (68821 voxels, peak = 71), gca=71.0 gca peak = 0.11462 (58) mri peak = 0.06297 (72) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (66922 voxels, overlap=0.080) Right_Cerebral_Cortex (42): linear fit = 1.25 x + 0.0 (66922 voxels, peak = 72), gca=72.2 gca peak = 0.25255 (66) mri peak = 0.15579 (85) Right_Caudate (50): linear fit = 1.25 x + 0.0 (475 voxels, overlap=0.019) Right_Caudate (50): linear fit = 1.25 x + 0.0 (475 voxels, peak = 83), gca=82.8 gca peak = 0.18480 (77) mri peak = 0.14440 (84) Left_Caudate (11): linear fit = 1.12 x + 0.0 (554 voxels, overlap=0.086) Left_Caudate (11): linear fit = 1.12 x + 0.0 (554 voxels, peak = 86), gca=85.9 gca peak = 0.12729 (58) mri peak = 0.06316 (72) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (30376 voxels, overlap=0.057) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (30376 voxels, peak = 71), gca=71.1 gca peak = 0.12622 (58) mri peak = 0.07054 (72) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (31398 voxels, overlap=0.034) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (31398 voxels, peak = 72), gca=72.2 gca peak = 0.15410 (88) mri peak = 0.11415 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6333 voxels, overlap=0.368) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6333 voxels, peak = 96), gca=96.4 gca peak = 0.15661 (88) mri peak = 0.09411 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5418 voxels, overlap=0.722) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5418 voxels, peak = 94), gca=93.7 gca peak = 0.30376 (59) mri peak = 0.11814 (72) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (472 voxels, overlap=0.062) Left_Amygdala (18): linear fit = 1.25 x + 0.0 (472 voxels, peak = 73), gca=73.5 gca peak = 0.35132 (58) mri peak = 0.11022 (78) Right_Amygdala (54): linear fit = 1.34 x + 0.0 (495 voxels, overlap=0.056) Right_Amygdala (54): linear fit = 1.34 x + 0.0 (495 voxels, peak = 77), gca=77.4 gca peak = 0.10548 (89) mri peak = 0.07002 (94) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (4457 voxels, overlap=0.692) Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (4457 voxels, peak = 97), gca=97.5 gca peak = 0.10706 (82) mri peak = 0.07285 (92) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3949 voxels, overlap=0.490) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3949 voxels, peak = 92), gca=92.2 gca peak = 0.08512 (74) mri peak = 0.10687 (90) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2094 voxels, overlap=0.180) Left_Putamen (12): linear fit = 1.14 x + 0.0 (2094 voxels, peak = 85), gca=84.7 gca peak = 0.08440 (78) mri peak = 0.10179 (89) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2289 voxels, overlap=0.235) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2289 voxels, peak = 87), gca=87.0 gca peak = 0.07263 (80) mri peak = 0.08112 (86) Brain_Stem (16): linear fit = 1.07 x + 0.0 (10788 voxels, overlap=0.615) Brain_Stem (16): linear fit = 1.07 x + 0.0 (10788 voxels, peak = 85), gca=85.2 gca peak = 0.13309 (90) mri peak = 0.09105 (99) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1334 voxels, overlap=0.681) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1334 voxels, peak = 98), gca=97.7 gca peak = 0.15558 (86) mri peak = 0.08603 (99) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1486 voxels, overlap=0.572) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1486 voxels, peak = 92), gca=92.5 gca peak = 0.17913 (26) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.17310 (16) mri peak = 0.12973 (27) Fourth_Ventricle (15): linear fit = 1.59 x + 0.0 (253 voxels, overlap=0.293) Fourth_Ventricle (15): linear fit = 1.59 x + 0.0 (253 voxels, peak = 25), gca=25.4 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.21424 (27) gca peak Left_Thalamus = 1.00000 (95) gca peak Third_Ventricle = 0.17913 (26) gca peak Fourth_Ventricle = 0.17310 (16) gca peak CSF = 0.22008 (37) gca peak Left_Accumbens_area = 0.78455 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09096 (57) gca peak Right_Inf_Lat_Vent = 0.24233 (28) gca peak Right_Accumbens_area = 0.41783 (64) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11536 (37) gca peak Fifth_Ventricle = 0.55384 (33) gca peak WM_hypointensities = 0.10945 (75) gca peak non_WM_hypointensities = 0.07381 (29) gca peak Optic_Chiasm = 0.66945 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.27 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.49 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.12399 (29) mri peak = 0.12222 (28) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (214 voxels, overlap=0.646) Left_Lateral_Ventricle (4): linear fit = 0.94 x + 0.0 (214 voxels, peak = 27), gca=27.1 gca peak = 0.14438 (19) mri peak = 0.12315 (28) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (227 voxels, overlap=0.327) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (227 voxels, peak = 27), gca=26.7 gca peak = 0.20311 (96) mri peak = 0.15990 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (793 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (793 voxels, peak = 96), gca=96.0 gca peak = 0.14488 (96) mri peak = 0.24369 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (665 voxels, overlap=0.996) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (665 voxels, peak = 96), gca=95.5 gca peak = 0.23103 (72) mri peak = 0.11008 (75) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (865 voxels, overlap=0.974) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (865 voxels, peak = 72), gca=72.0 gca peak = 0.29573 (72) mri peak = 0.08267 (76) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (896 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (896 voxels, peak = 72), gca=72.0 gca peak = 0.08264 (104) mri peak = 0.11447 (102) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47934 voxels, overlap=0.671) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47934 voxels, peak = 105), gca=104.5 gca peak = 0.08536 (105) mri peak = 0.12675 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45694 voxels, overlap=0.611) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (45694 voxels, peak = 105), gca=105.0 gca peak = 0.07921 (72) mri peak = 0.05816 (72) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (68821 voxels, overlap=0.936) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (68821 voxels, peak = 71), gca=70.9 gca peak = 0.09133 (72) mri peak = 0.06297 (72) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (66922 voxels, overlap=0.898) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (66922 voxels, peak = 71), gca=70.9 gca peak = 0.18410 (82) mri peak = 0.15579 (85) Right_Caudate (50): linear fit = 1.00 x + 0.0 (475 voxels, overlap=0.997) Right_Caudate (50): linear fit = 1.00 x + 0.0 (475 voxels, peak = 82), gca=82.0 gca peak = 0.20597 (86) mri peak = 0.14440 (84) Left_Caudate (11): linear fit = 1.00 x + 0.0 (554 voxels, overlap=0.767) Left_Caudate (11): linear fit = 1.00 x + 0.0 (554 voxels, peak = 86), gca=86.0 gca peak = 0.10530 (72) mri peak = 0.06316 (72) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (30376 voxels, overlap=0.939) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (30376 voxels, peak = 75), gca=74.5 gca peak = 0.10862 (72) mri peak = 0.07054 (72) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (31398 voxels, overlap=0.961) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (31398 voxels, peak = 72), gca=72.0 gca peak = 0.14354 (97) mri peak = 0.11415 (97) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6333 voxels, overlap=0.932) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6333 voxels, peak = 97), gca=96.5 gca peak = 0.14580 (93) mri peak = 0.09411 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5418 voxels, overlap=0.952) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5418 voxels, peak = 93), gca=92.5 gca peak = 0.31375 (73) mri peak = 0.11814 (72) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (472 voxels, overlap=1.021) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (472 voxels, peak = 73), gca=73.0 gca peak = 0.21965 (75) mri peak = 0.11022 (78) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (495 voxels, overlap=1.015) Right_Amygdala (54): linear fit = 0.99 x + 0.0 (495 voxels, peak = 74), gca=73.9 gca peak = 0.10051 (97) mri peak = 0.07002 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4457 voxels, overlap=0.990) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4457 voxels, peak = 97), gca=97.5 gca peak = 0.08901 (93) mri peak = 0.07285 (92) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3949 voxels, overlap=0.958) Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3949 voxels, peak = 92), gca=91.6 gca peak = 0.07725 (92) mri peak = 0.10687 (90) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2094 voxels, overlap=0.736) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2094 voxels, peak = 92), gca=92.0 gca peak = 0.08240 (84) mri peak = 0.10179 (89) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2289 voxels, overlap=0.750) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2289 voxels, peak = 85), gca=85.3 gca peak = 0.07773 (86) mri peak = 0.08112 (86) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10788 voxels, overlap=0.790) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10788 voxels, peak = 86), gca=85.6 gca peak = 0.11684 (98) mri peak = 0.09105 (99) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1334 voxels, overlap=0.865) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1334 voxels, peak = 98), gca=98.5 gca peak = 0.14251 (93) mri peak = 0.08603 (99) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1486 voxels, overlap=0.881) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1486 voxels, peak = 95), gca=95.3 gca peak = 0.13992 (39) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12099 (25) mri peak = 0.12973 (27) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (253 voxels, overlap=0.710) Fourth_Ventricle (15): linear fit = 1.07 x + 0.0 (253 voxels, peak = 27), gca=26.6 gca peak Unknown = 0.94959 ( 0) gca peak Left_Inf_Lat_Vent = 0.17508 (34) gca peak Left_Thalamus = 0.64824 (120) gca peak Third_Ventricle = 0.13992 (39) gca peak CSF = 0.14486 (55) gca peak Left_Accumbens_area = 0.66613 (69) gca peak Left_undetermined = 0.97815 (34) gca peak Left_vessel = 0.87251 (52) gca peak Left_choroid_plexus = 0.09080 (44) gca peak Right_Inf_Lat_Vent = 0.29639 (30) gca peak Right_Accumbens_area = 0.26457 (82) gca peak Right_vessel = 0.68147 (52) gca peak Right_choroid_plexus = 0.11434 (37) gca peak Fifth_Ventricle = 0.55752 (46) gca peak WM_hypointensities = 0.11024 (75) gca peak non_WM_hypointensities = 0.08301 (44) gca peak Optic_Chiasm = 0.66411 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.13 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 84010 voxels changed in iteration 0 of unlikely voxel relabeling 358 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 60749 gm and wm labels changed (%35 to gray, %65 to white out of all changed labels) 395 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 68755 changed. image ll: -2.114, PF=0.500 pass 2: 21122 changed. image ll: -2.113, PF=0.500 pass 3: 6631 changed. pass 4: 2568 changed. MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 44 minutes and 22 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /export/data/hippocampus/HMN/data/HMN002/mri/transforms/cc_up.lta HMN002 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /export/data/hippocampus/HMN/data/HMN002/mri/transforms/cc_up.lta reading aseg from /export/data/hippocampus/HMN/data/HMN002/mri/aseg.auto_noCCseg.mgz reading norm from /export/data/hippocampus/HMN/data/HMN002/mri/norm.mgz 32229 voxels in left wm, 35807 in right wm, xrange [123, 130] searching rotation angles z=[-5 9], y=[-8 6] searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 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 global minimum found at slice 126.3, rotations (-0.73, 1.97) final transformation (x=126.3, yr=-0.726, zr=1.974): 0.99933 -0.03445 -0.01267 6.28875; 0.03445 0.99941 -0.00044 40.75493; 0.01268 0.00000 0.99992 0.40966; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 129] in xformed coordinates best xformed slice 127 cc center is found at 127 83 126 eigenvectors: -0.00062 -0.00791 0.99997; -0.00101 -0.99997 -0.00791; 1.00000 -0.00101 0.00061; writing aseg with callosum to /export/data/hippocampus/HMN/data/HMN002/mri/aseg.auto.mgz... corpus callosum segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Mon Jan 25 16:28:59 EST 2016 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Jan 25 16:28:59 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_normalize -aseg aseg.presurf.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.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1250 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 80 (80), valley at 58 (58) csf peak at 40, setting threshold to 66 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 80 (80), valley at 58 (58) csf peak at 40, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 41 seconds. #-------------------------------------------- #@# Mask BFS Mon Jan 25 16:32:41 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1532998 voxels in mask (pct= 9.14) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Jan 25 16:32:42 EST 2016 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /export/data/hippocampus/HMN/data/HMN002/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux hostname hippocampus.umd.edu machine x86_64 user gengf input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt $Id: mri_binarize.c,v 1.41 2014/08/17 17:47:29 greve Exp $ cwd /export/data/hippocampus/HMN/data/HMN002/mri cmdline mri_binarize --i wm.mgz --min 1 --max 1 --o wm1.mgz --count wm1.txt sysname Linux hostname hippocampus.umd.edu machine x86_64 user gengf input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm1.mgz Binarizing based on threshold min 1 max 1 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done rm wm1.mgz wm255.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.3 +- 6.3 [80.0 --> 125.0] GM (78.0) : 77.4 +- 8.8 [30.0 --> 96.0] setting bottom of white matter range to 86.3 setting top of gray matter range to 95.1 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 7508 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4342 filled 662 bright non-wm voxels segmented. 4077 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.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.60 minutes reading wm segmentation from wm.seg.mgz... 344 voxels added to wm to prevent paths from MTL structures to cortex 5260 additional wm voxels added 0 additional wm voxels added SEG EDIT: 33259 voxels turned on, 40007 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 101 new 101 115,126,128 old 101 new 101 writing edited volume to wm.asegedit.mgz.... mri_pretess -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 27 found - 27 modified | TOTAL: 27 pass 2 (xy+): 0 found - 27 modified | TOTAL: 27 pass 1 (xy-): 42 found - 42 modified | TOTAL: 69 pass 2 (xy-): 0 found - 42 modified | TOTAL: 69 pass 1 (yz+): 49 found - 49 modified | TOTAL: 118 pass 2 (yz+): 0 found - 49 modified | TOTAL: 118 pass 1 (yz-): 52 found - 52 modified | TOTAL: 170 pass 2 (yz-): 0 found - 52 modified | TOTAL: 170 pass 1 (xz+): 31 found - 31 modified | TOTAL: 201 pass 2 (xz+): 0 found - 31 modified | TOTAL: 201 pass 1 (xz-): 30 found - 30 modified | TOTAL: 231 pass 2 (xz-): 0 found - 30 modified | TOTAL: 231 Iteration Number : 1 pass 1 (+++): 18 found - 18 modified | TOTAL: 18 pass 2 (+++): 0 found - 18 modified | TOTAL: 18 pass 1 (+++): 30 found - 30 modified | TOTAL: 48 pass 2 (+++): 0 found - 30 modified | TOTAL: 48 pass 1 (+++): 14 found - 14 modified | TOTAL: 62 pass 2 (+++): 0 found - 14 modified | TOTAL: 62 pass 1 (+++): 25 found - 25 modified | TOTAL: 87 pass 2 (+++): 0 found - 25 modified | TOTAL: 87 Iteration Number : 1 pass 1 (++): 217 found - 217 modified | TOTAL: 217 pass 2 (++): 0 found - 217 modified | TOTAL: 217 pass 1 (+-): 185 found - 185 modified | TOTAL: 402 pass 2 (+-): 0 found - 185 modified | TOTAL: 402 pass 1 (--): 159 found - 159 modified | TOTAL: 561 pass 2 (--): 0 found - 159 modified | TOTAL: 561 pass 1 (-+): 192 found - 192 modified | TOTAL: 753 pass 2 (-+): 0 found - 192 modified | TOTAL: 753 Iteration Number : 2 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 14 found - 14 modified | TOTAL: 25 pass 2 (xy-): 0 found - 14 modified | TOTAL: 25 pass 1 (yz+): 8 found - 8 modified | TOTAL: 33 pass 2 (yz+): 0 found - 8 modified | TOTAL: 33 pass 1 (yz-): 6 found - 6 modified | TOTAL: 39 pass 2 (yz-): 0 found - 6 modified | TOTAL: 39 pass 1 (xz+): 7 found - 7 modified | TOTAL: 46 pass 2 (xz+): 0 found - 7 modified | TOTAL: 46 pass 1 (xz-): 5 found - 5 modified | TOTAL: 51 pass 2 (xz-): 0 found - 5 modified | TOTAL: 51 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 1 found - 1 modified | TOTAL: 3 pass 2 (+++): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 7 found - 7 modified | TOTAL: 11 pass 2 (+-): 0 found - 7 modified | TOTAL: 11 pass 1 (--): 4 found - 4 modified | TOTAL: 15 pass 2 (--): 0 found - 4 modified | TOTAL: 15 pass 1 (-+): 1 found - 1 modified | TOTAL: 16 pass 2 (-+): 0 found - 1 modified | TOTAL: 16 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 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+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 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 = 1147 (out of 460426: 0.249117) 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 Mon Jan 25 16:35:33 EST 2016 /export/data/hippocampus/HMN/data/HMN002/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01535 -0.05267 -0.05124 9.04034; 0.04640 1.10335 0.09139 -9.85152; 0.04266 -0.12790 1.06561 -19.23201; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 914 (min = 350, max = 1400), aspect = 0.54 (min = 0.10, max = 0.75) no need to search using seed (124, 119, 144), TAL = (4.0, 16.0, 9.0) talairach voxel to voxel transform 0.98072 0.05177 0.04272 -7.53439; -0.03762 0.89542 -0.07860 7.64969; -0.04377 0.10540 0.92728 19.26759; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (124, 119, 144) --> (4.0, 16.0, 9.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (4.00, 16.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, 16.00, 9.00) SRC: (108.73, 98.90, 160.70) search lh wm seed point around talairach space (-14.00, 16.00, 9.00), SRC: (144.04, 97.55, 159.12) 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 Mon Jan 25 16:36:20 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 1 found - 1 modified | TOTAL: 1 pass 2 (xz-): 0 found - 1 modified | TOTAL: 1 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 1 (out of 221314: 0.000452) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ slice 60: 2758 vertices, 2942 faces slice 70: 10396 vertices, 10723 faces slice 80: 20728 vertices, 21114 faces slice 90: 32302 vertices, 32684 faces slice 100: 43955 vertices, 44353 faces slice 110: 56458 vertices, 56894 faces slice 120: 69209 vertices, 69657 faces slice 130: 81558 vertices, 81980 faces slice 140: 93067 vertices, 93503 faces slice 150: 103641 vertices, 103998 faces slice 160: 112471 vertices, 112845 faces slice 170: 122032 vertices, 122348 faces slice 180: 129246 vertices, 129539 faces slice 190: 134697 vertices, 134935 faces slice 200: 137865 vertices, 137965 faces slice 210: 138012 vertices, 138076 faces slice 220: 138012 vertices, 138076 faces slice 230: 138012 vertices, 138076 faces slice 240: 138012 vertices, 138076 faces slice 250: 138012 vertices, 138076 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 138012 voxel in cpt #1: X=-64 [v=138012,e=414228,f=276152] located at (-26.976357, -7.386945, 33.567589) For the whole surface: X=-64 [v=138012,e=414228,f=276152] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Jan 25 16:36:26 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 2 found - 2 modified | TOTAL: 3 pass 2 (yz+): 0 found - 2 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 223814: 0.002234) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ slice 60: 1004 vertices, 1115 faces slice 70: 6315 vertices, 6531 faces slice 80: 14595 vertices, 14973 faces slice 90: 25900 vertices, 26282 faces slice 100: 37884 vertices, 38271 faces slice 110: 49404 vertices, 49838 faces slice 120: 62726 vertices, 63163 faces slice 130: 76092 vertices, 76524 faces slice 140: 88460 vertices, 88908 faces slice 150: 100781 vertices, 101230 faces slice 160: 111999 vertices, 112400 faces slice 170: 121486 vertices, 121821 faces slice 180: 130024 vertices, 130326 faces slice 190: 136652 vertices, 136903 faces slice 200: 140729 vertices, 140926 faces slice 210: 141454 vertices, 141534 faces slice 220: 141454 vertices, 141534 faces slice 230: 141454 vertices, 141534 faces slice 240: 141454 vertices, 141534 faces slice 250: 141454 vertices, 141534 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 141454 voxel in cpt #1: X=-80 [v=141454,e=424602,f=283068] located at (30.312689, -2.012329, 32.503307) For the whole surface: X=-80 [v=141454,e=424602,f=283068] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Jan 25 16:36:33 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Mon Jan 25 16:36:38 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Jan 25 16:36:44 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 44.4 mm, total surface area = 73220 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.118 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.068 (target=0.015) step 025: RMS=0.059 (target=0.015) step 030: RMS=0.055 (target=0.015) step 035: RMS=0.050 (target=0.015) step 040: RMS=0.047 (target=0.015) step 045: RMS=0.045 (target=0.015) step 050: RMS=0.043 (target=0.015) step 055: RMS=0.043 (target=0.015) step 060: RMS=0.042 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# Inflation1 rh Mon Jan 25 16:37:25 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 44.2 mm, total surface area = 74788 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.7 minutes step 000: RMS=0.155 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.090 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.069 (target=0.015) step 025: RMS=0.063 (target=0.015) step 030: RMS=0.057 (target=0.015) step 035: RMS=0.052 (target=0.015) step 040: RMS=0.049 (target=0.015) step 045: RMS=0.047 (target=0.015) step 050: RMS=0.045 (target=0.015) step 055: RMS=0.044 (target=0.015) step 060: RMS=0.044 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Mon Jan 25 16:38:06 EST 2016 /export/data/hippocampus/HMN/data/HMN002/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 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.56 (0.00-->7.31) (max @ vno 47348 --> 48576) face area 0.03 +- 0.03 (-0.19-->0.93) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.318... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.181, avgs=0 005/300: dt: 0.9000, rms radial error=175.922, avgs=0 010/300: dt: 0.9000, rms radial error=175.365, avgs=0 015/300: dt: 0.9000, rms radial error=174.633, avgs=0 020/300: dt: 0.9000, rms radial error=173.799, avgs=0 025/300: dt: 0.9000, rms radial error=172.906, avgs=0 030/300: dt: 0.9000, rms radial error=171.980, avgs=0 035/300: dt: 0.9000, rms radial error=171.036, avgs=0 040/300: dt: 0.9000, rms radial error=170.088, avgs=0 045/300: dt: 0.9000, rms radial error=169.139, avgs=0 050/300: dt: 0.9000, rms radial error=168.191, avgs=0 055/300: dt: 0.9000, rms radial error=167.246, avgs=0 060/300: dt: 0.9000, rms radial error=166.304, avgs=0 065/300: dt: 0.9000, rms radial error=165.366, avgs=0 070/300: dt: 0.9000, rms radial error=164.433, avgs=0 075/300: dt: 0.9000, rms radial error=163.505, avgs=0 080/300: dt: 0.9000, rms radial error=162.582, avgs=0 085/300: dt: 0.9000, rms radial error=161.666, avgs=0 090/300: dt: 0.9000, rms radial error=160.757, avgs=0 095/300: dt: 0.9000, rms radial error=159.852, avgs=0 100/300: dt: 0.9000, rms radial error=158.953, avgs=0 105/300: dt: 0.9000, rms radial error=158.059, avgs=0 110/300: dt: 0.9000, rms radial error=157.169, avgs=0 115/300: dt: 0.9000, rms radial error=156.285, avgs=0 120/300: dt: 0.9000, rms radial error=155.406, avgs=0 125/300: dt: 0.9000, rms radial error=154.532, avgs=0 130/300: dt: 0.9000, rms radial error=153.662, avgs=0 135/300: dt: 0.9000, rms radial error=152.798, avgs=0 140/300: dt: 0.9000, rms radial error=151.938, avgs=0 145/300: dt: 0.9000, rms radial error=151.083, avgs=0 150/300: dt: 0.9000, rms radial error=150.233, avgs=0 155/300: dt: 0.9000, rms radial error=149.387, avgs=0 160/300: dt: 0.9000, rms radial error=148.546, avgs=0 165/300: dt: 0.9000, rms radial error=147.709, avgs=0 170/300: dt: 0.9000, rms radial error=146.877, avgs=0 175/300: dt: 0.9000, rms radial error=146.050, avgs=0 180/300: dt: 0.9000, rms radial error=145.227, avgs=0 185/300: dt: 0.9000, rms radial error=144.409, avgs=0 190/300: dt: 0.9000, rms radial error=143.596, avgs=0 195/300: dt: 0.9000, rms radial error=142.787, avgs=0 200/300: dt: 0.9000, rms radial error=141.982, avgs=0 205/300: dt: 0.9000, rms radial error=141.182, avgs=0 210/300: dt: 0.9000, rms radial error=140.386, avgs=0 215/300: dt: 0.9000, rms radial error=139.595, avgs=0 220/300: dt: 0.9000, rms radial error=138.808, avgs=0 225/300: dt: 0.9000, rms radial error=138.026, avgs=0 230/300: dt: 0.9000, rms radial error=137.248, avgs=0 235/300: dt: 0.9000, rms radial error=136.474, avgs=0 240/300: dt: 0.9000, rms radial error=135.705, avgs=0 245/300: dt: 0.9000, rms radial error=134.940, avgs=0 250/300: dt: 0.9000, rms radial error=134.179, avgs=0 255/300: dt: 0.9000, rms radial error=133.422, avgs=0 260/300: dt: 0.9000, rms radial error=132.670, avgs=0 265/300: dt: 0.9000, rms radial error=131.922, avgs=0 270/300: dt: 0.9000, rms radial error=131.178, avgs=0 275/300: dt: 0.9000, rms radial error=130.439, avgs=0 280/300: dt: 0.9000, rms radial error=129.703, avgs=0 285/300: dt: 0.9000, rms radial error=128.972, avgs=0 290/300: dt: 0.9000, rms radial error=128.244, avgs=0 295/300: dt: 0.9000, rms radial error=127.521, avgs=0 300/300: dt: 0.9000, rms radial error=126.802, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16032.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 2643.61 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00021 epoch 3 (K=160.0), pass 1, starting sse = 260.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00466 epoch 4 (K=640.0), pass 1, starting sse = 19.32 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/13 = 0.00712 final distance error %25.07 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours FSRUNTIME@ mris_sphere 0.0709 hours 1 threads #-------------------------------------------- #@# QSphere rh Mon Jan 25 16:42:21 EST 2016 /export/data/hippocampus/HMN/data/HMN002/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 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.55 (0.00-->6.97) (max @ vno 49010 --> 49011) face area 0.03 +- 0.03 (-0.18-->0.78) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.328... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.493, avgs=0 005/300: dt: 0.9000, rms radial error=175.237, avgs=0 010/300: dt: 0.9000, rms radial error=174.686, avgs=0 015/300: dt: 0.9000, rms radial error=173.963, avgs=0 020/300: dt: 0.9000, rms radial error=173.139, avgs=0 025/300: dt: 0.9000, rms radial error=172.258, avgs=0 030/300: dt: 0.9000, rms radial error=171.346, avgs=0 035/300: dt: 0.9000, rms radial error=170.416, avgs=0 040/300: dt: 0.9000, rms radial error=169.479, avgs=0 045/300: dt: 0.9000, rms radial error=168.539, avgs=0 050/300: dt: 0.9000, rms radial error=167.600, avgs=0 055/300: dt: 0.9000, rms radial error=166.662, avgs=0 060/300: dt: 0.9000, rms radial error=165.727, avgs=0 065/300: dt: 0.9000, rms radial error=164.796, avgs=0 070/300: dt: 0.9000, rms radial error=163.870, avgs=0 075/300: dt: 0.9000, rms radial error=162.948, avgs=0 080/300: dt: 0.9000, rms radial error=162.030, avgs=0 085/300: dt: 0.9000, rms radial error=161.118, avgs=0 090/300: dt: 0.9000, rms radial error=160.210, avgs=0 095/300: dt: 0.9000, rms radial error=159.306, avgs=0 100/300: dt: 0.9000, rms radial error=158.408, avgs=0 105/300: dt: 0.9000, rms radial error=157.514, avgs=0 110/300: dt: 0.9000, rms radial error=156.625, avgs=0 115/300: dt: 0.9000, rms radial error=155.741, avgs=0 120/300: dt: 0.9000, rms radial error=154.862, avgs=0 125/300: dt: 0.9000, rms radial error=153.988, avgs=0 130/300: dt: 0.9000, rms radial error=153.118, avgs=0 135/300: dt: 0.9000, rms radial error=152.253, avgs=0 140/300: dt: 0.9000, rms radial error=151.394, avgs=0 145/300: dt: 0.9000, rms radial error=150.539, avgs=0 150/300: dt: 0.9000, rms radial error=149.689, avgs=0 155/300: dt: 0.9000, rms radial error=148.844, avgs=0 160/300: dt: 0.9000, rms radial error=148.004, avgs=0 165/300: dt: 0.9000, rms radial error=147.168, avgs=0 170/300: dt: 0.9000, rms radial error=146.337, avgs=0 175/300: dt: 0.9000, rms radial error=145.510, avgs=0 180/300: dt: 0.9000, rms radial error=144.688, avgs=0 185/300: dt: 0.9000, rms radial error=143.871, avgs=0 190/300: dt: 0.9000, rms radial error=143.058, avgs=0 195/300: dt: 0.9000, rms radial error=142.249, avgs=0 200/300: dt: 0.9000, rms radial error=141.445, avgs=0 205/300: dt: 0.9000, rms radial error=140.646, avgs=0 210/300: dt: 0.9000, rms radial error=139.851, avgs=0 215/300: dt: 0.9000, rms radial error=139.061, avgs=0 220/300: dt: 0.9000, rms radial error=138.275, avgs=0 225/300: dt: 0.9000, rms radial error=137.493, avgs=0 230/300: dt: 0.9000, rms radial error=136.716, avgs=0 235/300: dt: 0.9000, rms radial error=135.943, avgs=0 240/300: dt: 0.9000, rms radial error=135.175, avgs=0 245/300: dt: 0.9000, rms radial error=134.411, avgs=0 250/300: dt: 0.9000, rms radial error=133.651, avgs=0 255/300: dt: 0.9000, rms radial error=132.895, avgs=0 260/300: dt: 0.9000, rms radial error=132.144, avgs=0 265/300: dt: 0.9000, rms radial error=131.397, avgs=0 270/300: dt: 0.9000, rms radial error=130.655, avgs=0 275/300: dt: 0.9000, rms radial error=129.916, avgs=0 280/300: dt: 0.9000, rms radial error=129.182, avgs=0 285/300: dt: 0.9000, rms radial error=128.452, avgs=0 290/300: dt: 0.9000, rms radial error=127.726, avgs=0 295/300: dt: 0.9000, rms radial error=127.004, avgs=0 300/300: dt: 0.9000, rms radial error=126.286, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16243.78 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00008 epoch 2 (K=40.0), pass 1, starting sse = 2593.55 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 236.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00345 epoch 4 (K=640.0), pass 1, starting sse = 17.11 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/13 = 0.00464 final distance error %24.03 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours FSRUNTIME@ mris_sphere 0.0726 hours 1 threads #-------------------------------------------- #@# Fix Topology lh Mon Jan 25 16:46:43 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology rh Mon Jan 25 16:46:43 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 HMN002 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 1.49 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ before topology correction, eno=-64 (nv=138012, nf=276152, ne=414228, g=33) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 6732 ambiguous faces found in tessellation segmenting defects... 37 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 37 defects to be corrected 0 vertices coincident reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3537 (-4.6768) -vertex loglikelihood: -5.8292 (-2.9146) -normal dot loglikelihood: -3.5920 (-3.5920) -quad curv loglikelihood: -6.0708 (-3.0354) Total Loglikelihood : -24.8457 CORRECTING DEFECT 0 (vertices=470, convex hull=242) After retessellation of defect 0, euler #=-33 (134110,401089,266946) : difference with theory (-34) = -1 CORRECTING DEFECT 1 (vertices=152, convex hull=40) After retessellation of defect 1, euler #=-32 (134114,401117,266971) : difference with theory (-33) = -1 CORRECTING DEFECT 2 (vertices=200, convex hull=47) After retessellation of defect 2, euler #=-31 (134123,401164,267010) : difference with theory (-32) = -1 CORRECTING DEFECT 3 (vertices=97, convex hull=132) After retessellation of defect 3, euler #=-30 (134176,401383,267177) : difference with theory (-31) = -1 CORRECTING DEFECT 4 (vertices=64, convex hull=112) After retessellation of defect 4, euler #=-29 (134219,401563,267315) : difference with theory (-30) = -1 CORRECTING DEFECT 5 (vertices=29, convex hull=54) After retessellation of defect 5, euler #=-28 (134229,401612,267355) : difference with theory (-29) = -1 CORRECTING DEFECT 6 (vertices=18, convex hull=53) After retessellation of defect 6, euler #=-27 (134238,401658,267393) : difference with theory (-28) = -1 CORRECTING DEFECT 7 (vertices=53, convex hull=75) After retessellation of defect 7, euler #=-26 (134247,401714,267441) : difference with theory (-27) = -1 CORRECTING DEFECT 8 (vertices=13, convex hull=25) After retessellation of defect 8, euler #=-25 (134248,401726,267453) : difference with theory (-26) = -1 CORRECTING DEFECT 9 (vertices=11, convex hull=29) After retessellation of defect 9, euler #=-24 (134250,401740,267466) : difference with theory (-25) = -1 CORRECTING DEFECT 10 (vertices=28, convex hull=60) After retessellation of defect 10, euler #=-23 (134263,401799,267513) : difference with theory (-24) = -1 CORRECTING DEFECT 11 (vertices=501, convex hull=251) After retessellation of defect 11, euler #=-22 (134280,401973,267671) : difference with theory (-23) = -1 CORRECTING DEFECT 12 (vertices=219, convex hull=60) After retessellation of defect 12, euler #=-21 (134305,402073,267747) : difference with theory (-22) = -1 CORRECTING DEFECT 13 (vertices=30, convex hull=78) After retessellation of defect 13, euler #=-20 (134322,402156,267814) : difference with theory (-21) = -1 CORRECTING DEFECT 14 (vertices=269, convex hull=308) After retessellation of defect 14, euler #=-19 (134447,402686,268220) : difference with theory (-20) = -1 CORRECTING DEFECT 15 (vertices=5, convex hull=29) After retessellation of defect 15, euler #=-18 (134449,402700,268233) : difference with theory (-19) = -1 CORRECTING DEFECT 16 (vertices=8, convex hull=19) After retessellation of defect 16, euler #=-17 (134452,402715,268246) : difference with theory (-18) = -1 CORRECTING DEFECT 17 (vertices=33, convex hull=29) After retessellation of defect 17, euler #=-16 (134455,402732,268261) : difference with theory (-17) = -1 CORRECTING DEFECT 18 (vertices=22, convex hull=58) After retessellation of defect 18, euler #=-15 (134467,402792,268310) : difference with theory (-16) = -1 CORRECTING DEFECT 19 (vertices=29, convex hull=76) After retessellation of defect 19, euler #=-14 (134484,402868,268370) : difference with theory (-15) = -1 CORRECTING DEFECT 20 (vertices=68, convex hull=92) After retessellation of defect 20, euler #=-13 (134511,402985,268461) : difference with theory (-14) = -1 CORRECTING DEFECT 21 (vertices=27, convex hull=22) After retessellation of defect 21, euler #=-12 (134518,403011,268481) : difference with theory (-13) = -1 CORRECTING DEFECT 22 (vertices=23, convex hull=35) After retessellation of defect 22, euler #=-11 (134523,403037,268503) : difference with theory (-12) = -1 CORRECTING DEFECT 23 (vertices=817, convex hull=291) After retessellation of defect 23, euler #=-11 (134561,403301,268729) : difference with theory (-11) = 0 CORRECTING DEFECT 24 (vertices=36, convex hull=58) After retessellation of defect 24, euler #=-10 (134580,403380,268790) : difference with theory (-10) = 0 CORRECTING DEFECT 25 (vertices=68, convex hull=65) After retessellation of defect 25, euler #=-9 (134593,403450,268848) : difference with theory (-9) = 0 CORRECTING DEFECT 26 (vertices=55, convex hull=76) After retessellation of defect 26, euler #=-8 (134609,403532,268915) : difference with theory (-8) = 0 CORRECTING DEFECT 27 (vertices=33, convex hull=59) After retessellation of defect 27, euler #=-7 (134621,403590,268962) : difference with theory (-7) = 0 CORRECTING DEFECT 28 (vertices=54, convex hull=87) After retessellation of defect 28, euler #=-6 (134652,403720,269062) : difference with theory (-6) = 0 CORRECTING DEFECT 29 (vertices=24, convex hull=69) After retessellation of defect 29, euler #=-5 (134663,403779,269111) : difference with theory (-5) = 0 CORRECTING DEFECT 30 (vertices=146, convex hull=89) After retessellation of defect 30, euler #=-4 (134686,403884,269194) : difference with theory (-4) = 0 CORRECTING DEFECT 31 (vertices=128, convex hull=36) After retessellation of defect 31, euler #=-3 (134695,403924,269226) : difference with theory (-3) = 0 CORRECTING DEFECT 32 (vertices=52, convex hull=108) After retessellation of defect 32, euler #=-2 (134723,404052,269327) : difference with theory (-2) = 0 CORRECTING DEFECT 33 (vertices=120, convex hull=111) After retessellation of defect 33, euler #=-1 (134760,404214,269453) : difference with theory (-1) = 0 CORRECTING DEFECT 34 (vertices=30, convex hull=71) After retessellation of defect 34, euler #=0 (134776,404289,269513) : difference with theory (0) = 0 CORRECTING DEFECT 35 (vertices=7, convex hull=22) After retessellation of defect 35, euler #=1 (134777,404300,269524) : difference with theory (1) = 0 CORRECTING DEFECT 36 (vertices=19, convex hull=61) After retessellation of defect 36, euler #=2 (134786,404352,269568) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.24 (0.04-->10.84) (max @ vno 267 --> 3480) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.24 (0.04-->10.84) (max @ vno 267 --> 3480) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 126 mutations (33.0%), 256 crossovers (67.0%), 382 vertices were eliminated building final representation... 3226 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134786, nf=269568, ne=404352, g=0) writing corrected surface to /export/data/hippocampus/HMN/data/HMN002/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 40.5 minutes 0 defective edges removing intersecting faces 000: 370 intersecting FSRUNTIME@ mris_fix_topology lh 0.6746 hours 1 threads mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 HMN002 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 1.49 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ before topology correction, eno=-80 (nv=141454, nf=283068, ne=424602, g=41) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 7 iterations marking ambiguous vertices... 6325 ambiguous faces found in tessellation segmenting defects... 45 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 44 into 43 44 defects to be corrected 0 vertices coincident reading input surface /export/data/hippocampus/HMN/data/HMN002/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2109 (-4.6054) -vertex loglikelihood: -5.7819 (-2.8909) -normal dot loglikelihood: -3.5952 (-3.5952) -quad curv loglikelihood: -6.2407 (-3.1204) Total Loglikelihood : -24.8287 CORRECTING DEFECT 0 (vertices=71, convex hull=97) After retessellation of defect 0, euler #=-41 (137746,411966,274179) : difference with theory (-41) = 0 CORRECTING DEFECT 1 (vertices=120, convex hull=119) After retessellation of defect 1, euler #=-40 (137775,412111,274296) : difference with theory (-40) = 0 CORRECTING DEFECT 2 (vertices=41, convex hull=75) After retessellation of defect 2, euler #=-39 (137784,412168,274345) : difference with theory (-39) = 0 CORRECTING DEFECT 3 (vertices=46, convex hull=67) After retessellation of defect 3, euler #=-38 (137809,412273,274426) : difference with theory (-38) = 0 CORRECTING DEFECT 4 (vertices=22, convex hull=55) After retessellation of defect 4, euler #=-37 (137817,412323,274469) : difference with theory (-37) = 0 CORRECTING DEFECT 5 (vertices=26, convex hull=52) After retessellation of defect 5, euler #=-36 (137831,412385,274518) : difference with theory (-36) = 0 CORRECTING DEFECT 6 (vertices=34, convex hull=68) After retessellation of defect 6, euler #=-35 (137855,412486,274596) : difference with theory (-35) = 0 CORRECTING DEFECT 7 (vertices=30, convex hull=62) After retessellation of defect 7, euler #=-34 (137864,412537,274639) : difference with theory (-34) = 0 CORRECTING DEFECT 8 (vertices=689, convex hull=215) After retessellation of defect 8, euler #=-33 (138020,413109,275056) : difference with theory (-33) = 0 CORRECTING DEFECT 9 (vertices=29, convex hull=67) After retessellation of defect 9, euler #=-32 (138038,413189,275119) : difference with theory (-32) = 0 CORRECTING DEFECT 10 (vertices=26, convex hull=49) After retessellation of defect 10, euler #=-31 (138049,413238,275158) : difference with theory (-31) = 0 CORRECTING DEFECT 11 (vertices=7, convex hull=20) After retessellation of defect 11, euler #=-30 (138050,413245,275165) : difference with theory (-30) = 0 CORRECTING DEFECT 12 (vertices=18, convex hull=21) After retessellation of defect 12, euler #=-29 (138050,413254,275175) : difference with theory (-29) = 0 CORRECTING DEFECT 13 (vertices=253, convex hull=46) After retessellation of defect 13, euler #=-28 (138074,413345,275243) : difference with theory (-28) = 0 CORRECTING DEFECT 14 (vertices=41, convex hull=69) After retessellation of defect 14, euler #=-27 (138098,413446,275321) : difference with theory (-27) = 0 CORRECTING DEFECT 15 (vertices=89, convex hull=77) After retessellation of defect 15, euler #=-26 (138114,413527,275387) : difference with theory (-26) = 0 CORRECTING DEFECT 16 (vertices=30, convex hull=51) After retessellation of defect 16, euler #=-25 (138129,413594,275440) : difference with theory (-25) = 0 CORRECTING DEFECT 17 (vertices=90, convex hull=96) After retessellation of defect 17, euler #=-24 (138141,413671,275506) : difference with theory (-24) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=64) After retessellation of defect 18, euler #=-23 (138150,413718,275545) : difference with theory (-23) = 0 CORRECTING DEFECT 19 (vertices=66, convex hull=32) After retessellation of defect 19, euler #=-22 (138156,413746,275568) : difference with theory (-22) = 0 CORRECTING DEFECT 20 (vertices=30, convex hull=44) After retessellation of defect 20, euler #=-21 (138171,413807,275615) : difference with theory (-21) = 0 CORRECTING DEFECT 21 (vertices=28, convex hull=83) After retessellation of defect 21, euler #=-20 (138180,413865,275665) : difference with theory (-20) = 0 CORRECTING DEFECT 22 (vertices=303, convex hull=83) After retessellation of defect 22, euler #=-19 (138206,413981,275756) : difference with theory (-19) = 0 CORRECTING DEFECT 23 (vertices=21, convex hull=47) After retessellation of defect 23, euler #=-18 (138219,414037,275800) : difference with theory (-18) = 0 CORRECTING DEFECT 24 (vertices=38, convex hull=57) After retessellation of defect 24, euler #=-17 (138243,414130,275870) : difference with theory (-17) = 0 CORRECTING DEFECT 25 (vertices=32, convex hull=44) After retessellation of defect 25, euler #=-17 (138252,414176,275907) : difference with theory (-16) = 1 CORRECTING DEFECT 26 (vertices=106, convex hull=63) After retessellation of defect 26, euler #=-16 (138273,414263,275974) : difference with theory (-15) = 1 CORRECTING DEFECT 27 (vertices=33, convex hull=66) After retessellation of defect 27, euler #=-15 (138282,414318,276021) : difference with theory (-14) = 1 CORRECTING DEFECT 28 (vertices=35, convex hull=25) After retessellation of defect 28, euler #=-14 (138284,414332,276034) : difference with theory (-13) = 1 CORRECTING DEFECT 29 (vertices=52, convex hull=51) After retessellation of defect 29, euler #=-13 (138296,414389,276080) : difference with theory (-12) = 1 CORRECTING DEFECT 30 (vertices=34, convex hull=58) After retessellation of defect 30, euler #=-12 (138307,414444,276125) : difference with theory (-11) = 1 CORRECTING DEFECT 31 (vertices=46, convex hull=96) After retessellation of defect 31, euler #=-11 (138330,414554,276213) : difference with theory (-10) = 1 CORRECTING DEFECT 32 (vertices=52, convex hull=76) After retessellation of defect 32, euler #=-10 (138355,414662,276297) : difference with theory (-9) = 1 CORRECTING DEFECT 33 (vertices=84, convex hull=45) After retessellation of defect 33, euler #=-9 (138364,414706,276333) : difference with theory (-8) = 1 CORRECTING DEFECT 34 (vertices=37, convex hull=69) After retessellation of defect 34, euler #=-8 (138373,414762,276381) : difference with theory (-7) = 1 CORRECTING DEFECT 35 (vertices=60, convex hull=66) After retessellation of defect 35, euler #=-7 (138382,414819,276430) : difference with theory (-6) = 1 CORRECTING DEFECT 36 (vertices=17, convex hull=62) After retessellation of defect 36, euler #=-6 (138387,414859,276466) : difference with theory (-5) = 1 CORRECTING DEFECT 37 (vertices=621, convex hull=167) After retessellation of defect 37, euler #=-5 (138481,415225,276739) : difference with theory (-4) = 1 CORRECTING DEFECT 38 (vertices=56, convex hull=83) After retessellation of defect 38, euler #=-4 (138505,415331,276822) : difference with theory (-3) = 1 CORRECTING DEFECT 39 (vertices=44, convex hull=18) After retessellation of defect 39, euler #=-3 (138506,415339,276830) : difference with theory (-2) = 1 CORRECTING DEFECT 40 (vertices=45, convex hull=86) After retessellation of defect 40, euler #=-2 (138530,415444,276912) : difference with theory (-1) = 1 CORRECTING DEFECT 41 (vertices=51, convex hull=82) After retessellation of defect 41, euler #=-1 (138546,415528,276981) : difference with theory (0) = 1 CORRECTING DEFECT 42 (vertices=69, convex hull=91) After retessellation of defect 42, euler #=0 (138561,415614,277053) : difference with theory (1) = 1 CORRECTING DEFECT 43 (vertices=82, convex hull=138) After retessellation of defect 43, euler #=2 (138601,415797,277198) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.24 (0.06-->8.58) (max @ vno 90439 --> 95076) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.24 (0.06-->8.58) (max @ vno 90439 --> 95076) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 171 mutations (35.6%), 309 crossovers (64.4%), 219 vertices were eliminated building final representation... 2853 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138601, nf=277198, ne=415797, g=0) writing corrected surface to /export/data/hippocampus/HMN/data/HMN002/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 33.4 minutes 0 defective edges removing intersecting faces 000: 320 intersecting 001: 15 intersecting FSRUNTIME@ mris_fix_topology rh 0.5560 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 134786 - 404352 + 269568 = 2 --> 0 holes F =2V-4: 269568 = 269572-4 (0) 2E=3F: 808704 = 808704 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 138601 - 415797 + 277198 = 2 --> 0 holes F =2V-4: 277198 = 277202-4 (0) 2E=3F: 831594 = 831594 (0) total defect index = 0 /export/data/hippocampus/HMN/data/HMN002/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 40 intersecting 001: 6 intersecting 002: 2 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /export/data/hippocampus/HMN/data/HMN002/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 27 intersecting 001: 4 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Jan 25 18:00:46 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs HMN002 lh only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline 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 1.162 2015/12/10 21:15:02 fischl Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading volume /export/data/hippocampus/HMN/data/HMN002/mri/filled.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/brain.finalsurfs.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/../mri/aseg.presurf.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... 21273 bright wm thresholded. 719 bright non-wm voxels segmented. reading original surface position from /export/data/hippocampus/HMN/data/HMN002/surf/lh.orig... computing class statistics... border white: 254757 voxels (1.52%) border gray 294746 voxels (1.76%) WM (101.0): 101.1 +- 7.1 [70.0 --> 110.0] GM (81.0) : 80.4 +- 9.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 69.0 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 60.0 (was 40) setting MAX_GRAY to 98.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 51.0 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->4.78) (max @ vno 84720 --> 134335) face area 0.28 +- 0.13 (0.00-->5.56) mean absolute distance = 0.69 +- 0.80 5479 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-4.3, GM=78+-6.1 mean inside = 98.0, mean outside = 83.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=86.1, 56 (56) missing vertices, mean dist 0.4 [0.5 (%30.8)->0.8 (%69.2))] %72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.09-->5.19) (max @ vno 61371 --> 61367) face area 0.28 +- 0.13 (0.00-->4.51) mean absolute distance = 0.37 +- 0.47 4269 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2283590.8, rms=8.115 001: dt: 0.5000, sse=1364148.5, rms=5.613 (30.836%) 002: dt: 0.5000, sse=981953.6, rms=4.123 (26.547%) 003: dt: 0.5000, sse=814698.9, rms=3.262 (20.878%) 004: dt: 0.5000, sse=741814.4, rms=2.797 (14.265%) 005: dt: 0.5000, sse=710142.6, rms=2.563 (8.365%) 006: dt: 0.5000, sse=699081.9, rms=2.450 (4.415%) 007: dt: 0.5000, sse=690454.6, rms=2.395 (2.232%) rms = 2.36, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=686796.3, rms=2.362 (1.375%) 009: dt: 0.2500, sse=615618.8, rms=1.542 (34.698%) 010: dt: 0.2500, sse=604398.2, rms=1.398 (9.391%) rms = 1.37, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=601759.9, rms=1.369 (2.062%) rms = 1.35, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=600300.8, rms=1.347 (1.586%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.5, 33 (4) missing vertices, mean dist -0.3 [0.4 (%81.9)->0.3 (%18.1))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.24 (0.07-->5.68) (max @ vno 67304 --> 68564) face area 0.35 +- 0.16 (0.00-->5.97) mean absolute distance = 0.23 +- 0.33 3381 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1197990.5, rms=4.431 013: dt: 0.5000, sse=878002.9, rms=2.634 (40.564%) 014: dt: 0.5000, sse=812458.3, rms=2.185 (17.034%) 015: dt: 0.5000, sse=794674.4, rms=2.033 (6.950%) rms = 2.16, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=748007.2, rms=1.529 (24.786%) 017: dt: 0.2500, sse=743475.3, rms=1.267 (17.126%) 018: dt: 0.2500, sse=726641.8, rms=1.200 (5.293%) rms = 1.18, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=727233.2, rms=1.183 (1.406%) rms = 1.17, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=723979.4, rms=1.166 (1.429%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=91.4, 38 (2) missing vertices, mean dist -0.1 [0.2 (%74.0)->0.2 (%26.0))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.03-->5.97) (max @ vno 67304 --> 68564) face area 0.34 +- 0.16 (0.00-->5.85) mean absolute distance = 0.19 +- 0.29 3055 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=833192.8, rms=2.589 021: dt: 0.5000, sse=751671.4, rms=1.763 (31.895%) rms = 1.86, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=708796.2, rms=1.319 (25.202%) 023: dt: 0.2500, sse=704647.8, rms=1.104 (16.320%) rms = 1.07, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=692130.4, rms=1.065 (3.460%) rms = 1.05, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=690430.6, rms=1.052 (1.297%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... mean border=92.0, 75 (0) missing vertices, mean dist -0.0 [0.2 (%57.3)->0.2 (%42.7))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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 /export/data/hippocampus/HMN/data/HMN002/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=695993.5, rms=1.271 026: dt: 0.5000, sse=692805.6, rms=1.050 (17.415%) rms = 1.41, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=674746.3, rms=0.877 (16.500%) rms = 0.87, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=674296.4, rms=0.871 (0.699%) rms = 0.85, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=670289.8, rms=0.852 (2.146%) positioning took 0.5 minutes generating cortex label... 8 non-cortical segments detected only using segment with 6255 vertices erasing segment 0 (vno[0] = 47551) erasing segment 2 (vno[0] = 68708) erasing segment 3 (vno[0] = 92851) erasing segment 4 (vno[0] = 94194) erasing segment 5 (vno[0] = 97086) erasing segment 6 (vno[0] = 97159) erasing segment 7 (vno[0] = 99041) writing cortex label to /export/data/hippocampus/HMN/data/HMN002/label/lh.cortex.label... writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.curv writing smoothed area to lh.area writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->6.19) (max @ vno 67304 --> 68564) face area 0.33 +- 0.16 (0.00-->5.60) refinement took 5.1 minutes #-------------------------------------------- #@# Make White Surf rh Mon Jan 25 18:05:50 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -noaparc -whiteonly -mgz -T1 brain.finalsurfs HMN002 rh only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline 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 1.162 2015/12/10 21:15:02 fischl Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading volume /export/data/hippocampus/HMN/data/HMN002/mri/filled.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/brain.finalsurfs.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/../mri/aseg.presurf.mgz... reading volume /export/data/hippocampus/HMN/data/HMN002/mri/wm.mgz... 21273 bright wm thresholded. 719 bright non-wm voxels segmented. reading original surface position from /export/data/hippocampus/HMN/data/HMN002/surf/rh.orig... computing class statistics... border white: 254757 voxels (1.52%) border gray 294746 voxels (1.76%) WM (101.0): 101.1 +- 7.1 [70.0 --> 110.0] GM (81.0) : 80.4 +- 9.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 69.0 (was 70) setting MAX_BORDER_WHITE to 113.1 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 60.0 (was 40) setting MAX_GRAY to 98.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 51.0 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.66) (max @ vno 137972 --> 137988) face area 0.28 +- 0.13 (0.00-->8.59) mean absolute distance = 0.71 +- 0.81 5721 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=106+-4.3, GM=78+-6.1 mean inside = 98.2, mean outside = 83.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=86.4, 81 (81) missing vertices, mean dist 0.4 [0.5 (%30.2)->0.8 (%69.8))] %73 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hippo, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.11-->6.09) (max @ vno 137898 --> 137900) face area 0.28 +- 0.13 (0.00-->6.92) mean absolute distance = 0.39 +- 0.50 4415 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2178827.8, rms=7.717 001: dt: 0.5000, sse=1298542.9, rms=5.265 (31.781%) 002: dt: 0.5000, sse=959611.1, rms=3.900 (25.910%) 003: dt: 0.5000, sse=815976.9, rms=3.147 (19.325%) 004: dt: 0.5000, sse=750375.1, rms=2.727 (13.352%) 005: dt: 0.5000, sse=720445.0, rms=2.505 (8.134%) 006: dt: 0.5000, sse=705350.8, rms=2.378 (5.060%) 007: dt: 0.5000, sse=700063.0, rms=2.320 (2.437%) rms = 2.27, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=696365.5, rms=2.275 (1.962%) 009: dt: 0.2500, sse=627152.2, rms=1.503 (33.913%) 010: dt: 0.2500, sse=616868.9, rms=1.367 (9.079%) rms = 1.34, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=615083.2, rms=1.336 (2.215%) rms = 1.31, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=615054.3, rms=1.315 (1.618%) positioning took 1.3 minutes inhibiting deformation at non-cortical midline structures... mean border=89.9, 87 (26) missing vertices, mean dist -0.3 [0.4 (%82.1)->0.3 (%17.9))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hippo, 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 +- 0.24 (0.09-->6.71) (max @ vno 137898 --> 137900) face area 0.35 +- 0.16 (0.00-->8.97) mean absolute distance = 0.24 +- 0.33 3920 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1243486.6, rms=4.495 013: dt: 0.5000, sse=902756.2, rms=2.723 (39.415%) 014: dt: 0.5000, sse=832267.5, rms=2.205 (19.025%) 015: dt: 0.5000, sse=805742.6, rms=2.001 (9.242%) rms = 2.10, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=763321.6, rms=1.533 (23.408%) 017: dt: 0.2500, sse=748676.4, rms=1.264 (17.544%) 018: dt: 0.2500, sse=744670.9, rms=1.180 (6.645%) rms = 1.15, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=739470.6, rms=1.147 (2.780%) rms = 1.13, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=737383.0, rms=1.128 (1.711%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=91.8, 94 (13) missing vertices, mean dist -0.1 [0.2 (%74.5)->0.2 (%25.5))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hippo, 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 +- 0.24 (0.07-->7.06) (max @ vno 137898 --> 137900) face area 0.33 +- 0.16 (0.00-->8.70) mean absolute distance = 0.19 +- 0.30 3351 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=860100.5, rms=2.642 021: dt: 0.5000, sse=769445.4, rms=1.730 (34.513%) rms = 1.78, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=725922.8, rms=1.300 (24.866%) 023: dt: 0.2500, sse=715862.9, rms=1.067 (17.892%) rms = 1.02, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=705449.9, rms=1.019 (4.571%) rms = 1.00, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=704328.5, rms=1.003 (1.494%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=92.4, 108 (2) missing vertices, mean dist -0.0 [0.2 (%57.7)->0.2 (%42.3))] %93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hippo, 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 /export/data/hippocampus/HMN/data/HMN002/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=710588.6, rms=1.243 026: dt: 0.5000, sse=712486.9, rms=0.999 (19.643%) rms = 1.34, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=685765.9, rms=0.831 (16.772%) rms = 0.83, time step reduction 2 of 3 to 0.125... rms = 0.82, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=684238.9, rms=0.818 (1.626%) positioning took 0.5 minutes generating cortex label... 11 non-cortical segments detected only using segment with 6261 vertices erasing segment 0 (vno[0] = 40709) erasing segment 1 (vno[0] = 41704) erasing segment 3 (vno[0] = 83989) erasing segment 4 (vno[0] = 91306) erasing segment 5 (vno[0] = 92446) erasing segment 6 (vno[0] = 95921) erasing segment 7 (vno[0] = 95970) erasing segment 8 (vno[0] = 98479) erasing segment 9 (vno[0] = 99774) erasing segment 10 (vno[0] = 99883) writing cortex label to /export/data/hippocampus/HMN/data/HMN002/label/rh.cortex.label... writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.curv writing smoothed area to rh.area writing curvature file /export/data/hippocampus/HMN/data/HMN002/surf/rh.area vertex spacing 0.89 +- 0.25 (0.02-->7.23) (max @ vno 137898 --> 137900) face area 0.33 +- 0.16 (0.00-->8.63) refinement took 5.1 minutes #-------------------------------------------- #@# Smooth2 lh Mon Jan 25 18:10:57 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm 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... #-------------------------------------------- #@# Smooth2 rh Mon Jan 25 18:11:02 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm 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 Mon Jan 25 18:11:08 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 44.3 mm, total surface area = 81813 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.173 (target=0.015) step 005: RMS=0.122 (target=0.015) step 010: RMS=0.091 (target=0.015) step 015: RMS=0.076 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.024 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.7 minutes #-------------------------------------------- #@# Inflation2 rh Mon Jan 25 18:11:48 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 44.2 mm, total surface area = 83639 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.173 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.092 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.056 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.041 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.7 minutes #-------------------------------------------- #@# Curv .H and .K lh Mon Jan 25 18:12:29 EST 2016 /export/data/hippocampus/HMN/data/HMN002/surf mris_curvature -w lh.white total integrated curvature = 0.774*4pi (9.725) --> 0 handles ICI = 147.6, FI = 1807.9, variation=27576.201 writing Gaussian curvature to ./lh.white.K...done. writing mean curvature to ./lh.white.H...done. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 148 vertices thresholded to be in k1 ~ [-0.23 1.56], k2 ~ [-0.14 0.05] total integrated curvature = 0.526*4pi (6.609) --> 0 handles ICI = 1.5, FI = 8.8, variation=154.123 121 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 87 vertices thresholded to be in [-0.15 0.25] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.017, std = 0.022 done. #-------------------------------------------- #@# Curv .H and .K rh Mon Jan 25 18:13:58 EST 2016 /export/data/hippocampus/HMN/data/HMN002/surf mris_curvature -w rh.white total integrated curvature = 1.619*4pi (20.343) --> -1 handles ICI = 151.8, FI = 1845.0, variation=28172.729 writing Gaussian curvature to ./rh.white.K...done. writing mean curvature to ./rh.white.H...done. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 180 vertices thresholded to be in k1 ~ [-0.28 2.48], k2 ~ [-0.11 0.08] total integrated curvature = 0.459*4pi (5.768) --> 1 handles ICI = 1.5, FI = 10.4, variation=175.824 134 vertices thresholded to be in [-0.05 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 100 vertices thresholded to be in [-0.16 0.53] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Mon Jan 25 18:15:31 EST 2016 /export/data/hippocampus/HMN/data/HMN002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm HMN002 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 [ HMN002/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 [ 268 ] Gb_filter = 0 WARN: S lookup min: -0.071232 WARN: S explicit min: 0.000000 vertex = 323 #----------------------------------------- #@# Curvature Stats rh Mon Jan 25 18:15:35 EST 2016 /export/data/hippocampus/HMN/data/HMN002/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm HMN002 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 [ HMN002/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 [ 234 ] Gb_filter = 0 WARN: S lookup min: -0.226645 WARN: S explicit min: 0.000000 vertex = 36 #-------------------------------------------- #@# Sphere lh Mon Jan 25 18:15:39 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.304... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=hippo, 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 %20.42 pass 1: epoch 2 of 3 starting distance error %20.32 unfolding complete - removing small folds... starting distance error %20.28 removing remaining folds... final distance error %20.29 MRISunfold() return, current seed 1234 -01: dt=0.0000, 137 negative triangles 200: dt=0.9900, 137 negative triangles 201: dt=0.9900, 66 negative triangles 202: dt=0.9900, 60 negative triangles 203: dt=0.9900, 59 negative triangles 204: dt=0.9900, 58 negative triangles 205: dt=0.9900, 53 negative triangles 206: dt=0.9900, 45 negative triangles 207: dt=0.9900, 52 negative triangles 208: dt=0.9900, 42 negative triangles 209: dt=0.9900, 50 negative triangles 210: dt=0.9900, 40 negative triangles 211: dt=0.9900, 34 negative triangles 212: dt=0.9900, 36 negative triangles 213: dt=0.9900, 32 negative triangles 214: dt=0.9900, 31 negative triangles 215: dt=0.9900, 30 negative triangles 216: dt=0.9900, 30 negative triangles 217: dt=0.9900, 27 negative triangles 218: dt=0.9900, 30 negative triangles 219: dt=0.9900, 28 negative triangles 220: dt=0.9900, 24 negative triangles 221: dt=0.9900, 24 negative triangles 222: dt=0.9900, 21 negative triangles 223: dt=0.9900, 20 negative triangles 224: dt=0.9900, 24 negative triangles 225: dt=0.9900, 23 negative triangles 226: dt=0.9900, 19 negative triangles 227: dt=0.9900, 22 negative triangles 228: dt=0.9900, 23 negative triangles 229: dt=0.9900, 19 negative triangles 230: dt=0.9900, 19 negative triangles 231: dt=0.9900, 20 negative triangles 232: dt=0.9900, 16 negative triangles 233: dt=0.9900, 16 negative triangles 234: dt=0.9900, 19 negative triangles 235: dt=0.9900, 19 negative triangles 236: dt=0.9900, 18 negative triangles 237: dt=0.9900, 14 negative triangles 238: dt=0.9900, 17 negative triangles 239: dt=0.9900, 15 negative triangles 240: dt=0.9900, 14 negative triangles 241: dt=0.9900, 13 negative triangles 242: dt=0.9900, 14 negative triangles 243: dt=0.9900, 7 negative triangles 244: dt=0.9900, 9 negative triangles 245: dt=0.9900, 6 negative triangles 246: dt=0.9900, 5 negative triangles 247: dt=0.9900, 5 negative triangles 248: dt=0.9900, 6 negative triangles 249: dt=0.9900, 5 negative triangles 250: dt=0.9900, 1 negative triangles 251: dt=0.9900, 5 negative triangles 252: dt=0.9900, 1 negative triangles 253: dt=0.9900, 5 negative triangles 254: dt=0.9900, 1 negative triangles 255: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.97 hours FSRUNTIME@ mris_sphere 0.9690 hours 1 threads #-------------------------------------------- #@# Sphere rh Mon Jan 25 19:13:48 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.307... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=hippo, 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 %19.46 pass 1: epoch 2 of 3 starting distance error %19.40 unfolding complete - removing small folds... starting distance error %19.35 removing remaining folds... final distance error %19.36 MRISunfold() return, current seed 1234 -01: dt=0.0000, 189 negative triangles 196: dt=0.9900, 189 negative triangles 197: dt=0.9900, 80 negative triangles 198: dt=0.9900, 63 negative triangles 199: dt=0.9900, 42 negative triangles 200: dt=0.9900, 41 negative triangles 201: dt=0.9900, 40 negative triangles 202: dt=0.9900, 43 negative triangles 203: dt=0.9900, 42 negative triangles 204: dt=0.9900, 35 negative triangles 205: dt=0.9900, 39 negative triangles 206: dt=0.9900, 34 negative triangles 207: dt=0.9900, 38 negative triangles 208: dt=0.9900, 30 negative triangles 209: dt=0.9900, 30 negative triangles 210: dt=0.9900, 31 negative triangles 211: dt=0.9900, 25 negative triangles 212: dt=0.9900, 26 negative triangles 213: dt=0.9900, 30 negative triangles 214: dt=0.9900, 28 negative triangles 215: dt=0.9900, 27 negative triangles 216: dt=0.9900, 27 negative triangles 217: dt=0.9900, 21 negative triangles 218: dt=0.9900, 26 negative triangles 219: dt=0.9900, 20 negative triangles 220: dt=0.9900, 31 negative triangles 221: dt=0.9900, 22 negative triangles 222: dt=0.9900, 23 negative triangles 223: dt=0.9900, 19 negative triangles 224: dt=0.9900, 19 negative triangles 225: dt=0.9900, 19 negative triangles 226: dt=0.9900, 18 negative triangles 227: dt=0.9900, 17 negative triangles 228: dt=0.9900, 17 negative triangles 229: dt=0.9900, 14 negative triangles 230: dt=0.9900, 14 negative triangles 231: dt=0.9900, 14 negative triangles 232: dt=0.9900, 19 negative triangles 233: dt=0.9900, 15 negative triangles 234: dt=0.9900, 9 negative triangles 235: dt=0.9900, 11 negative triangles 236: dt=0.9900, 10 negative triangles 237: dt=0.9900, 6 negative triangles 238: dt=0.9900, 3 negative triangles 239: dt=0.9900, 5 negative triangles 240: dt=0.9900, 6 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.95 hours FSRUNTIME@ mris_sphere 0.9451 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Mon Jan 25 20:10:30 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_register -curv ../surf/lh.sphere /cell_root/software/freesurfer/dev/sys/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /export/data/hippocampus/HMN/data/HMN002/scripts cmdline mris_register -curv ../surf/lh.sphere /cell_root/software/freesurfer/dev/sys/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /cell_root/software/freesurfer/dev/sys/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=hippo, 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=hippo, 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 = 0.640 curvature mean = 0.030, std = 0.932 curvature mean = 0.024, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 0.00) sse = 331973.4, tmin=1.1888 d=32.00 min @ (8.00, 8.00, 8.00) sse = 241004.1, tmin=2.4019 d=16.00 min @ (0.00, 0.00, -4.00) sse = 239682.1, tmin=3.6365 d=8.00 min @ (-2.00, -2.00, 2.00) sse = 226722.6, tmin=4.8773 d=4.00 min @ (1.00, 0.00, 0.00) sse = 226335.2, tmin=6.1296 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 225920.4, tmin=7.3842 d=1.00 min @ (0.25, 0.25, -0.25) sse = 225913.9, tmin=8.6397 d=0.50 min @ (-0.12, -0.12, 0.12) sse = 225842.3, tmin=9.9073 tol=1.0e+00, sigma=0.5, host=hippo, 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 9.91 min curvature mean = 0.022, std = 0.950 curvature mean = 0.011, std = 0.943 curvature mean = 0.022, std = 0.963 curvature mean = 0.005, std = 0.975 curvature mean = 0.021, std = 0.965 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.031, std = 0.306 curvature mean = 0.003, std = 0.066 curvature mean = 0.073, std = 0.336 curvature mean = 0.003, std = 0.079 curvature mean = 0.032, std = 0.521 curvature mean = 0.004, std = 0.085 curvature mean = 0.017, std = 0.660 curvature mean = 0.004, std = 0.087 curvature mean = 0.006, std = 0.774 MRISregister() return, current seed 0 -01: dt=0.0000, 58 negative triangles 116: dt=0.9900, 58 negative triangles expanding nbhd size to 1 117: dt=0.9900, 65 negative triangles 118: dt=0.9900, 43 negative triangles 119: dt=0.9900, 36 negative triangles 120: dt=0.9900, 48 negative triangles 121: dt=0.9900, 31 negative triangles 122: dt=0.9900, 29 negative triangles 123: dt=0.9900, 23 negative triangles 124: dt=0.9900, 25 negative triangles 125: dt=0.9900, 27 negative triangles 126: dt=0.9900, 26 negative triangles 127: dt=0.9900, 24 negative triangles 128: dt=0.9900, 23 negative triangles 129: dt=0.9900, 21 negative triangles 130: dt=0.9900, 21 negative triangles 131: dt=0.9900, 18 negative triangles 132: dt=0.9900, 18 negative triangles 133: dt=0.9900, 17 negative triangles 134: dt=0.9900, 17 negative triangles 135: dt=0.9900, 19 negative triangles 136: dt=0.9900, 18 negative triangles 137: dt=0.9900, 18 negative triangles 138: dt=0.9900, 16 negative triangles 139: dt=0.9900, 16 negative triangles 140: dt=0.9900, 16 negative triangles 141: dt=0.9900, 16 negative triangles 142: dt=0.9900, 16 negative triangles 143: dt=0.9900, 16 negative triangles 144: dt=0.9900, 15 negative triangles 145: dt=0.9900, 15 negative triangles 146: dt=0.9900, 11 negative triangles 147: dt=0.9900, 11 negative triangles 148: dt=0.9900, 9 negative triangles 149: dt=0.9900, 8 negative triangles 150: dt=0.9900, 9 negative triangles 151: dt=0.9900, 9 negative triangles 152: dt=0.9900, 10 negative triangles 153: dt=0.9900, 9 negative triangles 154: dt=0.9900, 9 negative triangles 155: dt=0.9900, 8 negative triangles 156: dt=0.9900, 6 negative triangles 157: dt=0.9900, 7 negative triangles 158: dt=0.9900, 5 negative triangles 159: dt=0.9900, 5 negative triangles 160: dt=0.9900, 7 negative triangles 161: dt=0.9900, 5 negative triangles 162: dt=0.9900, 5 negative triangles 163: dt=0.9900, 3 negative triangles 164: dt=0.9900, 1 negative triangles 165: dt=0.9900, 2 negative triangles 166: dt=0.9900, 1 negative triangles 167: dt=0.9900, 1 negative triangles 168: dt=0.9900, 1 negative triangles 169: dt=0.9900, 2 negative triangles 170: dt=0.9900, 1 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 0.91 hours FSRUNTIME@ mris_register 0.9082 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Mon Jan 25 21:04:59 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_register -curv ../surf/rh.sphere /cell_root/software/freesurfer/dev/sys/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /export/data/hippocampus/HMN/data/HMN002/scripts cmdline mris_register -curv ../surf/rh.sphere /cell_root/software/freesurfer/dev/sys/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /cell_root/software/freesurfer/dev/sys/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=hippo, 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=hippo, 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 = 0.634 curvature mean = 0.019, std = 0.929 curvature mean = 0.026, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 343478.5, tmin=1.2244 d=32.00 min @ (-8.00, 0.00, -8.00) sse = 321612.9, tmin=2.4843 d=16.00 min @ (4.00, -4.00, 4.00) sse = 276090.3, tmin=3.7565 d=8.00 min @ (-2.00, 0.00, -2.00) sse = 271301.4, tmin=5.0716 d=4.00 min @ (1.00, 0.00, 1.00) sse = 270246.8, tmin=6.3997 d=2.00 min @ (0.00, 0.50, -0.50) sse = 269387.7, tmin=7.7302 d=0.50 min @ (-0.12, 0.00, 0.00) sse = 269376.5, tmin=10.3572 tol=1.0e+00, sigma=0.5, host=hippo, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 10.36 min curvature mean = -0.004, std = 0.945 curvature mean = 0.011, std = 0.945 curvature mean = -0.008, std = 0.955 curvature mean = 0.005, std = 0.976 curvature mean = -0.010, std = 0.956 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.034, std = 0.339 curvature mean = 0.004, std = 0.070 curvature mean = 0.071, std = 0.303 curvature mean = 0.004, std = 0.084 curvature mean = 0.035, std = 0.471 curvature mean = 0.004, std = 0.090 curvature mean = 0.019, std = 0.601 curvature mean = 0.004, std = 0.092 curvature mean = 0.006, std = 0.714 MRISregister() return, current seed 0 -01: dt=0.0000, 84 negative triangles 121: dt=0.9900, 84 negative triangles expanding nbhd size to 1 122: dt=0.9900, 113 negative triangles 123: dt=0.9900, 83 negative triangles 124: dt=0.9900, 70 negative triangles 125: dt=0.9900, 84 negative triangles 126: dt=0.9900, 72 negative triangles 127: dt=0.9900, 75 negative triangles 128: dt=0.9900, 65 negative triangles 129: dt=0.9900, 62 negative triangles 130: dt=0.9900, 51 negative triangles 131: dt=0.9900, 49 negative triangles 132: dt=0.9900, 46 negative triangles 133: dt=0.9900, 42 negative triangles 134: dt=0.9900, 45 negative triangles 135: dt=0.9900, 37 negative triangles 136: dt=0.9900, 31 negative triangles 137: dt=0.9900, 34 negative triangles 138: dt=0.9900, 26 negative triangles 139: dt=0.9900, 25 negative triangles 140: dt=0.9900, 27 negative triangles 141: dt=0.9900, 14 negative triangles 142: dt=0.9900, 18 negative triangles 143: dt=0.9900, 13 negative triangles 144: dt=0.9900, 10 negative triangles 145: dt=0.9900, 10 negative triangles 146: dt=0.9900, 8 negative triangles 147: dt=0.9900, 8 negative triangles 148: dt=0.9900, 5 negative triangles 149: dt=0.9900, 4 negative triangles 150: dt=0.9900, 3 negative triangles 151: dt=0.9900, 2 negative triangles 152: dt=0.9900, 1 negative triangles 153: dt=0.9900, 2 negative triangles 154: dt=0.9900, 1 negative triangles 155: dt=0.9900, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.10 hours FSRUNTIME@ mris_register 1.0987 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Mon Jan 25 22:10:55 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts 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 #-------------------------------------------- #@# Jacobian white rh Mon Jan 25 22:10:57 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts 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 lh Mon Jan 25 22:10:59 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mrisp_paint -a 5 /cell_root/software/freesurfer/dev/sys/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 /cell_root/software/freesurfer/dev/sys/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Mon Jan 25 22:11:00 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mrisp_paint -a 5 /cell_root/software/freesurfer/dev/sys/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 /cell_root/software/freesurfer/dev/sys/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Mon Jan 25 22:11:02 EST 2016 /export/data/hippocampus/HMN/data/HMN002/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 HMN002 lh ../surf/lh.sphere.reg /cell_root/software/freesurfer/dev/sys/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.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ reading atlas from /cell_root/software/freesurfer/dev/sys/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... 1592 labels changed using aseg relabeling using gibbs priors... 000: 2975 changed, 134786 examined... 001: 698 changed, 12707 examined... 002: 152 changed, 3873 examined... 003: 50 changed, 880 examined... 004: 29 changed, 284 examined... 005: 16 changed, 164 examined... 006: 7 changed, 87 examined... 007: 1 changed, 42 examined... 008: 0 changed, 4 examined... 206 labels changed using aseg 000: 105 total segments, 64 labels (264 vertices) changed 001: 43 total segments, 4 labels (14 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 1 filter iterations complete (10 requested, 0 changed) Abort (core dumped) Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting