Mon Jan 23 12:03:18 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0 /usr/local/freesurfer/stable6/bin/recon-all -all -s nmr00327_6p0 -i /space/belle/1/users/mhibert/brain_tumor/subjects/nmr00327/mri/orig/001.mgz -openmp 4 subjid nmr00327_6p0 setenv SUBJECTS_DIR /autofs/space/belle_001/users/mhibert/brain_tumor/subjects FREESURFER_HOME /usr/local/freesurfer/stable6 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-20170118-8592379 Linux belle 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 8192 memorylocked 64 kbytes maxproc 128098 total used free shared buffers cached Mem: 32821692 4847376 27974316 298772 218120 2344580 -/+ buffers/cache: 2284676 30537016 Swap: 32767996 0 32767996 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:19-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:20-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.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: stable6 $ TimeStamp: 2017/01/23-17:03:20-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:21-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:22-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:22-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:23-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:23-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:24-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:24-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:25-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:25-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:26-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:26-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:27-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:27-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:28-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:28-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:29-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:29-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:30-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:31-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:31-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:32-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:32-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:33-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:33-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/01/23-17:03:34-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:34-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:35-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:35-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:36-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:36-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:37-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:37-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:38-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:38-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:39-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/01/23-17:03:39-GMT BuildTimeStamp: Jan 18 2017 09:15:54 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mhibert Machine: belle Platform: Linux PlatformVersion: 2.6.32-642.3.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable6/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/stable6/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0 mri_convert /autofs/space/megraid_archive/84/MEG-MRI/seder/freesurfer/nmr00327/mri/orig/001.mgz /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig/001.mgz mri_convert.bin /autofs/space/megraid_archive/84/MEG-MRI/seder/freesurfer/nmr00327/mri/orig/001.mgz /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/space/megraid_archive/84/MEG-MRI/seder/freesurfer/nmr00327/mri/orig/001.mgz... TR=8.56, TE=3.00, TI=0.00, flip angle=20.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Jan 23 12:03:53 EST 2017 Found 1 runs /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/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 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig/001.mgz /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/rawavg.mgz /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0 mri_convert /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/rawavg.mgz /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig.mgz --conform mri_convert.bin /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/rawavg.mgz /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/rawavg.mgz... TR=8.56, TE=3.00, TI=0.00, flip angle=20.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/transforms/talairach.xfm /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig.mgz /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jan 23 12:04:08 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri /usr/local/freesurfer/stable6/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux belle 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Mon Jan 23 12:04:08 EST 2017 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 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.9199 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9199/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9199/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.56, TE=3.00, TI=0.00, flip angle=20.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9199/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jan 23 12:04:10 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9199/nu0.mnc ./tmp.mri_nu_correct.mni.9199/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9199/0/ -iterations 1000 -distance 50 [mhibert@belle:/autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/] [2017-01-23 12:04:10] running: /usr/local/freesurfer/stable6/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9199/0/ ./tmp.mri_nu_correct.mni.9199/nu0.mnc ./tmp.mri_nu_correct.mni.9199/nu1.imp 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orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9199/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.9199/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Jan 23 12:05:40 EST 2017 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... Started at Mon Jan 23 12:05:40 EST 2017 Ended at Mon Jan 23 12:06:25 EST 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jan 23 12:06:27 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7043, pval=0.4932 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable6/bin/extract_talairach_avi_QA.awk /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/transforms/talairach_avi.log TalAviQA: 0.95527 z-score: -5 #-------------------------------------------- #@# Nu Intensity Correction Mon Jan 23 12:06:28 EST 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri /usr/local/freesurfer/stable6/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 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux belle 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Mon Jan 23 12:06:28 EST 2017 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 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.12545 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12545/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.12545/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=8.56, TE=3.00, TI=0.00, flip angle=20.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12545/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jan 23 12:06:29 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.12545/nu0.mnc ./tmp.mri_nu_correct.mni.12545/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12545/0/ [mhibert@belle:/autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/] [2017-01-23 12:06:29] running: /usr/local/freesurfer/stable6/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12545/0/ ./tmp.mri_nu_correct.mni.12545/nu0.mnc ./tmp.mri_nu_correct.mni.12545/nu1.imp Processing:.................................................................Done 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Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00192496 -------------------------------------------------------- Iteration 2 Mon Jan 23 12:07:06 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.12545/nu1.mnc ./tmp.mri_nu_correct.mni.12545/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12545/1/ [mhibert@belle:/autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/] [2017-01-23 12:07:06] running: /usr/local/freesurfer/stable6/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12545/1/ ./tmp.mri_nu_correct.mni.12545/nu1.mnc ./tmp.mri_nu_correct.mni.12545/nu2.imp 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: 45 CV of field change: 0.000985726 mri_binarize --i ./tmp.mri_nu_correct.mni.12545/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12545/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.12545/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12545/ones.mgz sysname Linux hostname belle machine x86_64 user mhibert input ./tmp.mri_nu_correct.mni.12545/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.12545/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.12545/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12545/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12545/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12545/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12545/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12545/input.mean.dat sysname Linux hostname belle machine x86_64 user mhibert UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12545/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.12545/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12545/ones.mgz --i ./tmp.mri_nu_correct.mni.12545/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12545/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12545/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12545/ones.mgz --i ./tmp.mri_nu_correct.mni.12545/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12545/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12545/output.mean.dat sysname Linux hostname belle machine x86_64 user mhibert UseRobust 0 Loading ./tmp.mri_nu_correct.mni.12545/ones.mgz Loading ./tmp.mri_nu_correct.mni.12545/nu2.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.12545/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.12545/nu2.mnc ./tmp.mri_nu_correct.mni.12545/nu2.mnc mul 1.11697400316466856797 Saving result to './tmp.mri_nu_correct.mni.12545/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.12545/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.12545/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.12545/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 6 seconds. mapping (10, 82) to ( 3, 110) Mon Jan 23 12:08:05 EST 2017 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Jan 23 12:08:05 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.05106 -0.10046 -0.05615 1.34946; 0.09440 0.92196 0.22991 -34.79473; 0.00786 -0.10881 1.16931 10.71896; 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 = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 103 gm peak at 78 (78), valley at 46 (46) csf peak at 39, setting threshold to 65 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 85 (85), valley at 44 (44) csf peak at 43, setting threshold to 71 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 25 seconds. #-------------------------------------------- #@# Skull Stripping Mon Jan 23 12:09:30 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_em_register -rusage /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/stable6/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable6/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=13.0 skull bounding box = (56, 41, 13) --> (212, 225, 235) using (108, 102, 124) as brain centroid... mean wm in atlas = 108, using box (89,79,97) --> (127, 124,151) to find MRI wm before smoothing, mri peak at 101 robust fit to distribution - 101 +- 6.9 after smoothing, mri peak at 101, scaling input intensities by 1.069 scaling channel 0 by 1.06931 initial log_p = -4.522 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.520296 @ (-9.091, -9.091, -9.091) max log p = -4.520296 @ (0.000, 0.000, 0.000) max log p = -4.464227 @ (6.818, 11.364, -2.273) max log p = -4.449519 @ (1.136, -3.409, 1.136) max log p = -4.431082 @ (0.568, 0.568, -0.568) max log p = -4.431082 @ (0.000, 0.000, 0.000) Found translation: (-0.6, -0.6, -10.8): log p = -4.431 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.271, old_max_log_p =-4.431 (thresh=-4.4) 1.07125 -0.03105 0.11590 -26.68016; 0.00000 1.19413 0.31997 -67.22388; -0.15634 -0.27175 1.01419 45.88009; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.255, old_max_log_p =-4.271 (thresh=-4.3) 1.15159 -0.03338 0.12459 -38.04683; 0.00000 1.19413 0.31997 -67.22388; -0.15634 -0.27175 1.01419 45.88009; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.255, old_max_log_p =-4.255 (thresh=-4.3) 1.15159 -0.03338 0.12459 -38.04683; 0.00000 1.19413 0.31997 -67.22388; -0.15634 -0.27175 1.01419 45.88009; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.199, old_max_log_p =-4.255 (thresh=-4.3) 1.08203 -0.04024 0.15017 -27.32515; 0.00000 1.17174 0.31397 -63.29765; -0.18891 -0.26548 0.99079 52.04800; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.198, old_max_log_p =-4.199 (thresh=-4.2) 1.06174 -0.03948 0.14735 -24.47139; 0.00000 1.17174 0.31397 -63.29765; -0.19246 -0.27046 1.00936 52.81909; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.181, old_max_log_p =-4.198 (thresh=-4.2) 1.05884 -0.03208 0.15802 -26.44242; -0.00867 1.16927 0.31203 -60.20028; -0.20180 -0.27099 1.01170 52.86750; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.180, old_max_log_p =-4.181 (thresh=-4.2) 1.05884 -0.03208 0.15802 -26.44242; -0.00868 1.17064 0.31239 -60.43744; -0.20251 -0.27194 1.01526 52.66324; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05884 -0.03208 0.15802 -26.44242; -0.00868 1.17064 0.31239 -60.43744; -0.20251 -0.27194 1.01526 52.66324; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.05884 -0.03208 0.15802 -26.44242; -0.00868 1.17064 0.31239 -60.43744; -0.20251 -0.27194 1.01526 52.66324; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.05884 -0.03208 0.15802 -26.44242; -0.00868 1.17064 0.31239 -60.43744; -0.20251 -0.27194 1.01526 52.66324; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.180 (old=-4.522) transform before final EM align: 1.05884 -0.03208 0.15802 -26.44242; -0.00868 1.17064 0.31239 -60.43744; -0.20251 -0.27194 1.01526 52.66324; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05884 -0.03208 0.15802 -26.44242; -0.00868 1.17064 0.31239 -60.43744; -0.20251 -0.27194 1.01526 52.66324; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.05884 -0.03208 0.15802 -26.44242; -0.00868 1.17064 0.31239 -60.43744; -0.20251 -0.27194 1.01526 52.66324; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.6 tol 0.000000 final transform: 1.05884 -0.03208 0.15802 -26.44242; -0.00868 1.17064 0.31239 -60.43744; -0.20251 -0.27194 1.01526 52.66324; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 950.909439 mri_em_register stimesec 1.525768 mri_em_register ru_maxrss 609812 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 157343 mri_em_register ru_majflt 1 mri_em_register ru_nswap 0 mri_em_register ru_inblock 149440 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 1259 mri_em_register ru_nivcsw 117324 registration took 4 minutes and 32 seconds. mri_watershed -rusage /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/stable6/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=135 y=116 z=123 r=82 first estimation of the main basin volume: 2336695 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=153, y=112, z=83, Imax=255 CSF=21, 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=8685867240 voxels, voxel volume =1.000 = 8685867240 mmm3 = 8685867.008 cm3 done. PostAnalyze...Basin Prior 1504 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=131,y=124, z=113, r=10472 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=23, CSF_MAX=72 , nb = 41750 RIGHT_CER CSF_MIN=0, CSF_intensity=14, CSF_MAX=55 , nb = -1031540460 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=61 , nb = 1099035382 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=23, CSF_MAX=71 , nb = -1094192121 LEFT_BRAIN CSF_MIN=0, CSF_intensity=23, CSF_MAX=68 , nb = 1077444042 OTHER CSF_MIN=2, CSF_intensity=14, CSF_MAX=37 , nb = 1072276548 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 72, 60, 56, 78 after analyzing : 50, 60, 60, 64 RIGHT_CER before analyzing : 55, 57, 59, 80 after analyzing : 55, 58, 59, 63 LEFT_CER before analyzing : 61, 59, 59, 79 after analyzing : 32, 59, 59, 64 RIGHT_BRAIN before analyzing : 71, 60, 56, 79 after analyzing : 50, 60, 60, 64 LEFT_BRAIN before analyzing : 68, 59, 56, 77 after analyzing : 49, 59, 59, 63 OTHER before analyzing : 37, 50, 63, 83 after analyzing : 37, 58, 63, 64 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...78 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.016 curvature mean = 68.507, std = 9.383 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.38, sigma = 15.63 after rotation: sse = 4.38, sigma = 15.63 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 8.66, its var is 46.94 before Erosion-Dilatation 4.77% of inacurate vertices after Erosion-Dilatation 6.71% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...51 iterations mri_strip_skull: done peeling brain Brain Size = 1430652 voxels, voxel volume = 1.000 mm3 = 1430652 mmm3 = 1430.652 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 21.109790 mri_watershed stimesec 0.230964 mri_watershed ru_maxrss 832320 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 215246 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 8920 mri_watershed ru_oublock 2472 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 4826 mri_watershed ru_nivcsw 3180 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Jan 23 12:14:22 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_em_register -rusage /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.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 = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (67, 61, 34) --> (197, 187, 210) using (110, 103, 122) as brain centroid... mean wm in atlas = 107, using box (94,88,100) --> (125, 118,143) to find MRI wm before smoothing, mri peak at 102 robust fit to distribution - 101 +- 6.5 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 initial log_p = -4.095 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.959537 @ (-9.091, -9.091, -9.091) max log p = -3.873952 @ (4.545, 4.545, -4.545) max log p = -3.850774 @ (2.273, -2.273, 2.273) max log p = -3.850774 @ (0.000, 0.000, 0.000) max log p = -3.841730 @ (-2.841, 3.977, 0.568) max log p = -3.840176 @ (1.989, -2.557, 2.557) Found translation: (-3.1, -5.4, -8.2): log p = -3.840 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.755, old_max_log_p =-3.840 (thresh=-3.8) 0.99144 -0.01704 0.12941 -14.60136; 0.00000 1.06580 0.14032 -29.55410; -0.12074 -0.11970 0.90924 32.68386; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.701, old_max_log_p =-3.755 (thresh=-3.8) 0.99144 -0.01704 0.12941 -14.60136; 0.00000 1.13375 0.14926 -39.04292; -0.12074 -0.11970 0.90924 32.68386; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.701, old_max_log_p =-3.701 (thresh=-3.7) 0.99144 -0.01704 0.12941 -14.60136; 0.00000 1.13375 0.14926 -39.04292; -0.12074 -0.11970 0.90924 32.68386; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.588, old_max_log_p =-3.701 (thresh=-3.7) 1.04735 -0.05579 0.13173 -21.23666; 0.03366 1.13256 0.15357 -42.00572; -0.12292 -0.12186 0.92565 31.37076; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.584, old_max_log_p =-3.588 (thresh=-3.6) 1.04789 -0.01870 0.13669 -26.43488; -0.00063 1.13378 0.14918 -38.95279; -0.12292 -0.12186 0.92565 31.37076; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.584, old_max_log_p =-3.584 (thresh=-3.6) 1.04789 -0.01870 0.13669 -26.43488; -0.00063 1.13378 0.14918 -38.95279; -0.12292 -0.12186 0.92565 31.37076; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.565, old_max_log_p =-3.584 (thresh=-3.6) 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.565, old_max_log_p =-3.565 (thresh=-3.6) 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.565 (old=-4.095) transform before final EM align: 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.1 tol 0.000000 final transform: 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 907.335064 mri_em_register stimesec 1.638750 mri_em_register ru_maxrss 599032 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 159130 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 140152 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 1249 mri_em_register ru_nivcsw 105172 registration took 4 minutes and 11 seconds. #-------------------------------------- #@# CA Normalize Mon Jan 23 12:18:34 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.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 '/usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (67, 61, 34) --> (197, 187, 210) using (110, 103, 122) as brain centroid... mean wm in atlas = 107, using box (94,88,100) --> (125, 118,143) to find MRI wm before smoothing, mri peak at 102 robust fit to distribution - 101 +- 6.5 after smoothing, mri peak at 102, scaling input intensities by 1.049 scaling channel 0 by 1.04902 using 246344 sample points... INFO: compute sample coordinates transform 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81447; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 65, 33) --> (198, 166, 210) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 132.0 1 of 21 (4.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 68, 29) --> (139, 169, 207) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 28 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (139, 145, 61) --> (186, 181, 118) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 132.0 3 of 12 (25.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (97, 145, 54) --> (141, 182, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 6 of 6 (100.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (119, 134, 96) --> (152, 197, 129) Brain_Stem: limiting intensities to 96.0 --> 132.0 13 of 16 (81.2%) samples deleted using 83 total control points for intensity normalization... bias field = 0.931 +- 0.054 0 of 60 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 65, 33) --> (198, 166, 210) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 14 of 122 (11.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 68, 29) --> (139, 169, 207) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 84 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (139, 145, 61) --> (186, 181, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 43 of 74 (58.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (97, 145, 54) --> (141, 182, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 44 (93.2%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (119, 134, 96) --> (152, 197, 129) Brain_Stem: limiting intensities to 88.0 --> 132.0 118 of 134 (88.1%) samples deleted using 458 total control points for intensity normalization... bias field = 1.016 +- 0.064 0 of 241 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (128, 65, 33) --> (198, 166, 210) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 204 (1.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (73, 68, 29) --> (139, 169, 207) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 185 (3.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (139, 145, 61) --> (186, 181, 118) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 80 of 112 (71.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (97, 145, 54) --> (141, 182, 115) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 49 of 54 (90.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (119, 134, 96) --> (152, 197, 129) Brain_Stem: limiting intensities to 88.0 --> 132.0 102 of 123 (82.9%) samples deleted using 678 total control points for intensity normalization... bias field = 0.994 +- 0.056 0 of 432 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 14 seconds. #-------------------------------------- #@# CA Reg Mon Jan 23 12:19:48 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_ca_register -rusage /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.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 = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.14 (predicted orig area = 7.0) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.092, neg=0, invalid=762 0001: dt=320.024197, rms=0.986 (9.710%), neg=0, invalid=762 0002: dt=221.952000, rms=0.959 (2.756%), neg=0, invalid=762 0003: dt=517.888000, rms=0.931 (2.844%), neg=0, invalid=762 0004: dt=129.472000, rms=0.919 (1.330%), neg=0, invalid=762 0005: dt=517.888000, rms=0.908 (1.210%), neg=0, invalid=762 0006: dt=221.952000, rms=0.903 (0.538%), neg=0, invalid=762 0007: dt=517.888000, rms=0.899 (0.412%), neg=0, invalid=762 0008: dt=130.348624, rms=0.896 (0.389%), neg=0, invalid=762 0009: dt=1775.616000, rms=0.887 (1.003%), neg=0, invalid=762 0010: dt=92.480000, rms=0.886 (0.076%), neg=0, invalid=762 0011: dt=92.480000, rms=0.886 (0.018%), neg=0, invalid=762 0012: dt=92.480000, rms=0.886 (0.016%), neg=0, invalid=762 0013: dt=92.480000, rms=0.886 (0.048%), neg=0, invalid=762 0014: dt=92.480000, rms=0.884 (0.146%), neg=0, invalid=762 0015: dt=92.480000, rms=0.883 (0.182%), neg=0, invalid=762 0016: dt=92.480000, rms=0.881 (0.163%), neg=0, invalid=762 0017: dt=92.480000, rms=0.880 (0.145%), neg=0, invalid=762 0018: dt=92.480000, rms=0.879 (0.106%), neg=0, invalid=762 0019: dt=92.480000, rms=0.879 (0.045%), neg=0, invalid=762 0020: dt=517.888000, rms=0.877 (0.127%), neg=0, invalid=762 0021: dt=129.472000, rms=0.877 (0.052%), neg=0, invalid=762 0022: dt=129.472000, rms=0.877 (0.026%), neg=0, invalid=762 0023: dt=129.472000, rms=0.877 (0.025%), neg=0, invalid=762 0024: dt=129.472000, rms=0.876 (0.052%), neg=0, invalid=762 0025: dt=129.472000, rms=0.876 (0.063%), neg=0, invalid=762 0026: dt=129.472000, rms=0.875 (0.067%), neg=0, invalid=762 0027: dt=129.472000, rms=0.875 (0.046%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.876, neg=0, invalid=762 0028: dt=129.472000, rms=0.872 (0.394%), neg=0, invalid=762 0029: dt=221.952000, rms=0.871 (0.125%), neg=0, invalid=762 0030: dt=221.952000, rms=0.870 (0.109%), neg=0, invalid=762 0031: dt=221.952000, rms=0.869 (0.127%), neg=0, invalid=762 0032: dt=221.952000, rms=0.868 (0.090%), neg=0, invalid=762 0033: dt=221.952000, rms=0.868 (0.073%), neg=0, invalid=762 0034: dt=1183.744000, rms=0.865 (0.288%), neg=0, invalid=762 0035: dt=110.976000, rms=0.865 (0.022%), neg=0, invalid=762 0036: dt=110.976000, rms=0.865 (0.010%), neg=0, invalid=762 0037: dt=110.976000, rms=0.865 (0.011%), neg=0, invalid=762 0038: dt=110.976000, rms=0.865 (0.007%), neg=0, invalid=762 0039: dt=110.976000, rms=0.865 (0.034%), neg=0, invalid=762 0040: dt=110.976000, rms=0.864 (0.055%), neg=0, invalid=762 0041: dt=110.976000, rms=0.864 (0.057%), neg=0, invalid=762 0042: dt=110.976000, rms=0.863 (0.062%), neg=0, invalid=762 0043: dt=110.976000, rms=0.863 (0.049%), neg=0, invalid=762 0044: dt=1479.680000, rms=0.862 (0.069%), neg=0, invalid=762 0045: dt=129.472000, rms=0.862 (0.054%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.872, neg=0, invalid=762 0046: dt=36.288000, rms=0.869 (0.389%), neg=0, invalid=762 0047: dt=93.416149, rms=0.866 (0.279%), neg=0, invalid=762 0048: dt=312.756325, rms=0.853 (1.535%), neg=0, invalid=762 0049: dt=26.711864, rms=0.851 (0.253%), neg=0, invalid=762 0050: dt=36.288000, rms=0.849 (0.145%), neg=0, invalid=762 0051: dt=36.288000, rms=0.848 (0.141%), neg=0, invalid=762 0052: dt=36.288000, rms=0.846 (0.226%), neg=0, invalid=762 0053: dt=36.288000, rms=0.844 (0.303%), neg=0, invalid=762 0054: dt=36.288000, rms=0.841 (0.352%), neg=0, invalid=762 0055: dt=36.288000, rms=0.838 (0.333%), neg=0, invalid=762 0056: dt=36.288000, rms=0.836 (0.254%), neg=0, invalid=762 0057: dt=36.288000, rms=0.834 (0.193%), neg=0, invalid=762 0058: dt=36.288000, rms=0.833 (0.165%), neg=0, invalid=762 0059: dt=36.288000, rms=0.832 (0.156%), neg=0, invalid=762 0060: dt=36.288000, rms=0.831 (0.102%), neg=0, invalid=762 0061: dt=36.288000, rms=0.830 (0.132%), neg=0, invalid=762 0062: dt=36.288000, rms=0.829 (0.108%), neg=0, invalid=762 0063: dt=36.288000, rms=0.828 (0.089%), neg=0, invalid=762 0064: dt=145.152000, rms=0.828 (0.055%), neg=0, invalid=762 0065: dt=145.152000, rms=0.828 (-0.143%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.829, neg=0, invalid=762 0066: dt=25.920000, rms=0.826 (0.317%), neg=0, invalid=762 0067: dt=31.104000, rms=0.826 (0.046%), neg=0, invalid=762 0068: dt=31.104000, rms=0.826 (0.038%), neg=0, invalid=762 0069: dt=31.104000, rms=0.825 (0.041%), neg=0, invalid=762 0070: dt=31.104000, rms=0.825 (0.061%), neg=0, invalid=762 0071: dt=31.104000, rms=0.824 (0.102%), neg=0, invalid=762 0072: dt=31.104000, rms=0.823 (0.115%), neg=0, invalid=762 0073: dt=31.104000, rms=0.822 (0.099%), neg=0, invalid=762 0074: dt=31.104000, rms=0.822 (0.067%), neg=0, invalid=762 0075: dt=62.208000, rms=0.821 (0.019%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.855, neg=0, invalid=762 0076: dt=20.150857, rms=0.847 (0.858%), neg=0, invalid=762 0077: dt=32.000000, rms=0.841 (0.689%), neg=0, invalid=762 0078: dt=11.200000, rms=0.839 (0.247%), neg=0, invalid=762 0079: dt=11.200000, rms=0.838 (0.200%), neg=0, invalid=762 0080: dt=11.200000, rms=0.835 (0.315%), neg=0, invalid=762 0081: dt=11.200000, rms=0.832 (0.417%), neg=0, invalid=762 0082: dt=11.200000, rms=0.828 (0.444%), neg=0, invalid=762 0083: dt=11.200000, rms=0.825 (0.401%), neg=0, invalid=762 0084: dt=11.200000, rms=0.824 (0.026%), neg=0, invalid=762 0085: dt=11.200000, rms=0.824 (0.051%), neg=0, invalid=762 0086: dt=11.200000, rms=0.823 (0.092%), neg=0, invalid=762 0087: dt=11.200000, rms=0.822 (0.112%), neg=0, invalid=762 0088: dt=11.200000, rms=0.821 (0.123%), neg=0, invalid=762 0089: dt=11.200000, rms=0.820 (0.162%), neg=0, invalid=762 0090: dt=11.200000, rms=0.819 (0.167%), neg=0, invalid=762 0091: dt=11.200000, rms=0.817 (0.170%), neg=0, invalid=762 0092: dt=11.200000, rms=0.816 (0.172%), neg=0, invalid=762 0093: dt=11.200000, rms=0.814 (0.164%), neg=0, invalid=762 0094: dt=11.200000, rms=0.813 (0.119%), neg=0, invalid=762 0095: dt=11.200000, rms=0.813 (0.088%), neg=0, invalid=762 0096: dt=0.000000, rms=0.813 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.814, neg=0, invalid=762 0097: dt=0.000000, rms=0.813 (0.120%), neg=0, invalid=762 0098: dt=0.000000, rms=0.813 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.884, neg=0, invalid=762 0099: dt=0.000000, rms=0.883 (0.102%), neg=0, invalid=762 0100: dt=0.000000, rms=0.883 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.884, neg=0, invalid=762 0101: dt=0.003375, rms=0.883 (0.102%), neg=0, invalid=762 0102: dt=0.000176, rms=0.883 (0.000%), neg=0, invalid=762 0103: dt=0.000176, rms=0.883 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.016, neg=0, invalid=762 0104: dt=1.591489, rms=0.996 (1.983%), neg=0, invalid=762 0105: dt=1.792000, rms=0.986 (0.972%), neg=0, invalid=762 0106: dt=1.090909, rms=0.981 (0.541%), neg=0, invalid=762 0107: dt=1.536000, rms=0.978 (0.335%), neg=0, invalid=762 0108: dt=1.536000, rms=0.974 (0.413%), neg=0, invalid=762 0109: dt=1.024000, rms=0.972 (0.180%), neg=0, invalid=762 0110: dt=1.024000, rms=0.969 (0.244%), neg=0, invalid=762 0111: dt=1.024000, rms=0.967 (0.233%), neg=0, invalid=762 0112: dt=1.024000, rms=0.966 (0.153%), neg=0, invalid=762 0113: dt=1.024000, rms=0.966 (-0.022%), neg=0, invalid=762 0114: dt=2.000000, rms=0.964 (0.208%), neg=0, invalid=762 0115: dt=1.536000, rms=0.963 (0.070%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.964, neg=0, invalid=762 0116: dt=1.792000, rms=0.961 (0.360%), neg=0, invalid=762 0117: dt=0.448000, rms=0.960 (0.038%), neg=0, invalid=762 0118: dt=0.448000, rms=0.960 (0.020%), neg=0, invalid=762 0119: dt=0.448000, rms=0.960 (0.035%), neg=0, invalid=762 0120: dt=0.448000, rms=0.959 (0.052%), neg=0, invalid=762 0121: dt=0.448000, rms=0.959 (0.058%), neg=0, invalid=762 0122: dt=0.448000, rms=0.958 (0.035%), neg=0, invalid=762 0123: dt=0.448000, rms=0.958 (-0.011%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.910, neg=0, invalid=762 0124: dt=0.448000, rms=0.889 (2.249%), neg=0, invalid=762 0125: dt=0.000000, rms=0.889 (0.002%), neg=0, invalid=762 0126: dt=0.050000, rms=0.889 (-0.114%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.891, neg=0, invalid=762 0127: dt=0.048000, rms=0.889 (0.156%), neg=0, invalid=762 0128: dt=0.007000, rms=0.889 (-0.002%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.10257 (19) Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (963 voxels, overlap=0.681) Left_Lateral_Ventricle (4): linear fit = 1.23 x + 0.0 (963 voxels, peak = 24), gca=24.5 gca peak = 0.15565 (16) mri peak = 0.10685 (30) Right_Lateral_Ventricle (43): linear fit = 1.62 x + 0.0 (838 voxels, overlap=0.350) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (838 voxels, peak = 26), gca=24.0 gca peak = 0.26829 (96) mri peak = 0.05694 (107) Right_Pallidum (52): linear fit = 1.15 x + 0.0 (693 voxels, overlap=0.039) Right_Pallidum (52): linear fit = 1.15 x + 0.0 (693 voxels, peak = 111), gca=110.9 gca peak = 0.20183 (93) mri peak = 0.05447 (93) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (640 voxels, overlap=1.009) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (640 voxels, peak = 90), gca=89.7 gca peak = 0.21683 (55) mri peak = 0.07937 (90) Right_Hippocampus (53): linear fit = 1.49 x + 0.0 (198 voxels, overlap=0.015) Right_Hippocampus (53): linear fit = 1.49 x + 0.0 (198 voxels, peak = 82), gca=81.7 gca peak = 0.30730 (58) mri peak = 0.06857 (69) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (667 voxels, overlap=0.104) Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (667 voxels, peak = 69), gca=68.7 gca peak = 0.11430 (101) mri peak = 0.06728 (107) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (53801 voxels, overlap=0.748) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (53801 voxels, peak = 107), gca=106.6 gca peak = 0.12076 (102) mri peak = 0.06956 (107) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (62382 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.07 x + 0.0 (62382 voxels, peak = 109), gca=108.6 gca peak = 0.14995 (59) mri peak = 0.04152 (84) Left_Cerebral_Cortex (3): linear fit = 1.41 x + 0.0 (16619 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.41 x + 0.0 (16619 voxels, peak = 83), gca=83.5 gca peak = 0.15082 (58) mri peak = 0.04346 (78) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (15581 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (15581 voxels, peak = 81), gca=81.5 gca peak = 0.14161 (67) mri peak = 0.11631 (100) Right_Caudate (50): linear fit = 1.43 x + 0.0 (584 voxels, overlap=0.046) Right_Caudate (50): linear fit = 1.43 x + 0.0 (584 voxels, peak = 96), gca=96.1 gca peak = 0.15243 (71) mri peak = 0.09524 (99) Left_Caudate (11): linear fit = 1.26 x + 0.0 (728 voxels, overlap=0.018) Left_Caudate (11): linear fit = 1.26 x + 0.0 (728 voxels, peak = 90), gca=89.8 gca peak = 0.13336 (57) mri peak = 0.03835 (73) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (11343 voxels, overlap=0.033) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (11343 voxels, peak = 74), gca=74.4 gca peak = 0.13252 (56) mri peak = 0.03211 (76) Right_Cerebellum_Cortex (47): linear fit = 1.39 x + 0.0 (16446 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.39 x + 0.0 (16446 voxels, peak = 78), gca=78.1 gca peak = 0.18181 (84) mri peak = 0.04217 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8356 voxels, overlap=0.954) Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (8356 voxels, peak = 85), gca=85.3 gca peak = 0.20573 (83) mri peak = 0.04184 (71) Right_Cerebellum_White_Matter (46): linear fit = 0.86 x + 0.0 (6662 voxels, overlap=0.833) Right_Cerebellum_White_Matter (46): linear fit = 0.86 x + 0.0 (6662 voxels, peak = 71), gca=71.0 gca peak = 0.21969 (57) mri peak = 0.07838 (64) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (361 voxels, overlap=0.296) Left_Amygdala (18): linear fit = 1.18 x + 0.0 (361 voxels, peak = 68), gca=67.5 gca peak = 0.39313 (56) mri peak = 1.00000 (50) Right_Amygdala: unreasonable value (49.0/50.0), not in range [50, 90] - rejecting gca peak = 0.14181 (85) mri peak = 0.06936 (108) Left_Thalamus_Proper (10): linear fit = 1.26 x + 0.0 (4223 voxels, overlap=0.009) Left_Thalamus_Proper (10): linear fit = 1.26 x + 0.0 (4223 voxels, peak = 108), gca=107.5 gca peak = 0.11978 (83) mri peak = 0.06863 (95) Right_Thalamus_Proper (49): linear fit = 1.18 x + 0.0 (1195 voxels, overlap=0.251) Right_Thalamus_Proper (49): linear fit = 1.18 x + 0.0 (1195 voxels, peak = 98), gca=98.4 gca peak = 0.13399 (79) mri peak = 0.06696 (95) Left_Putamen (12): linear fit = 1.20 x + 0.0 (1815 voxels, overlap=0.104) Left_Putamen (12): linear fit = 1.20 x + 0.0 (1815 voxels, peak = 94), gca=94.4 gca peak = 0.14159 (79) mri peak = 0.07031 (101) Right_Putamen (51): linear fit = 1.28 x + 0.0 (1818 voxels, overlap=0.016) Right_Putamen (51): linear fit = 1.28 x + 0.0 (1818 voxels, peak = 102), gca=101.5 gca peak = 0.10025 (80) mri peak = 0.08887 (84) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9607 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (9607 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06401 (93) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (862 voxels, overlap=0.529) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (862 voxels, peak = 93), gca=93.3 gca peak = 0.12801 (89) mri peak = 0.07703 (99) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (902 voxels, overlap=0.414) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (902 voxels, peak = 98), gca=98.3 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.05708 (21) Fourth_Ventricle (15): linear fit = 1.59 x + 0.0 (144 voxels, overlap=0.522) Fourth_Ventricle (15): linear fit = 1.59 x + 0.0 (144 voxels, peak = 33), gca=33.3 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Thalamus = 0.64095 (94) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Amygdala = 0.39313 (56) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Right_Amygdala based on Left_Amygdala = 1.18 x + 0: 68 estimating mean gm scale to be 1.31 x + 0.0 estimating mean wm scale to be 1.06 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 Right_Putamen too bright - rescaling by 0.954 (from 1.285) to 96.8 (was 101.5) Right_Pallidum too bright - rescaling by 0.941 (from 1.155) to 104.4 (was 110.9) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.919, neg=0, invalid=762 0129: dt=138.926829, rms=0.879 (4.371%), neg=0, invalid=762 0130: dt=129.472000, rms=0.866 (1.410%), neg=0, invalid=762 0131: dt=32.368000, rms=0.864 (0.264%), neg=0, invalid=762 0132: dt=8.092000, rms=0.863 (0.054%), neg=0, invalid=762 0133: dt=2.023000, rms=0.863 (0.015%), neg=0, invalid=762 0134: dt=0.252875, rms=0.863 (0.001%), neg=0, invalid=762 0135: dt=0.126438, rms=0.863 (0.001%), neg=0, invalid=762 0136: dt=0.063219, rms=0.863 (0.000%), neg=0, invalid=762 0137: dt=0.007902, rms=0.863 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.864, neg=0, invalid=762 0138: dt=0.000000, rms=0.863 (0.109%), neg=0, invalid=762 0139: dt=0.000000, rms=0.863 (0.000%), neg=0, invalid=762 0140: dt=0.001660, rms=0.863 (0.000%), neg=0, invalid=762 0141: dt=0.000830, rms=0.863 (0.000%), neg=0, invalid=762 0142: dt=0.000415, rms=0.863 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.864, neg=0, invalid=762 0143: dt=0.000000, rms=0.863 (0.109%), neg=0, invalid=762 0144: dt=0.000000, rms=0.863 (0.000%), neg=0, invalid=762 0145: dt=0.000002, rms=0.863 (0.000%), neg=0, invalid=762 0146: dt=0.000001, rms=0.863 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.864, neg=0, invalid=762 0147: dt=0.000000, rms=0.863 (0.109%), neg=0, invalid=762 0148: dt=0.000000, rms=0.863 (0.000%), neg=0, invalid=762 0149: dt=0.000002, rms=0.863 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.865, neg=0, invalid=762 0150: dt=2.800000, rms=0.857 (0.908%), neg=0, invalid=762 0151: dt=2.800000, rms=0.850 (0.780%), neg=0, invalid=762 0152: dt=2.800000, rms=0.844 (0.736%), neg=0, invalid=762 0153: dt=0.700000, rms=0.842 (0.186%), neg=0, invalid=762 0154: dt=0.700000, rms=0.841 (0.183%), neg=0, invalid=762 0155: dt=0.175000, rms=0.840 (0.045%), neg=0, invalid=762 0156: dt=0.175000, rms=0.840 (0.048%), neg=0, invalid=762 0157: dt=0.087500, rms=0.840 (0.022%), neg=0, invalid=762 0158: dt=0.021875, rms=0.840 (0.005%), neg=0, invalid=762 0159: dt=0.010937, rms=0.840 (0.003%), neg=0, invalid=762 0160: dt=0.005469, rms=0.840 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.841, neg=0, invalid=762 0161: dt=0.043750, rms=0.840 (0.119%), neg=0, invalid=762 0162: dt=0.002734, rms=0.840 (0.001%), neg=0, invalid=762 0163: dt=0.002734, rms=0.840 (0.001%), neg=0, invalid=762 0164: dt=0.000085, rms=0.840 (0.000%), neg=0, invalid=762 0165: dt=0.000043, rms=0.840 (0.000%), neg=0, invalid=762 0166: dt=0.000000, rms=0.840 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.842, neg=0, invalid=762 0167: dt=4.032000, rms=0.813 (3.459%), neg=0, invalid=762 0168: dt=3.456000, rms=0.793 (2.485%), neg=0, invalid=762 0169: dt=0.720000, rms=0.789 (0.452%), neg=0, invalid=762 0170: dt=0.045000, rms=0.789 (0.031%), neg=0, invalid=762 0171: dt=0.002813, rms=0.789 (0.002%), neg=0, invalid=762 0172: dt=0.000703, rms=0.789 (0.000%), neg=0, invalid=762 0173: dt=0.000352, rms=0.789 (0.000%), neg=0, invalid=762 0174: dt=0.000001, rms=0.789 (0.000%), neg=0, invalid=762 0175: dt=0.000000, rms=0.789 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.790, neg=0, invalid=762 0176: dt=0.000000, rms=0.789 (0.140%), neg=0, invalid=762 0177: dt=0.000000, rms=0.789 (0.000%), neg=0, invalid=762 0178: dt=0.000001, rms=0.789 (0.000%), neg=0, invalid=762 0179: dt=0.000000, rms=0.789 (0.000%), neg=0, invalid=762 0180: dt=0.000000, rms=0.789 (-0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.796, neg=0, invalid=762 0181: dt=1.792000, rms=0.776 (2.485%), neg=0, invalid=762 0182: dt=1.792000, rms=0.763 (1.649%), neg=0, invalid=762 0183: dt=1.792000, rms=0.755 (1.092%), neg=0, invalid=762 0184: dt=1.792000, rms=0.749 (0.750%), neg=0, invalid=762 0185: dt=1.536000, rms=0.746 (0.441%), neg=0, invalid=762 0186: dt=1.536000, rms=0.743 (0.358%), neg=0, invalid=762 0187: dt=1.536000, rms=0.741 (0.287%), neg=0, invalid=762 0188: dt=1.792000, rms=0.739 (0.286%), neg=0, invalid=762 0189: dt=1.536000, rms=0.737 (0.195%), neg=0, invalid=762 0190: dt=1.792000, rms=0.736 (0.200%), neg=0, invalid=762 0191: dt=1.536000, rms=0.735 (0.157%), neg=0, invalid=762 0192: dt=1.536000, rms=0.734 (0.129%), neg=0, invalid=762 0193: dt=1.792000, rms=0.733 (0.147%), neg=0, invalid=762 0194: dt=1.792000, rms=0.732 (0.115%), neg=0, invalid=762 0195: dt=1.792000, rms=0.731 (0.113%), neg=0, invalid=762 0196: dt=1.792000, rms=0.730 (0.100%), neg=0, invalid=762 0197: dt=1.792000, rms=0.730 (0.087%), neg=0, invalid=762 0198: dt=1.536000, rms=0.729 (0.071%), neg=0, invalid=762 0199: dt=1.792000, rms=0.729 (0.072%), neg=0, invalid=762 0200: dt=1.792000, rms=0.728 (0.062%), neg=0, invalid=762 0201: dt=1.792000, rms=0.728 (0.056%), neg=0, invalid=762 0202: dt=1.792000, rms=0.727 (0.051%), neg=0, invalid=762 0203: dt=1.792000, rms=0.727 (0.043%), neg=0, invalid=762 0204: dt=1.792000, rms=0.727 (0.048%), neg=0, invalid=762 0205: dt=1.792000, rms=0.726 (0.087%), neg=0, invalid=762 0206: dt=0.896000, rms=0.726 (0.009%), neg=0, invalid=762 0207: dt=0.896000, rms=0.726 (0.044%), neg=0, invalid=762 0208: dt=0.896000, rms=0.726 (0.016%), neg=0, invalid=762 0209: dt=0.896000, rms=0.725 (0.031%), neg=0, invalid=762 0210: dt=0.896000, rms=0.725 (0.044%), neg=0, invalid=762 0211: dt=0.896000, rms=0.725 (0.050%), neg=0, invalid=762 0212: dt=0.896000, rms=0.725 (0.012%), neg=0, invalid=762 0213: dt=0.896000, rms=0.724 (0.026%), neg=0, invalid=762 0214: dt=0.896000, rms=0.724 (0.026%), neg=0, invalid=762 0215: dt=0.896000, rms=0.724 (0.032%), neg=0, invalid=762 0216: dt=0.896000, rms=0.724 (0.044%), neg=0, invalid=762 0217: dt=0.896000, rms=0.723 (0.043%), neg=0, invalid=762 0218: dt=0.896000, rms=0.723 (0.060%), neg=0, invalid=762 0219: dt=0.896000, rms=0.723 (0.063%), neg=0, invalid=762 0220: dt=0.896000, rms=0.722 (0.063%), neg=0, invalid=762 0221: dt=0.896000, rms=0.722 (0.058%), neg=0, invalid=762 0222: dt=0.896000, rms=0.721 (0.048%), neg=0, invalid=762 0223: dt=0.896000, rms=0.721 (0.043%), neg=0, invalid=762 0224: dt=0.896000, rms=0.721 (-0.001%), neg=0, invalid=762 0225: dt=0.000375, rms=0.721 (0.000%), neg=0, invalid=762 0226: dt=0.000000, rms=0.721 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.722, neg=0, invalid=762 0227: dt=1.536000, rms=0.719 (0.363%), neg=0, invalid=762 0228: dt=1.536000, rms=0.718 (0.237%), neg=0, invalid=762 0229: dt=1.280000, rms=0.716 (0.177%), neg=0, invalid=762 0230: dt=1.536000, rms=0.715 (0.174%), neg=0, invalid=762 0231: dt=1.536000, rms=0.714 (0.171%), neg=0, invalid=762 0232: dt=1.792000, rms=0.713 (0.154%), neg=0, invalid=762 0233: dt=1.536000, rms=0.712 (0.125%), neg=0, invalid=762 0234: dt=1.792000, rms=0.711 (0.127%), neg=0, invalid=762 0235: dt=1.536000, rms=0.710 (0.098%), neg=0, invalid=762 0236: dt=1.536000, rms=0.710 (0.088%), neg=0, invalid=762 0237: dt=1.536000, rms=0.709 (0.085%), neg=0, invalid=762 0238: dt=1.280000, rms=0.709 (0.059%), neg=0, invalid=762 0239: dt=1.280000, rms=0.708 (0.062%), neg=0, invalid=762 0240: dt=1.536000, rms=0.708 (0.067%), neg=0, invalid=762 0241: dt=1.280000, rms=0.707 (0.053%), neg=0, invalid=762 0242: dt=1.536000, rms=0.707 (0.058%), neg=0, invalid=762 0243: dt=1.280000, rms=0.707 (0.052%), neg=0, invalid=762 0244: dt=1.280000, rms=0.706 (0.046%), neg=0, invalid=762 0245: dt=0.640000, rms=0.706 (0.019%), neg=0, invalid=762 0246: dt=0.640000, rms=0.706 (0.024%), neg=0, invalid=762 0247: dt=0.640000, rms=0.706 (0.042%), neg=0, invalid=762 0248: dt=0.640000, rms=0.705 (0.059%), neg=0, invalid=762 0249: dt=0.640000, rms=0.705 (0.065%), neg=0, invalid=762 0250: dt=0.640000, rms=0.704 (0.084%), neg=0, invalid=762 0251: dt=0.640000, rms=0.704 (0.083%), neg=0, invalid=762 0252: dt=0.640000, rms=0.703 (0.087%), neg=0, invalid=762 0253: dt=0.640000, rms=0.702 (0.088%), neg=0, invalid=762 0254: dt=0.640000, rms=0.702 (0.091%), neg=0, invalid=762 0255: dt=0.640000, rms=0.701 (0.087%), neg=0, invalid=762 0256: dt=0.640000, rms=0.701 (0.084%), neg=0, invalid=762 0257: dt=0.640000, rms=0.700 (0.076%), neg=0, invalid=762 0258: dt=0.640000, rms=0.700 (0.066%), neg=0, invalid=762 0259: dt=0.640000, rms=0.699 (0.064%), neg=0, invalid=762 0260: dt=0.640000, rms=0.699 (0.050%), neg=0, invalid=762 0261: dt=0.640000, rms=0.699 (0.043%), neg=0, invalid=762 0262: dt=0.640000, rms=0.698 (0.045%), neg=0, invalid=762 0263: dt=0.640000, rms=0.698 (0.042%), neg=0, invalid=762 0264: dt=0.640000, rms=0.698 (0.038%), neg=0, invalid=762 0265: dt=0.640000, rms=0.697 (0.040%), neg=0, invalid=762 0266: dt=0.640000, rms=0.697 (0.023%), neg=0, invalid=762 0267: dt=0.640000, rms=0.697 (0.030%), neg=0, invalid=762 0268: dt=0.640000, rms=0.697 (0.031%), neg=0, invalid=762 0269: dt=0.640000, rms=0.697 (0.029%), neg=0, invalid=762 0270: dt=0.640000, rms=0.696 (0.021%), neg=0, invalid=762 0271: dt=0.640000, rms=0.696 (0.021%), neg=0, invalid=762 0272: dt=0.020000, rms=0.696 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.683, neg=0, invalid=762 0273: dt=0.384000, rms=0.660 (3.449%), neg=0, invalid=762 0274: dt=0.320000, rms=0.651 (1.283%), neg=0, invalid=762 0275: dt=0.112000, rms=0.649 (0.295%), neg=0, invalid=762 0276: dt=0.384000, rms=0.644 (0.854%), neg=0, invalid=762 0277: dt=0.112000, rms=0.643 (0.136%), neg=0, invalid=762 0278: dt=0.320000, rms=0.641 (0.338%), neg=0, invalid=762 0279: dt=0.384000, rms=0.639 (0.323%), neg=0, invalid=762 0280: dt=0.320000, rms=0.638 (0.192%), neg=0, invalid=762 0281: dt=0.320000, rms=0.637 (0.162%), neg=0, invalid=762 0282: dt=0.384000, rms=0.636 (0.151%), neg=0, invalid=762 0283: dt=0.384000, rms=0.635 (0.127%), neg=0, invalid=762 0284: dt=0.320000, rms=0.634 (0.095%), neg=0, invalid=762 0285: dt=0.320000, rms=0.634 (0.069%), neg=0, invalid=762 0286: dt=0.384000, rms=0.633 (0.084%), neg=0, invalid=762 0287: dt=0.384000, rms=0.633 (0.053%), neg=0, invalid=762 0288: dt=0.384000, rms=0.633 (0.059%), neg=0, invalid=762 0289: dt=0.384000, rms=0.632 (0.046%), neg=0, invalid=762 0290: dt=0.384000, rms=0.632 (0.045%), neg=0, invalid=762 0291: dt=0.384000, rms=0.632 (0.063%), neg=0, invalid=762 0292: dt=0.192000, rms=0.631 (0.031%), neg=0, invalid=762 0293: dt=0.192000, rms=0.631 (0.052%), neg=0, invalid=762 0294: dt=0.192000, rms=0.631 (0.019%), neg=0, invalid=762 0295: dt=0.192000, rms=0.631 (0.025%), neg=0, invalid=762 0296: dt=0.192000, rms=0.630 (0.052%), neg=0, invalid=762 0297: dt=0.192000, rms=0.630 (0.043%), neg=0, invalid=762 0298: dt=0.192000, rms=0.630 (0.044%), neg=0, invalid=762 0299: dt=0.192000, rms=0.630 (0.022%), neg=0, invalid=762 0300: dt=0.192000, rms=0.630 (0.028%), neg=0, invalid=762 0301: dt=0.192000, rms=0.629 (0.023%), neg=0, invalid=762 0302: dt=0.192000, rms=0.629 (0.007%), neg=0, invalid=762 0303: dt=0.064000, rms=0.629 (0.000%), neg=0, invalid=762 0304: dt=0.064000, rms=0.629 (0.002%), neg=0, invalid=762 0305: dt=0.064000, rms=0.629 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=762 0306: dt=0.320000, rms=0.620 (1.649%), neg=0, invalid=762 0307: dt=0.320000, rms=0.616 (0.633%), neg=0, invalid=762 0308: dt=0.320000, rms=0.614 (0.343%), neg=0, invalid=762 0309: dt=0.112000, rms=0.614 (0.052%), neg=0, invalid=762 0310: dt=0.112000, rms=0.614 (0.049%), neg=0, invalid=762 0311: dt=0.112000, rms=0.613 (0.041%), neg=0, invalid=762 0312: dt=0.112000, rms=0.613 (0.062%), neg=0, invalid=762 0313: dt=0.112000, rms=0.613 (0.078%), neg=0, invalid=762 0314: dt=0.112000, rms=0.612 (0.062%), neg=0, invalid=762 0315: dt=0.112000, rms=0.612 (0.021%), neg=0, invalid=762 0316: dt=0.112000, rms=0.612 (-0.024%), neg=0, invalid=762 0317: dt=0.000000, rms=0.612 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.609, neg=0, invalid=762 0318: dt=0.000000, rms=0.608 (0.235%), neg=0, invalid=762 0319: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=762 0320: dt=0.000000, rms=0.608 (0.235%), neg=0, invalid=762 0321: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.609, neg=0, invalid=762 0322: dt=0.000000, rms=0.608 (0.235%), neg=0, invalid=762 0323: dt=0.000000, rms=0.608 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=762 0324: dt=9.072000, rms=0.608 (0.274%), neg=0, invalid=762 0325: dt=9.072000, rms=0.607 (0.026%), neg=0, invalid=762 0326: dt=9.072000, rms=0.607 (0.018%), neg=0, invalid=762 0327: dt=9.072000, rms=0.607 (0.000%), neg=0, invalid=762 0328: dt=9.072000, rms=0.607 (-0.036%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.609, neg=0, invalid=762 0329: dt=9.600000, rms=0.605 (0.619%), neg=0, invalid=762 0330: dt=4.800000, rms=0.605 (0.040%), neg=0, invalid=762 0331: dt=4.800000, rms=0.605 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.607, neg=0, invalid=762 0332: dt=25.220884, rms=0.598 (1.334%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 10 iterations, nbhd size=1, neg = 0 0333: dt=18.956522, rms=0.596 (0.459%), neg=0, invalid=762 0334: dt=11.200000, rms=0.594 (0.307%), neg=0, invalid=762 iter 0, gcam->neg = 319 after 27 iterations, nbhd size=1, neg = 0 0335: dt=128.000000, rms=0.590 (0.640%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 14 iterations, nbhd size=1, neg = 0 0336: dt=22.644068, rms=0.588 (0.369%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0337: dt=11.200000, rms=0.587 (0.196%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0338: dt=11.200000, rms=0.586 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0339: dt=11.200000, rms=0.585 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0340: dt=11.200000, rms=0.584 (0.157%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 13 iterations, nbhd size=1, neg = 0 0341: dt=11.200000, rms=0.583 (0.164%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 15 iterations, nbhd size=1, neg = 0 0342: dt=11.200000, rms=0.582 (0.198%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 14 iterations, nbhd size=1, neg = 0 0343: dt=11.200000, rms=0.581 (0.231%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 13 iterations, nbhd size=1, neg = 0 0344: dt=11.200000, rms=0.579 (0.266%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 12 iterations, nbhd size=1, neg = 0 0345: dt=11.200000, rms=0.578 (0.221%), neg=0, invalid=762 iter 0, gcam->neg = 39 after 15 iterations, nbhd size=1, neg = 0 0346: dt=11.200000, rms=0.577 (0.188%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 12 iterations, nbhd size=1, neg = 0 0347: dt=11.200000, rms=0.576 (0.173%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 17 iterations, nbhd size=1, neg = 0 0348: dt=11.200000, rms=0.575 (0.195%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 18 iterations, nbhd size=1, neg = 0 0349: dt=11.200000, rms=0.574 (0.145%), neg=0, invalid=762 iter 0, gcam->neg = 32 after 15 iterations, nbhd size=1, neg = 0 0350: dt=11.200000, rms=0.573 (0.132%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 26 iterations, nbhd size=1, neg = 0 0351: dt=11.200000, rms=0.573 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 23 after 19 iterations, nbhd size=1, neg = 0 0352: dt=11.200000, rms=0.572 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 17 after 14 iterations, nbhd size=1, neg = 0 0353: dt=11.200000, rms=0.571 (0.164%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 23 iterations, nbhd size=1, neg = 0 0354: dt=11.200000, rms=0.570 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 51 after 33 iterations, nbhd size=1, neg = 0 0355: dt=11.200000, rms=0.570 (0.055%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=1, neg = 0 0356: dt=25.600000, rms=0.570 (0.010%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 13 iterations, nbhd size=1, neg = 0 0357: dt=25.600000, rms=0.570 (0.059%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 16 iterations, nbhd size=1, neg = 0 0358: dt=25.600000, rms=0.570 (0.015%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 19 iterations, nbhd size=1, neg = 0 0359: dt=25.600000, rms=0.569 (0.015%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.581, neg=0, invalid=762 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0360: dt=1.500000, rms=0.579 (0.250%), neg=0, invalid=762 0361: dt=0.000211, rms=0.579 (0.000%), neg=0, invalid=762 0362: dt=0.000211, rms=0.579 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.581, neg=0, invalid=762 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0363: dt=4.454545, rms=0.579 (0.374%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 13 iterations, nbhd size=1, neg = 0 0364: dt=7.142857, rms=0.578 (0.091%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0365: dt=7.142857, rms=0.577 (0.142%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=1, neg = 0 0366: dt=7.142857, rms=0.576 (0.150%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 18 iterations, nbhd size=1, neg = 0 0367: dt=7.142857, rms=0.576 (0.128%), neg=0, invalid=762 iter 0, gcam->neg = 25 after 24 iterations, nbhd size=1, neg = 0 0368: dt=7.142857, rms=0.575 (0.077%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 11 iterations, nbhd size=1, neg = 0 0369: dt=7.142857, rms=0.573 (0.434%), neg=0, invalid=762 iter 0, gcam->neg = 64 after 16 iterations, nbhd size=1, neg = 0 0370: dt=7.142857, rms=0.569 (0.626%), neg=0, invalid=762 iter 0, gcam->neg = 55 after 17 iterations, nbhd size=1, neg = 0 0371: dt=7.142857, rms=0.565 (0.701%), neg=0, invalid=762 iter 0, gcam->neg = 75 after 17 iterations, nbhd size=1, neg = 0 0372: dt=7.142857, rms=0.562 (0.496%), neg=0, invalid=762 iter 0, gcam->neg = 79 after 17 iterations, nbhd size=1, neg = 0 0373: dt=7.142857, rms=0.561 (0.290%), neg=0, invalid=762 iter 0, gcam->neg = 75 after 18 iterations, nbhd size=1, neg = 0 0374: dt=7.142857, rms=0.560 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 102 after 16 iterations, nbhd size=1, neg = 0 0375: dt=7.142857, rms=0.560 (-0.079%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0376: dt=4.500000, rms=0.560 (0.025%), neg=0, invalid=762 0377: dt=2.304000, rms=0.560 (0.001%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.572, neg=0, invalid=762 0378: dt=0.000000, rms=0.570 (0.249%), neg=0, invalid=762 0379: dt=0.000000, rms=0.570 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.572, neg=0, invalid=762 0380: dt=0.000000, rms=0.570 (0.249%), neg=0, invalid=762 0381: dt=0.000000, rms=0.570 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.555, neg=0, invalid=762 iter 0, gcam->neg = 1147 after 21 iterations, nbhd size=1, neg = 0 0382: dt=1.436674, rms=0.538 (3.081%), neg=0, invalid=762 0383: dt=0.007000, rms=0.538 (-0.005%), neg=0, invalid=762 0384: dt=0.007000, rms=0.538 (0.000%), neg=0, invalid=762 0385: dt=0.007000, rms=0.538 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=762 0386: dt=0.256000, rms=0.536 (0.660%), neg=0, invalid=762 0387: dt=0.112000, rms=0.535 (0.095%), neg=0, invalid=762 0388: dt=0.112000, rms=0.535 (0.074%), neg=0, invalid=762 0389: dt=0.112000, rms=0.534 (0.055%), neg=0, invalid=762 0390: dt=0.112000, rms=0.534 (-0.017%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0391: dt=0.000000, rms=0.533 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0392: dt=0.000000, rms=0.533 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0393: dt=0.000000, rms=0.533 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0394: dt=6.480000, rms=0.533 (0.007%), neg=0, invalid=762 0395: dt=2.268000, rms=0.533 (0.001%), neg=0, invalid=762 0396: dt=2.268000, rms=0.533 (0.001%), neg=0, invalid=762 0397: dt=2.268000, rms=0.533 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.533, neg=0, invalid=762 0398: dt=2.800000, rms=0.532 (0.049%), neg=0, invalid=762 0399: dt=0.700000, rms=0.532 (0.004%), neg=0, invalid=762 0400: dt=0.700000, rms=0.532 (0.001%), neg=0, invalid=762 0401: dt=0.700000, rms=0.532 (-0.005%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.532, neg=0, invalid=762 0402: dt=25.600000, rms=0.530 (0.420%), neg=0, invalid=762 0403: dt=11.200000, rms=0.529 (0.182%), neg=0, invalid=762 0404: dt=11.200000, rms=0.529 (0.115%), neg=0, invalid=762 0405: dt=11.200000, rms=0.528 (0.152%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0406: dt=11.200000, rms=0.527 (0.150%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 13 iterations, nbhd size=1, neg = 0 0407: dt=11.200000, rms=0.526 (0.101%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 12 iterations, nbhd size=1, neg = 0 0408: dt=11.200000, rms=0.526 (0.093%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 14 iterations, nbhd size=2, neg = 0 0409: dt=44.800000, rms=0.526 (-0.012%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.528, neg=0, invalid=762 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 0410: dt=2.082192, rms=0.527 (0.046%), neg=0, invalid=762 0411: dt=0.009000, rms=0.527 (0.000%), neg=0, invalid=762 0412: dt=0.009000, rms=0.527 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.527, neg=0, invalid=762 iter 0, gcam->neg = 10 after 13 iterations, nbhd size=1, neg = 0 0413: dt=16.265193, rms=0.522 (0.999%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0414: dt=6.058824, rms=0.520 (0.451%), neg=0, invalid=762 iter 0, gcam->neg = 95 after 18 iterations, nbhd size=1, neg = 0 0415: dt=9.473684, rms=0.519 (0.187%), neg=0, invalid=762 iter 0, gcam->neg = 86 after 18 iterations, nbhd size=1, neg = 0 0416: dt=9.473684, rms=0.519 (-0.079%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 0417: dt=0.000060, rms=0.522 (0.000%), neg=0, invalid=762 0418: dt=0.000000, rms=0.522 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.522, neg=0, invalid=762 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=1, neg = 0 0419: dt=1.792000, rms=0.521 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 270 after 17 iterations, nbhd size=1, neg = 0 0420: dt=3.197026, rms=0.519 (0.395%), neg=0, invalid=762 0421: dt=1.792000, rms=0.518 (0.228%), neg=0, invalid=762 0422: dt=1.792000, rms=0.517 (0.336%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0423: dt=1.792000, rms=0.514 (0.416%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 18 iterations, nbhd size=1, neg = 0 0424: dt=1.792000, rms=0.513 (0.321%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 0425: dt=1.792000, rms=0.511 (0.387%), neg=0, invalid=762 iter 0, gcam->neg = 15 after 13 iterations, nbhd size=1, neg = 0 0426: dt=1.792000, rms=0.510 (0.239%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 13 iterations, nbhd size=1, neg = 0 0427: dt=1.792000, rms=0.508 (0.228%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 14 iterations, nbhd size=1, neg = 0 0428: dt=1.792000, rms=0.508 (0.129%), neg=0, invalid=762 iter 0, gcam->neg = 18 after 20 iterations, nbhd size=1, neg = 0 0429: dt=1.792000, rms=0.507 (0.159%), neg=0, invalid=762 iter 0, gcam->neg = 51 after 18 iterations, nbhd size=1, neg = 0 0430: dt=1.792000, rms=0.507 (-0.037%), neg=0, invalid=762 0431: dt=1.792000, rms=0.507 (0.054%), neg=0, invalid=762 0432: dt=1.024000, rms=0.507 (0.014%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.503, neg=0, invalid=762 iter 0, gcam->neg = 780 after 21 iterations, nbhd size=1, neg = 0 0433: dt=1.310223, rms=0.500 (0.702%), neg=0, invalid=762 0434: dt=0.028000, rms=0.500 (0.005%), neg=0, invalid=762 0435: dt=0.028000, rms=0.500 (-0.003%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.500, neg=0, invalid=762 0436: dt=0.256000, rms=0.498 (0.391%), neg=0, invalid=762 0437: dt=0.384000, rms=0.496 (0.353%), neg=0, invalid=762 iter 0, gcam->neg = 194 after 12 iterations, nbhd size=1, neg = 0 0438: dt=0.734043, rms=0.493 (0.510%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0439: dt=0.448000, rms=0.492 (0.305%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 0 iterations, nbhd size=0, neg = 0 0440: dt=0.491453, rms=0.490 (0.451%), neg=0, invalid=762 0441: dt=0.320000, rms=0.489 (0.174%), neg=0, invalid=762 0442: dt=0.320000, rms=0.487 (0.352%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 10 iterations, nbhd size=1, neg = 0 0443: dt=0.320000, rms=0.486 (0.279%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0444: dt=0.320000, rms=0.485 (0.168%), neg=0, invalid=762 iter 0, gcam->neg = 19 after 11 iterations, nbhd size=1, neg = 0 0445: dt=0.320000, rms=0.485 (0.100%), neg=0, invalid=762 iter 0, gcam->neg = 21 after 11 iterations, nbhd size=1, neg = 0 0446: dt=0.320000, rms=0.484 (0.010%), neg=0, invalid=762 0447: dt=0.112000, rms=0.484 (0.029%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 12 iterations, nbhd size=1, neg = 0 0448: dt=0.384000, rms=0.484 (0.033%), neg=0, invalid=762 0449: dt=0.048000, rms=0.484 (0.002%), neg=0, invalid=762 0450: dt=0.048000, rms=0.484 (0.002%), neg=0, invalid=762 0451: dt=0.048000, rms=0.484 (0.001%), neg=0, invalid=762 0452: dt=0.048000, rms=0.484 (0.001%), neg=0, invalid=762 0453: dt=0.048000, rms=0.484 (0.004%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0454: dt=0.048000, rms=0.484 (0.005%), neg=0, invalid=762 0455: dt=0.048000, rms=0.484 (0.013%), neg=0, invalid=762 0456: dt=0.048000, rms=0.484 (0.016%), neg=0, invalid=762 0457: dt=0.048000, rms=0.484 (0.018%), neg=0, invalid=762 0458: dt=0.048000, rms=0.484 (0.020%), neg=0, invalid=762 0459: dt=0.048000, rms=0.484 (0.022%), neg=0, invalid=762 0460: dt=0.048000, rms=0.484 (0.023%), neg=0, invalid=762 0461: dt=0.048000, rms=0.483 (0.024%), neg=0, invalid=762 0462: dt=0.048000, rms=0.483 (0.023%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 30 minutes and 53 seconds. mri_ca_register utimesec 6655.706178 mri_ca_register stimesec 9.423567 mri_ca_register ru_maxrss 1340152 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 7879070 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 70056 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 15364 mri_ca_register ru_nivcsw 760725 FSRUNTIME@ mri_ca_register 1.5147 hours 4 threads #-------------------------------------- #@# SubCort Seg Mon Jan 23 13:50:41 EST 2017 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname belle machine x86_64 setenv SUBJECTS_DIR /autofs/space/belle_001/users/mhibert/brain_tumor/subjects cd /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 4 == 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 /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.99 Atlas used for the 3D morph was /usr/local/freesurfer/stable6/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.11347 (25) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (659 voxels, overlap=0.766) Left_Lateral_Ventricle (4): linear fit = 1.36 x + 0.0 (659 voxels, peak = 27), gca=27.1 gca peak = 0.17677 (13) mri peak = 0.11303 (25) Right_Lateral_Ventricle (43): linear fit = 1.84 x + 0.0 (2378 voxels, overlap=0.306) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2378 voxels, peak = 24), gca=19.5 gca peak = 0.28129 (95) mri peak = 0.09141 (113) Right_Pallidum (52): linear fit = 1.20 x + 0.0 (357 voxels, overlap=0.027) Right_Pallidum (52): linear fit = 1.20 x + 0.0 (357 voxels, peak = 114), gca=113.5 gca peak = 0.16930 (96) mri peak = 0.06668 (112) Left_Pallidum (13): linear fit = 1.23 x + 0.0 (578 voxels, overlap=0.036) Left_Pallidum (13): linear fit = 1.23 x + 0.0 (578 voxels, peak = 118), gca=117.6 gca peak = 0.24553 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30264 (59) mri peak = 0.07514 (72) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (354 voxels, overlap=0.025) Left_Hippocampus (17): linear fit = 1.27 x + 0.0 (354 voxels, peak = 75), gca=75.2 gca peak = 0.07580 (103) mri peak = 0.07241 (107) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (37471 voxels, overlap=0.693) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (37471 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.07567 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (56446 voxels, overlap=0.567) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (56446 voxels, peak = 109), gca=108.7 gca peak = 0.09712 (58) mri peak = 0.04400 (80) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (22262 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (22262 voxels, peak = 78), gca=78.0 gca peak = 0.11620 (58) mri peak = 0.04938 (78) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (14870 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.40 x + 0.0 (14870 voxels, peak = 81), gca=81.5 gca peak = 0.30970 (66) mri peak = 0.08779 (96) Right_Caudate (50): linear fit = 1.38 x + 0.0 (496 voxels, overlap=0.024) Right_Caudate (50): linear fit = 1.38 x + 0.0 (496 voxels, peak = 91), gca=91.4 gca peak = 0.15280 (69) mri peak = 0.11957 (91) Left_Caudate (11): linear fit = 1.26 x + 0.0 (582 voxels, overlap=0.025) Left_Caudate (11): linear fit = 1.26 x + 0.0 (582 voxels, peak = 87), gca=87.3 gca peak = 0.13902 (56) mri peak = 0.05199 (68) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (18058 voxels, overlap=0.132) Left_Cerebellum_Cortex (8): linear fit = 1.23 x + 0.0 (18058 voxels, peak = 69), gca=68.6 gca peak = 0.14777 (55) mri peak = 0.04621 (71) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (17649 voxels, overlap=0.148) Right_Cerebellum_Cortex (47): linear fit = 1.26 x + 0.0 (17649 voxels, peak = 70), gca=69.6 gca peak = 0.16765 (84) mri peak = 0.06749 (87) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5347 voxels, overlap=0.864) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5347 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.06521 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6346 voxels, overlap=0.935) Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6346 voxels, peak = 87), gca=86.9 gca peak = 0.29869 (57) mri peak = 0.12617 (66) Left_Amygdala (18): linear fit = 1.14 x + 0.0 (367 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.14 x + 0.0 (367 voxels, peak = 65), gca=65.3 gca peak = 0.33601 (57) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11131 (90) mri peak = 0.06644 (109) Left_Thalamus_Proper (10): linear fit = 1.21 x + 0.0 (3145 voxels, overlap=0.009) Left_Thalamus_Proper (10): linear fit = 1.21 x + 0.0 (3145 voxels, peak = 108), gca=108.5 gca peak = 0.11793 (83) mri peak = 0.06100 (101) Right_Thalamus_Proper (49): linear fit = 1.26 x + 0.0 (976 voxels, overlap=0.010) Right_Thalamus_Proper (49): linear fit = 1.26 x + 0.0 (976 voxels, peak = 105), gca=105.0 gca peak = 0.08324 (81) mri peak = 0.06955 (96) Left_Putamen (12): linear fit = 1.23 x + 0.0 (1216 voxels, overlap=0.014) Left_Putamen (12): linear fit = 1.23 x + 0.0 (1216 voxels, peak = 99), gca=99.2 gca peak = 0.10360 (77) mri peak = 0.08686 (96) Right_Putamen (51): linear fit = 1.25 x + 0.0 (471 voxels, overlap=0.015) Right_Putamen (51): linear fit = 1.25 x + 0.0 (471 voxels, peak = 97), gca=96.6 gca peak = 0.08424 (78) mri peak = 0.07854 (84) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9222 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9222 voxels, peak = 86), gca=86.2 gca peak = 0.12631 (89) mri peak = 0.07143 (101) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (943 voxels, overlap=0.015) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (943 voxels, peak = 105), gca=105.5 gca peak = 0.14500 (87) mri peak = 0.06507 (99) Left_VentralDC (28): linear fit = 1.15 x + 0.0 (1051 voxels, overlap=0.270) Left_VentralDC (28): linear fit = 1.15 x + 0.0 (1051 voxels, peak = 100), gca=100.5 gca peak = 0.14975 (24) mri peak = 0.11940 (23) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (134 voxels, overlap=0.937) Third_Ventricle (14): linear fit = 0.94 x + 0.0 (134 voxels, peak = 22), gca=22.4 gca peak = 0.19357 (14) mri peak = 0.14911 (21) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (165 voxels, overlap=0.727) Fourth_Ventricle (15): linear fit = 1.25 x + 0.0 (165 voxels, peak = 17), gca=17.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Thalamus = 1.00000 (94) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Hippocampus = 0.24553 (55) gca peak Right_Amygdala = 0.33601 (57) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 1.27 x + 0: 75 setting label Right_Amygdala based on Left_Amygdala = 1.14 x + 0: 65 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 1.26 x + 0.0 Left_Putamen too bright - rescaling by 0.976 (from 1.225) to 96.9 (was 99.2) Left_Pallidum too bright - rescaling by 0.888 (from 1.225) to 104.4 (was 117.6) Right_Putamen too bright - rescaling by 1.003 (from 1.255) to 96.9 (was 96.6) Right_Pallidum too bright - rescaling by 0.920 (from 1.195) to 104.4 (was 113.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13790 (25) mri peak = 0.11347 (25) Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (659 voxels, overlap=0.877) Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (659 voxels, peak = 24), gca=24.1 gca peak = 0.14120 (19) mri peak = 0.11303 (25) Right_Lateral_Ventricle (43): linear fit = 1.17 x + 0.0 (2378 voxels, overlap=0.723) Right_Lateral_Ventricle (43): linear fit = 1.17 x + 0.0 (2378 voxels, peak = 22), gca=22.3 gca peak = 0.22825 (105) mri peak = 0.09141 (113) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (357 voxels, overlap=0.427) Right_Pallidum (52): linear fit = 1.09 x + 0.0 (357 voxels, peak = 114), gca=113.9 gca peak = 0.15856 (103) mri peak = 0.06668 (112) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (578 voxels, overlap=0.182) Left_Pallidum (13): linear fit = 1.12 x + 0.0 (578 voxels, peak = 116), gca=115.9 gca peak = 0.22392 (71) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.24132 (72) mri peak = 0.07514 (72) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (354 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (354 voxels, peak = 71), gca=70.9 gca peak = 0.07548 (107) mri peak = 0.07241 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37471 voxels, overlap=0.825) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (37471 voxels, peak = 107), gca=107.0 gca peak = 0.07816 (109) mri peak = 0.07567 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (56446 voxels, overlap=0.761) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (56446 voxels, peak = 109), gca=109.0 gca peak = 0.07295 (78) mri peak = 0.04400 (80) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (22262 voxels, overlap=0.955) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (22262 voxels, peak = 78), gca=78.0 gca peak = 0.08224 (81) mri peak = 0.04938 (78) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14870 voxels, overlap=0.949) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (14870 voxels, peak = 80), gca=79.8 gca peak = 0.22027 (91) mri peak = 0.08779 (96) Right_Caudate (50): linear fit = 1.00 x + 0.0 (496 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (496 voxels, peak = 91), gca=91.0 gca peak = 0.14925 (98) mri peak = 0.11957 (91) Left_Caudate (11): linear fit = 1.00 x + 0.0 (582 voxels, overlap=1.000) Left_Caudate (11): linear fit = 1.00 x + 0.0 (582 voxels, peak = 98), gca=98.0 gca peak = 0.11797 (68) mri peak = 0.05199 (68) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18058 voxels, overlap=0.990) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (18058 voxels, peak = 68), gca=68.0 gca peak = 0.12166 (69) mri peak = 0.04621 (71) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (17649 voxels, overlap=0.993) Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (17649 voxels, peak = 68), gca=68.0 gca peak = 0.15888 (90) mri peak = 0.06749 (87) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (5347 voxels, overlap=0.984) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (5347 voxels, peak = 88), gca=87.8 gca peak = 0.18134 (87) mri peak = 0.06521 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6346 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6346 voxels, peak = 87), gca=86.6 gca peak = 0.29872 (67) mri peak = 0.12617 (66) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (367 voxels, overlap=0.991) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (367 voxels, peak = 67), gca=67.0 gca peak = 0.23168 (65) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10207 (106) mri peak = 0.06644 (109) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3145 voxels, overlap=0.803) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3145 voxels, peak = 108), gca=107.6 gca peak = 0.09606 (102) mri peak = 0.06100 (101) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (976 voxels, overlap=0.868) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (976 voxels, peak = 103), gca=102.5 gca peak = 0.07880 (90) mri peak = 0.06955 (96) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1216 voxels, overlap=0.846) Left_Putamen (12): linear fit = 1.02 x + 0.0 (1216 voxels, peak = 92), gca=92.2 gca peak = 0.08663 (95) mri peak = 0.08686 (96) Right_Putamen (51): linear fit = 1.00 x + 0.0 (471 voxels, overlap=0.791) Right_Putamen (51): linear fit = 1.00 x + 0.0 (471 voxels, peak = 95), gca=95.0 gca peak = 0.07171 (86) mri peak = 0.07854 (84) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9222 voxels, overlap=0.801) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9222 voxels, peak = 86), gca=86.4 gca peak = 0.11318 (100) mri peak = 0.07143 (101) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (943 voxels, overlap=0.738) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (943 voxels, peak = 100), gca=100.5 gca peak = 0.14671 (99) mri peak = 0.06507 (99) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1051 voxels, overlap=0.953) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1051 voxels, peak = 99), gca=99.5 gca peak = 0.21418 (24) mri peak = 0.11940 (23) Third_Ventricle (14): linear fit = 1.14 x + 0.0 (134 voxels, overlap=0.997) Third_Ventricle (14): linear fit = 1.14 x + 0.0 (134 voxels, peak = 27), gca=27.5 gca peak = 0.16542 (20) mri peak = 0.14911 (21) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (165 voxels, overlap=0.627) Fourth_Ventricle (15): linear fit = 1.12 x + 0.0 (165 voxels, peak = 22), gca=22.5 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.14444 (41) gca peak Left_Thalamus = 0.64095 (106) gca peak CSF = 0.19962 (45) gca peak Left_Accumbens_area = 0.51391 (78) gca peak Left_undetermined = 0.96707 (31) gca peak Left_vessel = 0.75962 (52) gca peak Left_choroid_plexus = 0.11874 (35) gca peak Right_Inf_Lat_Vent = 0.19636 (29) gca peak Right_Hippocampus = 0.22392 (71) gca peak Right_Amygdala = 0.23168 (65) gca peak Right_Accumbens_area = 0.32409 (89) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14507 (37) gca peak Fifth_Ventricle = 0.78028 (39) gca peak WM_hypointensities = 0.08084 (79) gca peak non_WM_hypointensities = 0.09744 (45) gca peak Optic_Chiasm = 0.49837 (76) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 0.99 x + 0: 71 setting label Right_Amygdala based on Left_Amygdala = 1.00 x + 0: 67 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 1.10 x + 0.0 Left_Pallidum too bright - rescaling by 0.904 (from 1.125) to 104.8 (was 115.9) Right_Pallidum too bright - rescaling by 0.920 (from 1.085) to 104.8 (was 113.9) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 120844 voxels changed in iteration 0 of unlikely voxel relabeling 323 voxels changed in iteration 1 of unlikely voxel relabeling 17 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 123371 gm and wm labels changed (%32 to gray, %68 to white out of all changed labels) 735 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 110263 changed. image ll: -2.231, PF=0.500 pass 2: 27124 changed. image ll: -2.227, PF=0.500 pass 3: 7610 changed. pass 4: 2648 changed. 92285 voxels changed in iteration 0 of unlikely voxel relabeling 675 voxels changed in iteration 1 of unlikely voxel relabeling 16 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 9807 voxels changed in iteration 0 of unlikely voxel relabeling 127 voxels changed in iteration 1 of unlikely voxel relabeling 69 voxels changed in iteration 2 of unlikely voxel relabeling 13 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 7302 voxels changed in iteration 0 of unlikely voxel relabeling 68 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 1 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 6595 voxels changed in iteration 0 of unlikely voxel relabeling 66 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3260.322355 mri_ca_label stimesec 0.624905 mri_ca_label ru_maxrss 2105284 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 678897 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 480 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 466 mri_ca_label ru_nivcsw 331362 auto-labeling took 53 minutes and 33 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/transforms/cc_up.lta nmr00327_6p0 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/transforms/cc_up.lta reading aseg from /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/norm.mgz 118945 voxels in left wm, 98830 in right wm, xrange [120, 141] searching rotation angles z=[-5 9], y=[-1 13] searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.6 global minimum found at slice 129.0, rotations (5.60, 2.86) final transformation (x=129.0, yr=5.600, zr=2.861): 0.99399 -0.04991 0.09746 -6.28667; 0.04968 0.99875 0.00487 14.15524; -0.09759 0.00000 0.99523 24.14690; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 130] in xformed coordinates best xformed slice 127 cc center is found at 127 107 117 eigenvectors: -0.00082 -0.00535 0.99999; 0.03690 -0.99930 -0.00531; 0.99932 0.03690 0.00102; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri/aseg.auto.mgz... corpus callosum segmentation took 1.9 minutes #-------------------------------------- #@# Merge ASeg Mon Jan 23 14:46:06 EST 2017 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Jan 23 14:46:06 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz assuming input volume is MGH (Van der Kouwe) MP-RAGE 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... 2083 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 110 white matter peak found at 108 gm peak at 86 (86), valley at 41 (41) csf peak at 27, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 82 (82), valley at 38 (38) csf peak at 41, setting threshold to 68 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 1 minutes and 58 seconds. #-------------------------------------------- #@# Mask BFS Mon Jan 23 14:48:05 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1420696 voxels in mask (pct= 8.47) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Jan 23 14:48:07 EST 2017 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 104.2 +- 7.7 [79.0 --> 125.0] GM (70.0) : 65.3 +- 14.2 [30.0 --> 95.0] setting bottom of white matter range to 79.5 setting top of gray matter range to 93.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 29171 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3508 filled 22955 bright non-wm voxels segmented. 14240 diagonally connected voxels added... white matter segmentation took 1.5 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE 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 0.53 minutes reading wm segmentation from wm.seg.mgz... 1945 voxels added to wm to prevent paths from MTL structures to cortex 7327 additional wm voxels added 0 additional wm voxels added SEG EDIT: 52370 voxels turned on, 21912 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 107 new 107 115,126,128 old 107 new 107 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 127 found - 127 modified | TOTAL: 127 pass 2 (xy+): 0 found - 127 modified | TOTAL: 127 pass 1 (xy-): 113 found - 113 modified | TOTAL: 240 pass 2 (xy-): 0 found - 113 modified | TOTAL: 240 pass 1 (yz+): 116 found - 116 modified | TOTAL: 356 pass 2 (yz+): 0 found - 116 modified | TOTAL: 356 pass 1 (yz-): 116 found - 116 modified | TOTAL: 472 pass 2 (yz-): 0 found - 116 modified | TOTAL: 472 pass 1 (xz+): 135 found - 135 modified | TOTAL: 607 pass 2 (xz+): 0 found - 135 modified | TOTAL: 607 pass 1 (xz-): 133 found - 133 modified | TOTAL: 740 pass 2 (xz-): 0 found - 133 modified | TOTAL: 740 Iteration Number : 1 pass 1 (+++): 341 found - 341 modified | TOTAL: 341 pass 2 (+++): 0 found - 341 modified | TOTAL: 341 pass 1 (+++): 384 found - 384 modified | TOTAL: 725 pass 2 (+++): 0 found - 384 modified | TOTAL: 725 pass 1 (+++): 417 found - 417 modified | TOTAL: 1142 pass 2 (+++): 0 found - 417 modified | TOTAL: 1142 pass 1 (+++): 370 found - 370 modified | TOTAL: 1512 pass 2 (+++): 0 found - 370 modified | TOTAL: 1512 Iteration Number : 1 pass 1 (++): 285 found - 285 modified | TOTAL: 285 pass 2 (++): 0 found - 285 modified | TOTAL: 285 pass 1 (+-): 370 found - 370 modified | TOTAL: 655 pass 2 (+-): 3 found - 373 modified | TOTAL: 658 pass 3 (+-): 0 found - 373 modified | TOTAL: 658 pass 1 (--): 365 found - 365 modified | TOTAL: 1023 pass 2 (--): 2 found - 367 modified | TOTAL: 1025 pass 3 (--): 0 found - 367 modified | TOTAL: 1025 pass 1 (-+): 389 found - 389 modified | TOTAL: 1414 pass 2 (-+): 0 found - 389 modified | TOTAL: 1414 Iteration Number : 2 pass 1 (xy+): 96 found - 96 modified | TOTAL: 96 pass 2 (xy+): 0 found - 96 modified | TOTAL: 96 pass 1 (xy-): 100 found - 100 modified | TOTAL: 196 pass 2 (xy-): 0 found - 100 modified | TOTAL: 196 pass 1 (yz+): 84 found - 84 modified | TOTAL: 280 pass 2 (yz+): 0 found - 84 modified | TOTAL: 280 pass 1 (yz-): 108 found - 108 modified | TOTAL: 388 pass 2 (yz-): 0 found - 108 modified | TOTAL: 388 pass 1 (xz+): 88 found - 88 modified | TOTAL: 476 pass 2 (xz+): 0 found - 88 modified | TOTAL: 476 pass 1 (xz-): 104 found - 104 modified | TOTAL: 580 pass 2 (xz-): 0 found - 104 modified | TOTAL: 580 Iteration Number : 2 pass 1 (+++): 29 found - 29 modified | TOTAL: 29 pass 2 (+++): 0 found - 29 modified | TOTAL: 29 pass 1 (+++): 43 found - 43 modified | TOTAL: 72 pass 2 (+++): 0 found - 43 modified | TOTAL: 72 pass 1 (+++): 47 found - 47 modified | TOTAL: 119 pass 2 (+++): 0 found - 47 modified | TOTAL: 119 pass 1 (+++): 30 found - 30 modified | TOTAL: 149 pass 2 (+++): 0 found - 30 modified | TOTAL: 149 Iteration Number : 2 pass 1 (++): 60 found - 60 modified | TOTAL: 60 pass 2 (++): 0 found - 60 modified | TOTAL: 60 pass 1 (+-): 46 found - 46 modified | TOTAL: 106 pass 2 (+-): 0 found - 46 modified | TOTAL: 106 pass 1 (--): 40 found - 40 modified | TOTAL: 146 pass 2 (--): 0 found - 40 modified | TOTAL: 146 pass 1 (-+): 55 found - 55 modified | TOTAL: 201 pass 2 (-+): 0 found - 55 modified | TOTAL: 201 Iteration Number : 3 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 13 found - 13 modified | TOTAL: 30 pass 2 (xy-): 0 found - 13 modified | TOTAL: 30 pass 1 (yz+): 14 found - 14 modified | TOTAL: 44 pass 2 (yz+): 0 found - 14 modified | TOTAL: 44 pass 1 (yz-): 14 found - 14 modified | TOTAL: 58 pass 2 (yz-): 0 found - 14 modified | TOTAL: 58 pass 1 (xz+): 12 found - 12 modified | TOTAL: 70 pass 2 (xz+): 0 found - 12 modified | TOTAL: 70 pass 1 (xz-): 18 found - 18 modified | TOTAL: 88 pass 2 (xz-): 0 found - 18 modified | TOTAL: 88 Iteration Number : 3 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 pass 1 (+++): 4 found - 4 modified | TOTAL: 10 pass 2 (+++): 0 found - 4 modified | TOTAL: 10 pass 1 (+++): 2 found - 2 modified | TOTAL: 12 pass 2 (+++): 0 found - 2 modified | TOTAL: 12 Iteration Number : 3 pass 1 (++): 8 found - 8 modified | TOTAL: 8 pass 2 (++): 0 found - 8 modified | TOTAL: 8 pass 1 (+-): 7 found - 7 modified | TOTAL: 15 pass 2 (+-): 0 found - 7 modified | TOTAL: 15 pass 1 (--): 7 found - 7 modified | TOTAL: 22 pass 2 (--): 0 found - 7 modified | TOTAL: 22 pass 1 (-+): 10 found - 10 modified | TOTAL: 32 pass 2 (-+): 0 found - 10 modified | TOTAL: 32 Iteration Number : 4 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 3 found - 3 modified | TOTAL: 9 pass 2 (xz-): 0 found - 3 modified | TOTAL: 9 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 4740 (out of 629524: 0.752950) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Jan 23 14:50:13 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/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 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81448; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.04899 -0.03729 0.13438 -24.93768; 0.01655 1.13598 0.15175 -41.81448; -0.12320 -0.12215 0.92782 31.19715; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1234 (min = 350, max = 1400), aspect = 0.63 (min = 0.10, max = 0.75) no need to search using seed (122, 121, 146), TAL = (6.0, 18.0, 7.0) talairach voxel to voxel transform 0.93681 0.01589 -0.13828 28.34021; -0.02975 0.86458 -0.13710 39.68726; 0.12048 0.11593 1.04138 -24.63599; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (122, 121, 146) --> (6.0, 18.0, 7.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (6.00, 18.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(24.00, 18.00, 7.00) SRC: (107.50, 121.19, 153.96) search lh wm seed point around talairach space (-12.00, 18.00, 7.00), SRC: (141.23, 120.12, 158.30) 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 23 14:50:42 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 0 found - 0 modified | TOTAL: 10 pass 1 (yz+): 3 found - 3 modified | TOTAL: 13 pass 2 (yz+): 0 found - 3 modified | TOTAL: 13 pass 1 (yz-): 3 found - 3 modified | TOTAL: 16 pass 2 (yz-): 0 found - 3 modified | TOTAL: 16 pass 1 (xz+): 10 found - 10 modified | TOTAL: 26 pass 2 (xz+): 0 found - 10 modified | TOTAL: 26 pass 1 (xz-): 11 found - 11 modified | TOTAL: 37 pass 2 (xz-): 0 found - 11 modified | TOTAL: 37 Iteration Number : 1 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 5 pass 2 (+++): 0 found - 4 modified | TOTAL: 5 pass 1 (+++): 2 found - 2 modified | TOTAL: 7 pass 2 (+++): 0 found - 2 modified | TOTAL: 7 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 7 found - 7 modified | TOTAL: 9 pass 2 (--): 0 found - 7 modified | TOTAL: 9 pass 1 (-+): 3 found - 3 modified | TOTAL: 12 pass 2 (-+): 0 found - 3 modified | TOTAL: 12 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 62 (out of 344827: 0.017980) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 40: 1369 vertices, 1507 faces slice 50: 8228 vertices, 8630 faces slice 60: 18978 vertices, 19626 faces slice 70: 33317 vertices, 34264 faces slice 80: 49246 vertices, 50345 faces slice 90: 65359 vertices, 66712 faces slice 100: 81356 vertices, 82791 faces slice 110: 97972 vertices, 99537 faces slice 120: 113561 vertices, 115238 faces slice 130: 129259 vertices, 131098 faces slice 140: 143814 vertices, 145757 faces slice 150: 158084 vertices, 160046 faces slice 160: 169679 vertices, 171629 faces slice 170: 180409 vertices, 182428 faces slice 180: 190358 vertices, 192390 faces slice 190: 198596 vertices, 200616 faces slice 200: 205137 vertices, 207107 faces slice 210: 208180 vertices, 209972 faces slice 220: 208180 vertices, 209972 faces slice 230: 208180 vertices, 209972 faces slice 240: 208180 vertices, 209972 faces slice 250: 208180 vertices, 209972 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... 208180 voxel in cpt #1: X=-1792 [v=208180,e=629916,f=419944] located at (-30.875887, -12.623018, 12.353026) For the whole surface: X=-1792 [v=208180,e=629916,f=419944] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Mon Jan 23 14:50:48 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 5 found - 5 modified | TOTAL: 9 pass 2 (xy-): 0 found - 5 modified | TOTAL: 9 pass 1 (yz+): 4 found - 4 modified | TOTAL: 13 pass 2 (yz+): 0 found - 4 modified | TOTAL: 13 pass 1 (yz-): 16 found - 16 modified | TOTAL: 29 pass 2 (yz-): 0 found - 16 modified | TOTAL: 29 pass 1 (xz+): 8 found - 8 modified | TOTAL: 37 pass 2 (xz+): 0 found - 8 modified | TOTAL: 37 pass 1 (xz-): 12 found - 12 modified | TOTAL: 49 pass 2 (xz-): 0 found - 12 modified | TOTAL: 49 Iteration Number : 1 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 2 found - 2 modified | TOTAL: 3 pass 2 (+++): 0 found - 2 modified | TOTAL: 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 3 Iteration Number : 1 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 2 found - 2 modified | TOTAL: 9 pass 2 (+-): 0 found - 2 modified | TOTAL: 9 pass 1 (--): 3 found - 3 modified | TOTAL: 12 pass 2 (--): 0 found - 3 modified | TOTAL: 12 pass 1 (-+): 3 found - 3 modified | TOTAL: 15 pass 2 (-+): 0 found - 3 modified | TOTAL: 15 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 69 (out of 280380: 0.024609) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 628 vertices, 703 faces slice 40: 5124 vertices, 5395 faces slice 50: 13327 vertices, 13710 faces slice 60: 23822 vertices, 24372 faces slice 70: 37131 vertices, 37741 faces slice 80: 51352 vertices, 51914 faces slice 90: 62625 vertices, 63312 faces slice 100: 74940 vertices, 75673 faces slice 110: 85297 vertices, 86052 faces slice 120: 95252 vertices, 96059 faces slice 130: 104237 vertices, 105111 faces slice 140: 113381 vertices, 114216 faces slice 150: 121544 vertices, 122426 faces slice 160: 130921 vertices, 131903 faces slice 170: 140318 vertices, 141343 faces slice 180: 148591 vertices, 149605 faces slice 190: 155229 vertices, 156201 faces slice 200: 160438 vertices, 161337 faces slice 210: 161490 vertices, 162258 faces slice 220: 161490 vertices, 162258 faces slice 230: 161490 vertices, 162258 faces slice 240: 161490 vertices, 162258 faces slice 250: 161490 vertices, 162258 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... 161490 voxel in cpt #1: X=-768 [v=161490,e=486774,f=324516] located at (22.238714, -18.377367, 16.122887) For the whole surface: X=-768 [v=161490,e=486774,f=324516] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Jan 23 14:50:52 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/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 23 14:50:58 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/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 23 14:51:02 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 49.1 mm, total surface area = 95174 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes step 000: RMS=0.230 (target=0.015) step 005: RMS=0.182 (target=0.015) step 010: RMS=0.162 (target=0.015) step 015: RMS=0.155 (target=0.015) step 020: RMS=0.149 (target=0.015) step 025: RMS=0.145 (target=0.015) step 030: RMS=0.141 (target=0.015) step 035: RMS=0.137 (target=0.015) step 040: RMS=0.135 (target=0.015) step 045: RMS=0.132 (target=0.015) step 050: RMS=0.131 (target=0.015) step 055: RMS=0.131 (target=0.015) step 060: RMS=0.130 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 49.867419 mris_inflate stimesec 0.256960 mris_inflate ru_maxrss 328816 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 49150 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 576 mris_inflate ru_oublock 14728 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 38511 mris_inflate ru_nivcsw 5718 #-------------------------------------------- #@# Inflation1 rh Mon Jan 23 14:51:22 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 50.0 mm, total surface area = 75049 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.2 minutes step 000: RMS=0.211 (target=0.015) step 005: RMS=0.165 (target=0.015) step 010: RMS=0.143 (target=0.015) step 015: RMS=0.133 (target=0.015) step 020: RMS=0.128 (target=0.015) step 025: RMS=0.123 (target=0.015) step 030: RMS=0.118 (target=0.015) step 035: RMS=0.118 (target=0.015) step 040: RMS=0.116 (target=0.015) step 045: RMS=0.114 (target=0.015) step 050: RMS=0.112 (target=0.015) step 055: RMS=0.112 (target=0.015) step 060: RMS=0.112 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 38.643125 mris_inflate stimesec 0.144977 mris_inflate ru_maxrss 253400 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 37980 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 11400 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 29152 mris_inflate ru_nivcsw 4514 #-------------------------------------------- #@# QSphere lh Mon Jan 23 14:51:36 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/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 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.83 +- 0.63 (0.00-->6.67) (max @ vno 151991 --> 152010) face area 0.02 +- 0.03 (-0.33-->0.59) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.277... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.605, avgs=0 005/300: dt: 0.9000, rms radial error=177.345, avgs=0 010/300: dt: 0.9000, rms radial error=176.785, avgs=0 015/300: dt: 0.9000, rms radial error=176.050, avgs=0 020/300: dt: 0.9000, rms radial error=175.213, avgs=0 025/300: dt: 0.9000, rms radial error=174.318, avgs=0 030/300: dt: 0.9000, rms radial error=173.389, avgs=0 035/300: dt: 0.9000, rms radial error=172.442, avgs=0 040/300: dt: 0.9000, rms radial error=171.486, avgs=0 045/300: dt: 0.9000, rms radial error=170.528, avgs=0 050/300: dt: 0.9000, rms radial error=169.572, avgs=0 055/300: dt: 0.9000, rms radial error=168.618, avgs=0 060/300: dt: 0.9000, rms radial error=167.669, avgs=0 065/300: dt: 0.9000, rms radial error=166.724, avgs=0 070/300: dt: 0.9000, rms radial error=165.783, avgs=0 075/300: dt: 0.9000, rms radial error=164.847, avgs=0 080/300: dt: 0.9000, rms radial error=163.917, avgs=0 085/300: dt: 0.9000, rms radial error=162.992, avgs=0 090/300: dt: 0.9000, rms radial error=162.072, avgs=0 095/300: dt: 0.9000, rms radial error=161.160, avgs=0 100/300: dt: 0.9000, rms radial error=160.253, avgs=0 105/300: dt: 0.9000, rms radial error=159.351, avgs=0 110/300: dt: 0.9000, rms radial error=158.454, avgs=0 115/300: dt: 0.9000, rms radial error=157.561, avgs=0 120/300: dt: 0.9000, rms radial error=156.673, avgs=0 125/300: dt: 0.9000, rms radial error=155.790, avgs=0 130/300: dt: 0.9000, rms radial error=154.912, avgs=0 135/300: dt: 0.9000, rms radial error=154.039, avgs=0 140/300: dt: 0.9000, rms radial error=153.171, avgs=0 145/300: dt: 0.9000, rms radial error=152.307, avgs=0 150/300: dt: 0.9000, rms radial error=151.449, avgs=0 155/300: dt: 0.9000, rms radial error=150.595, avgs=0 160/300: dt: 0.9000, rms radial error=149.747, avgs=0 165/300: dt: 0.9000, rms radial error=148.903, avgs=0 170/300: dt: 0.9000, rms radial error=148.065, avgs=0 175/300: dt: 0.9000, rms radial error=147.232, avgs=0 180/300: dt: 0.9000, rms radial error=146.403, avgs=0 185/300: dt: 0.9000, rms radial error=145.579, avgs=0 190/300: dt: 0.9000, rms radial error=144.759, avgs=0 195/300: dt: 0.9000, rms radial error=143.944, avgs=0 200/300: dt: 0.9000, rms radial error=143.133, avgs=0 205/300: dt: 0.9000, rms radial error=142.327, avgs=0 210/300: dt: 0.9000, rms radial error=141.525, avgs=0 215/300: dt: 0.9000, rms radial error=140.728, avgs=0 220/300: dt: 0.9000, rms radial error=139.935, avgs=0 225/300: dt: 0.9000, rms radial error=139.147, avgs=0 230/300: dt: 0.9000, rms radial error=138.363, avgs=0 235/300: dt: 0.9000, rms radial error=137.584, avgs=0 240/300: dt: 0.9000, rms radial error=136.809, avgs=0 245/300: dt: 0.9000, rms radial error=136.038, avgs=0 250/300: dt: 0.9000, rms radial error=135.273, avgs=0 255/300: dt: 0.9000, rms radial error=134.511, avgs=0 260/300: dt: 0.9000, rms radial error=133.754, avgs=0 265/300: dt: 0.9000, rms radial error=133.001, avgs=0 270/300: dt: 0.9000, rms radial error=132.252, avgs=0 275/300: dt: 0.9000, rms radial error=131.507, avgs=0 280/300: dt: 0.9000, rms radial error=130.767, avgs=0 285/300: dt: 0.9000, rms radial error=130.030, avgs=0 290/300: dt: 0.9000, rms radial error=129.298, avgs=0 295/300: dt: 0.9000, rms radial error=128.570, avgs=0 300/300: dt: 0.9000, rms radial error=127.846, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 26069.99 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 5187.58 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 3 (K=160.0), pass 1, starting sse = 912.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00344 epoch 4 (K=640.0), pass 1, starting sse = 196.39 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00737 final distance error %33.29 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 294.612212 mris_sphere stimesec 0.265959 mris_sphere ru_maxrss 329036 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 49204 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 14728 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 43291 mris_sphere ru_nivcsw 33481 FSRUNTIME@ mris_sphere 0.0344 hours 1 threads #-------------------------------------------- #@# QSphere rh Mon Jan 23 14:53:40 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/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 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.83 +- 0.67 (0.00-->10.42) (max @ vno 64751 --> 66026) face area 0.02 +- 0.03 (-0.29-->0.77) == Number of threads available to mris_sphere for OpenMP = 4 == scaling brain by 0.272... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=178.244, avgs=0 005/300: dt: 0.9000, rms radial error=177.983, avgs=0 010/300: dt: 0.9000, rms radial error=177.421, avgs=0 015/300: dt: 0.9000, rms radial error=176.681, avgs=0 020/300: dt: 0.9000, rms radial error=175.836, avgs=0 025/300: dt: 0.9000, rms radial error=174.931, avgs=0 030/300: dt: 0.9000, rms radial error=173.991, avgs=0 035/300: dt: 0.9000, rms radial error=173.038, avgs=0 040/300: dt: 0.9000, rms radial error=172.080, avgs=0 045/300: dt: 0.9000, rms radial error=171.120, avgs=0 050/300: dt: 0.9000, rms radial error=170.160, avgs=0 055/300: dt: 0.9000, rms radial error=169.203, avgs=0 060/300: dt: 0.9000, rms radial error=168.249, avgs=0 065/300: dt: 0.9000, rms radial error=167.300, avgs=0 070/300: dt: 0.9000, rms radial error=166.354, avgs=0 075/300: dt: 0.9000, rms radial error=165.414, avgs=0 080/300: dt: 0.9000, rms radial error=164.478, avgs=0 085/300: dt: 0.9000, rms radial error=163.547, avgs=0 090/300: dt: 0.9000, rms radial error=162.621, avgs=0 095/300: dt: 0.9000, rms radial error=161.700, avgs=0 100/300: dt: 0.9000, rms radial error=160.784, avgs=0 105/300: dt: 0.9000, rms radial error=159.873, avgs=0 110/300: dt: 0.9000, rms radial error=158.967, avgs=0 115/300: dt: 0.9000, rms radial error=158.065, avgs=0 120/300: dt: 0.9000, rms radial error=157.169, avgs=0 125/300: dt: 0.9000, rms radial error=156.277, avgs=0 130/300: dt: 0.9000, rms radial error=155.390, avgs=0 135/300: dt: 0.9000, rms radial error=154.508, avgs=0 140/300: dt: 0.9000, rms radial error=153.630, avgs=0 145/300: dt: 0.9000, rms radial error=152.758, avgs=0 150/300: dt: 0.9000, rms radial error=151.890, avgs=0 155/300: dt: 0.9000, rms radial error=151.027, avgs=0 160/300: dt: 0.9000, rms radial error=150.169, avgs=0 165/300: dt: 0.9000, rms radial error=149.315, avgs=0 170/300: dt: 0.9000, rms radial error=148.466, avgs=0 175/300: dt: 0.9000, rms radial error=147.622, avgs=0 180/300: dt: 0.9000, rms radial error=146.782, avgs=0 185/300: dt: 0.9000, rms radial error=145.947, avgs=0 190/300: dt: 0.9000, rms radial error=145.117, avgs=0 195/300: dt: 0.9000, rms radial error=144.291, avgs=0 200/300: dt: 0.9000, rms radial error=143.472, avgs=0 205/300: dt: 0.9000, rms radial error=142.659, avgs=0 210/300: dt: 0.9000, rms radial error=141.850, avgs=0 215/300: dt: 0.9000, rms radial error=141.046, avgs=0 220/300: dt: 0.9000, rms radial error=140.247, avgs=0 225/300: dt: 0.9000, rms radial error=139.452, avgs=0 230/300: dt: 0.9000, rms radial error=138.661, avgs=0 235/300: dt: 0.9000, rms radial error=137.875, avgs=0 240/300: dt: 0.9000, rms radial error=137.093, avgs=0 245/300: dt: 0.9000, rms radial error=136.316, avgs=0 250/300: dt: 0.9000, rms radial error=135.543, avgs=0 255/300: dt: 0.9000, rms radial error=134.774, avgs=0 260/300: dt: 0.9000, rms radial error=134.010, avgs=0 265/300: dt: 0.9000, rms radial error=133.249, avgs=0 270/300: dt: 0.9000, rms radial error=132.493, avgs=0 275/300: dt: 0.9000, rms radial error=131.742, avgs=0 280/300: dt: 0.9000, rms radial error=130.994, avgs=0 285/300: dt: 0.9000, rms radial error=130.251, avgs=0 290/300: dt: 0.9000, rms radial error=129.512, avgs=0 295/300: dt: 0.9000, rms radial error=128.777, avgs=0 300/300: dt: 0.9000, rms radial error=128.047, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20193.69 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 2 (K=40.0), pass 1, starting sse = 4048.25 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 3 (K=160.0), pass 1, starting sse = 669.41 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00124 epoch 4 (K=640.0), pass 1, starting sse = 106.26 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00466 final distance error %37.94 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.03 hours mris_sphere utimesec 219.974558 mris_sphere stimesec 0.247962 mris_sphere ru_maxrss 253608 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 38529 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 11400 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 34291 mris_sphere ru_nivcsw 26060 FSRUNTIME@ mris_sphere 0.0256 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Mon Jan 23 14:55:12 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Mon Jan 23 14:55:12 EST 2017 /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Mon Jan 23 14:55:12 EST 2017 mris_fix_topology -rusage /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 nmr00327_6p0 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 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-1792 (nv=208180, nf=419944, ne=629916, g=897) 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... 135126 ambiguous faces found in tessellation segmenting defects... 264 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 5 into 0 -merging segment 18 into 0 -merging segment 23 into 0 -merging segment 30 into 0 -merging segment 8 into 0 -merging segment 15 into 0 -merging segment 25 into 0 -merging segment 28 into 7 -merging segment 38 into 35 -merging segment 70 into 40 -merging segment 92 into 40 -merging segment 131 into 40 -merging segment 133 into 40 -merging segment 67 into 66 -merging segment 84 into 66 -merging segment 97 into 76 -merging segment 40 into 78 -merging segment 91 into 89 -merging segment 138 into 93 -merging segment 120 into 117 -merging segment 130 into 119 -merging segment 124 into 123 -merging segment 127 into 123 -merging segment 128 into 125 -merging segment 147 into 136 -merging segment 172 into 167 -merging segment 177 into 174 -merging segment 199 into 187 -merging segment 202 into 191 -merging segment 208 into 194 -merging segment 210 into 205 -merging segment 215 into 205 -merging segment 219 into 205 -merging segment 225 into 209 -merging segment 244 into 239 -merging segment 247 into 243 -merging segment 251 into 250 -merging segment 254 into 253 224 defects to be corrected 0 vertices coincident reading input surface /autofs/space/belle_001/users/mhibert/brain_tumor/subjects/nmr00327_6p0/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.0460 (-4.5230) -vertex loglikelihood: -6.6409 (-3.3205) -normal dot loglikelihood: -3.5376 (-3.5376) -quad curv loglikelihood: -6.2507 (-3.1254) Total Loglikelihood : -25.4753 CORRECTING DEFECT 0 (vertices=17861, convex hull=5847, v0=24) XL defect detected...