Wed Jan 9 20:30:54 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan /usr/local/freesurfer/bin/recon-all -s chong_lan -i /mnt/hgfs/DATA/Social_anxiety_disorder/SAD/3DT1/chen_lan//0001.dcm subjid chong_lan setenv SUBJECTS_DIR /mnt/hgfs/DATA/Freesurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux fslvm6.localdomain 2.6.32-279.5.2.el6.x86_64 #1 SMP Fri Aug 24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 8057928 2372152 5685776 0 78860 1699052 -/+ buffers/cache: 594240 7463688 Swap: 4128760 0 4128760 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:30:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /mnt/hgfs/DATA/Freesurfer/chong_lan mri_convert /mnt/hgfs/DATA/Social_anxiety_disorder/SAD/3DT1/chen_lan/0001.dcm /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig/001.mgz mri_convert /mnt/hgfs/DATA/Social_anxiety_disorder/SAD/3DT1/chen_lan/0001.dcm /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /mnt/hgfs/DATA/Social_anxiety_disorder/SAD/3DT1/chen_lan/0001.dcm... Starting DICOMRead2() dcmfile = /mnt/hgfs/DATA/Social_anxiety_disorder/SAD/3DT1/chen_lan/0001.dcm dcmdir = /mnt/hgfs/DATA/Social_anxiety_disorder/SAD/3DT1/chen_lan Ref Series No = 6 Found 158 files, checking for dicoms Found 156 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 156 ndcmfiles = 156 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=8.53, TE=3.40, TI=400.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig/001.mgz... #------------------------------------------ recon-all -s chong_lan finished without error at Wed Jan 9 20:41:41 EST 2013 New invocation of recon-all Wed Jan 9 20:42:52 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan /usr/local/freesurfer/bin/recon-all -s chong_lan -all subjid chong_lan setenv SUBJECTS_DIR /mnt/hgfs/DATA/Freesurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux fslvm6.localdomain 2.6.32-279.5.2.el6.x86_64 #1 SMP Fri Aug 24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 8057928 2455432 5602496 0 79280 1780820 -/+ buffers/cache: 595332 7462596 Swap: 4128760 0 4128760 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/10-01:42:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: fsl Machine: fslvm6.localdomain Platform: Linux PlatformVersion: 2.6.32-279.5.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed Jan 9 20:42:56 EST 2013 Found 1 runs /mnt/hgfs/DATA/Freesurfer/chong_lan/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 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig/001.mgz /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/rawavg.mgz /mnt/hgfs/DATA/Freesurfer/chong_lan mri_convert /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/rawavg.mgz /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig.mgz --conform mri_convert /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/rawavg.mgz /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/rawavg.mgz... TR=8.53, TE=3.40, TI=400.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) Original Data has (0.46875, 0.46875, 1) mm size and (512, 512, 156) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig.mgz... mri_add_xform_to_header -c /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/transforms/talairach.xfm /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig.mgz /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Jan 9 20:43:26 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Jan 9 20:44:17 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7582, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/transforms/talairach_avi.log TalAviQA: 0.97504 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Jan 9 20:44:18 EST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux fslvm6.localdomain 2.6.32-279.5.2.el6.x86_64 #1 SMP Fri Aug 24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux Wed Jan 9 20:44:18 EST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.24936 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24936/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24936/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=8.53, TE=3.40, TI=400.00, flip angle=12.00 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.24936/nu0.mnc... Outputting Volume: ............................................................ -------------------------------------------------------- Iteration 1 Wed Jan 9 20:44:51 EST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24936/nu0.mnc ./tmp.mri_nu_correct.mni.24936/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24936/0/ [fsl@fslvm6.localdomain:/mnt/hgfs/DATA/Freesurfer/chong_lan/mri/] [2013-01-09 20:44:51] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24936/0/ ./tmp.mri_nu_correct.mni.24936/nu0.mnc ./tmp.mri_nu_correct.mni.24936/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000981059 [fsl@fslvm6.localdomain:/mnt/hgfs/DATA/Freesurfer/chong_lan/mri/] [2013-01-09 20:46:17] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24936/nu0.mnc ./tmp.mri_nu_correct.mni.24936/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Jan 9 20:47:18 EST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.24936/nu1.mnc ./tmp.mri_nu_correct.mni.24936/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.24936/1/ [fsl@fslvm6.localdomain:/mnt/hgfs/DATA/Freesurfer/chong_lan/mri/] [2013-01-09 20:47:19] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.24936/1/ ./tmp.mri_nu_correct.mni.24936/nu1.mnc ./tmp.mri_nu_correct.mni.24936/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 16 CV of field change: 0.000949803 [fsl@fslvm6.localdomain:/mnt/hgfs/DATA/Freesurfer/chong_lan/mri/] [2013-01-09 20:48:36] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.24936/nu1.mnc ./tmp.mri_nu_correct.mni.24936/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.24936/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24936/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/hgfs/DATA/Freesurfer/chong_lan/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.24936/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.24936/ones.mgz sysname Linux hostname fslvm6.localdomain machine x86_64 user fsl input ./tmp.mri_nu_correct.mni.24936/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.24936/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24936/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24936/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24936/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24936/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.24936/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24936/input.mean.dat sysname Linux hostname fslvm6.localdomain machine x86_64 user fsl Loading ./tmp.mri_nu_correct.mni.24936/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.24936/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24936/ones.mgz --i ./tmp.mri_nu_correct.mni.24936/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24936/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24936/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.24936/ones.mgz --i ./tmp.mri_nu_correct.mni.24936/nu2.mnc --sum ./tmp.mri_nu_correct.mni.24936/sum.junk --avgwf ./tmp.mri_nu_correct.mni.24936/output.mean.dat sysname Linux hostname fslvm6.localdomain machine x86_64 user fsl Loading ./tmp.mri_nu_correct.mni.24936/ones.mgz Loading ./tmp.mri_nu_correct.mni.24936/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.24936/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.24936/nu2.mnc ./tmp.mri_nu_correct.mni.24936/nu2.mnc mul 1.06560358890701468189 Saving result to './tmp.mri_nu_correct.mni.24936/nu2.mnc' (type = MINC )Outputting Volume: ............................................................ [ ok ] mri_convert ./tmp.mri_nu_correct.mni.24936/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.24936/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.24936/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 9 seconds. mapping (10, 100) to ( 3, 110) Wed Jan 9 20:51:09 EST 2013 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Wed Jan 9 20:51:10 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.081 -0.032 0.001 6.589; 0.066 1.059 0.366 -24.625; -0.025 -0.255 1.148 41.700; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 2 minutes and 14 seconds. MRIsplineNormalize(): npeaks = 15 Starting OpenSpline(): npoints = 15 white matter peak found at 111 white matter peak found at 109 gm peak at 55 (55), valley at 37 (37) csf peak at 28, setting threshold to 46 white matter peak found at 111 white matter peak found at 110 gm peak at 57 (57), valley at 38 (38) csf peak at 29, setting threshold to 47 #-------------------------------------------- #@# Skull Stripping Wed Jan 9 20:53:24 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (49, 49, 39) --> (206, 207, 225) using (101, 102, 132) as brain centroid... mean wm in atlas = 126, using box (82,83,109) --> (120, 121,154) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 initial log_p = -10412.8 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-1.7, 2.8, -22.2): log p = -10357.330 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10335.5, old_max_log_p =-10357.3 (thresh=-10347.0) 1.150 0.000 0.000 -20.824; 0.000 1.194 0.320 -61.136; 0.000 -0.259 0.966 12.820; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10330.5, old_max_log_p =-10335.5 (thresh=-10325.2) 1.150 0.000 0.000 -20.824; 0.000 1.312 0.063 -34.694; 0.000 0.063 1.092 -41.464; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10312.3, old_max_log_p =-10330.5 (thresh=-10320.2) 1.170 0.040 0.010 -27.438; -0.036 1.361 0.173 -51.630; 0.000 -0.058 1.082 -22.843; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10311.9, old_max_log_p =-10312.3 (thresh=-10302.0) 1.148 -0.001 -0.031 -16.650; 0.002 1.359 0.208 -60.538; 0.039 -0.099 1.055 -17.792; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10307.4, old_max_log_p =-10311.9 (thresh=-10301.6) 1.151 0.020 -0.011 -21.955; -0.017 1.360 0.208 -58.360; 0.020 -0.099 1.052 -15.018; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15104 0.01977 -0.01064 -21.95466; -0.01688 1.36007 0.20802 -58.36036; 0.02002 -0.09902 1.05169 -15.01840; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.15104 0.01977 -0.01064 -21.95466; -0.01688 1.36007 0.20802 -58.36036; 0.02002 -0.09902 1.05169 -15.01840; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 10307.4 tol 0.000010 Resulting transform: 1.151 0.020 -0.011 -21.955; -0.017 1.360 0.208 -58.360; 0.020 -0.099 1.052 -15.018; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10307.4 (old=-10412.8) transform before final EM align: 1.151 0.020 -0.011 -21.955; -0.017 1.360 0.208 -58.360; 0.020 -0.099 1.052 -15.018; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.15104 0.01977 -0.01064 -21.95466; -0.01688 1.36007 0.20802 -58.36036; 0.02002 -0.09902 1.05169 -15.01840; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.15104 0.01977 -0.01064 -21.95466; -0.01688 1.36007 0.20802 -58.36036; 0.02002 -0.09902 1.05169 -15.01840; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1145304.2 tol 0.000000 final transform: 1.151 0.020 -0.011 -21.955; -0.017 1.360 0.208 -58.360; 0.020 -0.099 1.052 -15.018; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 22 minutes and 42 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=105 z=126 r=72 first estimation of the main basin volume: 1586332 voxels Looking for seedpoints 2 found in the cerebellum 13 found in the rest of the brain global maximum in x=150, y=100, z=93, 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=17957695018 voxels, voxel volume =1.000 = 17957695018 mmm3 = 17957695.488 cm3 done. PostAnalyze...Basin Prior 354 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=113, z=124, r=9157 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=29 , nb = 45522 RIGHT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=32 , nb = 3132 LEFT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=37 , nb = 3078 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=28 , nb = 19350 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=28 , nb = 18936 OTHER CSF_MIN=0, CSF_intensity=14, CSF_MAX=34 , nb = 1026 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 29, 28, 27, 50 after analyzing : 22, 28, 28, 33 RIGHT_CER before analyzing : 32, 29, 27, 64 after analyzing : 22, 29, 29, 37 LEFT_CER before analyzing : 37, 36, 36, 64 after analyzing : 26, 36, 36, 43 RIGHT_BRAIN before analyzing : 28, 27, 27, 51 after analyzing : 21, 27, 27, 33 LEFT_BRAIN before analyzing : 28, 27, 27, 51 after analyzing : 21, 27, 27, 33 OTHER before analyzing : 34, 47, 58, 73 after analyzing : 34, 54, 58, 58 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...65 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 68.054, std = 7.639 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.95, sigma = 4.00 after rotation: sse = 2.95, sigma = 4.00 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.06, its var is 3.76 before Erosion-Dilatation 0.33% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...29 iterations mri_strip_skull: done peeling brain Brain Size = 1492418 voxels, voxel volume = 1.000 mm3 = 1492418 mmm3 = 1492.418 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Jan 9 21:16:31 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (60, 57, 53) --> (195, 181, 211) using (105, 98, 132) as brain centroid... mean wm in atlas = 107, using box (88,83,113) --> (121, 113,151) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 initial log_p = -7514.2 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-2.8, 5.1, -19.9): log p = -7290.771 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7183.2, old_max_log_p =-7290.8 (thresh=-7283.5) 1.064 0.000 0.000 -11.106; 0.000 1.135 0.169 -31.416; 0.000 -0.120 1.071 -15.159; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7183.2, old_max_log_p =-7183.2 (thresh=-7176.0) 1.064 0.000 0.000 -11.106; 0.000 1.135 0.169 -31.416; 0.000 -0.120 1.071 -15.159; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7093.7, old_max_log_p =-7183.2 (thresh=-7176.0) 1.040 0.070 0.053 -22.867; -0.066 1.135 0.278 -38.369; -0.034 -0.223 1.029 8.015; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7093.7, old_max_log_p =-7093.7 (thresh=-7086.6) 1.040 0.070 0.053 -22.867; -0.066 1.135 0.278 -38.369; -0.034 -0.223 1.029 8.015; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7078.4, old_max_log_p =-7093.7 (thresh=-7086.6) 1.040 0.051 0.048 -20.096; -0.049 1.138 0.279 -40.509; -0.034 -0.223 1.026 8.357; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7078.4, old_max_log_p =-7078.4 (thresh=-7071.4) 1.040 0.051 0.048 -20.096; -0.049 1.138 0.279 -40.509; -0.034 -0.223 1.026 8.357; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03998 0.05125 0.04806 -20.09595; -0.04874 1.13774 0.27906 -40.50945; -0.03401 -0.22250 1.02571 8.35691; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.03998 0.05125 0.04806 -20.09595; -0.04874 1.13774 0.27906 -40.50945; -0.03401 -0.22250 1.02571 8.35691; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 7078.4 tol 0.000010 Resulting transform: 1.040 0.051 0.048 -20.096; -0.049 1.138 0.279 -40.509; -0.034 -0.223 1.026 8.357; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -7078.4 (old=-7514.2) transform before final EM align: 1.040 0.051 0.048 -20.096; -0.049 1.138 0.279 -40.509; -0.034 -0.223 1.026 8.357; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03998 0.05125 0.04806 -20.09595; -0.04874 1.13774 0.27906 -40.50945; -0.03401 -0.22250 1.02571 8.35691; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.03998 0.05125 0.04806 -20.09595; -0.04874 1.13774 0.27906 -40.50945; -0.03401 -0.22250 1.02571 8.35691; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 842356.3 tol 0.000000 final transform: 1.040 0.051 0.048 -20.096; -0.049 1.138 0.279 -40.509; -0.034 -0.223 1.026 8.357; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 20 minutes and 49 seconds. #-------------------------------------- #@# CA Normalize Wed Jan 9 21:37:21 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (60, 57, 53) --> (195, 181, 211) using (105, 98, 132) as brain centroid... mean wm in atlas = 107, using box (88,83,113) --> (121, 113,151) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.019 scaling channel 0 by 1.01905 using 244171 sample points... INFO: compute sample coordinates transform 1.040 0.051 0.048 -20.096; -0.049 1.138 0.279 -40.509; -0.034 -0.223 1.026 8.357; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 58, 52) --> (192, 159, 208) Left_Cerebral_White_Matter: limiting intensities to 115.0 --> 255.0 3 of 17 (17.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 58, 50) --> (131, 153, 207) Right_Cerebral_White_Matter: limiting intensities to 124.0 --> 255.0 8 of 11 (72.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 135, 79) --> (175, 175, 129) Left_Cerebellum_White_Matter: limiting intensities to 93.0 --> 255.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 135, 75) --> (129, 172, 128) Right_Cerebellum_White_Matter: limiting intensities to 92.0 --> 255.0 0 of 11 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 125, 111) --> (143, 186, 139) Brain_Stem: limiting intensities to 88.0 --> 255.0 0 of 9 (0.0%) samples deleted using 56 total control points for intensity normalization... bias field = 0.899 +- 0.046 0 of 45 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 58, 52) --> (192, 159, 208) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 238.0 3 of 79 (3.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 58, 50) --> (131, 153, 207) Right_Cerebral_White_Matter: limiting intensities to 117.0 --> 238.0 61 of 69 (88.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 135, 79) --> (175, 175, 129) Left_Cerebellum_White_Matter: limiting intensities to 72.0 --> 238.0 0 of 53 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 135, 75) --> (129, 172, 128) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 238.0 0 of 47 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 125, 111) --> (143, 186, 139) Brain_Stem: limiting intensities to 71.0 --> 238.0 0 of 77 (0.0%) samples deleted using 325 total control points for intensity normalization... bias field = 1.008 +- 0.059 0 of 261 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 58, 52) --> (192, 159, 208) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 247.0 8 of 163 (4.9%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 58, 50) --> (131, 153, 207) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 247.0 51 of 195 (26.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 135, 79) --> (175, 175, 129) Left_Cerebellum_White_Matter: limiting intensities to 78.0 --> 247.0 0 of 58 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (83, 135, 75) --> (129, 172, 128) Right_Cerebellum_White_Matter: limiting intensities to 76.0 --> 247.0 0 of 48 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 125, 111) --> (143, 186, 139) Brain_Stem: limiting intensities to 73.0 --> 247.0 0 of 135 (0.0%) samples deleted using 599 total control points for intensity normalization... bias field = 1.007 +- 0.057 1 of 540 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 42 seconds. #-------------------------------------- #@# CA Reg Wed Jan 9 21:39:03 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.28 (predicted orig area = 6.2) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.938, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24863.436 ms 0001: dt=129.472000, rms=0.846 (9.856%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24977.693 ms 0002: dt=129.472000, rms=0.830 (1.815%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26635.984 ms 0003: dt=295.936000, rms=0.810 (2.449%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25267.779 ms 0004: dt=73.984000, rms=0.802 (0.962%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26937.871 ms 0005: dt=517.888000, rms=0.788 (1.707%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26564.293 ms 0006: dt=129.472000, rms=0.783 (0.684%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26407.768 ms 0007: dt=92.480000, rms=0.782 (0.126%), neg=0, invalid=766 0008: dt=92.480000, rms=0.780 (0.273%), neg=0, invalid=766 0009: dt=92.480000, rms=0.777 (0.388%), neg=0, invalid=766 0010: dt=92.480000, rms=0.773 (0.466%), neg=0, invalid=766 0011: dt=92.480000, rms=0.769 (0.509%), neg=0, invalid=766 0012: dt=92.480000, rms=0.765 (0.551%), neg=0, invalid=766 0013: dt=92.480000, rms=0.761 (0.551%), neg=0, invalid=766 0014: dt=92.480000, rms=0.757 (0.469%), neg=0, invalid=766 0015: dt=92.480000, rms=0.754 (0.386%), neg=0, invalid=766 0016: dt=92.480000, rms=0.752 (0.355%), neg=0, invalid=766 0017: dt=92.480000, rms=0.749 (0.387%), neg=0, invalid=766 0018: dt=92.480000, rms=0.746 (0.348%), neg=0, invalid=766 0019: dt=92.480000, rms=0.744 (0.307%), neg=0, invalid=766 0020: dt=92.480000, rms=0.742 (0.318%), neg=0, invalid=766 0021: dt=92.480000, rms=0.739 (0.346%), neg=0, invalid=766 0022: dt=92.480000, rms=0.736 (0.331%), neg=0, invalid=766 0023: dt=92.480000, rms=0.734 (0.322%), neg=0, invalid=766 0024: dt=92.480000, rms=0.732 (0.305%), neg=0, invalid=766 0025: dt=92.480000, rms=0.730 (0.279%), neg=0, invalid=766 0026: dt=92.480000, rms=0.728 (0.266%), neg=0, invalid=766 0027: dt=92.480000, rms=0.726 (0.257%), neg=0, invalid=766 0028: dt=92.480000, rms=0.724 (0.247%), neg=0, invalid=766 0029: dt=92.480000, rms=0.723 (0.212%), neg=0, invalid=766 0030: dt=92.480000, rms=0.721 (0.198%), neg=0, invalid=766 0031: dt=92.480000, rms=0.720 (0.192%), neg=0, invalid=766 0032: dt=92.480000, rms=0.718 (0.217%), neg=0, invalid=766 0033: dt=92.480000, rms=0.717 (0.180%), neg=0, invalid=766 0034: dt=92.480000, rms=0.716 (0.142%), neg=0, invalid=766 0035: dt=92.480000, rms=0.715 (0.105%), neg=0, invalid=766 0036: dt=92.480000, rms=0.714 (0.150%), neg=0, invalid=766 0037: dt=92.480000, rms=0.713 (0.165%), neg=0, invalid=766 0038: dt=92.480000, rms=0.712 (0.135%), neg=0, invalid=766 0039: dt=92.480000, rms=0.711 (0.090%), neg=0, invalid=766 0040: dt=92.480000, rms=0.711 (0.076%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29815.182 ms 0041: dt=295.936000, rms=0.710 (0.121%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28982.434 ms 0042: dt=23.120000, rms=0.710 (0.003%), neg=0, invalid=766 0043: dt=23.120000, rms=0.710 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.710, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28077.912 ms 0044: dt=32.368000, rms=0.710 (0.028%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30264.877 ms 0045: dt=73.984000, rms=0.710 (0.030%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30443.346 ms 0046: dt=221.952000, rms=0.709 (0.092%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30276.115 ms 0047: dt=0.000000, rms=0.709 (-0.002%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.718, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28622.428 ms 0048: dt=145.152000, rms=0.708 (1.502%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26038.977 ms 0049: dt=36.288000, rms=0.703 (0.665%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28166.018 ms 0050: dt=145.152000, rms=0.693 (1.372%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25952.934 ms 0051: dt=36.288000, rms=0.689 (0.640%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27908.090 ms 0052: dt=145.152000, rms=0.684 (0.634%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26151.504 ms 0053: dt=36.288000, rms=0.680 (0.622%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25936.027 ms 0054: dt=36.288000, rms=0.679 (0.148%), neg=0, invalid=766 0055: dt=36.288000, rms=0.677 (0.309%), neg=0, invalid=766 0056: dt=36.288000, rms=0.675 (0.377%), neg=0, invalid=766 0057: dt=36.288000, rms=0.671 (0.462%), neg=0, invalid=766 0058: dt=36.288000, rms=0.668 (0.517%), neg=0, invalid=766 0059: dt=36.288000, rms=0.663 (0.677%), neg=0, invalid=766 0060: dt=36.288000, rms=0.659 (0.634%), neg=0, invalid=766 0061: dt=36.288000, rms=0.655 (0.600%), neg=0, invalid=766 0062: dt=36.288000, rms=0.652 (0.565%), neg=0, invalid=766 0063: dt=36.288000, rms=0.648 (0.567%), neg=0, invalid=766 0064: dt=36.288000, rms=0.645 (0.457%), neg=0, invalid=766 0065: dt=36.288000, rms=0.643 (0.343%), neg=0, invalid=766 0066: dt=36.288000, rms=0.641 (0.279%), neg=0, invalid=766 0067: dt=36.288000, rms=0.639 (0.265%), neg=0, invalid=766 0068: dt=36.288000, rms=0.637 (0.274%), neg=0, invalid=766 0069: dt=36.288000, rms=0.636 (0.219%), neg=0, invalid=766 0070: dt=36.288000, rms=0.635 (0.148%), neg=0, invalid=766 0071: dt=36.288000, rms=0.634 (0.154%), neg=0, invalid=766 0072: dt=36.288000, rms=0.633 (0.180%), neg=0, invalid=766 0073: dt=36.288000, rms=0.632 (0.133%), neg=0, invalid=766 0074: dt=36.288000, rms=0.631 (0.140%), neg=0, invalid=766 0075: dt=36.288000, rms=0.630 (0.135%), neg=0, invalid=766 0076: dt=36.288000, rms=0.629 (0.157%), neg=0, invalid=766 0077: dt=36.288000, rms=0.629 (0.133%), neg=0, invalid=766 0078: dt=36.288000, rms=0.628 (0.111%), neg=0, invalid=766 0079: dt=36.288000, rms=0.627 (0.105%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27759.410 ms 0080: dt=36.288000, rms=0.627 (0.044%), neg=0, invalid=766 0081: dt=36.288000, rms=0.627 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27679.098 ms 0082: dt=36.288000, rms=0.627 (0.058%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29625.584 ms 0083: dt=36.288000, rms=0.626 (0.031%), neg=0, invalid=766 0084: dt=36.288000, rms=0.626 (-0.020%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.661, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29623.854 ms 0085: dt=0.175000, rms=0.661 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29492.021 ms 0086: dt=0.100000, rms=0.661 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.661, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29338.248 ms 0087: dt=0.125000, rms=0.661 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29839.340 ms 0088: dt=0.002344, rms=0.661 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.760, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27739.219 ms 0089: dt=4.794020, rms=0.734 (3.498%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27828.123 ms 0090: dt=3.456000, rms=0.731 (0.343%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28396.953 ms 0091: dt=1.008000, rms=0.731 (0.027%), neg=0, invalid=766 0092: dt=1.008000, rms=0.731 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.731, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25905.629 ms 0093: dt=0.000000, rms=0.731 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.815, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27761.621 ms 0094: dt=1.124736, rms=0.810 (0.553%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25820.172 ms 0095: dt=1.792000, rms=0.803 (0.924%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26075.736 ms 0096: dt=0.448000, rms=0.802 (0.070%), neg=0, invalid=766 0097: dt=0.448000, rms=0.802 (0.056%), neg=0, invalid=766 0098: dt=0.448000, rms=0.801 (0.069%), neg=0, invalid=766 0099: dt=0.448000, rms=0.801 (0.048%), neg=0, invalid=766 0100: dt=0.448000, rms=0.801 (-0.019%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.801, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25926.754 ms 0101: dt=1.536000, rms=0.798 (0.407%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24509.859 ms 0102: dt=0.000000, rms=0.798 (0.002%), neg=0, invalid=766 0103: dt=0.100000, rms=0.798 (-0.016%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.738, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24222.668 ms 0104: dt=0.080000, rms=0.733 (0.719%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24320.424 ms 0105: dt=0.080000, rms=0.731 (0.291%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22389.703 ms 0106: dt=0.028000, rms=0.730 (0.065%), neg=0, invalid=766 0107: dt=0.028000, rms=0.730 (0.060%), neg=0, invalid=766 0108: dt=0.028000, rms=0.729 (0.107%), neg=0, invalid=766 0109: dt=0.028000, rms=0.729 (0.046%), neg=0, invalid=766 0110: dt=0.028000, rms=0.728 (0.084%), neg=0, invalid=766 0111: dt=0.028000, rms=0.727 (0.111%), neg=0, invalid=766 0112: dt=0.028000, rms=0.727 (0.131%), neg=0, invalid=766 0113: dt=0.028000, rms=0.726 (0.138%), neg=0, invalid=766 0114: dt=0.028000, rms=0.725 (0.137%), neg=0, invalid=766 0115: dt=0.014000, rms=0.724 (0.005%), neg=0, invalid=766 0116: dt=0.014000, rms=0.724 (0.010%), neg=0, invalid=766 0117: dt=0.014000, rms=0.724 (0.013%), neg=0, invalid=766 0118: dt=0.014000, rms=0.724 (0.018%), neg=0, invalid=766 0119: dt=0.014000, rms=0.724 (0.020%), neg=0, invalid=766 0120: dt=0.014000, rms=0.724 (0.025%), neg=0, invalid=766 0121: dt=0.014000, rms=0.724 (0.030%), neg=0, invalid=766 0122: dt=0.014000, rms=0.724 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24258.021 ms 0123: dt=0.096000, rms=0.723 (0.042%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22710.094 ms 0124: dt=0.028000, rms=0.723 (0.011%), neg=0, invalid=766 0125: dt=0.028000, rms=0.723 (0.011%), neg=0, invalid=766 0126: dt=0.028000, rms=0.723 (0.021%), neg=0, invalid=766 0127: dt=0.028000, rms=0.723 (0.010%), neg=0, invalid=766 0128: dt=0.028000, rms=0.723 (0.019%), neg=0, invalid=766 0129: dt=0.028000, rms=0.723 (0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26061.668 ms 0130: dt=0.384000, rms=0.714 (1.138%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22464.262 ms 0131: dt=0.000000, rms=0.714 (-0.001%), neg=0, invalid=766 0132: dt=0.050000, rms=0.714 (-0.363%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.10486 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (1325 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1325 voxels, peak = 6), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.12784 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (697 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (697 voxels, peak = 9), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.07362 (89) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (418 voxels, overlap=0.360) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (418 voxels, peak = 90), gca=90.0 gca peak = 0.19192 (97) mri peak = 0.07754 (99) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (313 voxels, overlap=0.756) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (313 voxels, peak = 87), gca=87.3 gca peak = 0.24007 (63) mri peak = 0.08914 (55) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (526 voxels, overlap=0.482) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (526 voxels, peak = 55), gca=55.1 gca peak = 0.29892 (64) mri peak = 0.06110 (61) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (358 voxels, overlap=0.424) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (358 voxels, peak = 56), gca=56.0 gca peak = 0.12541 (104) mri peak = 0.05073 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (58631 voxels, overlap=0.930) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (58631 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.05428 (109) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (58797 voxels, overlap=0.866) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (58797 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.03326 (58) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (15479 voxels, overlap=0.274) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (15479 voxels, peak = 55), gca=55.1 gca peak = 0.13270 (63) mri peak = 0.03858 (56) Right_Cerebral_Cortex (42): linear fit = 0.88 x + 0.0 (17275 voxels, overlap=0.270) Right_Cerebral_Cortex (42): linear fit = 0.88 x + 0.0 (17275 voxels, peak = 55), gca=55.1 gca peak = 0.15182 (70) mri peak = 0.09296 (56) Right_Caudate (50): linear fit = 0.80 x + 0.0 (304 voxels, overlap=0.002) Right_Caudate (50): linear fit = 0.80 x + 0.0 (304 voxels, peak = 56), gca=56.0 gca peak = 0.14251 (76) mri peak = 0.07711 (68) Left_Caudate (11): linear fit = 0.82 x + 0.0 (631 voxels, overlap=0.183) Left_Caudate (11): linear fit = 0.82 x + 0.0 (631 voxels, peak = 63), gca=62.7 gca peak = 0.12116 (60) mri peak = 0.03415 (58) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (16105 voxels, overlap=0.965) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (16105 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.03210 (59) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (21309 voxels, overlap=0.953) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (21309 voxels, peak = 63), gca=62.5 gca peak = 0.22684 (88) mri peak = 0.05244 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (8660 voxels, overlap=0.903) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (8660 voxels, peak = 92), gca=92.4 gca peak = 0.21067 (87) mri peak = 0.06179 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7882 voxels, overlap=0.867) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7882 voxels, peak = 91), gca=91.3 gca peak = 0.25455 (62) mri peak = 0.10612 (55) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (265 voxels, overlap=0.658) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (265 voxels, peak = 54), gca=54.2 gca peak = 0.39668 (62) mri peak = 0.13688 (58) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (293 voxels, overlap=0.931) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (293 voxels, peak = 57), gca=57.4 gca peak = 0.10129 (93) mri peak = 0.04191 (84) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4764 voxels, overlap=0.951) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (4764 voxels, peak = 91), gca=90.7 gca peak = 0.12071 (89) mri peak = 0.05685 (85) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3829 voxels, overlap=0.971) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3829 voxels, peak = 87), gca=86.8 gca peak = 0.13716 (82) mri peak = 0.05470 (71) Left_Putamen (12): linear fit = 0.93 x + 0.0 (1941 voxels, overlap=0.408) Left_Putamen (12): linear fit = 0.93 x + 0.0 (1941 voxels, peak = 76), gca=75.8 gca peak = 0.15214 (84) mri peak = 0.05311 (72) Right_Putamen (51): linear fit = 0.85 x + 0.0 (2256 voxels, overlap=0.325) Right_Putamen (51): linear fit = 0.85 x + 0.0 (2256 voxels, peak = 71), gca=71.4 gca peak = 0.08983 (85) mri peak = 0.06518 (88) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10621 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10621 voxels, peak = 89), gca=89.2 gca peak = 0.11809 (92) mri peak = 0.06703 (104) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1061 voxels, overlap=0.721) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1061 voxels, peak = 104), gca=103.5 gca peak = 0.12914 (94) mri peak = 0.06463 (104) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1282 voxels, overlap=0.684) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1282 voxels, peak = 103), gca=103.4 gca peak = 0.21100 (36) mri peak = 0.16786 (12) gca peak = 0.13542 (27) mri peak = 0.10669 (20) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (249 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.60 x + 0.0 (249 voxels, peak = 16), gca=16.2 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.88 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.742, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27963.551 ms 0133: dt=129.472000, rms=0.736 (0.816%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 118665.539 ms 0134: dt=129.472000, rms=0.733 (0.360%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27681.277 ms 0135: dt=129.472000, rms=0.732 (0.177%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29600.963 ms 0136: dt=129.472000, rms=0.730 (0.156%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27987.777 ms 0137: dt=110.976000, rms=0.730 (0.122%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29687.217 ms 0138: dt=110.976000, rms=0.729 (0.098%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27942.564 ms 0139: dt=110.976000, rms=0.728 (0.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29931.018 ms 0140: dt=110.976000, rms=0.728 (0.071%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28030.621 ms 0141: dt=110.976000, rms=0.727 (0.086%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29589.354 ms 0142: dt=92.480000, rms=0.727 (0.064%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27778.838 ms 0143: dt=129.472000, rms=0.726 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29907.221 ms 0144: dt=73.984000, rms=0.726 (0.059%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27760.568 ms 0145: dt=295.936000, rms=0.725 (0.113%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27824.668 ms 0146: dt=73.984000, rms=0.724 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28018.359 ms 0147: dt=129.472000, rms=0.724 (0.066%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29735.031 ms 0148: dt=110.976000, rms=0.723 (0.043%), neg=0, invalid=766 0149: dt=110.976000, rms=0.723 (0.060%), neg=0, invalid=766 0150: dt=110.976000, rms=0.722 (0.099%), neg=0, invalid=766 0151: dt=110.976000, rms=0.721 (0.107%), neg=0, invalid=766 0152: dt=110.976000, rms=0.720 (0.150%), neg=0, invalid=766 0153: dt=110.976000, rms=0.719 (0.143%), neg=0, invalid=766 0154: dt=110.976000, rms=0.718 (0.151%), neg=0, invalid=766 0155: dt=110.976000, rms=0.717 (0.119%), neg=0, invalid=766 0156: dt=110.976000, rms=0.716 (0.120%), neg=0, invalid=766 0157: dt=110.976000, rms=0.716 (0.107%), neg=0, invalid=766 0158: dt=110.976000, rms=0.715 (0.111%), neg=0, invalid=766 0159: dt=110.976000, rms=0.714 (0.085%), neg=0, invalid=766 0160: dt=110.976000, rms=0.714 (0.100%), neg=0, invalid=766 0161: dt=110.976000, rms=0.713 (0.096%), neg=0, invalid=766 0162: dt=110.976000, rms=0.712 (0.100%), neg=0, invalid=766 0163: dt=110.976000, rms=0.711 (0.100%), neg=0, invalid=766 0164: dt=110.976000, rms=0.711 (0.107%), neg=0, invalid=766 0165: dt=110.976000, rms=0.710 (0.120%), neg=0, invalid=766 0166: dt=110.976000, rms=0.709 (0.112%), neg=0, invalid=766 0167: dt=110.976000, rms=0.708 (0.111%), neg=0, invalid=766 0168: dt=110.976000, rms=0.707 (0.111%), neg=0, invalid=766 0169: dt=110.976000, rms=0.707 (0.114%), neg=0, invalid=766 0170: dt=110.976000, rms=0.706 (0.105%), neg=0, invalid=766 0171: dt=110.976000, rms=0.705 (0.099%), neg=0, invalid=766 0172: dt=110.976000, rms=0.705 (0.100%), neg=0, invalid=766 0173: dt=110.976000, rms=0.704 (0.099%), neg=0, invalid=766 0174: dt=110.976000, rms=0.703 (0.095%), neg=0, invalid=766 0175: dt=110.976000, rms=0.702 (0.095%), neg=0, invalid=766 0176: dt=110.976000, rms=0.702 (0.086%), neg=0, invalid=766 0177: dt=110.976000, rms=0.701 (0.082%), neg=0, invalid=766 0178: dt=110.976000, rms=0.701 (0.081%), neg=0, invalid=766 0179: dt=110.976000, rms=0.700 (0.075%), neg=0, invalid=766 0180: dt=110.976000, rms=0.700 (0.067%), neg=0, invalid=766 0181: dt=110.976000, rms=0.699 (0.064%), neg=0, invalid=766 0182: dt=110.976000, rms=0.699 (0.061%), neg=0, invalid=766 0183: dt=110.976000, rms=0.698 (0.062%), neg=0, invalid=766 0184: dt=110.976000, rms=0.698 (0.056%), neg=0, invalid=766 0185: dt=110.976000, rms=0.698 (0.052%), neg=0, invalid=766 0186: dt=110.976000, rms=0.697 (0.060%), neg=0, invalid=766 0187: dt=110.976000, rms=0.697 (0.059%), neg=0, invalid=766 0188: dt=110.976000, rms=0.696 (0.063%), neg=0, invalid=766 0189: dt=110.976000, rms=0.696 (0.055%), neg=0, invalid=766 0190: dt=110.976000, rms=0.696 (0.050%), neg=0, invalid=766 0191: dt=110.976000, rms=0.695 (0.047%), neg=0, invalid=766 0192: dt=110.976000, rms=0.695 (0.050%), neg=0, invalid=766 0193: dt=110.976000, rms=0.695 (0.051%), neg=0, invalid=766 0194: dt=110.976000, rms=0.694 (0.050%), neg=0, invalid=766 0195: dt=110.976000, rms=0.694 (0.046%), neg=0, invalid=766 0196: dt=110.976000, rms=0.694 (0.054%), neg=0, invalid=766 0197: dt=110.976000, rms=0.693 (0.048%), neg=0, invalid=766 0198: dt=110.976000, rms=0.693 (0.044%), neg=0, invalid=766 0199: dt=110.976000, rms=0.693 (0.039%), neg=0, invalid=766 0200: dt=110.976000, rms=0.692 (0.040%), neg=0, invalid=766 0201: dt=110.976000, rms=0.692 (0.041%), neg=0, invalid=766 0202: dt=110.976000, rms=0.692 (0.044%), neg=0, invalid=766 0203: dt=110.976000, rms=0.692 (0.037%), neg=0, invalid=766 0204: dt=110.976000, rms=0.691 (0.035%), neg=0, invalid=766 0205: dt=110.976000, rms=0.691 (0.037%), neg=0, invalid=766 0206: dt=110.976000, rms=0.691 (0.035%), neg=0, invalid=766 0207: dt=110.976000, rms=0.691 (0.031%), neg=0, invalid=766 0208: dt=110.976000, rms=0.690 (0.028%), neg=0, invalid=766 0209: dt=110.976000, rms=0.690 (0.029%), neg=0, invalid=766 0210: dt=110.976000, rms=0.690 (0.027%), neg=0, invalid=766 0211: dt=110.976000, rms=0.690 (0.024%), neg=0, invalid=766 0212: dt=110.976000, rms=0.690 (0.029%), neg=0, invalid=766 0213: dt=110.976000, rms=0.690 (0.029%), neg=0, invalid=766 0214: dt=110.976000, rms=0.689 (0.026%), neg=0, invalid=766 0215: dt=110.976000, rms=0.689 (0.024%), neg=0, invalid=766 0216: dt=110.976000, rms=0.689 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27699.633 ms 0217: dt=369.920000, rms=0.689 (0.003%), neg=0, invalid=766 0218: dt=369.920000, rms=0.689 (-0.191%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.689, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27922.379 ms 0219: dt=221.952000, rms=0.688 (0.146%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25929.893 ms 0220: dt=110.976000, rms=0.688 (0.030%), neg=0, invalid=766 0221: dt=110.976000, rms=0.688 (0.025%), neg=0, invalid=766 0222: dt=110.976000, rms=0.687 (0.029%), neg=0, invalid=766 0223: dt=110.976000, rms=0.687 (0.021%), neg=0, invalid=766 0224: dt=110.976000, rms=0.687 (0.041%), neg=0, invalid=766 0225: dt=110.976000, rms=0.687 (0.048%), neg=0, invalid=766 0226: dt=110.976000, rms=0.686 (0.028%), neg=0, invalid=766 0227: dt=110.976000, rms=0.686 (0.031%), neg=0, invalid=766 0228: dt=110.976000, rms=0.686 (0.027%), neg=0, invalid=766 0229: dt=110.976000, rms=0.686 (0.045%), neg=0, invalid=766 0230: dt=110.976000, rms=0.686 (0.008%), neg=0, invalid=766 0231: dt=110.976000, rms=0.686 (0.012%), neg=0, invalid=766 0232: dt=110.976000, rms=0.686 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22497.426 ms 0233: dt=32.368000, rms=0.686 (0.001%), neg=0, invalid=766 0234: dt=32.368000, rms=0.686 (0.001%), neg=0, invalid=766 0235: dt=32.368000, rms=0.686 (0.002%), neg=0, invalid=766 0236: dt=16.184000, rms=0.685 (0.001%), neg=0, invalid=766 0237: dt=1.011500, rms=0.685 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.687, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26060.832 ms 0238: dt=103.680000, rms=0.680 (0.997%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26014.713 ms 0239: dt=82.944000, rms=0.677 (0.478%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26417.572 ms 0240: dt=31.104000, rms=0.674 (0.531%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26009.801 ms 0241: dt=36.288000, rms=0.672 (0.249%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 28388.818 ms 0242: dt=62.208000, rms=0.669 (0.387%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24288.910 ms 0243: dt=25.920000, rms=0.668 (0.260%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26021.014 ms 0244: dt=82.944000, rms=0.665 (0.405%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24501.684 ms 0245: dt=20.736000, rms=0.663 (0.281%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24238.529 ms 0246: dt=36.288000, rms=0.662 (0.231%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22838.438 ms 0247: dt=9.072000, rms=0.661 (0.048%), neg=0, invalid=766 0248: dt=9.072000, rms=0.661 (0.051%), neg=0, invalid=766 0249: dt=9.072000, rms=0.661 (0.049%), neg=0, invalid=766 0250: dt=1.134000, rms=0.660 (0.005%), neg=0, invalid=766 0251: dt=0.283500, rms=0.660 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 19125.967 ms 0252: dt=0.121500, rms=0.660 (0.001%), neg=0, invalid=766 0253: dt=0.007594, rms=0.660 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.660, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22451.379 ms 0254: dt=0.002215, rms=0.660 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 12141.710 ms 0255: dt=0.000000, rms=0.660 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.668, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 12172.946 ms 0256: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.668, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 12117.009 ms 0257: dt=0.000000, rms=0.668 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.691, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26814.014 ms 0258: dt=4.032000, rms=0.668 (3.387%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27569.086 ms 0259: dt=11.520000, rms=0.623 (6.650%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24155.561 ms 0260: dt=4.032000, rms=0.618 (0.852%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24337.705 ms 0261: dt=4.032000, rms=0.613 (0.739%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25962.859 ms 0262: dt=13.824000, rms=0.601 (2.093%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25989.820 ms 0263: dt=16.128000, rms=0.594 (1.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25964.795 ms 0264: dt=2.880000, rms=0.593 (0.207%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26008.316 ms 0265: dt=13.824000, rms=0.590 (0.573%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25968.129 ms 0266: dt=3.185185, rms=0.589 (0.140%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26218.553 ms 0267: dt=7.157895, rms=0.588 (0.220%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25938.889 ms 0268: dt=4.032000, rms=0.587 (0.121%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26143.484 ms 0269: dt=5.280000, rms=0.586 (0.141%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25997.266 ms 0270: dt=4.032000, rms=0.585 (0.106%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26379.555 ms 0271: dt=6.315789, rms=0.585 (0.145%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25933.551 ms 0272: dt=3.471698, rms=0.584 (0.091%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26345.840 ms 0273: dt=6.400000, rms=0.583 (0.136%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26075.664 ms 0274: dt=4.137931, rms=0.583 (0.089%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26257.455 ms 0275: dt=5.000000, rms=0.582 (0.106%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25920.857 ms 0276: dt=5.176471, rms=0.582 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26123.740 ms 0277: dt=4.333333, rms=0.581 (0.081%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26134.557 ms 0278: dt=6.000000, rms=0.581 (0.106%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26186.496 ms 0279: dt=4.032000, rms=0.580 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26011.123 ms 0280: dt=5.142857, rms=0.580 (0.098%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26242.238 ms 0281: dt=4.032000, rms=0.579 (0.052%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25964.152 ms 0282: dt=4.857143, rms=0.579 (0.080%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26218.877 ms 0283: dt=4.533333, rms=0.579 (0.054%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26209.895 ms 0284: dt=5.090909, rms=0.578 (0.080%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26172.193 ms 0285: dt=4.032000, rms=0.578 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26055.705 ms 0286: dt=5.090909, rms=0.577 (0.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24579.801 ms 0287: dt=4.032000, rms=0.577 (0.043%), neg=0, invalid=766 0288: dt=4.032000, rms=0.577 (0.058%), neg=0, invalid=766 0289: dt=4.032000, rms=0.576 (0.084%), neg=0, invalid=766 0290: dt=4.032000, rms=0.576 (0.109%), neg=0, invalid=766 0291: dt=4.032000, rms=0.575 (0.148%), neg=0, invalid=766 0292: dt=4.032000, rms=0.574 (0.178%), neg=0, invalid=766 0293: dt=4.032000, rms=0.573 (0.176%), neg=0, invalid=766 0294: dt=4.032000, rms=0.572 (0.181%), neg=0, invalid=766 0295: dt=4.032000, rms=0.571 (0.163%), neg=0, invalid=766 0296: dt=4.032000, rms=0.570 (0.160%), neg=0, invalid=766 0297: dt=4.032000, rms=0.569 (0.138%), neg=0, invalid=766 0298: dt=4.032000, rms=0.569 (0.003%), neg=0, invalid=766 0299: dt=4.032000, rms=0.569 (0.003%), neg=0, invalid=766 0300: dt=4.032000, rms=0.569 (0.019%), neg=0, invalid=766 0301: dt=4.032000, rms=0.569 (0.015%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26095.557 ms 0302: dt=6.912000, rms=0.569 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26248.176 ms 0303: dt=4.032000, rms=0.569 (0.026%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 25793.119 ms 0304: dt=4.032000, rms=0.569 (0.011%), neg=0, invalid=766 0305: dt=4.032000, rms=0.569 (0.009%), neg=0, invalid=766 0306: dt=4.032000, rms=0.568 (0.021%), neg=0, invalid=766 0307: dt=4.032000, rms=0.568 (0.028%), neg=0, invalid=766 0308: dt=4.032000, rms=0.568 (0.044%), neg=0, invalid=766 0309: dt=4.032000, rms=0.568 (0.049%), neg=0, invalid=766 0310: dt=4.032000, rms=0.568 (0.039%), neg=0, invalid=766 0311: dt=4.032000, rms=0.567 (0.050%), neg=0, invalid=766 0312: dt=4.032000, rms=0.567 (0.054%), neg=0, invalid=766 0313: dt=4.032000, rms=0.567 (0.065%), neg=0, invalid=766 0314: dt=4.032000, rms=0.566 (0.057%), neg=0, invalid=766 0315: dt=4.032000, rms=0.566 (0.061%), neg=0, invalid=766 0316: dt=4.032000, rms=0.566 (0.057%), neg=0, invalid=766 0317: dt=4.032000, rms=0.565 (0.055%), neg=0, invalid=766 0318: dt=4.032000, rms=0.565 (0.042%), neg=0, invalid=766 0319: dt=4.032000, rms=0.565 (0.050%), neg=0, invalid=766 0320: dt=4.032000, rms=0.564 (0.052%), neg=0, invalid=766 0321: dt=4.032000, rms=0.564 (0.045%), neg=0, invalid=766 0322: dt=4.032000, rms=0.564 (0.045%), neg=0, invalid=766 0323: dt=4.032000, rms=0.564 (0.035%), neg=0, invalid=766 0324: dt=4.032000, rms=0.564 (0.042%), neg=0, invalid=766 0325: dt=4.032000, rms=0.563 (0.037%), neg=0, invalid=766 0326: dt=4.032000, rms=0.563 (0.038%), neg=0, invalid=766 0327: dt=4.032000, rms=0.563 (0.031%), neg=0, invalid=766 0328: dt=4.032000, rms=0.563 (0.042%), neg=0, invalid=766 0329: dt=4.032000, rms=0.562 (0.037%), neg=0, invalid=766 0330: dt=4.032000, rms=0.562 (0.030%), neg=0, invalid=766 0331: dt=4.032000, rms=0.562 (0.029%), neg=0, invalid=766 0332: dt=4.032000, rms=0.562 (0.028%), neg=0, invalid=766 0333: dt=4.032000, rms=0.562 (0.017%), neg=0, invalid=766 0334: dt=4.032000, rms=0.562 (0.026%), neg=0, invalid=766 0335: dt=4.032000, rms=0.562 (0.017%), neg=0, invalid=766 0336: dt=4.032000, rms=0.561 (0.026%), neg=0, invalid=766 0337: dt=4.032000, rms=0.561 (0.019%), neg=0, invalid=766 0338: dt=4.032000, rms=0.561 (0.021%), neg=0, invalid=766 0339: dt=4.032000, rms=0.561 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26130.994 ms 0340: dt=4.032000, rms=0.561 (0.008%), neg=0, invalid=766 0341: dt=4.032000, rms=0.561 (0.005%), neg=0, invalid=766 0342: dt=4.032000, rms=0.561 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.561, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26103.180 ms 0343: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.586, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24494.545 ms 0344: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.586, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24350.590 ms 0345: dt=0.000000, rms=0.586 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.544, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24396.883 ms 0346: dt=0.185988, rms=0.534 (1.752%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 20836.811 ms 0347: dt=0.007000, rms=0.534 (0.040%), neg=0, invalid=766 0348: dt=0.007000, rms=0.534 (0.041%), neg=0, invalid=766 0349: dt=0.007000, rms=0.533 (0.078%), neg=0, invalid=766 0350: dt=0.007000, rms=0.533 (0.110%), neg=0, invalid=766 0351: dt=0.007000, rms=0.532 (0.134%), neg=0, invalid=766 0352: dt=0.007000, rms=0.531 (0.159%), neg=0, invalid=766 0353: dt=0.007000, rms=0.530 (0.176%), neg=0, invalid=766 0354: dt=0.007000, rms=0.529 (0.191%), neg=0, invalid=766 0355: dt=0.007000, rms=0.528 (0.201%), neg=0, invalid=766 0356: dt=0.007000, rms=0.527 (0.207%), neg=0, invalid=766 0357: dt=0.007000, rms=0.526 (0.206%), neg=0, invalid=766 0358: dt=0.007000, rms=0.525 (0.207%), neg=0, invalid=766 0359: dt=0.007000, rms=0.524 (0.206%), neg=0, invalid=766 0360: dt=0.007000, rms=0.523 (0.204%), neg=0, invalid=766 0361: dt=0.007000, rms=0.522 (0.195%), neg=0, invalid=766 0362: dt=0.007000, rms=0.521 (0.190%), neg=0, invalid=766 0363: dt=0.007000, rms=0.520 (0.179%), neg=0, invalid=766 0364: dt=0.007000, rms=0.519 (0.168%), neg=0, invalid=766 0365: dt=0.007000, rms=0.518 (0.157%), neg=0, invalid=766 0366: dt=0.007000, rms=0.517 (0.145%), neg=0, invalid=766 0367: dt=0.007000, rms=0.517 (0.134%), neg=0, invalid=766 0368: dt=0.007000, rms=0.516 (0.119%), neg=0, invalid=766 0369: dt=0.007000, rms=0.515 (0.112%), neg=0, invalid=766 0370: dt=0.007000, rms=0.515 (0.096%), neg=0, invalid=766 0371: dt=0.007000, rms=0.514 (0.085%), neg=0, invalid=766 0372: dt=0.007000, rms=0.514 (0.076%), neg=0, invalid=766 0373: dt=0.007000, rms=0.514 (0.064%), neg=0, invalid=766 0374: dt=0.007000, rms=0.513 (0.054%), neg=0, invalid=766 0375: dt=0.007000, rms=0.513 (0.046%), neg=0, invalid=766 0376: dt=0.007000, rms=0.513 (0.043%), neg=0, invalid=766 0377: dt=0.007000, rms=0.513 (0.034%), neg=0, invalid=766 0378: dt=0.007000, rms=0.513 (0.025%), neg=0, invalid=766 0379: dt=0.007000, rms=0.513 (0.021%), neg=0, invalid=766 0380: dt=0.007000, rms=0.512 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22278.365 ms 0381: dt=0.000000, rms=0.512 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.512, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24641.365 ms 0382: dt=0.112000, rms=0.511 (0.269%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24512.338 ms 0383: dt=0.100427, rms=0.510 (0.186%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 21118.521 ms 0384: dt=0.007000, rms=0.510 (0.013%), neg=0, invalid=766 0385: dt=0.007000, rms=0.510 (0.008%), neg=0, invalid=766 0386: dt=0.007000, rms=0.510 (0.018%), neg=0, invalid=766 0387: dt=0.007000, rms=0.510 (0.024%), neg=0, invalid=766 0388: dt=0.007000, rms=0.510 (0.034%), neg=0, invalid=766 0389: dt=0.007000, rms=0.509 (0.037%), neg=0, invalid=766 0390: dt=0.007000, rms=0.509 (0.043%), neg=0, invalid=766 0391: dt=0.007000, rms=0.509 (0.049%), neg=0, invalid=766 0392: dt=0.007000, rms=0.509 (0.047%), neg=0, invalid=766 0393: dt=0.007000, rms=0.508 (0.055%), neg=0, invalid=766 0394: dt=0.007000, rms=0.508 (0.052%), neg=0, invalid=766 0395: dt=0.007000, rms=0.508 (0.051%), neg=0, invalid=766 0396: dt=0.007000, rms=0.508 (0.051%), neg=0, invalid=766 0397: dt=0.007000, rms=0.507 (0.047%), neg=0, invalid=766 0398: dt=0.007000, rms=0.507 (0.051%), neg=0, invalid=766 0399: dt=0.007000, rms=0.507 (0.044%), neg=0, invalid=766 0400: dt=0.007000, rms=0.507 (0.043%), neg=0, invalid=766 0401: dt=0.007000, rms=0.507 (0.039%), neg=0, invalid=766 0402: dt=0.007000, rms=0.506 (0.040%), neg=0, invalid=766 0403: dt=0.007000, rms=0.506 (0.032%), neg=0, invalid=766 0404: dt=0.007000, rms=0.506 (0.032%), neg=0, invalid=766 0405: dt=0.007000, rms=0.506 (0.027%), neg=0, invalid=766 0406: dt=0.007000, rms=0.506 (0.025%), neg=0, invalid=766 0407: dt=0.007000, rms=0.506 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 22474.807 ms 0408: dt=0.000000, rms=0.506 (-0.000%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.504, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29411.359 ms iter 0, gcam->neg = 104 after 23 iterations, nbhd size=2, neg = 0 0409: dt=32.000000, rms=0.494 (1.867%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29484.404 ms iter 0, gcam->neg = 23 after 38 iterations, nbhd size=4, neg = 0 0410: dt=19.200000, rms=0.493 (0.360%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29499.939 ms iter 0, gcam->neg = 14 after 6 iterations, nbhd size=1, neg = 0 0411: dt=19.200000, rms=0.491 (0.357%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29213.244 ms iter 0, gcam->neg = 11 after 25 iterations, nbhd size=3, neg = 0 0412: dt=11.200000, rms=0.490 (0.210%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0413: dt=11.200000, rms=0.489 (0.127%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 33 iterations, nbhd size=4, neg = 0 0414: dt=11.200000, rms=0.488 (0.144%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 42 iterations, nbhd size=1, neg = 0 0415: dt=11.200000, rms=0.488 (0.153%), neg=0, invalid=766 iter 0, gcam->neg = 36 after 48 iterations, nbhd size=1, neg = 0 0416: dt=11.200000, rms=0.487 (0.138%), neg=0, invalid=766 iter 0, gcam->neg = 39 after 54 iterations, nbhd size=4, neg = 0 0417: dt=11.200000, rms=0.487 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 47 after 64 iterations, nbhd size=1, neg = 0 0418: dt=11.200000, rms=0.487 (-0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29700.787 ms iter 0, gcam->neg = 7 after 23 iterations, nbhd size=3, neg = 0 0419: dt=11.200000, rms=0.486 (0.159%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30226.656 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0420: dt=11.200000, rms=0.486 (0.119%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29869.840 ms iter 0, gcam->neg = 23 after 50 iterations, nbhd size=3, neg = 0 0421: dt=32.000000, rms=0.481 (0.944%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31775.932 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0422: dt=8.165517, rms=0.480 (0.265%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29602.510 ms 0423: dt=11.200000, rms=0.479 (0.160%), neg=0, invalid=766 0424: dt=11.200000, rms=0.478 (0.117%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0425: dt=11.200000, rms=0.478 (0.186%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 31 iterations, nbhd size=4, neg = 0 0426: dt=11.200000, rms=0.476 (0.277%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 30 iterations, nbhd size=4, neg = 0 0427: dt=11.200000, rms=0.475 (0.229%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 51 iterations, nbhd size=3, neg = 0 0428: dt=11.200000, rms=0.474 (0.222%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 44 iterations, nbhd size=4, neg = 0 0429: dt=11.200000, rms=0.473 (0.153%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 45 iterations, nbhd size=1, neg = 0 0430: dt=11.200000, rms=0.473 (0.095%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 53 iterations, nbhd size=1, neg = 0 0431: dt=11.200000, rms=0.472 (0.152%), neg=0, invalid=766 iter 0, gcam->neg = 32 after 62 iterations, nbhd size=1, neg = 0 0432: dt=11.200000, rms=0.471 (0.140%), neg=0, invalid=766 iter 0, gcam->neg = 29 after 55 iterations, nbhd size=1, neg = 0 0433: dt=11.200000, rms=0.471 (0.139%), neg=0, invalid=766 iter 0, gcam->neg = 28 after 59 iterations, nbhd size=1, neg = 0 0434: dt=11.200000, rms=0.470 (0.147%), neg=0, invalid=766 iter 0, gcam->neg = 31 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13679.824 ms iter 1, dt=0.002000: new neg 0, old_neg 1, delta 1, rms=0.002 (18.941%) 0435: dt=11.200000, rms=0.469 (0.142%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0436: dt=11.200000, rms=0.469 (0.049%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0437: dt=11.200000, rms=0.469 (0.065%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0438: dt=11.200000, rms=0.469 (0.042%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29549.635 ms 0439: dt=11.200000, rms=0.469 (0.030%), neg=0, invalid=766 0440: dt=11.200000, rms=0.468 (0.034%), neg=0, invalid=766 0441: dt=11.200000, rms=0.468 (0.034%), neg=0, invalid=766 0442: dt=11.200000, rms=0.468 (0.047%), neg=0, invalid=766 0443: dt=11.200000, rms=0.468 (0.050%), neg=0, invalid=766 0444: dt=11.200000, rms=0.468 (0.037%), neg=0, invalid=766 0445: dt=11.200000, rms=0.467 (0.044%), neg=0, invalid=766 0446: dt=11.200000, rms=0.467 (0.040%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31196.312 ms 0447: dt=1.008000, rms=0.472 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29609.182 ms 0448: dt=1.008000, rms=0.472 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31128.773 ms 0449: dt=0.576000, rms=0.472 (0.000%), neg=0, invalid=766 0450: dt=0.576000, rms=0.472 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 183097.922 ms 0451: dt=4.032000, rms=0.472 (0.044%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 29742.623 ms iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0452: dt=4.032000, rms=0.471 (0.069%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30463.127 ms 0453: dt=0.000000, rms=0.471 (-0.011%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39819.125 ms 0454: dt=0.000063, rms=0.479 (0.000%), neg=0, invalid=766 0455: dt=0.000063, rms=0.479 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31332.725 ms iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0456: dt=0.285714, rms=0.479 (0.025%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31340.979 ms iter 0, gcam->neg = 14 after 9 iterations, nbhd size=1, neg = 0 0457: dt=0.240000, rms=0.479 (0.046%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 684282.938 ms iter 0, gcam->neg = 21 after 8 iterations, nbhd size=1, neg = 0 0458: dt=0.834646, rms=0.478 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31457.447 ms iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0459: dt=0.458333, rms=0.478 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0460: dt=0.458333, rms=0.478 (-0.003%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31721.361 ms iter 0, gcam->neg = 1072 after 22 iterations, nbhd size=2, neg = 0 0461: dt=1.358805, rms=0.434 (7.334%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31255.967 ms 0462: dt=0.000188, rms=0.434 (-0.004%), neg=0, invalid=766 0463: dt=0.000188, rms=0.434 (0.001%), neg=0, invalid=766 0464: dt=0.000188, rms=0.434 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31101.311 ms 0465: dt=0.000188, rms=0.434 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38111.422 ms 0466: dt=0.000016, rms=0.434 (0.000%), neg=0, invalid=766 0467: dt=0.000016, rms=0.434 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.426, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30981.930 ms iter 0, gcam->neg = 350 after 29 iterations, nbhd size=3, neg = 0 0468: dt=0.309720, rms=0.419 (1.625%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 212389.328 ms 0469: dt=0.000438, rms=0.419 (-0.018%), neg=0, invalid=766 0470: dt=0.000438, rms=0.419 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0471: dt=0.000438, rms=0.419 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0472: dt=0.000438, rms=0.419 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0473: dt=0.000438, rms=0.419 (0.003%), neg=0, invalid=766 0474: dt=0.000438, rms=0.419 (0.003%), neg=0, invalid=766 0475: dt=0.000438, rms=0.419 (0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31072.484 ms iter 0, gcam->neg = 76 after 18 iterations, nbhd size=2, neg = 0 0476: dt=0.082692, rms=0.418 (0.365%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31252.391 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0477: dt=0.001250, rms=0.418 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0478: dt=0.001250, rms=0.418 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0479: dt=0.001250, rms=0.417 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0480: dt=0.001250, rms=0.417 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0481: dt=0.001250, rms=0.417 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0482: dt=0.001250, rms=0.417 (0.018%), neg=0, invalid=766 0483: dt=0.001250, rms=0.417 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0484: dt=0.001250, rms=0.417 (0.025%), neg=0, invalid=766 0485: dt=0.001250, rms=0.417 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0486: dt=0.001250, rms=0.417 (0.029%), neg=0, invalid=766 0487: dt=0.001250, rms=0.417 (0.030%), neg=0, invalid=766 0488: dt=0.001250, rms=0.417 (0.031%), neg=0, invalid=766 0489: dt=0.001250, rms=0.416 (0.034%), neg=0, invalid=766 0490: dt=0.001250, rms=0.416 (0.037%), neg=0, invalid=766 0491: dt=0.001250, rms=0.416 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0492: dt=0.001250, rms=0.416 (0.033%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31118.574 ms iter 0, gcam->neg = 163 after 36 iterations, nbhd size=3, neg = 0 0493: dt=0.256000, rms=0.413 (0.613%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31191.967 ms 0494: dt=0.001000, rms=0.413 (-0.002%), neg=0, invalid=766 0495: dt=0.001000, rms=0.413 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 13 iterations, nbhd size=2, neg = 0 0496: dt=0.001000, rms=0.413 (-0.008%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30941.648 ms iter 0, gcam->neg = 50 after 16 iterations, nbhd size=2, neg = 0 0497: dt=0.048000, rms=0.412 (0.263%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30892.574 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0498: dt=0.001750, rms=0.412 (-0.000%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0499: dt=0.001750, rms=0.412 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0500: dt=0.001750, rms=0.412 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0501: dt=0.001750, rms=0.412 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0502: dt=0.001750, rms=0.412 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0503: dt=0.001750, rms=0.411 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0504: dt=0.001750, rms=0.411 (0.039%), neg=0, invalid=766 0505: dt=0.001750, rms=0.411 (0.043%), neg=0, invalid=766 0506: dt=0.001750, rms=0.411 (0.046%), neg=0, invalid=766 0507: dt=0.001750, rms=0.411 (0.046%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0508: dt=0.001750, rms=0.410 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0509: dt=0.001750, rms=0.410 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0510: dt=0.001750, rms=0.410 (0.053%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0511: dt=0.001750, rms=0.410 (0.051%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31428.328 ms iter 0, gcam->neg = 159 after 29 iterations, nbhd size=3, neg = 0 0512: dt=0.112000, rms=0.407 (0.582%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31091.896 ms iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0513: dt=0.000438, rms=0.407 (-0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0514: dt=0.000438, rms=0.407 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0515: dt=0.000438, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0516: dt=0.000438, rms=0.407 (0.005%), neg=0, invalid=766 0517: dt=0.000438, rms=0.407 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0518: dt=0.000438, rms=0.407 (0.008%), neg=0, invalid=766 0519: dt=0.000438, rms=0.407 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0520: dt=0.000438, rms=0.407 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0521: dt=0.000438, rms=0.407 (0.010%), neg=0, invalid=766 0522: dt=0.000438, rms=0.407 (0.012%), neg=0, invalid=766 0523: dt=0.000438, rms=0.407 (0.011%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30533.514 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0524: dt=0.500000, rms=0.408 (-0.185%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.408, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30700.521 ms iter 0, gcam->neg = 40 after 44 iterations, nbhd size=3, neg = 0 0525: dt=6.436782, rms=0.407 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30850.730 ms iter 0, gcam->neg = 19 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13378.657 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0526: dt=1.200000, rms=0.407 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30703.881 ms iter 0, gcam->neg = 25 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 223948.688 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0527: dt=0.180000, rms=0.407 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30842.787 ms iter 0, gcam->neg = 66 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13386.695 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0528: dt=0.864000, rms=0.407 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30906.965 ms iter 0, gcam->neg = 19 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13944.327 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0529: dt=0.096000, rms=0.407 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30474.377 ms iter 0, gcam->neg = 20 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13454.494 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0530: dt=0.112000, rms=0.407 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 405154.688 ms iter 0, gcam->neg = 1 after 19 iterations, nbhd size=3, neg = 0 0531: dt=0.000063, rms=0.407 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33254.953 ms iter 0, gcam->neg = 2 after 37 iterations, nbhd size=2, neg = 0 0532: dt=0.000250, rms=0.407 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32511.062 ms iter 0, gcam->neg = 1 after 26 iterations, nbhd size=4, neg = 0 0533: dt=0.000109, rms=0.407 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 26 iterations, nbhd size=4, neg = 0 0534: dt=0.000109, rms=0.407 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 28 iterations, nbhd size=4, neg = 0 0535: dt=0.000109, rms=0.407 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 30 iterations, nbhd size=1, neg = 0 0536: dt=0.000109, rms=0.407 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 32 iterations, nbhd size=1, neg = 0 0537: dt=0.000109, rms=0.407 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 36 iterations, nbhd size=2, neg = 0 0538: dt=0.000109, rms=0.407 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 36 iterations, nbhd size=2, neg = 0 0539: dt=0.000109, rms=0.407 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 39 iterations, nbhd size=2, neg = 0 0540: dt=0.000109, rms=0.407 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 37 iterations, nbhd size=2, neg = 0 0541: dt=0.000109, rms=0.407 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 37 iterations, nbhd size=2, neg = 0 0542: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 33 iterations, nbhd size=1, neg = 0 0543: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 29 iterations, nbhd size=1, neg = 0 0544: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 29 iterations, nbhd size=1, neg = 0 0545: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 29 iterations, nbhd size=1, neg = 0 0546: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 29 iterations, nbhd size=4, neg = 0 0547: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 28 iterations, nbhd size=4, neg = 0 0548: dt=0.000109, rms=0.407 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 28 iterations, nbhd size=4, neg = 0 0549: dt=0.000109, rms=0.407 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 28 iterations, nbhd size=4, neg = 0 0550: dt=0.000109, rms=0.407 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 28 iterations, nbhd size=4, neg = 0 0551: dt=0.000109, rms=0.407 (0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32637.305 ms iter 0, gcam->neg = 1 after 20 iterations, nbhd size=3, neg = 0 0552: dt=0.000438, rms=0.407 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32573.021 ms iter 0, gcam->neg = 2 after 29 iterations, nbhd size=4, neg = 0 0553: dt=0.001500, rms=0.407 (0.011%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32603.725 ms iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0554: dt=0.000109, rms=0.407 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0555: dt=0.000109, rms=0.407 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 19 iterations, nbhd size=3, neg = 0 0556: dt=0.000109, rms=0.407 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 16 iterations, nbhd size=2, neg = 0 0557: dt=0.000109, rms=0.407 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 22 iterations, nbhd size=3, neg = 0 0558: dt=0.000109, rms=0.407 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 26 iterations, nbhd size=4, neg = 0 0559: dt=0.000109, rms=0.407 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 17 iterations, nbhd size=3, neg = 0 0560: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 20 iterations, nbhd size=3, neg = 0 0561: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 24 iterations, nbhd size=4, neg = 0 0562: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 22 iterations, nbhd size=3, neg = 0 0563: dt=0.000109, rms=0.407 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 23 iterations, nbhd size=4, neg = 0 0564: dt=0.000109, rms=0.407 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 21 iterations, nbhd size=3, neg = 0 0565: dt=0.000109, rms=0.407 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 24 iterations, nbhd size=3, neg = 0 0566: dt=0.000109, rms=0.407 (0.005%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32474.014 ms iter 0, gcam->neg = 1 after 36 iterations, nbhd size=2, neg = 0 0567: dt=0.000109, rms=0.407 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32614.262 ms iter 0, gcam->neg = 1 after 48 iterations, nbhd size=4, neg = 0 0568: dt=0.000438, rms=0.407 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32414.502 ms iter 0, gcam->neg = 4 after 53 iterations, nbhd size=4, neg = 0 0569: dt=0.001750, rms=0.407 (0.009%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32605.947 ms iter 0, gcam->neg = 3 after 48 iterations, nbhd size=4, neg = 0 0570: dt=0.001500, rms=0.407 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 45 iterations, nbhd size=3, neg = 0 0571: dt=0.001500, rms=0.407 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 51 iterations, nbhd size=4, neg = 0 0572: dt=0.001500, rms=0.407 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 54 iterations, nbhd size=4, neg = 0 0573: dt=0.001500, rms=0.407 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 52 iterations, nbhd size=3, neg = 0 0574: dt=0.001500, rms=0.407 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 48 iterations, nbhd size=3, neg = 0 0575: dt=0.001500, rms=0.406 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 51 iterations, nbhd size=3, neg = 0 0576: dt=0.001500, rms=0.406 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 43 iterations, nbhd size=4, neg = 0 0577: dt=0.001500, rms=0.406 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 48 iterations, nbhd size=3, neg = 0 0578: dt=0.001500, rms=0.406 (0.042%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 51 iterations, nbhd size=3, neg = 0 0579: dt=0.001500, rms=0.406 (0.043%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 39 iterations, nbhd size=4, neg = 0 0580: dt=0.001500, rms=0.406 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13412.365 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.001 (0.003%) ---------- unfolding failed - restoring original position -------------------- 0581: dt=0.001500, rms=0.406 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32534.168 ms iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0582: dt=0.000438, rms=0.406 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32569.527 ms iter 0, gcam->neg = 1 after 16 iterations, nbhd size=2, neg = 0 0583: dt=0.000750, rms=0.406 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32710.246 ms iter 0, gcam->neg = 1 after 19 iterations, nbhd size=3, neg = 0 0584: dt=0.000438, rms=0.406 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 21 iterations, nbhd size=3, neg = 0 0585: dt=0.000438, rms=0.406 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 20 iterations, nbhd size=3, neg = 0 0586: dt=0.000438, rms=0.406 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 22 iterations, nbhd size=3, neg = 0 0587: dt=0.000438, rms=0.405 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 28 iterations, nbhd size=4, neg = 0 0588: dt=0.000438, rms=0.405 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 20 iterations, nbhd size=3, neg = 0 0589: dt=0.000438, rms=0.405 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 26 iterations, nbhd size=3, neg = 0 0590: dt=0.000438, rms=0.405 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 28 iterations, nbhd size=4, neg = 0 0591: dt=0.000438, rms=0.405 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 25 iterations, nbhd size=3, neg = 0 0592: dt=0.000438, rms=0.405 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 23 iterations, nbhd size=3, neg = 0 0593: dt=0.000438, rms=0.405 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 30 iterations, nbhd size=4, neg = 0 0594: dt=0.000438, rms=0.405 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 52 iterations, nbhd size=4, neg = 0 0595: dt=0.000438, rms=0.405 (0.017%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.405, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 31455.807 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0596: dt=0.000016, rms=0.405 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32630.006 ms iter 0, gcam->neg = 1 after 15 iterations, nbhd size=2, neg = 0 0597: dt=0.000078, rms=0.405 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32852.613 ms iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.000, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 13580.527 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.000 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0598: dt=0.000438, rms=0.405 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.405, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32832.355 ms iter 0, gcam->neg = 1 after 25 iterations, nbhd size=4, neg = 0 0599: dt=0.000438, rms=0.405 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32558.801 ms iter 0, gcam->neg = 4 after 31 iterations, nbhd size=4, neg = 0 0600: dt=0.001750, rms=0.405 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32526.418 ms iter 0, gcam->neg = 5 after 30 iterations, nbhd size=4, neg = 0 0601: dt=0.004000, rms=0.405 (0.029%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32865.230 ms iter 0, gcam->neg = 3 after 23 iterations, nbhd size=4, neg = 0 0602: dt=0.001750, rms=0.405 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 23 iterations, nbhd size=4, neg = 0 0603: dt=0.001750, rms=0.405 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 26 iterations, nbhd size=4, neg = 0 0604: dt=0.001750, rms=0.405 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 26 iterations, nbhd size=4, neg = 0 0605: dt=0.001750, rms=0.404 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 31 iterations, nbhd size=3, neg = 0 0606: dt=0.001750, rms=0.404 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 31 iterations, nbhd size=4, neg = 0 0607: dt=0.001750, rms=0.404 (0.049%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 40 iterations, nbhd size=1, neg = 0 0608: dt=0.001750, rms=0.404 (0.055%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 33 iterations, nbhd size=4, neg = 0 0609: dt=0.001750, rms=0.404 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 34 iterations, nbhd size=4, neg = 0 0610: dt=0.001750, rms=0.403 (0.064%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 25 iterations, nbhd size=3, neg = 0 0611: dt=0.001750, rms=0.403 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 13 after 27 iterations, nbhd size=3, neg = 0 0612: dt=0.001750, rms=0.403 (0.074%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 34 iterations, nbhd size=4, neg = 0 0613: dt=0.001750, rms=0.403 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 37 iterations, nbhd size=4, neg = 0 0614: dt=0.001750, rms=0.402 (0.073%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 29 iterations, nbhd size=3, neg = 0 0615: dt=0.001750, rms=0.402 (0.081%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 32 iterations, nbhd size=4, neg = 0 0616: dt=0.001750, rms=0.402 (0.077%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 7 hours, 54 minutes and 37 seconds. #-------------------------------------- #@# CA Reg Inv Thu Jan 10 05:33:41 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Thu Jan 10 05:35:13 EST 2013 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11582330 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 13 minutes and 2 seconds. #-------------------------------------- #@# SkullLTA Thu Jan 10 05:48:16 EST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (49, 49, 39) --> (206, 207, 226) using (101, 102, 133) as brain centroid... mean wm in atlas = 126, using box (82,83,110) --> (120, 121,156) to find MRI wm before smoothing, mri peak at 106 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10317.8, old_max_log_p =-10371.9 (thresh=-10361.6) 1.040 0.051 0.048 -20.096; -0.060 1.407 0.345 -78.692; -0.037 -0.239 1.103 1.031; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10317.8, old_max_log_p =-10317.8 (thresh=-10307.4) 1.040 0.051 0.048 -20.096; -0.060 1.407 0.345 -78.692; -0.037 -0.239 1.103 1.031; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10305.9, old_max_log_p =-10317.8 (thresh=-10307.4) 1.022 0.006 0.039 -11.456; -0.022 1.367 0.263 -65.103; -0.040 -0.144 1.101 -9.519; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10305.9, old_max_log_p =-10305.9 (thresh=-10295.6) 1.022 0.006 0.039 -11.456; -0.022 1.367 0.263 -65.103; -0.040 -0.144 1.101 -9.519; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10300.4, old_max_log_p =-10305.9 (thresh=-10295.6) 1.021 0.025 0.079 -18.428; -0.037 1.366 0.243 -61.366; -0.073 -0.121 1.099 -7.597; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02058 0.02486 0.07896 -18.42799; -0.03746 1.36563 0.24349 -61.36623; -0.07313 -0.12116 1.09943 -7.59707; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02058 0.02486 0.07896 -18.42799; -0.03746 1.36563 0.24349 -61.36623; -0.07313 -0.12116 1.09943 -7.59707; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = 10300.4 tol 0.000010 Resulting transform: 1.021 0.025 0.079 -18.428; -0.037 1.366 0.243 -61.366; -0.073 -0.121 1.099 -7.597; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10300.4 (old=-10371.9) transform before final EM align: 1.021 0.025 0.079 -18.428; -0.037 1.366 0.243 -61.366; -0.073 -0.121 1.099 -7.597; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02058 0.02486 0.07896 -18.42799; -0.03746 1.36563 0.24349 -61.36623; -0.07313 -0.12116 1.09943 -7.59707; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.02058 0.02486 0.07896 -18.42799; -0.03746 1.36563 0.24349 -61.36623; -0.07313 -0.12116 1.09943 -7.59707; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 1145196.9 tol 0.000000 final transform: 1.021 0.025 0.079 -18.428; -0.037 1.366 0.243 -61.366; -0.073 -0.121 1.099 -7.597; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 98 minutes and 39 seconds. #-------------------------------------- #@# SubCort Seg Thu Jan 10 07:26:56 EST 2013 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.11474 (11) Left_Lateral_Ventricle (4): linear fit = 0.38 x + 0.0 (1753 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1753 voxels, peak = 10), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.10638 (11) Right_Lateral_Ventricle (43): linear fit = 0.45 x + 0.0 (1847 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.45 x + 0.0 (1847 voxels, peak = 9), gca=9.0 gca peak = 0.28003 (97) mri peak = 0.09627 (89) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (327 voxels, overlap=0.557) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (327 voxels, peak = 87), gca=87.3 gca peak = 0.18160 (96) mri peak = 0.09511 (99) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (346 voxels, overlap=0.762) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (346 voxels, peak = 94), gca=93.6 gca peak = 0.27536 (62) mri peak = 0.09736 (55) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (735 voxels, overlap=0.266) Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (735 voxels, peak = 54), gca=54.2 gca peak = 0.32745 (63) mri peak = 0.08142 (61) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (750 voxels, overlap=0.587) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (750 voxels, peak = 55), gca=55.1 gca peak = 0.08597 (105) mri peak = 0.05828 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (33823 voxels, overlap=0.744) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (33823 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.05572 (111) Left_Cerebral_White_Matter (2): linear fit = 1.08 x + 0.0 (32907 voxels, overlap=0.709) Left_Cerebral_White_Matter (2): linear fit = 1.08 x + 0.0 (32907 voxels, peak = 114), gca=114.0 gca peak = 0.07826 (63) mri peak = 0.03845 (55) Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (22671 voxels, overlap=0.445) Left_Cerebral_Cortex (3): linear fit = 0.90 x + 0.0 (22671 voxels, peak = 57), gca=56.7 gca peak = 0.08598 (64) mri peak = 0.03641 (56) Right_Cerebral_Cortex (42): linear fit = 0.88 x + 0.0 (22741 voxels, overlap=0.424) Right_Cerebral_Cortex (42): linear fit = 0.88 x + 0.0 (22741 voxels, peak = 56), gca=56.0 gca peak = 0.24164 (71) mri peak = 0.08092 (62) Right_Caudate (50): linear fit = 0.82 x + 0.0 (1063 voxels, overlap=0.000) Right_Caudate (50): linear fit = 0.82 x + 0.0 (1063 voxels, peak = 59), gca=58.6 gca peak = 0.18227 (75) mri peak = 0.09285 (64) Left_Caudate (11): linear fit = 0.80 x + 0.0 (1068 voxels, overlap=0.000) Left_Caudate (11): linear fit = 0.80 x + 0.0 (1068 voxels, peak = 60), gca=60.0 gca peak = 0.10629 (62) mri peak = 0.04122 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (20947 voxels, overlap=0.988) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (20947 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.03760 (60) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (23612 voxels, overlap=0.989) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (23612 voxels, peak = 60), gca=60.5 gca peak = 0.17849 (88) mri peak = 0.09318 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4596 voxels, overlap=0.920) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4596 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.08911 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5114 voxels, overlap=0.895) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5114 voxels, peak = 90), gca=90.3 gca peak = 0.41688 (64) mri peak = 0.13699 (54) Left_Amygdala (18): linear fit = 0.85 x + 0.0 (358 voxels, overlap=0.300) Left_Amygdala (18): linear fit = 0.85 x + 0.0 (358 voxels, peak = 54), gca=54.4 gca peak = 0.42394 (62) mri peak = 0.13880 (58) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (386 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (386 voxels, peak = 57), gca=57.4 gca peak = 0.10041 (96) mri peak = 0.05237 (84) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3932 voxels, overlap=0.813) Left_Thalamus_Proper (10): linear fit = 0.95 x + 0.0 (3932 voxels, peak = 91), gca=91.2 gca peak = 0.13978 (88) mri peak = 0.06569 (85) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3695 voxels, overlap=0.951) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (3695 voxels, peak = 86), gca=85.8 gca peak = 0.08514 (81) mri peak = 0.06729 (70) Left_Putamen (12): linear fit = 0.85 x + 0.0 (1585 voxels, overlap=0.418) Left_Putamen (12): linear fit = 0.85 x + 0.0 (1585 voxels, peak = 69), gca=68.8 gca peak = 0.09624 (82) mri peak = 0.06594 (72) Right_Putamen (51): linear fit = 0.85 x + 0.0 (1507 voxels, overlap=0.313) Right_Putamen (51): linear fit = 0.85 x + 0.0 (1507 voxels, peak = 70), gca=69.7 gca peak = 0.07543 (88) mri peak = 0.06368 (88) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10666 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (10666 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.06956 (104) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1367 voxels, overlap=0.801) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (1367 voxels, peak = 104), gca=104.5 gca peak = 0.17004 (92) mri peak = 0.06304 (98) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1364 voxels, overlap=0.847) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1364 voxels, peak = 97), gca=96.6 gca peak = 0.21361 (36) mri peak = 0.16418 (17) Third_Ventricle (14): linear fit = 0.43 x + 0.0 (67 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.43 x + 0.0 (67 voxels, peak = 15), gca=15.3 gca peak = 0.26069 (23) mri peak = 0.14876 (16) Fourth_Ventricle (15): linear fit = 0.65 x + 0.0 (180 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.65 x + 0.0 (180 voxels, peak = 15), gca=14.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.88 x + 0.0 estimating mean wm scale to be 1.06 x + 0.0 estimating mean csf scale to be 0.43 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31598 (11) mri peak = 0.11474 (11) Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1753 voxels, overlap=0.997) Left_Lateral_Ventricle (4): linear fit = 0.93 x + 0.0 (1753 voxels, peak = 10), gca=10.2 gca peak = 0.25469 (10) mri peak = 0.10638 (11) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (1847 voxels, overlap=0.996) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (1847 voxels, peak = 10), gca=10.5 gca peak = 0.26609 (88) mri peak = 0.09627 (89) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (327 voxels, overlap=0.996) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (327 voxels, peak = 88), gca=88.0 gca peak = 0.20066 (93) mri peak = 0.09511 (99) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (346 voxels, overlap=0.988) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (346 voxels, peak = 93), gca=93.0 gca peak = 0.29893 (54) mri peak = 0.09736 (55) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (735 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (735 voxels, peak = 54), gca=54.0 gca peak = 0.33450 (55) mri peak = 0.08142 (61) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (750 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (750 voxels, peak = 51), gca=50.9 gca peak = 0.08006 (112) mri peak = 0.05828 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (33823 voxels, overlap=0.883) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (33823 voxels, peak = 112), gca=112.0 gca peak = 0.08557 (114) mri peak = 0.05572 (111) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32907 voxels, overlap=0.885) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32907 voxels, peak = 114), gca=114.0 gca peak = 0.08440 (57) mri peak = 0.03845 (55) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22671 voxels, overlap=0.788) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (22671 voxels, peak = 58), gca=58.4 gca peak = 0.09689 (55) mri peak = 0.03641 (56) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22741 voxels, overlap=0.952) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (22741 voxels, peak = 55), gca=55.0 gca peak = 0.27509 (61) mri peak = 0.08092 (62) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1063 voxels, overlap=0.995) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1063 voxels, peak = 61), gca=61.0 gca peak = 0.20113 (60) mri peak = 0.09285 (64) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1068 voxels, overlap=0.998) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1068 voxels, peak = 62), gca=61.5 gca peak = 0.10135 (62) mri peak = 0.04122 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (20947 voxels, overlap=0.997) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (20947 voxels, peak = 64), gca=63.5 gca peak = 0.12659 (61) mri peak = 0.03760 (60) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (23612 voxels, overlap=0.996) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (23612 voxels, peak = 63), gca=62.5 gca peak = 0.16848 (92) mri peak = 0.09318 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4596 voxels, overlap=0.944) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4596 voxels, peak = 92), gca=92.0 gca peak = 0.15998 (91) mri peak = 0.08911 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5114 voxels, overlap=0.996) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5114 voxels, peak = 91), gca=91.0 gca peak = 0.32434 (54) mri peak = 0.13699 (54) Left_Amygdala (18): linear fit = 0.98 x + 0.0 (358 voxels, overlap=0.998) Left_Amygdala (18): linear fit = 0.98 x + 0.0 (358 voxels, peak = 53), gca=52.7 gca peak = 0.43504 (58) mri peak = 0.13880 (58) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (386 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.98 x + 0.0 (386 voxels, peak = 57), gca=56.6 gca peak = 0.10153 (91) mri peak = 0.05237 (84) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3932 voxels, overlap=0.997) Left_Thalamus_Proper (10): linear fit = 0.98 x + 0.0 (3932 voxels, peak = 89), gca=88.7 gca peak = 0.11173 (86) mri peak = 0.06569 (85) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3695 voxels, overlap=0.995) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3695 voxels, peak = 86), gca=86.0 gca peak = 0.11225 (70) mri peak = 0.06729 (70) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1585 voxels, overlap=0.997) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1585 voxels, peak = 70), gca=70.0 gca peak = 0.10657 (70) mri peak = 0.06594 (72) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1507 voxels, overlap=0.999) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1507 voxels, peak = 70), gca=70.0 gca peak = 0.07366 (90) mri peak = 0.06368 (88) Brain_Stem (16): linear fit = 0.98 x + 0.0 (10666 voxels, overlap=0.818) Brain_Stem (16): linear fit = 0.98 x + 0.0 (10666 voxels, peak = 88), gca=87.8 gca peak = 0.13487 (104) mri peak = 0.06956 (104) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1367 voxels, overlap=0.839) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1367 voxels, peak = 107), gca=106.6 gca peak = 0.13380 (98) mri peak = 0.06304 (98) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1364 voxels, overlap=0.909) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1364 voxels, peak = 100), gca=100.4 gca peak = 0.30327 (15) mri peak = 0.16418 (17) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (67 voxels, overlap=0.991) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (67 voxels, peak = 15), gca=15.0 gca peak = 0.43815 (10) mri peak = 0.14876 (16) Fourth_Ventricle (15): linear fit = 1.55 x + 0.0 (180 voxels, overlap=0.816) Fourth_Ventricle (15): linear fit = 1.55 x + 0.0 (180 voxels, peak = 16), gca=15.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.27467 (31) gca peak Fourth_Ventricle = 0.43815 (10) gca peak CSF = 0.32925 (17) gca peak Left_Accumbens_area = 0.61266 (56) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.43530 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31271 (28) gca peak Right_Accumbens_area = 0.50574 (59) gca peak Right_vessel = 0.52656 (60) gca peak Right_choroid_plexus = 0.10191 (48) gca peak Fifth_Ventricle = 0.46192 (20) gca peak WM_hypointensities = 0.15252 (87) gca peak non_WM_hypointensities = 0.11967 (56) gca peak Optic_Chiasm = 0.34840 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.98 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.99 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 12763 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels) 223 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 97305 changed. image ll: -2.197, PF=1.000 pass 2: 19242 changed. image ll: -2.195, PF=1.000 pass 3: 7917 changed. pass 4: 3812 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 61 minutes and 8 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/transforms/cc_up.lta chong_lan will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/transforms/cc_up.lta reading aseg from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.auto_noCCseg.mgz reading norm from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/norm.mgz 17083 voxels in left wm, 37148 in right wm, xrange [123, 132] searching rotation angles z=[-8 6], y=[-4 10] searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.5 searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 global minimum found at slice 128.0, rotations (2.27, -0.49) final transformation (x=128.0, yr=2.275, zr=-0.487): 0.999 0.009 0.040 -5.703; -0.008 1.000 -0.000 20.133; -0.040 -0.000 0.999 10.177; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 139 114 eigenvectors: -0.002 0.005 1.000; -0.093 -0.996 0.005; 0.996 -0.093 0.002; writing aseg with callosum to /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Thu Jan 10 08:28:50 EST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Jan 10 08:28:50 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 6212 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 5 minutes and 59 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 107 gm peak at 56 (56), valley at 24 (24) csf peak at 10, setting threshold to 40 white matter peak found at 111 white matter peak found at 110 gm peak at 58 (58), valley at 25 (25) csf peak at 10, setting threshold to 42 #-------------------------------------------- #@# Mask BFS Thu Jan 10 08:34:51 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1465950 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Jan 10 08:35:24 EST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 107.0 +- 5.5 [80.0 --> 125.0] GM (66.0) : 64.7 +- 11.6 [30.0 --> 96.0] setting bottom of white matter range to 76.3 setting top of gray matter range to 87.9 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 10384 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4357 filled 2132 bright non-wm voxels segmented. 3792 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.52 minutes reading wm segmentation from wm.seg.mgz... 378 voxels added to wm to prevent paths from MTL structures to cortex 1355 additional wm voxels added 0 additional wm voxels added SEG EDIT: 57795 voxels turned on, 46231 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 101 new 101 115,126,128 old 101 new 101 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 24 found - 24 modified | TOTAL: 24 pass 2 (xy+): 0 found - 24 modified | TOTAL: 24 pass 1 (xy-): 36 found - 36 modified | TOTAL: 60 pass 2 (xy-): 0 found - 36 modified | TOTAL: 60 pass 1 (yz+): 47 found - 47 modified | TOTAL: 107 pass 2 (yz+): 0 found - 47 modified | TOTAL: 107 pass 1 (yz-): 25 found - 25 modified | TOTAL: 132 pass 2 (yz-): 0 found - 25 modified | TOTAL: 132 pass 1 (xz+): 21 found - 21 modified | TOTAL: 153 pass 2 (xz+): 0 found - 21 modified | TOTAL: 153 pass 1 (xz-): 29 found - 29 modified | TOTAL: 182 pass 2 (xz-): 0 found - 29 modified | TOTAL: 182 Iteration Number : 1 pass 1 (+++): 21 found - 21 modified | TOTAL: 21 pass 2 (+++): 0 found - 21 modified | TOTAL: 21 pass 1 (+++): 13 found - 13 modified | TOTAL: 34 pass 2 (+++): 0 found - 13 modified | TOTAL: 34 pass 1 (+++): 10 found - 10 modified | TOTAL: 44 pass 2 (+++): 0 found - 10 modified | TOTAL: 44 pass 1 (+++): 26 found - 26 modified | TOTAL: 70 pass 2 (+++): 0 found - 26 modified | TOTAL: 70 Iteration Number : 1 pass 1 (++): 143 found - 143 modified | TOTAL: 143 pass 2 (++): 0 found - 143 modified | TOTAL: 143 pass 1 (+-): 167 found - 167 modified | TOTAL: 310 pass 2 (+-): 0 found - 167 modified | TOTAL: 310 pass 1 (--): 117 found - 117 modified | TOTAL: 427 pass 2 (--): 0 found - 117 modified | TOTAL: 427 pass 1 (-+): 135 found - 135 modified | TOTAL: 562 pass 2 (-+): 0 found - 135 modified | TOTAL: 562 Iteration Number : 2 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 3 found - 3 modified | TOTAL: 10 pass 2 (xy-): 0 found - 3 modified | TOTAL: 10 pass 1 (yz+): 10 found - 10 modified | TOTAL: 20 pass 2 (yz+): 0 found - 10 modified | TOTAL: 20 pass 1 (yz-): 7 found - 7 modified | TOTAL: 27 pass 2 (yz-): 0 found - 7 modified | TOTAL: 27 pass 1 (xz+): 6 found - 6 modified | TOTAL: 33 pass 2 (xz+): 0 found - 6 modified | TOTAL: 33 pass 1 (xz-): 5 found - 5 modified | TOTAL: 38 pass 2 (xz-): 0 found - 5 modified | TOTAL: 38 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 6 found - 6 modified | TOTAL: 8 pass 2 (+-): 0 found - 6 modified | TOTAL: 8 pass 1 (--): 3 found - 3 modified | TOTAL: 11 pass 2 (--): 0 found - 3 modified | TOTAL: 11 pass 1 (-+): 2 found - 2 modified | TOTAL: 13 pass 2 (-+): 0 found - 2 modified | TOTAL: 13 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+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 869 (out of 488878: 0.177754) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Jan 10 08:37:40 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/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 1.040 0.051 0.048 -20.096; -0.049 1.138 0.279 -40.509; -0.034 -0.223 1.026 8.357; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.040 0.051 0.048 -20.096; -0.049 1.138 0.279 -40.509; -0.034 -0.223 1.026 8.357; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1029 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75) no need to search using seed (124, 114, 93), TAL = (4.0, -35.0, 14.0) talairach voxel to voxel transform 0.958 -0.049 -0.031 17.521; 0.032 0.833 -0.228 36.281; 0.039 0.179 0.924 0.304; 0.000 0.000 0.000 1.000; segmentation indicates cc at (124, 114, 93) --> (4.0, -35.0, 14.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (4.00, -35.00, 14.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -35.00, 14.00) SRC: (110.54, 113.37, 110.78) search lh wm seed point around talairach space (-14.00, -35.00, 14.00), SRC: (145.04, 114.50, 112.17) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu Jan 10 08:38:35 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 2 found - 2 modified | TOTAL: 7 pass 2 (xy-): 0 found - 2 modified | TOTAL: 7 pass 1 (yz+): 3 found - 3 modified | TOTAL: 10 pass 2 (yz+): 0 found - 3 modified | TOTAL: 10 pass 1 (yz-): 0 found - 0 modified | TOTAL: 10 pass 1 (xz+): 1 found - 1 modified | TOTAL: 11 pass 2 (xz+): 0 found - 1 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 2 found - 2 modified | TOTAL: 2 pass 2 (--): 0 found - 2 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 13 (out of 234246: 0.005550) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 60: 1294 vertices, 1398 faces slice 70: 6062 vertices, 6309 faces slice 80: 15296 vertices, 15682 faces slice 90: 26170 vertices, 26531 faces slice 100: 36849 vertices, 37211 faces slice 110: 47836 vertices, 48209 faces slice 120: 58692 vertices, 59109 faces slice 130: 70350 vertices, 70783 faces slice 140: 80884 vertices, 81335 faces slice 150: 92166 vertices, 92602 faces slice 160: 101902 vertices, 102323 faces slice 170: 109600 vertices, 109964 faces slice 180: 116296 vertices, 116657 faces slice 190: 122474 vertices, 122788 faces slice 200: 127942 vertices, 128247 faces slice 210: 131793 vertices, 131984 faces slice 220: 131950 vertices, 132100 faces slice 230: 131950 vertices, 132100 faces slice 240: 131950 vertices, 132100 faces slice 250: 131950 vertices, 132100 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 131950 voxel in cpt #1: X=-150 [v=131950,e=396300,f=264200] located at (-28.058817, -0.777673, 19.062265) For the whole surface: X=-150 [v=131950,e=396300,f=264200] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Jan 10 08:38:47 EST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Thu Jan 10 08:38:54 EST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts avg radius = 45.7 mm, total surface area = 68887 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.109 (target=0.015) step 005: RMS=0.083 (target=0.015) step 010: RMS=0.065 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.052 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.045 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.041 (target=0.015) step 045: RMS=0.040 (target=0.015) step 050: RMS=0.040 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.038 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Jan 10 08:39:27 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.01 +- 0.61 (0.00-->7.41) (max @ vno 89643 --> 89644) face area 0.03 +- 0.04 (-0.30-->0.75) scaling brain by 0.321... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.442, avgs=0 005/300: dt: 0.9000, rms radial error=176.182, avgs=0 010/300: dt: 0.9000, rms radial error=175.625, avgs=0 015/300: dt: 0.9000, rms radial error=174.894, avgs=0 020/300: dt: 0.9000, rms radial error=174.062, avgs=0 025/300: dt: 0.9000, rms radial error=173.171, avgs=0 030/300: dt: 0.9000, rms radial error=172.252, avgs=0 035/300: dt: 0.9000, rms radial error=171.316, avgs=0 040/300: dt: 0.9000, rms radial error=170.374, avgs=0 045/300: dt: 0.9000, rms radial error=169.430, avgs=0 050/300: dt: 0.9000, rms radial error=168.488, avgs=0 055/300: dt: 0.9000, rms radial error=167.548, avgs=0 060/300: dt: 0.9000, rms radial error=166.613, avgs=0 065/300: dt: 0.9000, rms radial error=165.682, avgs=0 070/300: dt: 0.9000, rms radial error=164.756, avgs=0 075/300: dt: 0.9000, rms radial error=163.833, avgs=0 080/300: dt: 0.9000, rms radial error=162.918, avgs=0 085/300: dt: 0.9000, rms radial error=162.006, avgs=0 090/300: dt: 0.9000, rms radial error=161.099, avgs=0 095/300: dt: 0.9000, rms radial error=160.198, avgs=0 100/300: dt: 0.9000, rms radial error=159.302, avgs=0 105/300: dt: 0.9000, rms radial error=158.410, avgs=0 110/300: dt: 0.9000, rms radial error=157.523, avgs=0 115/300: dt: 0.9000, rms radial error=156.640, avgs=0 120/300: dt: 0.9000, rms radial error=155.762, avgs=0 125/300: dt: 0.9000, rms radial error=154.888, avgs=0 130/300: dt: 0.9000, rms radial error=154.019, avgs=0 135/300: dt: 0.9000, rms radial error=153.154, avgs=0 140/300: dt: 0.9000, rms radial error=152.294, avgs=0 145/300: dt: 0.9000, rms radial error=151.439, avgs=0 150/300: dt: 0.9000, rms radial error=150.588, avgs=0 155/300: dt: 0.9000, rms radial error=149.742, avgs=0 160/300: dt: 0.9000, rms radial error=148.901, avgs=0 165/300: dt: 0.9000, rms radial error=148.064, avgs=0 170/300: dt: 0.9000, rms radial error=147.231, avgs=0 175/300: dt: 0.9000, rms radial error=146.404, avgs=0 180/300: dt: 0.9000, rms radial error=145.580, avgs=0 185/300: dt: 0.9000, rms radial error=144.761, avgs=0 190/300: dt: 0.9000, rms radial error=143.947, avgs=0 195/300: dt: 0.9000, rms radial error=143.137, avgs=0 200/300: dt: 0.9000, rms radial error=142.331, avgs=0 205/300: dt: 0.9000, rms radial error=141.530, avgs=0 210/300: dt: 0.9000, rms radial error=140.733, avgs=0 215/300: dt: 0.9000, rms radial error=139.941, avgs=0 220/300: dt: 0.9000, rms radial error=139.153, avgs=0 225/300: dt: 0.9000, rms radial error=138.369, avgs=0 230/300: dt: 0.9000, rms radial error=137.590, avgs=0 235/300: dt: 0.9000, rms radial error=136.815, avgs=0 240/300: dt: 0.9000, rms radial error=136.044, avgs=0 245/300: dt: 0.9000, rms radial error=135.278, avgs=0 250/300: dt: 0.9000, rms radial error=134.516, avgs=0 255/300: dt: 0.9000, rms radial error=133.758, avgs=0 260/300: dt: 0.9000, rms radial error=133.004, avgs=0 265/300: dt: 0.9000, rms radial error=132.255, avgs=0 270/300: dt: 0.9000, rms radial error=131.509, avgs=0 275/300: dt: 0.9000, rms radial error=130.768, avgs=0 280/300: dt: 0.9000, rms radial error=130.031, avgs=0 285/300: dt: 0.9000, rms radial error=129.298, avgs=0 290/300: dt: 0.9000, rms radial error=128.570, avgs=0 295/300: dt: 0.9000, rms radial error=127.845, avgs=0 300/300: dt: 0.9000, rms radial error=127.124, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15356.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 2554.14 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 = 274.76 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00599 epoch 4 (K=640.0), pass 1, starting sse = 24.24 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/12 = 0.00651 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Jan 10 08:43:19 EST 2013 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 chong_lan lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-150 (nv=131950, nf=264200, ne=396300, g=76) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 10538 ambiguous faces found in tessellation segmenting defects... 66 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 27 into 26 -merging segment 38 into 34 -merging segment 46 into 43 -merging segment 51 into 48 -merging segment 42 into 50 61 defects to be corrected 0 vertices coincident reading input surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8276 (-4.9138) -vertex loglikelihood: -6.9788 (-3.4894) -normal dot loglikelihood: -3.5569 (-3.5569) -quad curv loglikelihood: -5.9355 (-2.9678) Total Loglikelihood : -26.2988 CORRECTING DEFECT 0 (vertices=18, convex hull=38) After retessellation of defect 0, euler #=-61 (125604,374477,248812) : difference with theory (-58) = 3 CORRECTING DEFECT 1 (vertices=29, convex hull=59) After retessellation of defect 1, euler #=-60 (125616,374536,248860) : difference with theory (-57) = 3 CORRECTING DEFECT 2 (vertices=6, convex hull=23) After retessellation of defect 2, euler #=-59 (125617,374544,248868) : difference with theory (-56) = 3 CORRECTING DEFECT 3 (vertices=12, convex hull=25) After retessellation of defect 3, euler #=-58 (125618,374551,248875) : difference with theory (-55) = 3 CORRECTING DEFECT 4 (vertices=5, convex hull=17) After retessellation of defect 4, euler #=-57 (125619,374558,248882) : difference with theory (-54) = 3 CORRECTING DEFECT 5 (vertices=25, convex hull=32) After retessellation of defect 5, euler #=-56 (125620,374571,248895) : difference with theory (-53) = 3 CORRECTING DEFECT 6 (vertices=107, convex hull=101) After retessellation of defect 6, euler #=-55 (125664,374749,249030) : difference with theory (-52) = 3 CORRECTING DEFECT 7 (vertices=39, convex hull=108) After retessellation of defect 7, euler #=-54 (125686,374853,249113) : difference with theory (-51) = 3 CORRECTING DEFECT 8 (vertices=107, convex hull=119) After retessellation of defect 8, euler #=-53 (125734,375050,249263) : difference with theory (-50) = 3 CORRECTING DEFECT 9 (vertices=58, convex hull=38) After retessellation of defect 9, euler #=-52 (125740,375080,249288) : difference with theory (-49) = 3 CORRECTING DEFECT 10 (vertices=154, convex hull=125) After retessellation of defect 10, euler #=-52 (125792,375299,249455) : difference with theory (-48) = 4 CORRECTING DEFECT 11 (vertices=30, convex hull=65) After retessellation of defect 11, euler #=-51 (125801,375351,249499) : difference with theory (-47) = 4 CORRECTING DEFECT 12 (vertices=37, convex hull=80) After retessellation of defect 12, euler #=-50 (125820,375443,249573) : difference with theory (-46) = 4 CORRECTING DEFECT 13 (vertices=48, convex hull=47) After retessellation of defect 13, euler #=-49 (125830,375491,249612) : difference with theory (-45) = 4 CORRECTING DEFECT 14 (vertices=20, convex hull=34) After retessellation of defect 14, euler #=-48 (125832,375509,249629) : difference with theory (-44) = 4 CORRECTING DEFECT 15 (vertices=41, convex hull=77) After retessellation of defect 15, euler #=-47 (125857,375617,249713) : difference with theory (-43) = 4 CORRECTING DEFECT 16 (vertices=48, convex hull=81) After retessellation of defect 16, euler #=-46 (125866,375680,249768) : difference with theory (-42) = 4 CORRECTING DEFECT 17 (vertices=50, convex hull=89) After retessellation of defect 17, euler #=-45 (125897,375811,249869) : difference with theory (-41) = 4 CORRECTING DEFECT 18 (vertices=43, convex hull=60) After retessellation of defect 18, euler #=-44 (125924,375913,249945) : difference with theory (-40) = 4 CORRECTING DEFECT 19 (vertices=50, convex hull=89) After retessellation of defect 19, euler #=-43 (125961,376058,250054) : difference with theory (-39) = 4 CORRECTING DEFECT 20 (vertices=57, convex hull=57) After retessellation of defect 20, euler #=-42 (125985,376157,250130) : difference with theory (-38) = 4 CORRECTING DEFECT 21 (vertices=137, convex hull=178) After retessellation of defect 21, euler #=-41 (126006,376303,250256) : difference with theory (-37) = 4 CORRECTING DEFECT 22 (vertices=171, convex hull=141) After retessellation of defect 22, euler #=-40 (126035,376462,250387) : difference with theory (-36) = 4 CORRECTING DEFECT 23 (vertices=17, convex hull=30) After retessellation of defect 23, euler #=-39 (126038,376482,250405) : difference with theory (-35) = 4 CORRECTING DEFECT 24 (vertices=20, convex hull=25) After retessellation of defect 24, euler #=-38 (126039,376492,250415) : difference with theory (-34) = 4 CORRECTING DEFECT 25 (vertices=102, convex hull=122) After retessellation of defect 25, euler #=-37 (126087,376693,250569) : difference with theory (-33) = 4 CORRECTING DEFECT 26 (vertices=439, convex hull=285) After retessellation of defect 26, euler #=-35 (126188,377145,250922) : difference with theory (-32) = 3 CORRECTING DEFECT 27 (vertices=11, convex hull=32) After retessellation of defect 27, euler #=-34 (126190,377160,250936) : difference with theory (-31) = 3 CORRECTING DEFECT 28 (vertices=45, convex hull=40) After retessellation of defect 28, euler #=-33 (126198,377200,250969) : difference with theory (-30) = 3 CORRECTING DEFECT 29 (vertices=322, convex hull=126) After retessellation of defect 29, euler #=-32 (126265,377463,251166) : difference with theory (-29) = 3 CORRECTING DEFECT 30 (vertices=923, convex hull=328) After retessellation of defect 30, euler #=-31 (126518,378391,251842) : difference with theory (-28) = 3 CORRECTING DEFECT 31 (vertices=91, convex hull=114) After retessellation of defect 31, euler #=-30 (126541,378514,251943) : difference with theory (-27) = 3 CORRECTING DEFECT 32 (vertices=33, convex hull=62) After retessellation of defect 32, euler #=-29 (126559,378593,252005) : difference with theory (-26) = 3 CORRECTING DEFECT 33 (vertices=204, convex hull=171) After retessellation of defect 33, euler #=-27 (126617,378860,252216) : difference with theory (-25) = 2 CORRECTING DEFECT 34 (vertices=27, convex hull=66) After retessellation of defect 34, euler #=-26 (126630,378923,252267) : difference with theory (-24) = 2 CORRECTING DEFECT 35 (vertices=81, convex hull=130) After retessellation of defect 35, euler #=-25 (126667,379091,252399) : difference with theory (-23) = 2 CORRECTING DEFECT 36 (vertices=22, convex hull=70) After retessellation of defect 36, euler #=-24 (126680,379156,252452) : difference with theory (-22) = 2 CORRECTING DEFECT 37 (vertices=32, convex hull=60) After retessellation of defect 37, euler #=-23 (126697,379228,252508) : difference with theory (-21) = 2 CORRECTING DEFECT 38 (vertices=192, convex hull=172) After retessellation of defect 38, euler #=-22 (126738,379437,252677) : difference with theory (-20) = 2 CORRECTING DEFECT 39 (vertices=13, convex hull=23) After retessellation of defect 39, euler #=-21 (126742,379456,252693) : difference with theory (-19) = 2 CORRECTING DEFECT 40 (vertices=186, convex hull=109) After retessellation of defect 40, euler #=-19 (126814,379724,252891) : difference with theory (-18) = 1 CORRECTING DEFECT 41 (vertices=53, convex hull=106) After retessellation of defect 41, euler #=-18 (126837,379837,252982) : difference with theory (-17) = 1 CORRECTING DEFECT 42 (vertices=112, convex hull=125) After retessellation of defect 42, euler #=-17 (126850,379937,253070) : difference with theory (-16) = 1 CORRECTING DEFECT 43 (vertices=51, convex hull=78) After retessellation of defect 43, euler #=-16 (126882,380062,253164) : difference with theory (-15) = 1 CORRECTING DEFECT 44 (vertices=128, convex hull=89) After retessellation of defect 44, euler #=-14 (126891,380125,253220) : difference with theory (-14) = 0 CORRECTING DEFECT 45 (vertices=56, convex hull=54) After retessellation of defect 45, euler #=-13 (126900,380176,253263) : difference with theory (-13) = 0 CORRECTING DEFECT 46 (vertices=396, convex hull=283) After retessellation of defect 46, euler #=-12 (127029,380711,253670) : difference with theory (-12) = 0 CORRECTING DEFECT 47 (vertices=6, convex hull=17) After retessellation of defect 47, euler #=-11 (127031,380720,253678) : difference with theory (-11) = 0 CORRECTING DEFECT 48 (vertices=35, convex hull=57) After retessellation of defect 48, euler #=-10 (127049,380793,253734) : difference with theory (-10) = 0 CORRECTING DEFECT 49 (vertices=35, convex hull=71) After retessellation of defect 49, euler #=-9 (127070,380886,253807) : difference with theory (-9) = 0 CORRECTING DEFECT 50 (vertices=8, convex hull=25) After retessellation of defect 50, euler #=-8 (127071,380896,253817) : difference with theory (-8) = 0 CORRECTING DEFECT 51 (vertices=468, convex hull=98) After retessellation of defect 51, euler #=-7 (127112,381068,253949) : difference with theory (-7) = 0 CORRECTING DEFECT 52 (vertices=19, convex hull=50) After retessellation of defect 52, euler #=-6 (127119,381107,253982) : difference with theory (-6) = 0 CORRECTING DEFECT 53 (vertices=58, convex hull=20) After retessellation of defect 53, euler #=-5 (127122,381121,253994) : difference with theory (-5) = 0 CORRECTING DEFECT 54 (vertices=6, convex hull=17) After retessellation of defect 54, euler #=-4 (127123,381130,254003) : difference with theory (-4) = 0 CORRECTING DEFECT 55 (vertices=125, convex hull=59) After retessellation of defect 55, euler #=-3 (127132,381180,254045) : difference with theory (-3) = 0 CORRECTING DEFECT 56 (vertices=241, convex hull=166) After retessellation of defect 56, euler #=-2 (127157,381337,254178) : difference with theory (-2) = 0 CORRECTING DEFECT 57 (vertices=415, convex hull=200) After retessellation of defect 57, euler #=-1 (127251,381720,254468) : difference with theory (-1) = 0 CORRECTING DEFECT 58 (vertices=9, convex hull=21) After retessellation of defect 58, euler #=0 (127253,381729,254476) : difference with theory (0) = 0 CORRECTING DEFECT 59 (vertices=26, convex hull=22) After retessellation of defect 59, euler #=1 (127255,381743,254489) : difference with theory (1) = 0 CORRECTING DEFECT 60 (vertices=42, convex hull=41) After retessellation of defect 60, euler #=2 (127256,381762,254508) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.04-->10.34) (max @ vno 61904 --> 68646) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.04-->10.34) (max @ vno 61904 --> 68646) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 214 mutations (38.0%), 349 crossovers (62.0%), 424 vertices were eliminated building final representation... 4694 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=127256, nf=254508, ne=381762, g=0) writing corrected surface to /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 48.6 minutes 0 defective edges removing intersecting faces 000: 591 intersecting 001: 48 intersecting 002: 22 intersecting 003: 13 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 127256 - 381762 + 254508 = 2 --> 0 holes F =2V-4: 254508 = 254512-4 (0) 2E=3F: 763524 = 763524 (0) total defect index = 0 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 158 intersecting 001: 26 intersecting 002: 21 intersecting 003: 15 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Jan 10 09:32:08 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs chong_lan lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/filled.mgz... reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/brain.finalsurfs.mgz... reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/wm.mgz... 15908 bright wm thresholded. 2155 bright non-wm voxels segmented. reading original surface position from /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.orig... computing class statistics... border white: 235458 voxels (1.40%) border gray 280839 voxels (1.67%) WM (90.0): 91.5 +- 10.1 [70.0 --> 110.0] GM (74.0) : 71.8 +- 13.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 45.3 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 31.5 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->4.48) (max @ vno 61904 --> 68646) face area 0.28 +- 0.13 (0.00-->4.05) mean absolute distance = 0.67 +- 0.87 3288 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=59 using class modes intead of means.... mean inside = 91.2, mean outside = 66.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=73.4, 90 (90) missing vertices, mean dist 0.3 [0.6 (%34.0)->0.7 (%66.0))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fslvm, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.28 (0.07-->4.77) (max @ vno 55807 --> 126037) face area 0.28 +- 0.14 (0.00-->3.23) mean absolute distance = 0.34 +- 0.64 3112 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6470782.0, rms=12.97 001: dt: 0.5000, sse=6870029.0, rms=9.16 002: dt: 0.5000, sse=7468743.5, rms=7.21 003: dt: 0.5000, sse=7716151.5, rms=6.10 004: dt: 0.5000, sse=8080667.5, rms=5.54 005: dt: 0.5000, sse=8113021.5, rms=5.22 006: dt: 0.5000, sse=8324963.5, rms=5.08 007: dt: 0.5000, sse=8234054.5, rms=4.96 008: dt: 0.5000, sse=8375818.0, rms=4.91 009: dt: 0.5000, sse=8238411.0, rms=4.84 rms = 4.81, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=8347062.0, rms=4.81 011: dt: 0.2500, sse=5432012.5, rms=3.47 012: dt: 0.2500, sse=5114291.0, rms=3.02 013: dt: 0.2500, sse=4813682.5, rms=2.94 014: dt: 0.2500, sse=4788079.5, rms=2.85 rms = 2.83, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4661948.5, rms=2.83 016: dt: 0.1250, sse=4328380.0, rms=2.44 017: dt: 0.1250, sse=4275048.5, rms=2.39 rms = 2.39, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4275048.5, rms=2.39 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=77.1, 134 (39) missing vertices, mean dist -0.2 [0.4 (%70.1)->0.2 (%29.9))] %73 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fslvm, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.27 (0.04-->5.14) (max @ vno 48579 --> 48580) face area 0.35 +- 0.18 (0.00-->4.15) mean absolute distance = 0.28 +- 0.49 3154 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4912443.5, rms=5.27 019: dt: 0.5000, sse=5440342.0, rms=4.17 rms = 4.63, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=4897947.0, rms=2.98 021: dt: 0.2500, sse=4768313.5, rms=2.54 022: dt: 0.2500, sse=4722795.0, rms=2.25 rms = 2.24, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4707874.5, rms=2.24 024: dt: 0.1250, sse=4500672.5, rms=1.93 rms = 1.89, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4436986.0, rms=1.89 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=79.3, 171 (34) missing vertices, mean dist -0.1 [0.3 (%62.7)->0.2 (%37.3))] %79 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fslvm, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.27 (0.08-->5.31) (max @ vno 48579 --> 48580) face area 0.34 +- 0.17 (0.00-->4.08) mean absolute distance = 0.26 +- 0.41 3552 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4636744.5, rms=3.54 rms = 4.01, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4531412.5, rms=2.57 027: dt: 0.2500, sse=4564599.5, rms=1.98 rms = 1.94, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4654162.5, rms=1.94 029: dt: 0.1250, sse=4542931.0, rms=1.72 rms = 1.70, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4494057.0, rms=1.70 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group mean border=80.2, 140 (7) missing vertices, mean dist -0.1 [0.3 (%53.0)->0.2 (%47.0))] %82 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fslvm, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4537320.0, rms=2.22 rms = 3.00, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4682126.0, rms=1.56 032: dt: 0.2500, sse=4966645.0, rms=1.31 rms = 1.34, time step reduction 2 of 3 to 0.125... rms = 1.29, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4962180.0, rms=1.29 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 19 non-cortical segments detected only using segment with 1543 vertices erasing segment 1 (vno[0] = 57123) erasing segment 2 (vno[0] = 74442) erasing segment 3 (vno[0] = 80803) erasing segment 4 (vno[0] = 82998) erasing segment 5 (vno[0] = 87058) erasing segment 6 (vno[0] = 88054) erasing segment 7 (vno[0] = 89128) erasing segment 8 (vno[0] = 91046) erasing segment 9 (vno[0] = 91931) erasing segment 10 (vno[0] = 92840) erasing segment 11 (vno[0] = 93711) erasing segment 12 (vno[0] = 96989) erasing segment 13 (vno[0] = 97868) erasing segment 14 (vno[0] = 98636) erasing segment 15 (vno[0] = 99376) erasing segment 16 (vno[0] = 100062) erasing segment 17 (vno[0] = 100124) erasing segment 18 (vno[0] = 100720) writing cortex label to /mnt/hgfs/DATA/Freesurfer/chong_lan/label/lh.cortex.label... LabelWrite: saving to /mnt/hgfs/DATA/Freesurfer/chong_lan/label/lh.cortex.label writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.curv writing smoothed area to lh.area writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.area vertex spacing 0.90 +- 0.27 (0.07-->5.40) (max @ vno 48579 --> 48580) face area 0.34 +- 0.17 (0.00-->4.05) refinement took 5.2 minutes #-------------------------------------------- #@# Smooth2 lh Thu Jan 10 09:37:20 EST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Thu Jan 10 09:37:26 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 45.5 mm, total surface area = 78426 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.121 (target=0.015) step 005: RMS=0.085 (target=0.015) step 010: RMS=0.063 (target=0.015) step 015: RMS=0.052 (target=0.015) step 020: RMS=0.043 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.020 (target=0.015) step 050: RMS=0.018 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 267 vertices thresholded to be in k1 ~ [-0.19 0.34], k2 ~ [-0.10 0.06] total integrated curvature = 0.509*4pi (6.401) --> 0 handles ICI = 1.4, FI = 8.1, variation=142.506 144 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 141 vertices thresholded to be in [-0.12 0.17] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.021 done. #----------------------------------------- #@# Curvature Stats lh Thu Jan 10 09:39:23 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm chong_lan lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ chong_lan/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 237 ] Gb_filter = 0 WARN: S lookup min: -0.074659 WARN: S explicit min: 0.000000 vertex = 61 #-------------------------------------------- #@# Sphere lh Thu Jan 10 09:39:29 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 0.77 hours scaling brain by 0.299... pass 1: epoch 1 of 3 starting distance error %21.26 pass 1: epoch 2 of 3 starting distance error %21.24 unfolding complete - removing small folds... starting distance error %21.16 removing remaining folds... final distance error %21.18 #-------------------------------------------- #@# Surf Reg lh Thu Jan 10 10:25:55 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = -0.000, std = 0.601 curvature mean = 0.032, std = 0.940 curvature mean = 0.019, std = 0.866 curvature mean = 0.015, std = 0.955 curvature mean = 0.010, std = 0.944 curvature mean = 0.014, std = 0.968 curvature mean = 0.004, std = 0.975 curvature mean = 0.013, std = 0.971 curvature mean = 0.001, std = 0.989 curvature mean = -0.030, std = 0.300 curvature mean = 0.003, std = 0.067 curvature mean = 0.076, std = 0.331 curvature mean = 0.003, std = 0.079 curvature mean = 0.042, std = 0.515 curvature mean = 0.003, std = 0.085 curvature mean = 0.023, std = 0.656 curvature mean = 0.003, std = 0.088 curvature mean = 0.009, std = 0.767 expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Thu Jan 10 10:50:22 EST 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Jan 10 10:50:28 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Thu Jan 10 10:50:31 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 chong_lan lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1121 labels changed using aseg relabeling using gibbs priors... 000: 2965 changed, 127256 examined... 001: 692 changed, 12640 examined... 002: 164 changed, 3865 examined... 003: 60 changed, 1007 examined... 004: 30 changed, 344 examined... 005: 19 changed, 162 examined... 006: 13 changed, 121 examined... 007: 3 changed, 72 examined... 008: 2 changed, 19 examined... 009: 3 changed, 16 examined... 010: 1 changed, 14 examined... 011: 3 changed, 8 examined... 012: 0 changed, 14 examined... 237 labels changed using aseg 000: 115 total segments, 74 labels (337 vertices) changed 001: 42 total segments, 1 labels (1 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 34 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1493 vertices marked for relabeling... 1493 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 48 seconds. #-------------------------------------------- #@# Make Pial Surf lh Thu Jan 10 10:51:19 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs chong_lan lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/filled.mgz... reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/brain.finalsurfs.mgz... reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/wm.mgz... 15908 bright wm thresholded. 2155 bright non-wm voxels segmented. reading original surface position from /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.orig... computing class statistics... border white: 235458 voxels (1.40%) border gray 280839 voxels (1.67%) WM (90.0): 91.5 +- 10.1 [70.0 --> 110.0] GM (74.0) : 71.8 +- 13.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 45.3 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 59.0 (was 85) setting MAX_CSF to 31.5 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 52.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 17.8 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=59 using class modes intead of means.... mean inside = 91.2, mean outside = 66.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->4.48) (max @ vno 61904 --> 68646) face area 0.28 +- 0.13 (0.00-->4.05) mean absolute distance = 0.67 +- 0.87 3301 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 45 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown mean border=73.4, 90 (90) missing vertices, mean dist 0.3 [0.6 (%34.0)->0.7 (%66.0))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fslvm, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.28 (0.07-->4.77) (max @ vno 55807 --> 126037) face area 0.28 +- 0.14 (0.00-->3.23) mean absolute distance = 0.35 +- 0.64 3120 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6473247.0, rms=12.97 001: dt: 0.5000, sse=6871158.0, rms=9.16 002: dt: 0.5000, sse=7471642.5, rms=7.21 003: dt: 0.5000, sse=7720438.5, rms=6.10 004: dt: 0.5000, sse=8084701.0, rms=5.54 005: dt: 0.5000, sse=8118063.5, rms=5.23 006: dt: 0.5000, sse=8329046.0, rms=5.08 007: dt: 0.5000, sse=8239429.5, rms=4.97 008: dt: 0.5000, sse=8382001.0, rms=4.91 009: dt: 0.5000, sse=8245329.0, rms=4.84 rms = 4.81, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=8352994.5, rms=4.81 011: dt: 0.2500, sse=5437488.0, rms=3.48 012: dt: 0.2500, sse=5119149.5, rms=3.03 013: dt: 0.2500, sse=4817996.0, rms=2.95 014: dt: 0.2500, sse=4792075.0, rms=2.85 rms = 2.83, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=4666206.0, rms=2.83 016: dt: 0.1250, sse=4332387.5, rms=2.45 017: dt: 0.1250, sse=4278869.5, rms=2.39 rms = 2.39, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=4278869.5, rms=2.39 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 62 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown mean border=77.1, 135 (39) missing vertices, mean dist -0.2 [0.4 (%70.1)->0.2 (%29.9))] %73 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fslvm, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.27 (0.04-->5.14) (max @ vno 48579 --> 48580) face area 0.35 +- 0.18 (0.00-->4.15) mean absolute distance = 0.28 +- 0.49 3166 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4916327.5, rms=5.27 019: dt: 0.5000, sse=5444654.0, rms=4.18 rms = 4.63, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=4902291.0, rms=2.98 021: dt: 0.2500, sse=4772979.5, rms=2.54 022: dt: 0.2500, sse=4727519.0, rms=2.25 rms = 2.25, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=4712960.0, rms=2.25 024: dt: 0.1250, sse=4505661.5, rms=1.93 rms = 1.89, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=4441940.0, rms=1.89 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 62 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown mean border=79.3, 174 (34) missing vertices, mean dist -0.1 [0.3 (%62.7)->0.2 (%37.3))] %79 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fslvm, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.27 (0.08-->5.31) (max @ vno 48579 --> 48580) face area 0.34 +- 0.17 (0.00-->4.08) mean absolute distance = 0.26 +- 0.41 3549 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4642098.0, rms=3.55 rms = 4.01, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=4536891.0, rms=2.57 027: dt: 0.2500, sse=4570153.0, rms=1.98 rms = 1.94, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=4659576.5, rms=1.94 029: dt: 0.1250, sse=4548197.5, rms=1.73 rms = 1.70, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=4499659.0, rms=1.70 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 62 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 6 with 11 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 8 with 3 points - only 0.00% unknown mean border=80.2, 144 (7) missing vertices, mean dist -0.1 [0.3 (%53.0)->0.2 (%47.0))] %83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fslvm, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4542611.5, rms=2.22 rms = 3.00, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=4688061.0, rms=1.56 032: dt: 0.2500, sse=4973598.0, rms=1.32 rms = 1.34, time step reduction 2 of 3 to 0.125... rms = 1.30, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=4969157.0, rms=1.30 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=48.0, 74 (74) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.2 (%100.0))] %16 local maxima, %55 large gradients and %24 min vals, 1978 gradients ignored tol=1.0e-04, sigma=2.0, host=fslvm, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=27050468.0, rms=31.76 001: dt: 0.5000, sse=19460718.0, rms=26.34 002: dt: 0.5000, sse=14275283.0, rms=21.85 003: dt: 0.5000, sse=11316016.0, rms=18.36 004: dt: 0.5000, sse=9915743.0, rms=15.73 005: dt: 0.5000, sse=9116611.0, rms=13.79 006: dt: 0.5000, sse=8677608.0, rms=12.42 007: dt: 0.5000, sse=8382479.0, rms=11.42 008: dt: 0.5000, sse=8262139.5, rms=10.58 009: dt: 0.5000, sse=8130869.0, rms=9.86 010: dt: 0.5000, sse=8141343.0, rms=9.25 011: dt: 0.5000, sse=8139273.5, rms=8.68 012: dt: 0.5000, sse=8188490.0, rms=8.09 013: dt: 0.5000, sse=8167375.5, rms=7.49 014: dt: 0.5000, sse=8229076.0, rms=6.91 015: dt: 0.5000, sse=8223410.5, rms=6.48 016: dt: 0.5000, sse=8351956.5, rms=6.17 017: dt: 0.5000, sse=8325871.5, rms=5.97 018: dt: 0.5000, sse=8428964.0, rms=5.82 019: dt: 0.5000, sse=8383107.0, rms=5.74 020: dt: 0.5000, sse=8470729.0, rms=5.65 rms = 5.62, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=8404670.0, rms=5.62 022: dt: 0.2500, sse=6377001.5, rms=4.98 023: dt: 0.2500, sse=6215038.0, rms=4.78 rms = 4.78, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=6058894.0, rms=4.78 025: dt: 0.1250, sse=5729078.5, rms=4.58 rms = 4.54, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=5684975.0, rms=4.54 positioning took 2.4 minutes mean border=46.1, 1041 (16) missing vertices, mean dist 0.2 [0.2 (%50.0)->0.8 (%50.0))] %35 local maxima, %38 large gradients and %21 min vals, 927 gradients ignored tol=1.0e-04, sigma=1.0, host=fslvm, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6294037.0, rms=5.83 027: dt: 0.5000, sse=6732584.5, rms=5.62 028: dt: 0.5000, sse=8479933.0, rms=5.51 rms = 5.49, time step reduction 1 of 3 to 0.250... 029: dt: 0.5000, sse=8020534.5, rms=5.49 030: dt: 0.2500, sse=6830251.5, rms=4.72 031: dt: 0.2500, sse=6758975.5, rms=4.45 rms = 4.48, time step reduction 2 of 3 to 0.125... 032: dt: 0.1250, sse=6601975.5, rms=4.35 033: dt: 0.1250, sse=6362502.5, rms=4.22 rms = 4.18, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=6289257.5, rms=4.18 positioning took 0.8 minutes mean border=44.1, 1281 (16) missing vertices, mean dist 0.2 [0.2 (%43.8)->0.6 (%56.2))] %50 local maxima, %23 large gradients and %21 min vals, 1055 gradients ignored tol=1.0e-04, sigma=0.5, host=fslvm, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6531453.0, rms=5.14 rms = 5.32, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=6319795.0, rms=4.71 036: dt: 0.2500, sse=6282912.0, rms=4.44 037: dt: 0.2500, sse=6543470.0, rms=4.38 rms = 4.33, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=6698513.0, rms=4.33 039: dt: 0.1250, sse=6383971.0, rms=4.06 040: dt: 0.1250, sse=6390947.5, rms=3.98 rms = 3.96, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=6401201.5, rms=3.96 positioning took 0.7 minutes mean border=43.0, 2470 (13) missing vertices, mean dist 0.1 [0.2 (%47.2)->0.5 (%52.8))] %54 local maxima, %18 large gradients and %21 min vals, 933 gradients ignored tol=1.0e-04, sigma=0.2, host=fslvm, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6472265.5, rms=4.31 rms = 4.87, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=6366367.5, rms=4.07 043: dt: 0.2500, sse=6612603.0, rms=3.97 rms = 4.00, time step reduction 2 of 3 to 0.125... 044: dt: 0.1250, sse=6539738.5, rms=3.91 045: dt: 0.1250, sse=6494864.5, rms=3.83 rms = 3.78, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=6513703.5, rms=3.78 positioning took 0.6 minutes writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.area.pial vertex spacing 1.06 +- 0.46 (0.09-->9.58) (max @ vno 89125 --> 89124) face area 0.44 +- 0.35 (0.00-->8.22) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 127256 vertices processed 25000 of 127256 vertices processed 50000 of 127256 vertices processed 75000 of 127256 vertices processed 100000 of 127256 vertices processed 125000 of 127256 vertices processed 0 of 127256 vertices processed 25000 of 127256 vertices processed 50000 of 127256 vertices processed 75000 of 127256 vertices processed 100000 of 127256 vertices processed 125000 of 127256 vertices processed thickness calculation complete, 778:1043 truncations. 49012 vertices at 0 distance 75410 vertices at 1 distance 68442 vertices at 2 distance 30972 vertices at 3 distance 11206 vertices at 4 distance 4052 vertices at 5 distance 1477 vertices at 6 distance 600 vertices at 7 distance 329 vertices at 8 distance 205 vertices at 9 distance 132 vertices at 10 distance 87 vertices at 11 distance 77 vertices at 12 distance 56 vertices at 13 distance 49 vertices at 14 distance 48 vertices at 15 distance 43 vertices at 16 distance 32 vertices at 17 distance 32 vertices at 18 distance 21 vertices at 19 distance 26 vertices at 20 distance writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.thickness positioning took 10.7 minutes #-------------------------------------------- #@# Surf Volume lh Thu Jan 10 11:02:03 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats lh Thu Jan 10 11:02:05 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab chong_lan lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/wm.mgz... reading input surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.white... reading input pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.pial... reading input white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1370 966 2400 2.499 0.504 0.119 0.032 10 1.9 bankssts 903 612 1326 1.979 0.604 0.176 0.070 22 2.8 caudalanteriorcingulate 4318 2938 9151 2.447 0.780 0.150 0.103 87 10.6 caudalmiddlefrontal 1990 1391 3143 1.976 0.574 0.196 0.092 58 7.2 cuneus 711 527 2481 3.061 0.877 0.231 0.138 35 3.8 entorhinal 4767 3342 10036 2.519 0.729 0.167 0.067 96 13.5 fusiform 7089 4932 15182 2.504 0.811 0.155 0.067 139 17.7 inferiorparietal 4696 3227 10584 2.632 0.865 0.181 0.104 133 17.4 inferiortemporal 1615 1078 3344 2.719 0.834 0.160 0.059 35 3.7 isthmuscingulate 6481 4194 11230 2.324 0.707 0.173 0.106 194 27.6 lateraloccipital 3363 2370 7956 2.869 0.905 0.168 0.082 70 10.9 lateralorbitofrontal 3936 2798 6736 2.274 0.665 0.180 0.077 78 12.5 lingual 2648 1804 5494 2.564 0.888 0.177 0.133 149 14.1 medialorbitofrontal 4099 2817 10299 2.793 0.809 0.157 0.071 109 11.1 middletemporal 948 636 2344 3.126 0.700 0.145 0.053 16 2.0 parahippocampal 1744 1224 3668 2.413 0.711 0.153 0.056 26 4.3 paracentral 2122 1443 4596 2.611 0.614 0.150 0.063 34 5.6 parsopercularis 814 527 1745 2.542 0.853 0.205 0.174 67 7.1 parsorbitalis 1747 1140 3728 2.677 0.671 0.151 0.068 38 4.8 parstriangularis 1458 1021 1854 1.787 0.475 0.165 0.070 30 4.3 pericalcarine 6823 4464 10873 2.031 0.717 0.161 0.155 232 30.1 postcentral 1275 878 2574 2.584 0.771 0.165 0.079 27 3.7 posteriorcingulate 7115 4832 14042 2.456 0.682 0.147 0.059 112 17.9 precentral 6014 4144 11945 2.427 0.780 0.164 0.069 117 15.6 precuneus 1305 938 2680 2.391 0.779 0.183 0.113 43 5.6 rostralanteriorcingulate 8320 5481 16020 2.435 0.751 0.179 0.130 481 37.6 rostralmiddlefrontal 9535 6719 20624 2.480 0.822 0.166 0.073 187 31.0 superiorfrontal 7813 5346 14013 2.194 0.707 0.158 0.105 174 39.6 superiorparietal 4704 3220 11016 2.707 0.799 0.179 0.591 7275 203.8 superiortemporal 4997 3385 10448 2.475 0.799 0.162 0.073 101 14.4 supramarginal 287 186 901 3.421 0.468 0.210 0.121 10 1.4 frontalpole 603 373 1074 2.416 1.145 0.259 0.220 52 6.9 temporalpole 620 399 981 2.334 0.391 0.139 0.049 8 1.3 transversetemporal 3058 1999 6450 2.865 1.055 0.140 0.119 128 16.1 insula #----------------------------------------- #@# Cortical Parc 2 lh Thu Jan 10 11:02:21 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 chong_lan lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 55 labels changed using aseg relabeling using gibbs priors... 000: 8697 changed, 127256 examined... 001: 2029 changed, 33286 examined... 002: 614 changed, 10416 examined... 003: 237 changed, 3359 examined... 004: 117 changed, 1347 examined... 005: 67 changed, 642 examined... 006: 33 changed, 388 examined... 007: 21 changed, 178 examined... 008: 14 changed, 120 examined... 009: 5 changed, 72 examined... 010: 2 changed, 32 examined... 011: 1 changed, 16 examined... 012: 2 changed, 7 examined... 013: 3 changed, 11 examined... 014: 1 changed, 11 examined... 015: 2 changed, 8 examined... 016: 2 changed, 10 examined... 017: 0 changed, 10 examined... 29 labels changed using aseg 000: 250 total segments, 167 labels (1714 vertices) changed 001: 96 total segments, 12 labels (30 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 123 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 871 vertices marked for relabeling... 871 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 50 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Thu Jan 10 11:03:12 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab chong_lan lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/wm.mgz... reading input surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.white... reading input pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.pial... reading input white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1205 786 2086 2.391 0.751 0.197 0.154 205 6.1 G_and_S_frontomargin 1420 972 3046 2.526 0.834 0.170 0.069 27 3.7 G_and_S_occipital_inf 1154 830 2725 2.503 0.694 0.180 0.076 25 3.6 G_and_S_paracentral 1340 912 3256 2.735 0.603 0.178 0.092 32 4.4 G_and_S_subcentral 556 339 1418 2.790 0.796 0.203 0.489 72 3.9 G_and_S_transv_frontopol 1965 1451 3722 2.186 0.715 0.168 0.087 45 7.0 G_and_S_cingul-Ant 1162 846 1784 1.944 0.604 0.156 0.054 18 2.7 G_and_S_cingul-Mid-Ant 1031 721 2025 2.321 0.771 0.155 0.077 20 2.7 G_and_S_cingul-Mid-Post 520 362 1568 3.137 0.602 0.195 0.079 16 1.5 G_cingul-Post-dorsal 344 214 548 2.348 0.907 0.156 0.067 9 0.8 G_cingul-Post-ventral 1858 1340 3189 2.023 0.601 0.209 0.117 68 7.8 G_cuneus 1409 942 3783 2.898 0.534 0.174 0.080 32 4.9 G_front_inf-Opercular 258 173 728 2.884 0.646 0.158 0.062 6 0.6 G_front_inf-Orbital 1093 690 2867 2.970 0.564 0.177 0.092 35 4.1 G_front_inf-Triangul 5118 3386 12596 2.695 0.826 0.181 0.096 155 20.6 G_front_middle 6611 4613 16682 2.753 0.787 0.179 0.085 156 25.2 G_front_sup 458 277 1192 3.160 0.717 0.222 0.370 53 9.0 G_Ins_lg_and_S_cent_ins 501 349 1605 3.583 1.071 0.152 0.173 24 2.6 G_insular_short 2100 1384 5544 2.934 0.612 0.177 0.101 72 7.2 G_occipital_middle 1544 1021 2782 2.175 0.659 0.175 0.107 54 6.2 G_occipital_sup 2230 1556 5713 2.794 0.697 0.179 0.075 57 7.6 G_oc-temp_lat-fusifor 2722 1965 5218 2.325 0.622 0.204 0.097 68 11.0 G_oc-temp_med-Lingual 1141 820 3746 3.180 0.779 0.188 0.084 31 3.9 G_oc-temp_med-Parahip 2057 1421 5434 2.854 0.911 0.222 0.178 136 16.2 G_orbital 2646 1877 7490 2.848 0.900 0.188 0.095 76 10.3 G_pariet_inf-Angular 2479 1690 6360 2.753 0.793 0.177 0.089 63 8.4 G_pariet_inf-Supramar 3101 2149 7166 2.492 0.809 0.193 0.110 99 13.5 G_parietal_sup 2793 1747 4884 2.209 0.655 0.195 0.297 178 21.1 G_postcentral 2792 1891 7255 2.786 0.663 0.166 0.142 79 9.5 G_precentral 2714 1899 7146 2.799 0.682 0.186 0.077 68 8.8 G_precuneus 1002 680 2432 2.567 0.777 0.238 0.253 116 9.9 G_rectus 392 275 917 3.155 0.987 0.159 0.072 10 1.1 G_subcallosal 608 392 1093 2.439 0.432 0.151 0.055 9 1.4 G_temp_sup-G_T_transv 1805 1275 6036 3.260 0.685 0.218 0.145 91 10.3 G_temp_sup-Lateral 479 290 1183 3.394 1.044 0.281 4.995 7156 187.4 G_temp_sup-Plan_polar 532 378 1179 2.514 0.607 0.151 0.069 10 1.6 G_temp_sup-Plan_tempo 2498 1708 7277 3.001 0.895 0.208 0.141 93 11.9 G_temporal_inf 2486 1690 7687 3.099 0.723 0.168 0.083 85 7.4 G_temporal_middle 313 200 417 2.293 0.424 0.103 0.027 2 0.4 Lat_Fis-ant-Horizont 178 123 293 2.469 0.320 0.118 0.038 1 0.2 Lat_Fis-ant-Vertical 812 541 1060 2.123 0.501 0.117 0.032 6 1.1 Lat_Fis-post 1920 1204 2756 2.102 0.663 0.204 0.189 92 14.0 Pole_occipital 1547 1032 2673 2.124 0.712 0.239 0.175 96 11.8 Pole_temporal 2055 1390 2791 2.055 0.808 0.149 0.059 30 4.6 S_calcarine 3158 2110 3626 1.823 0.581 0.125 0.042 27 6.0 S_central 1009 716 1519 2.021 0.624 0.138 0.046 11 2.1 S_cingul-Marginalis 420 284 827 2.731 0.910 0.126 0.060 5 1.1 S_circular_insula_ant 1469 960 2294 2.405 0.824 0.111 0.042 39 2.9 S_circular_insula_inf 1779 1215 2484 2.164 0.685 0.130 0.048 18 3.7 S_circular_insula_sup 780 575 1263 2.125 0.663 0.148 0.048 11 1.4 S_collat_transv_ant 202 143 344 2.383 0.453 0.163 0.063 3 0.5 S_collat_transv_post 2107 1450 3389 2.279 0.512 0.129 0.044 32 3.6 S_front_inf 1572 1083 2361 2.105 0.594 0.168 0.089 42 6.7 S_front_middle 3192 2218 5486 2.193 0.695 0.142 0.051 35 6.9 S_front_sup 345 236 415 1.798 0.485 0.130 0.039 3 0.6 S_interm_prim-Jensen 3052 2068 4165 2.007 0.498 0.128 0.108 39 21.5 S_intrapariet_and_P_trans 1049 708 1571 2.165 0.587 0.133 0.038 10 1.8 S_oc_middle_and_Lunatus 1637 1087 2323 2.174 0.582 0.119 0.032 13 2.3 S_oc_sup_and_transversal 681 443 938 2.165 0.580 0.119 0.044 8 1.1 S_occipital_ant 851 576 1169 2.183 0.680 0.152 0.061 13 1.9 S_oc-temp_lat 1910 1333 3356 2.639 0.681 0.139 0.046 22 3.6 S_oc-temp_med_and_Lingual 378 263 561 2.386 0.592 0.156 0.058 5 0.8 S_orbital_lateral 891 605 1436 2.209 0.910 0.128 0.055 20 2.0 S_orbital_med-olfact 1419 966 2809 2.920 0.934 0.144 0.050 17 3.0 S_orbital-H_Shaped 2163 1449 2959 2.031 0.649 0.149 0.052 29 4.7 S_parieto_occipital 1134 699 1408 2.335 0.813 0.154 0.065 27 2.7 S_pericallosal 2956 1971 3605 1.837 0.552 0.130 0.048 33 5.6 S_postcentral 1514 1018 2410 2.280 0.539 0.120 0.040 13 2.4 S_precentral-inf-part 1393 957 1933 1.975 0.623 0.131 0.039 12 2.5 S_precentral-sup-part 769 525 1377 2.549 0.886 0.152 0.056 11 1.7 S_suborbital 1394 953 2163 2.149 0.678 0.144 0.069 22 2.8 S_subparietal 1871 1298 2742 2.118 0.620 0.124 0.033 17 2.8 S_temporal_inf 5007 3474 8263 2.370 0.618 0.130 0.044 60 10.2 S_temporal_sup 237 169 390 2.138 0.520 0.107 0.032 1 0.4 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Thu Jan 10 11:03:29 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 4 found - 4 modified | TOTAL: 5 pass 2 (yz+): 0 found - 4 modified | TOTAL: 5 pass 1 (yz-): 0 found - 0 modified | TOTAL: 5 pass 1 (xz+): 0 found - 0 modified | TOTAL: 5 pass 1 (xz-): 2 found - 2 modified | TOTAL: 7 pass 2 (xz-): 0 found - 2 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 10 (out of 237177: 0.004216) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 60: 2265 vertices, 2432 faces slice 70: 9324 vertices, 9691 faces slice 80: 19868 vertices, 20282 faces slice 90: 32023 vertices, 32469 faces slice 100: 43148 vertices, 43553 faces slice 110: 54294 vertices, 54691 faces slice 120: 65692 vertices, 66094 faces slice 130: 77122 vertices, 77581 faces slice 140: 87587 vertices, 88024 faces slice 150: 98023 vertices, 98438 faces slice 160: 107301 vertices, 107687 faces slice 170: 114407 vertices, 114750 faces slice 180: 120620 vertices, 120939 faces slice 190: 126381 vertices, 126686 faces slice 200: 131308 vertices, 131586 faces slice 210: 133506 vertices, 133628 faces slice 220: 133506 vertices, 133628 faces slice 230: 133506 vertices, 133628 faces slice 240: 133506 vertices, 133628 faces slice 250: 133506 vertices, 133628 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 133506 voxel in cpt #1: X=-122 [v=133506,e=400884,f=267256] located at (28.031355, -5.565113, 19.002180) For the whole surface: X=-122 [v=133506,e=400884,f=267256] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Jan 10 11:03:40 EST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Thu Jan 10 11:03:47 EST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts avg radius = 45.9 mm, total surface area = 69383 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.109 (target=0.015) step 005: RMS=0.082 (target=0.015) step 010: RMS=0.065 (target=0.015) step 015: RMS=0.057 (target=0.015) step 020: RMS=0.051 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.043 (target=0.015) step 040: RMS=0.042 (target=0.015) step 045: RMS=0.041 (target=0.015) step 050: RMS=0.040 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.040 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Jan 10 11:04:20 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.00 +- 0.62 (0.00-->7.21) (max @ vno 93498 --> 94549) face area 0.03 +- 0.03 (-0.21-->0.71) scaling brain by 0.321... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.440, avgs=0 005/300: dt: 0.9000, rms radial error=176.181, avgs=0 010/300: dt: 0.9000, rms radial error=175.625, avgs=0 015/300: dt: 0.9000, rms radial error=174.894, avgs=0 020/300: dt: 0.9000, rms radial error=174.062, avgs=0 025/300: dt: 0.9000, rms radial error=173.171, avgs=0 030/300: dt: 0.9000, rms radial error=172.249, avgs=0 035/300: dt: 0.9000, rms radial error=171.311, avgs=0 040/300: dt: 0.9000, rms radial error=170.364, avgs=0 045/300: dt: 0.9000, rms radial error=169.415, avgs=0 050/300: dt: 0.9000, rms radial error=168.467, avgs=0 055/300: dt: 0.9000, rms radial error=167.523, avgs=0 060/300: dt: 0.9000, rms radial error=166.582, avgs=0 065/300: dt: 0.9000, rms radial error=165.645, avgs=0 070/300: dt: 0.9000, rms radial error=164.713, avgs=0 075/300: dt: 0.9000, rms radial error=163.785, avgs=0 080/300: dt: 0.9000, rms radial error=162.862, avgs=0 085/300: dt: 0.9000, rms radial error=161.946, avgs=0 090/300: dt: 0.9000, rms radial error=161.035, avgs=0 095/300: dt: 0.9000, rms radial error=160.129, avgs=0 100/300: dt: 0.9000, rms radial error=159.227, avgs=0 105/300: dt: 0.9000, rms radial error=158.331, avgs=0 110/300: dt: 0.9000, rms radial error=157.439, avgs=0 115/300: dt: 0.9000, rms radial error=156.552, avgs=0 120/300: dt: 0.9000, rms radial error=155.669, avgs=0 125/300: dt: 0.9000, rms radial error=154.792, avgs=0 130/300: dt: 0.9000, rms radial error=153.919, avgs=0 135/300: dt: 0.9000, rms radial error=153.050, avgs=0 140/300: dt: 0.9000, rms radial error=152.187, avgs=0 145/300: dt: 0.9000, rms radial error=151.327, avgs=0 150/300: dt: 0.9000, rms radial error=150.473, avgs=0 155/300: dt: 0.9000, rms radial error=149.623, avgs=0 160/300: dt: 0.9000, rms radial error=148.778, avgs=0 165/300: dt: 0.9000, rms radial error=147.938, avgs=0 170/300: dt: 0.9000, rms radial error=147.102, avgs=0 175/300: dt: 0.9000, rms radial error=146.271, avgs=0 180/300: dt: 0.9000, rms radial error=145.445, avgs=0 185/300: dt: 0.9000, rms radial error=144.624, avgs=0 190/300: dt: 0.9000, rms radial error=143.807, avgs=0 195/300: dt: 0.9000, rms radial error=142.995, avgs=0 200/300: dt: 0.9000, rms radial error=142.187, avgs=0 205/300: dt: 0.9000, rms radial error=141.385, avgs=0 210/300: dt: 0.9000, rms radial error=140.586, avgs=0 215/300: dt: 0.9000, rms radial error=139.792, avgs=0 220/300: dt: 0.9000, rms radial error=139.003, avgs=0 225/300: dt: 0.9000, rms radial error=138.217, avgs=0 230/300: dt: 0.9000, rms radial error=137.437, avgs=0 235/300: dt: 0.9000, rms radial error=136.660, avgs=0 240/300: dt: 0.9000, rms radial error=135.888, avgs=0 245/300: dt: 0.9000, rms radial error=135.120, avgs=0 250/300: dt: 0.9000, rms radial error=134.357, avgs=0 255/300: dt: 0.9000, rms radial error=133.598, avgs=0 260/300: dt: 0.9000, rms radial error=132.845, avgs=0 265/300: dt: 0.9000, rms radial error=132.096, avgs=0 270/300: dt: 0.9000, rms radial error=131.351, avgs=0 275/300: dt: 0.9000, rms radial error=130.610, avgs=0 280/300: dt: 0.9000, rms radial error=129.873, avgs=0 285/300: dt: 0.9000, rms radial error=129.141, avgs=0 290/300: dt: 0.9000, rms radial error=128.412, avgs=0 295/300: dt: 0.9000, rms radial error=127.688, avgs=0 300/300: dt: 0.9000, rms radial error=126.967, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15534.62 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2598.11 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00005 epoch 3 (K=160.0), pass 1, starting sse = 289.02 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00572 epoch 4 (K=640.0), pass 1, starting sse = 28.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00757 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Jan 10 11:08:07 EST 2013 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 chong_lan rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-122 (nv=133506, nf=267256, ne=400884, g=62) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 11754 ambiguous faces found in tessellation segmenting defects... 67 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 1 66 defects to be corrected 0 vertices coincident reading input surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.8088 (-4.9044) -vertex loglikelihood: -6.9644 (-3.4822) -normal dot loglikelihood: -3.5599 (-3.5599) -quad curv loglikelihood: -6.3747 (-3.1873) Total Loglikelihood : -26.7078 CORRECTING DEFECT 0 (vertices=64, convex hull=23) After retessellation of defect 0, euler #=-63 (126699,378019,251257) : difference with theory (-63) = 0 CORRECTING DEFECT 1 (vertices=64, convex hull=71) After retessellation of defect 1, euler #=-61 (126714,378095,251320) : difference with theory (-62) = -1 CORRECTING DEFECT 2 (vertices=24, convex hull=47) After retessellation of defect 2, euler #=-60 (126722,378140,251358) : difference with theory (-61) = -1 CORRECTING DEFECT 3 (vertices=6, convex hull=29) After retessellation of defect 3, euler #=-59 (126723,378153,251371) : difference with theory (-60) = -1 CORRECTING DEFECT 4 (vertices=54, convex hull=38) After retessellation of defect 4, euler #=-58 (126727,378178,251393) : difference with theory (-59) = -1 CORRECTING DEFECT 5 (vertices=64, convex hull=70) After retessellation of defect 5, euler #=-57 (126741,378250,251452) : difference with theory (-58) = -1 CORRECTING DEFECT 6 (vertices=30, convex hull=48) After retessellation of defect 6, euler #=-56 (126750,378293,251487) : difference with theory (-57) = -1 CORRECTING DEFECT 7 (vertices=39, convex hull=84) After retessellation of defect 7, euler #=-55 (126773,378402,251574) : difference with theory (-56) = -1 CORRECTING DEFECT 8 (vertices=33, convex hull=64) After retessellation of defect 8, euler #=-54 (126792,378483,251637) : difference with theory (-55) = -1 CORRECTING DEFECT 9 (vertices=59, convex hull=112) After retessellation of defect 9, euler #=-53 (126834,378655,251768) : difference with theory (-54) = -1 CORRECTING DEFECT 10 (vertices=73, convex hull=94) After retessellation of defect 10, euler #=-52 (126857,378768,251859) : difference with theory (-53) = -1 CORRECTING DEFECT 11 (vertices=117, convex hull=98) After retessellation of defect 11, euler #=-51 (126889,378909,251969) : difference with theory (-52) = -1 CORRECTING DEFECT 12 (vertices=48, convex hull=79) After retessellation of defect 12, euler #=-50 (126914,379021,252057) : difference with theory (-51) = -1 CORRECTING DEFECT 13 (vertices=18, convex hull=46) After retessellation of defect 13, euler #=-49 (126922,379063,252092) : difference with theory (-50) = -1 CORRECTING DEFECT 14 (vertices=31, convex hull=37) After retessellation of defect 14, euler #=-48 (126927,379091,252116) : difference with theory (-49) = -1 CORRECTING DEFECT 15 (vertices=79, convex hull=68) After retessellation of defect 15, euler #=-47 (126939,379152,252166) : difference with theory (-48) = -1 CORRECTING DEFECT 16 (vertices=93, convex hull=72) After retessellation of defect 16, euler #=-46 (126948,379212,252218) : difference with theory (-47) = -1 CORRECTING DEFECT 17 (vertices=19, convex hull=25) After retessellation of defect 17, euler #=-45 (126950,379224,252229) : difference with theory (-46) = -1 CORRECTING DEFECT 18 (vertices=21, convex hull=55) After retessellation of defect 18, euler #=-44 (126963,379281,252274) : difference with theory (-45) = -1 CORRECTING DEFECT 19 (vertices=374, convex hull=232) After retessellation of defect 19, euler #=-43 (127026,379575,252506) : difference with theory (-44) = -1 CORRECTING DEFECT 20 (vertices=86, convex hull=157) After retessellation of defect 20, euler #=-42 (127075,379796,252679) : difference with theory (-43) = -1 CORRECTING DEFECT 21 (vertices=196, convex hull=164) After retessellation of defect 21, euler #=-41 (127097,379938,252800) : difference with theory (-42) = -1 CORRECTING DEFECT 22 (vertices=22, convex hull=69) After retessellation of defect 22, euler #=-40 (127106,379992,252846) : difference with theory (-41) = -1 CORRECTING DEFECT 23 (vertices=8, convex hull=29) After retessellation of defect 23, euler #=-39 (127110,380012,252863) : difference with theory (-40) = -1 CORRECTING DEFECT 24 (vertices=86, convex hull=68) After retessellation of defect 24, euler #=-38 (127126,380087,252923) : difference with theory (-39) = -1 CORRECTING DEFECT 25 (vertices=167, convex hull=54) After retessellation of defect 25, euler #=-37 (127150,380188,253001) : difference with theory (-38) = -1 CORRECTING DEFECT 26 (vertices=67, convex hull=94) After retessellation of defect 26, euler #=-36 (127191,380346,253119) : difference with theory (-37) = -1 CORRECTING DEFECT 27 (vertices=31, convex hull=45) After retessellation of defect 27, euler #=-35 (127196,380379,253148) : difference with theory (-36) = -1 CORRECTING DEFECT 28 (vertices=34, convex hull=63) After retessellation of defect 28, euler #=-34 (127222,380480,253224) : difference with theory (-35) = -1 CORRECTING DEFECT 29 (vertices=20, convex hull=63) After retessellation of defect 29, euler #=-33 (127231,380535,253271) : difference with theory (-34) = -1 CORRECTING DEFECT 30 (vertices=65, convex hull=90) After retessellation of defect 30, euler #=-32 (127258,380659,253369) : difference with theory (-33) = -1 CORRECTING DEFECT 31 (vertices=23, convex hull=48) After retessellation of defect 31, euler #=-31 (127268,380707,253408) : difference with theory (-32) = -1 CORRECTING DEFECT 32 (vertices=88, convex hull=35) After retessellation of defect 32, euler #=-30 (127279,380752,253443) : difference with theory (-31) = -1 CORRECTING DEFECT 33 (vertices=72, convex hull=104) After retessellation of defect 33, euler #=-29 (127294,380841,253518) : difference with theory (-30) = -1 CORRECTING DEFECT 34 (vertices=56, convex hull=93) After retessellation of defect 34, euler #=-28 (127312,380944,253604) : difference with theory (-29) = -1 CORRECTING DEFECT 35 (vertices=52, convex hull=65) After retessellation of defect 35, euler #=-27 (127323,381004,253654) : difference with theory (-28) = -1 CORRECTING DEFECT 36 (vertices=197, convex hull=124) After retessellation of defect 36, euler #=-26 (127361,381187,253800) : difference with theory (-27) = -1 CORRECTING DEFECT 37 (vertices=153, convex hull=51) After retessellation of defect 37, euler #=-25 (127375,381252,253852) : difference with theory (-26) = -1 CORRECTING DEFECT 38 (vertices=779, convex hull=165) After retessellation of defect 38, euler #=-24 (127460,381603,254119) : difference with theory (-25) = -1 CORRECTING DEFECT 39 (vertices=353, convex hull=138) After retessellation of defect 39, euler #=-23 (127493,381774,254258) : difference with theory (-24) = -1 CORRECTING DEFECT 40 (vertices=170, convex hull=103) After retessellation of defect 40, euler #=-22 (127539,381960,254399) : difference with theory (-23) = -1 CORRECTING DEFECT 41 (vertices=23, convex hull=70) After retessellation of defect 41, euler #=-21 (127548,382010,254441) : difference with theory (-22) = -1 CORRECTING DEFECT 42 (vertices=47, convex hull=87) After retessellation of defect 42, euler #=-20 (127569,382104,254515) : difference with theory (-21) = -1 CORRECTING DEFECT 43 (vertices=84, convex hull=41) After retessellation of defect 43, euler #=-19 (127581,382157,254557) : difference with theory (-20) = -1 CORRECTING DEFECT 44 (vertices=872, convex hull=251) After retessellation of defect 44, euler #=-18 (127757,382807,255032) : difference with theory (-19) = -1 CORRECTING DEFECT 45 (vertices=30, convex hull=44) After retessellation of defect 45, euler #=-17 (127758,382831,255056) : difference with theory (-18) = -1 CORRECTING DEFECT 46 (vertices=19, convex hull=36) After retessellation of defect 46, euler #=-16 (127761,382852,255075) : difference with theory (-17) = -1 CORRECTING DEFECT 47 (vertices=31, convex hull=58) After retessellation of defect 47, euler #=-15 (127778,382925,255132) : difference with theory (-16) = -1 CORRECTING DEFECT 48 (vertices=12, convex hull=16) After retessellation of defect 48, euler #=-14 (127780,382937,255143) : difference with theory (-15) = -1 CORRECTING DEFECT 49 (vertices=101, convex hull=51) After retessellation of defect 49, euler #=-13 (127796,383004,255195) : difference with theory (-14) = -1 CORRECTING DEFECT 50 (vertices=6, convex hull=16) After retessellation of defect 50, euler #=-12 (127796,383007,255199) : difference with theory (-13) = -1 CORRECTING DEFECT 51 (vertices=6, convex hull=21) After retessellation of defect 51, euler #=-11 (127799,383023,255213) : difference with theory (-12) = -1 CORRECTING DEFECT 52 (vertices=409, convex hull=113) After retessellation of defect 52, euler #=-10 (127837,383195,255348) : difference with theory (-11) = -1 CORRECTING DEFECT 53 (vertices=81, convex hull=78) After retessellation of defect 53, euler #=-10 (127882,383364,255472) : difference with theory (-10) = 0 CORRECTING DEFECT 54 (vertices=23, convex hull=30) After retessellation of defect 54, euler #=-9 (127886,383383,255488) : difference with theory (-9) = 0 CORRECTING DEFECT 55 (vertices=9, convex hull=32) After retessellation of defect 55, euler #=-8 (127888,383399,255503) : difference with theory (-8) = 0 CORRECTING DEFECT 56 (vertices=496, convex hull=144) After retessellation of defect 56, euler #=-7 (127916,383546,255623) : difference with theory (-7) = 0 CORRECTING DEFECT 57 (vertices=36, convex hull=61) After retessellation of defect 57, euler #=-6 (127932,383619,255681) : difference with theory (-6) = 0 CORRECTING DEFECT 58 (vertices=41, convex hull=91) After retessellation of defect 58, euler #=-5 (127953,383722,255764) : difference with theory (-5) = 0 CORRECTING DEFECT 59 (vertices=196, convex hull=64) After retessellation of defect 59, euler #=-4 (127970,383802,255828) : difference with theory (-4) = 0 CORRECTING DEFECT 60 (vertices=97, convex hull=60) After retessellation of defect 60, euler #=-3 (127979,383853,255871) : difference with theory (-3) = 0 CORRECTING DEFECT 61 (vertices=33, convex hull=69) After retessellation of defect 61, euler #=-2 (127996,383930,255932) : difference with theory (-2) = 0 CORRECTING DEFECT 62 (vertices=27, convex hull=27) After retessellation of defect 62, euler #=-1 (127997,383943,255945) : difference with theory (-1) = 0 CORRECTING DEFECT 63 (vertices=30, convex hull=41) After retessellation of defect 63, euler #=0 (128001,383967,255966) : difference with theory (0) = 0 CORRECTING DEFECT 64 (vertices=35, convex hull=67) After retessellation of defect 64, euler #=1 (128016,384036,256021) : difference with theory (1) = 0 CORRECTING DEFECT 65 (vertices=27, convex hull=29) After retessellation of defect 65, euler #=2 (128018,384048,256032) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.25 (0.05-->9.34) (max @ vno 106643 --> 111157) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.25 (0.05-->9.34) (max @ vno 106643 --> 111157) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 239 mutations (34.4%), 456 crossovers (65.6%), 476 vertices were eliminated building final representation... 5488 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=128018, nf=256032, ne=384048, g=0) writing corrected surface to /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 44.9 minutes 0 defective edges removing intersecting faces 000: 532 intersecting 001: 15 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 128018 - 384048 + 256032 = 2 --> 0 holes F =2V-4: 256032 = 256036-4 (0) 2E=3F: 768096 = 768096 (0) total defect index = 0 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 62 intersecting 001: 11 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Jan 10 11:53:13 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs chong_lan rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/filled.mgz... reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/brain.finalsurfs.mgz... reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/wm.mgz... 16247 bright wm thresholded. 2173 bright non-wm voxels segmented. reading original surface position from /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.orig... computing class statistics... border white: 235458 voxels (1.40%) border gray 280839 voxels (1.67%) WM (90.0): 91.6 +- 10.1 [70.0 --> 110.0] GM (74.0) : 71.6 +- 13.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 42.2 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 28.4 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 14.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->5.06) (max @ vno 54957 --> 127089) face area 0.28 +- 0.13 (0.00-->6.73) mean absolute distance = 0.67 +- 0.81 3823 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=56 using class modes intead of means.... mean inside = 91.3, mean outside = 67.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=71.9, 146 (146) missing vertices, mean dist 0.4 [0.5 (%30.6)->0.8 (%69.4))] %74 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fslvm, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.06-->6.13) (max @ vno 54957 --> 127089) face area 0.28 +- 0.14 (0.00-->5.34) mean absolute distance = 0.33 +- 0.56 3057 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6764728.0, rms=13.40 001: dt: 0.5000, sse=7038291.0, rms=9.64 002: dt: 0.5000, sse=7491348.5, rms=7.63 003: dt: 0.5000, sse=7708622.0, rms=6.41 004: dt: 0.5000, sse=8036784.0, rms=5.77 005: dt: 0.5000, sse=8136162.0, rms=5.36 006: dt: 0.5000, sse=8325912.0, rms=5.19 007: dt: 0.5000, sse=8309906.5, rms=5.03 rms = 4.98, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=8373753.0, rms=4.98 009: dt: 0.2500, sse=5430337.0, rms=3.65 010: dt: 0.2500, sse=5094619.5, rms=3.21 011: dt: 0.2500, sse=4810048.5, rms=3.13 012: dt: 0.2500, sse=4769484.0, rms=3.02 rms = 2.99, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=4643882.5, rms=2.99 014: dt: 0.1250, sse=4304200.0, rms=2.60 015: dt: 0.1250, sse=4250826.5, rms=2.54 rms = 2.53, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4218223.0, rms=2.53 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=75.7, 159 (53) missing vertices, mean dist -0.2 [0.4 (%71.5)->0.3 (%28.5))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fslvm, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.27 (0.07-->6.53) (max @ vno 53980 --> 55024) face area 0.35 +- 0.18 (0.00-->6.89) mean absolute distance = 0.26 +- 0.44 3439 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4940365.5, rms=5.58 017: dt: 0.5000, sse=5555209.5, rms=4.19 rms = 4.71, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4974741.0, rms=2.98 019: dt: 0.2500, sse=4813756.5, rms=2.59 020: dt: 0.2500, sse=4764681.0, rms=2.32 rms = 2.34, time step reduction 2 of 3 to 0.125... 021: dt: 0.1250, sse=4668059.0, rms=2.18 022: dt: 0.1250, sse=4535871.0, rms=1.98 rms = 1.94, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4473881.0, rms=1.94 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=78.0, 153 (31) missing vertices, mean dist -0.1 [0.3 (%63.4)->0.2 (%36.6))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fslvm, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.06-->6.72) (max @ vno 53980 --> 55024) face area 0.34 +- 0.17 (0.00-->6.92) mean absolute distance = 0.25 +- 0.39 3425 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4689285.5, rms=3.65 rms = 4.11, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4587696.5, rms=2.65 025: dt: 0.2500, sse=4628746.5, rms=2.03 rms = 2.01, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4724538.0, rms=2.01 027: dt: 0.1250, sse=4592922.5, rms=1.77 rms = 1.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4549763.0, rms=1.74 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=78.8, 183 (23) missing vertices, mean dist -0.0 [0.3 (%53.3)->0.2 (%46.7))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fslvm, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4594930.0, rms=2.24 rms = 3.02, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4749535.0, rms=1.61 030: dt: 0.2500, sse=5031728.0, rms=1.36 rms = 1.39, time step reduction 2 of 3 to 0.125... rms = 1.34, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5028726.0, rms=1.34 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 15 non-cortical segments detected only using segment with 1621 vertices erasing segment 1 (vno[0] = 80921) erasing segment 2 (vno[0] = 89080) erasing segment 3 (vno[0] = 91000) erasing segment 4 (vno[0] = 91876) erasing segment 5 (vno[0] = 92192) erasing segment 6 (vno[0] = 92902) erasing segment 7 (vno[0] = 92974) erasing segment 8 (vno[0] = 93063) erasing segment 9 (vno[0] = 93956) erasing segment 10 (vno[0] = 94072) erasing segment 11 (vno[0] = 94892) erasing segment 12 (vno[0] = 94999) erasing segment 13 (vno[0] = 99605) erasing segment 14 (vno[0] = 103447) writing cortex label to /mnt/hgfs/DATA/Freesurfer/chong_lan/label/rh.cortex.label... LabelWrite: saving to /mnt/hgfs/DATA/Freesurfer/chong_lan/label/rh.cortex.label writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.curv writing smoothed area to rh.area writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.area vertex spacing 0.90 +- 0.26 (0.06-->6.73) (max @ vno 53980 --> 55024) face area 0.34 +- 0.17 (0.00-->7.03) refinement took 5.0 minutes #-------------------------------------------- #@# Smooth2 rh Thu Jan 10 11:58:13 EST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Thu Jan 10 11:58:20 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 46.0 mm, total surface area = 79226 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.120 (target=0.015) step 005: RMS=0.083 (target=0.015) step 010: RMS=0.062 (target=0.015) step 015: RMS=0.051 (target=0.015) step 020: RMS=0.042 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.023 (target=0.015) step 045: RMS=0.021 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.018 (target=0.015) step 060: RMS=0.017 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 279 vertices thresholded to be in k1 ~ [-0.29 0.62], k2 ~ [-0.15 0.10] total integrated curvature = 0.480*4pi (6.031) --> 1 handles ICI = 1.4, FI = 8.9, variation=151.333 194 vertices thresholded to be in [-0.03 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 142 vertices thresholded to be in [-0.14 0.25] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Thu Jan 10 12:00:14 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm chong_lan rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ chong_lan/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 214 ] Gb_filter = 0 WARN: S lookup min: -0.533532 WARN: S explicit min: 0.000000 vertex = 588 #-------------------------------------------- #@# Sphere rh Thu Jan 10 12:00:21 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.03 hours scaling brain by 0.299... pass 1: epoch 1 of 3 starting distance error %21.47 pass 1: epoch 2 of 3 starting distance error %21.45 unfolding complete - removing small folds... starting distance error %21.34 removing remaining folds... final distance error %21.37 #-------------------------------------------- #@# Surf Reg rh Thu Jan 10 13:02:24 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = -0.000, std = 0.599 curvature mean = 0.031, std = 0.936 curvature mean = 0.015, std = 0.868 curvature mean = 0.020, std = 0.944 curvature mean = 0.006, std = 0.945 curvature mean = 0.018, std = 0.955 curvature mean = 0.003, std = 0.975 curvature mean = 0.017, std = 0.956 curvature mean = 0.001, std = 0.989 curvature mean = -0.026, std = 0.285 curvature mean = 0.006, std = 0.069 curvature mean = 0.060, std = 0.352 curvature mean = 0.006, std = 0.082 curvature mean = 0.035, std = 0.543 curvature mean = 0.006, std = 0.088 curvature mean = 0.020, std = 0.684 curvature mean = 0.006, std = 0.091 curvature mean = 0.007, std = 0.797 expanding nbhd size to 1 1108: 117 negative triangles #-------------------------------------------- #@# Jacobian white rh Thu Jan 10 13:36:41 EST 2013 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu Jan 10 13:36:44 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Jan 10 13:36:47 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 chong_lan rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1247 labels changed using aseg relabeling using gibbs priors... 000: 2759 changed, 128018 examined... 001: 651 changed, 11968 examined... 002: 173 changed, 3653 examined... 003: 59 changed, 1009 examined... 004: 21 changed, 355 examined... 005: 8 changed, 122 examined... 006: 4 changed, 47 examined... 007: 3 changed, 23 examined... 008: 2 changed, 12 examined... 009: 0 changed, 10 examined... 165 labels changed using aseg 000: 100 total segments, 63 labels (380 vertices) changed 001: 40 total segments, 3 labels (7 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 55 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1350 vertices marked for relabeling... 1350 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 43 seconds. #-------------------------------------------- #@# Make Pial Surf rh Thu Jan 10 13:37:31 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs chong_lan rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/filled.mgz... reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/brain.finalsurfs.mgz... reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/wm.mgz... 16247 bright wm thresholded. 2173 bright non-wm voxels segmented. reading original surface position from /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.orig... computing class statistics... border white: 235458 voxels (1.40%) border gray 280839 voxels (1.67%) WM (90.0): 91.6 +- 10.1 [70.0 --> 110.0] GM (74.0) : 71.6 +- 13.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 42.2 (was 70) setting MAX_BORDER_WHITE to 112.1 (was 105) setting MIN_BORDER_WHITE to 56.0 (was 85) setting MAX_CSF to 28.4 (was 40) setting MAX_GRAY to 91.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 49.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 14.6 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=56 using class modes intead of means.... mean inside = 91.3, mean outside = 67.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.03-->5.06) (max @ vno 54957 --> 127089) face area 0.28 +- 0.13 (0.00-->6.73) mean absolute distance = 0.67 +- 0.81 3825 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 13 points - only 0.00% unknown mean border=71.9, 146 (146) missing vertices, mean dist 0.4 [0.5 (%30.6)->0.8 (%69.4))] %74 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=fslvm, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.06-->6.13) (max @ vno 54957 --> 127089) face area 0.28 +- 0.14 (0.00-->5.34) mean absolute distance = 0.33 +- 0.56 3058 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=6765164.0, rms=13.40 001: dt: 0.5000, sse=7039138.0, rms=9.64 002: dt: 0.5000, sse=7492768.0, rms=7.63 003: dt: 0.5000, sse=7710249.0, rms=6.41 004: dt: 0.5000, sse=8038068.0, rms=5.77 005: dt: 0.5000, sse=8138688.5, rms=5.36 006: dt: 0.5000, sse=8326686.5, rms=5.19 007: dt: 0.5000, sse=8311488.5, rms=5.03 rms = 4.98, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=8375772.0, rms=4.98 009: dt: 0.2500, sse=5430820.0, rms=3.65 010: dt: 0.2500, sse=5095200.5, rms=3.21 011: dt: 0.2500, sse=4810448.0, rms=3.13 012: dt: 0.2500, sse=4770060.0, rms=3.02 rms = 2.99, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=4646003.0, rms=2.99 014: dt: 0.1250, sse=4306131.0, rms=2.60 015: dt: 0.1250, sse=4252168.0, rms=2.54 rms = 2.53, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4219038.0, rms=2.53 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 6 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown mean border=75.7, 159 (53) missing vertices, mean dist -0.2 [0.4 (%71.5)->0.3 (%28.5))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=fslvm, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.91 +- 0.27 (0.07-->6.53) (max @ vno 53980 --> 55024) face area 0.35 +- 0.18 (0.00-->6.89) mean absolute distance = 0.26 +- 0.44 3457 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4941041.5, rms=5.58 017: dt: 0.5000, sse=5556840.0, rms=4.19 rms = 4.71, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=4976513.0, rms=2.98 019: dt: 0.2500, sse=4815697.0, rms=2.59 020: dt: 0.2500, sse=4764981.5, rms=2.32 rms = 2.34, time step reduction 2 of 3 to 0.125... 021: dt: 0.1250, sse=4668395.5, rms=2.18 022: dt: 0.1250, sse=4535295.0, rms=1.98 rms = 1.94, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4474001.5, rms=1.94 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown mean border=78.0, 150 (31) missing vertices, mean dist -0.1 [0.3 (%63.4)->0.2 (%36.6))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=fslvm, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.26 (0.06-->6.72) (max @ vno 53980 --> 55024) face area 0.34 +- 0.17 (0.00-->6.92) mean absolute distance = 0.25 +- 0.39 3441 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4689651.5, rms=3.65 rms = 4.11, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=4587789.5, rms=2.65 025: dt: 0.2500, sse=4627687.5, rms=2.03 rms = 2.01, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=4725491.0, rms=2.01 027: dt: 0.1250, sse=4591350.5, rms=1.77 rms = 1.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=4548809.5, rms=1.74 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group deleting segment 0 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 4 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown mean border=78.8, 174 (23) missing vertices, mean dist -0.0 [0.3 (%53.2)->0.2 (%46.8))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=fslvm, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4593878.0, rms=2.24 rms = 3.02, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4747667.0, rms=1.61 030: dt: 0.2500, sse=5028693.5, rms=1.36 rms = 1.39, time step reduction 2 of 3 to 0.125... rms = 1.34, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5025967.5, rms=1.34 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=45.6, 145 (145) missing vertices, mean dist 1.6 [0.3 (%0.0)->2.4 (%100.0))] %13 local maxima, %50 large gradients and %33 min vals, 2014 gradients ignored tol=1.0e-04, sigma=2.0, host=fslvm, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=29196352.0, rms=32.93 001: dt: 0.5000, sse=21062568.0, rms=27.41 002: dt: 0.5000, sse=15484685.0, rms=22.85 003: dt: 0.5000, sse=12069167.0, rms=19.28 004: dt: 0.5000, sse=10253342.0, rms=16.55 005: dt: 0.5000, sse=9205617.0, rms=14.53 006: dt: 0.5000, sse=8735529.0, rms=13.15 007: dt: 0.5000, sse=8458864.0, rms=12.14 008: dt: 0.5000, sse=8342305.5, rms=11.32 009: dt: 0.5000, sse=8277776.5, rms=10.61 010: dt: 0.5000, sse=8301986.0, rms=9.98 011: dt: 0.5000, sse=8289626.5, rms=9.36 012: dt: 0.5000, sse=8318086.0, rms=8.69 013: dt: 0.5000, sse=8215416.5, rms=7.99 014: dt: 0.5000, sse=8272967.5, rms=7.34 015: dt: 0.5000, sse=8267946.0, rms=6.80 016: dt: 0.5000, sse=8384966.5, rms=6.41 017: dt: 0.5000, sse=8453807.0, rms=6.14 018: dt: 0.5000, sse=8495037.0, rms=5.95 019: dt: 0.5000, sse=8526391.0, rms=5.83 020: dt: 0.5000, sse=8527932.0, rms=5.75 021: dt: 0.5000, sse=8536949.0, rms=5.69 022: dt: 0.5000, sse=8589565.0, rms=5.63 rms = 5.58, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, sse=8583432.0, rms=5.58 024: dt: 0.2500, sse=6520426.0, rms=4.99 025: dt: 0.2500, sse=6388788.5, rms=4.78 rms = 4.77, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=6229729.0, rms=4.77 027: dt: 0.1250, sse=5889469.0, rms=4.61 rms = 4.58, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5832474.0, rms=4.58 positioning took 2.6 minutes mean border=44.2, 1582 (26) missing vertices, mean dist 0.2 [0.2 (%52.5)->0.7 (%47.5))] %30 local maxima, %36 large gradients and %29 min vals, 916 gradients ignored tol=1.0e-04, sigma=1.0, host=fslvm, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6336183.5, rms=5.47 029: dt: 0.5000, sse=6947393.0, rms=5.41 rms = 5.40, time step reduction 1 of 3 to 0.250... 030: dt: 0.5000, sse=8644755.0, rms=5.40 031: dt: 0.2500, sse=6742089.0, rms=4.74 032: dt: 0.2500, sse=6890981.5, rms=4.53 rms = 4.54, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=6737032.0, rms=4.45 034: dt: 0.1250, sse=6480705.5, rms=4.32 rms = 4.30, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=6419619.5, rms=4.30 positioning took 0.7 minutes mean border=42.5, 1829 (18) missing vertices, mean dist 0.2 [0.2 (%44.9)->0.5 (%55.1))] %44 local maxima, %21 large gradients and %29 min vals, 1016 gradients ignored tol=1.0e-04, sigma=0.5, host=fslvm, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6593462.0, rms=4.99 rms = 5.31, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=6412265.0, rms=4.65 037: dt: 0.2500, sse=6479854.0, rms=4.48 rms = 4.46, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=6742863.5, rms=4.46 039: dt: 0.1250, sse=6519395.5, rms=4.26 rms = 4.21, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=6538908.5, rms=4.21 positioning took 0.5 minutes mean border=41.5, 3475 (17) missing vertices, mean dist 0.1 [0.2 (%47.4)->0.4 (%52.6))] %47 local maxima, %17 large gradients and %28 min vals, 896 gradients ignored tol=1.0e-04, sigma=0.2, host=fslvm, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=6601136.0, rms=4.51 rms = 5.00, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=6497216.5, rms=4.30 042: dt: 0.2500, sse=6805647.0, rms=4.20 rms = 4.19, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=6962955.0, rms=4.19 044: dt: 0.1250, sse=6818312.5, rms=3.99 045: dt: 0.1250, sse=6846331.0, rms=3.94 rms = 3.93, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=6875275.0, rms=3.93 positioning took 0.6 minutes writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.area.pial vertex spacing 1.06 +- 0.46 (0.06-->8.46) (max @ vno 97252 --> 96481) face area 0.44 +- 0.35 (0.00-->7.85) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 128018 vertices processed 25000 of 128018 vertices processed 50000 of 128018 vertices processed 75000 of 128018 vertices processed 100000 of 128018 vertices processed 125000 of 128018 vertices processed 0 of 128018 vertices processed 25000 of 128018 vertices processed 50000 of 128018 vertices processed 75000 of 128018 vertices processed 100000 of 128018 vertices processed 125000 of 128018 vertices processed thickness calculation complete, 1196:1199 truncations. 48923 vertices at 0 distance 69145 vertices at 1 distance 68871 vertices at 2 distance 34485 vertices at 3 distance 13556 vertices at 4 distance 5053 vertices at 5 distance 2056 vertices at 6 distance 842 vertices at 7 distance 459 vertices at 8 distance 274 vertices at 9 distance 168 vertices at 10 distance 131 vertices at 11 distance 106 vertices at 12 distance 91 vertices at 13 distance 45 vertices at 14 distance 53 vertices at 15 distance 41 vertices at 16 distance 32 vertices at 17 distance 29 vertices at 18 distance 31 vertices at 19 distance 35 vertices at 20 distance writing curvature file /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.thickness positioning took 13.1 minutes #-------------------------------------------- #@# Surf Volume rh Thu Jan 10 13:50:38 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Parcellation Stats rh Thu Jan 10 13:50:40 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab chong_lan rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/wm.mgz... reading input surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.white... reading input pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.pial... reading input white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1337 935 2259 2.538 0.465 0.124 0.038 12 1.9 bankssts 1025 731 2083 2.340 0.681 0.176 0.077 25 3.0 caudalanteriorcingulate 3511 2433 7621 2.529 0.787 0.153 0.061 56 8.9 caudalmiddlefrontal 2312 1620 3771 2.074 0.556 0.186 0.089 56 8.5 cuneus 395 294 1171 3.266 0.874 0.262 0.201 60 3.6 entorhinal 4763 3292 10383 2.747 0.719 0.161 0.074 129 17.3 fusiform 8663 5963 19959 2.695 0.824 0.156 0.070 187 25.0 inferiorparietal 4116 2737 10473 3.029 0.885 0.170 0.126 703 20.2 inferiortemporal 1452 955 3012 2.675 1.024 0.159 0.069 29 3.8 isthmuscingulate 6845 4527 12575 2.482 0.749 0.169 0.080 155 22.4 lateraloccipital 2932 2073 7601 2.958 0.904 0.190 0.125 98 14.9 lateralorbitofrontal 3994 2830 6785 2.210 0.671 0.174 0.090 84 15.2 lingual 2126 1531 4834 2.633 0.957 0.181 0.115 70 6.8 medialorbitofrontal 4559 3104 12527 3.083 0.727 0.161 0.080 137 17.3 middletemporal 761 507 1676 2.842 0.807 0.124 0.054 9 1.4 parahippocampal 1694 1206 3340 2.319 0.657 0.150 0.050 21 3.7 paracentral 2301 1592 5240 2.756 0.667 0.152 0.059 40 5.8 parsopercularis 1053 699 2851 2.999 0.606 0.182 0.378 95 5.9 parsorbitalis 1985 1344 4773 2.818 0.731 0.163 0.068 43 5.9 parstriangularis 2064 1440 2358 1.736 0.540 0.160 0.070 36 6.1 pericalcarine 6254 4151 10298 2.106 0.672 0.156 0.129 154 20.3 postcentral 1871 1287 3438 2.375 0.745 0.170 0.072 38 5.5 posteriorcingulate 6265 4226 13250 2.640 0.693 0.140 0.050 75 13.2 precentral 5641 3906 11209 2.540 0.674 0.150 0.055 87 13.1 precuneus 726 495 1417 2.372 0.842 0.163 0.075 16 2.3 rostralanteriorcingulate 8930 6125 19395 2.623 0.777 0.179 0.091 223 30.8 rostralmiddlefrontal 9305 6494 20058 2.548 0.769 0.161 0.084 172 25.6 superiorfrontal 8454 5804 16289 2.331 0.747 0.157 0.064 178 23.1 superiorparietal 5493 3690 11838 2.686 0.732 0.166 0.095 154 18.8 superiortemporal 4906 3325 9942 2.532 0.789 0.146 0.059 72 12.1 supramarginal 427 277 1038 2.733 0.814 0.241 0.488 34 12.6 frontalpole 515 345 1099 2.347 0.827 0.244 0.284 41 6.8 temporalpole 494 317 858 2.491 0.509 0.160 0.065 8 1.3 transversetemporal 3143 2128 6773 3.089 1.012 0.163 0.172 197 14.5 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Jan 10 13:50:56 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 chong_lan rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 41 labels changed using aseg relabeling using gibbs priors... 000: 9461 changed, 128018 examined... 001: 2238 changed, 35792 examined... 002: 656 changed, 11520 examined... 003: 283 changed, 3624 examined... 004: 153 changed, 1647 examined... 005: 88 changed, 854 examined... 006: 45 changed, 485 examined... 007: 25 changed, 268 examined... 008: 18 changed, 141 examined... 009: 8 changed, 85 examined... 010: 4 changed, 50 examined... 011: 1 changed, 19 examined... 012: 0 changed, 5 examined... 18 labels changed using aseg 000: 268 total segments, 188 labels (2356 vertices) changed 001: 89 total segments, 9 labels (32 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 120 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 920 vertices marked for relabeling... 920 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 50 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Jan 10 13:51:46 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab chong_lan rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/wm.mgz... reading input surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.white... reading input pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.pial... reading input white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1099 722 2458 2.813 0.830 0.204 0.247 50 14.9 G_and_S_frontomargin 1498 1004 3033 2.854 0.563 0.147 0.048 21 3.1 G_and_S_occipital_inf 1113 816 2596 2.456 0.673 0.189 0.092 31 4.0 G_and_S_paracentral 1519 1034 3455 2.704 0.690 0.175 0.075 33 4.9 G_and_S_subcentral 980 658 2422 2.916 0.556 0.199 0.117 27 4.8 G_and_S_transv_frontopol 2284 1632 4490 2.384 0.706 0.162 0.135 49 6.0 G_and_S_cingul-Ant 1401 995 2698 2.352 0.652 0.160 0.073 25 4.0 G_and_S_cingul-Mid-Ant 1415 980 2435 2.229 0.714 0.170 0.072 27 4.2 G_and_S_cingul-Mid-Post 524 353 1407 3.063 0.846 0.191 0.090 13 1.8 G_cingul-Post-dorsal 206 130 674 3.457 0.807 0.182 0.088 5 0.7 G_cingul-Post-ventral 2015 1437 3235 1.986 0.585 0.197 0.090 53 7.3 G_cuneus 1016 715 2985 3.088 0.636 0.183 0.082 27 3.4 G_front_inf-Opercular 273 165 852 3.474 0.571 0.176 0.070 6 0.8 G_front_inf-Orbital 1122 766 3486 3.190 0.595 0.196 0.086 34 4.2 G_front_inf-Triangul 4515 3176 12782 2.879 0.788 0.194 0.105 136 18.4 G_front_middle 5983 4198 15274 2.783 0.741 0.175 0.080 136 19.0 G_front_sup 405 273 1100 3.579 1.058 0.178 0.166 70 2.0 G_Ins_lg_and_S_cent_ins 479 371 1582 3.429 0.843 0.276 0.291 40 6.0 G_insular_short 2364 1630 6793 3.202 0.658 0.188 0.102 74 9.9 G_occipital_middle 1666 1166 3351 2.256 0.715 0.186 0.087 66 6.6 G_occipital_sup 2124 1432 5562 3.138 0.562 0.172 0.061 50 5.3 G_oc-temp_lat-fusifor 2615 1882 4922 2.302 0.789 0.196 0.109 66 11.7 G_oc-temp_med-Lingual 1081 746 2988 3.283 0.871 0.148 0.064 22 2.5 G_oc-temp_med-Parahip 2465 1714 7546 3.207 0.722 0.212 0.266 171 15.2 G_orbital 3134 2130 9482 3.055 0.891 0.174 0.088 88 11.2 G_pariet_inf-Angular 2309 1590 6003 2.874 0.757 0.168 0.074 47 7.0 G_pariet_inf-Supramar 2727 1893 6627 2.624 0.877 0.175 0.078 64 9.0 G_parietal_sup 1939 1281 3807 2.258 0.646 0.186 0.293 88 10.2 G_postcentral 2552 1729 7055 2.976 0.648 0.158 0.064 42 7.0 G_precentral 2471 1759 6402 2.735 0.708 0.183 0.081 64 8.0 G_precuneus 544 429 1628 2.923 1.028 0.248 0.220 35 2.5 G_rectus 300 189 569 2.842 0.826 0.121 0.059 5 0.7 G_subcallosal 444 281 808 2.539 0.552 0.178 0.083 10 1.5 G_temp_sup-G_T_transv 1975 1331 6065 3.223 0.648 0.198 0.153 77 9.8 G_temp_sup-Lateral 703 456 1407 2.678 0.870 0.193 0.146 40 3.9 G_temp_sup-Plan_polar 689 490 1311 2.339 0.465 0.111 0.031 5 0.9 G_temp_sup-Plan_tempo 2334 1540 7465 3.319 0.930 0.195 0.166 674 14.9 G_temporal_inf 2715 1846 9041 3.391 0.655 0.168 0.072 68 8.4 G_temporal_middle 311 212 494 2.342 0.695 0.115 0.034 2 0.5 Lat_Fis-ant-Horizont 224 145 438 2.394 0.692 0.143 0.069 4 0.6 Lat_Fis-ant-Vertical 1415 929 1878 2.152 0.458 0.132 0.046 15 2.9 Lat_Fis-post 3160 2072 4427 2.005 0.642 0.192 0.119 103 15.9 Pole_occipital 1577 1120 3255 2.270 0.724 0.286 0.329 229 27.2 Pole_temporal 2067 1431 2930 2.247 0.839 0.140 0.051 27 4.4 S_calcarine 2760 1807 3219 1.906 0.579 0.113 0.035 18 4.3 S_central 1089 771 1667 2.144 0.507 0.130 0.040 10 1.8 S_cingul-Marginalis 528 346 1029 2.811 1.001 0.172 0.178 26 4.2 S_circular_insula_ant 1312 858 2175 2.667 1.001 0.112 0.043 10 2.3 S_circular_insula_inf 1417 936 2232 2.549 0.674 0.130 0.185 59 4.2 S_circular_insula_sup 1144 802 1948 2.325 0.727 0.145 0.055 17 2.8 S_collat_transv_ant 272 177 347 2.003 0.330 0.140 0.046 3 0.5 S_collat_transv_post 2018 1395 3189 2.308 0.587 0.135 0.041 22 3.5 S_front_inf 2453 1656 3787 2.223 0.636 0.157 0.066 40 6.5 S_front_middle 2791 1959 4782 2.214 0.639 0.143 0.049 30 5.9 S_front_sup 875 584 1308 2.180 0.831 0.139 0.049 11 1.9 S_interm_prim-Jensen 3107 2137 4718 2.033 0.498 0.138 0.046 40 6.1 S_intrapariet_and_P_trans 1040 687 1664 2.270 0.625 0.137 0.047 11 2.1 S_oc_middle_and_Lunatus 1661 1126 2355 2.222 0.422 0.129 0.036 14 2.6 S_oc_sup_and_transversal 934 618 1760 2.622 0.679 0.133 0.043 10 1.7 S_occipital_ant 765 545 1448 2.743 0.652 0.118 0.028 6 1.0 S_oc-temp_lat 1723 1198 2669 2.309 0.482 0.114 0.031 20 2.1 S_oc-temp_med_and_Lingual 490 321 683 2.344 0.581 0.149 0.067 10 1.3 S_orbital_lateral 432 327 900 2.408 1.006 0.125 0.038 3 0.7 S_orbital_med-olfact 1180 843 2480 2.761 0.840 0.159 0.057 17 2.8 S_orbital-H_Shaped 1976 1310 2873 2.342 0.508 0.123 0.037 16 3.3 S_parieto_occipital 1570 1006 1741 1.894 0.554 0.141 0.046 24 2.9 S_pericallosal 2827 1873 3524 1.924 0.449 0.125 0.040 24 4.7 S_postcentral 1761 1172 2923 2.472 0.616 0.120 0.036 17 2.7 S_precentral-inf-part 981 665 1500 2.165 0.624 0.134 0.043 9 1.7 S_precentral-sup-part 350 240 737 2.930 1.086 0.162 0.071 7 0.8 S_suborbital 1611 1114 3031 2.506 0.728 0.149 0.053 22 3.6 S_subparietal 1055 687 1621 2.712 0.599 0.129 0.046 10 1.7 S_temporal_inf 6213 4230 10305 2.506 0.552 0.128 0.042 70 10.4 S_temporal_sup 225 146 366 2.451 0.395 0.112 0.031 1 0.3 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Thu Jan 10 13:52:03 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon chong_lan SUBJECTS_DIR is /mnt/hgfs/DATA/Freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 41 writing volume /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Jan 10 14:02:36 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject chong_lan $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject chong_lan sysname Linux hostname fslvm6.localdomain machine x86_64 user fsl atlas_icv (eTIV) = 1374815 mm^3 (det: 1.416994 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 212109 rh white matter volume 219454 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 233222.913698, pTot = 463734.604419 c = 230511.690721 rh surface-based volumes (mm3): wTot = 240967.252047, pTot = 480987.330951 c = 240020.078903 Computing SupraTentVolCor SupraTentVolCor = 62108.000 SupraTentVol = 1006829.935 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 7326 7326 4 5 Left-Inf-Lat-Vent 410 410 5 7 Left-Cerebellum-White-Matter 11915 11915 6 8 Left-Cerebellum-Cortex 43887 43887 7 10 Left-Thalamus-Proper 6910 6910 8 11 Left-Caudate 3865 3865 9 12 Left-Putamen 5696 5696 10 13 Left-Pallidum 1677 1677 11 14 3rd-Ventricle 1042 1042 12 15 4th-Ventricle 1354 1354 13 16 Brain-Stem 17976 17976 14 17 Left-Hippocampus 3609 3609 15 18 Left-Amygdala 1037 1037 16 24 CSF 1110 1110 17 26 Left-Accumbens-area 559 559 18 28 Left-VentralDC 4723 4723 19 30 Left-vessel 45 45 20 31 Left-choroid-plexus 1635 1635 23 43 Right-Lateral-Ventricle 8096 8096 24 44 Right-Inf-Lat-Vent 368 368 25 46 Right-Cerebellum-White-Matter 13241 13241 26 47 Right-Cerebellum-Cortex 46033 46033 27 49 Right-Thalamus-Proper 6726 6726 28 50 Right-Caudate 3942 3942 29 51 Right-Putamen 5871 5871 30 52 Right-Pallidum 1665 1665 31 53 Right-Hippocampus 3874 3874 32 54 Right-Amygdala 1403 1403 33 58 Right-Accumbens-area 546 546 34 60 Right-VentralDC 4649 4649 35 62 Right-vessel 94 94 36 63 Right-choroid-plexus 1707 1707 37 72 5th-Ventricle 3 3 38 77 WM-hypointensities 2382 2382 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 37 37 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 288 288 45 251 CC_Posterior 931 931 46 252 CC_Mid_Posterior 434 434 47 253 CC_Central 503 503 48 254 CC_Mid_Anterior 548 548 49 255 CC_Anterior 818 818 Reporting on 45 segmentations SubCortGrayVol = 164648 #----------------------------------------- #@# AParc-to-ASeg Thu Jan 10 14:10:17 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan mri_aparc2aseg --s chong_lan --volmask SUBJECTS_DIR /mnt/hgfs/DATA/Freesurfer subject chong_lan outvol /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.white Reading lh pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.pial Loading lh annotations from /mnt/hgfs/DATA/Freesurfer/chong_lan/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.white Reading rh pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.pial Loading rh annotations from /mnt/hgfs/DATA/Freesurfer/chong_lan/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 463724 Used brute-force search on 0 voxels Writing output aseg to /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aparc+aseg.mgz /mnt/hgfs/DATA/Freesurfer/chong_lan mri_aparc2aseg --s chong_lan --volmask --a2009s SUBJECTS_DIR /mnt/hgfs/DATA/Freesurfer subject chong_lan outvol /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.white Reading lh pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.pial Loading lh annotations from /mnt/hgfs/DATA/Freesurfer/chong_lan/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.white Reading rh pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.pial Loading rh annotations from /mnt/hgfs/DATA/Freesurfer/chong_lan/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 463724 Used brute-force search on 0 voxels Writing output aseg to /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu Jan 10 14:13:50 EST 2013 /mnt/hgfs/DATA/Freesurfer/chong_lan mri_aparc2aseg --s chong_lan --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /mnt/hgfs/DATA/Freesurfer subject chong_lan outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aparc+aseg.mgz Reading lh white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.white Reading lh pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/lh.pial Loading lh annotations from /mnt/hgfs/DATA/Freesurfer/chong_lan/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.white Reading rh pial surface /mnt/hgfs/DATA/Freesurfer/chong_lan/surf/rh.pial Loading rh annotations from /mnt/hgfs/DATA/Freesurfer/chong_lan/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) mghRead(/mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aparc+aseg.mgz): could not read 262144 bytes at slice 184 Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/ribbon.mgz Loading filled from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7968 vertices from left hemi Ripped 7706 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aseg.mgz Loading Ctx Seg File /mnt/hgfs/DATA/Freesurfer/chong_lan/mri/aparc+aseg.mgz Linux fslvm6.localdomain 2.6.32-279.5.2.el6.x86_64 #1 SMP Fri Aug 24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s chong_lan exited with ERRORS at Thu Jan 10 14:14:02 EST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting