Tue Nov 15 03:14:19 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260 /home/virtualuser/freesurfer/bin/recon-all -i vo0260/t1.nii -subjid avo0260 subjid avo0260 setenv SUBJECTS_DIR /home/virtualuser/freesurfer/subjects FREESURFER_HOME /home/virtualuser/freesurfer Actual FREESURFER_HOME /home/virtualuser/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited total used free shared buffers cached Mem: 1285388 1173464 111924 0 97992 920544 -/+ buffers/cache: 154928 1130460 Swap: 530104 0 530104 ######################################## program versions used $Id: recon-all,v 1.395 2011/05/18 23:01:39 krish 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: 2011/11/15-08:14:19-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/15-08:14:19-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:19-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:19-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:20-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:20-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:20-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:20-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_label2label.c,v 1.40 2011/03/02 00:04:22 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:20-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:20-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:20-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:20-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:21-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:21-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:21-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:21-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:21-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:21-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:21-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:21-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:22-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:22-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:22-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:22-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:22-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:22-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:22-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:22-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:23-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:23-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:23-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:23-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/15-08:14:23-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/15-08:14:23-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:23-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:23-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:24-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/15-08:14:24-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /home/virtualuser/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/virtualuser/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/virtualuser/freesurfer/subjects/avo0260 mri_convert /home/virtualuser/SUBJECTS_DIR/vo0260/t1.nii /home/virtualuser/freesurfer/subjects/avo0260/mri/orig/001.mgz mri_convert /home/virtualuser/SUBJECTS_DIR/vo0260/t1.nii /home/virtualuser/freesurfer/subjects/avo0260/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/SUBJECTS_DIR/vo0260/t1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -3.01484e-09, -1) j_ras = (-3.01484e-09, -1, 3.01484e-09) k_ras = (-1, 3.01484e-09, 0) writing to /home/virtualuser/freesurfer/subjects/avo0260/mri/orig/001.mgz... #------------------------------------------ recon-all -s avo0260 finished without error at Tue Nov 15 03:14:30 EST 2011 New invocation of recon-all Fri Nov 18 01:13:53 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260 /home/virtualuser/freesurfer/bin/recon-all -subjid avo0260 -autorecon1 subjid avo0260 setenv SUBJECTS_DIR /home/virtualuser/freesurfer/subjects FREESURFER_HOME /home/virtualuser/freesurfer Actual FREESURFER_HOME /home/virtualuser/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited total used free shared buffers cached Mem: 1285388 114872 1170516 0 9072 39724 -/+ buffers/cache: 66076 1219312 Swap: 530104 91052 439052 ######################################## program versions used $Id: recon-all,v 1.395 2011/05/18 23:01:39 krish 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: 2011/11/18-06:13:53-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/18-06:13:54-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:55-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:55-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:56-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:56-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:56-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:57-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_label2label.c,v 1.40 2011/03/02 00:04:22 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:57-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:57-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:57-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:58-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:58-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:58-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:59-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:59-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:59-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:13:59-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:00-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:00-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:00-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:00-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:01-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:01-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:01-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:02-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:02-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:02-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:02-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:03-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:03-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:03-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/18-06:14:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/18-06:14:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:05-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-06:14:05-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /home/virtualuser/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/virtualuser/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri Nov 18 01:14:05 EST 2011 Found 1 runs /home/virtualuser/freesurfer/subjects/avo0260/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 /home/virtualuser/freesurfer/subjects/avo0260/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/avo0260/mri/rawavg.mgz /home/virtualuser/freesurfer/subjects/avo0260 mri_convert /home/virtualuser/freesurfer/subjects/avo0260/mri/rawavg.mgz /home/virtualuser/freesurfer/subjects/avo0260/mri/orig.mgz --conform mri_convert /home/virtualuser/freesurfer/subjects/avo0260/mri/rawavg.mgz /home/virtualuser/freesurfer/subjects/avo0260/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/avo0260/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -3.01484e-09, -1) j_ras = (-3.01484e-09, -1, 3.01484e-09) k_ras = (-1, 3.01484e-09, 0) Original Data has (1.03079, 1.02027, 1.21479) mm size and (256, 256, 166) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/virtualuser/freesurfer/subjects/avo0260/mri/orig.mgz... mri_add_xform_to_header -c /home/virtualuser/freesurfer/subjects/avo0260/mri/transforms/talairach.xfm /home/virtualuser/freesurfer/subjects/avo0260/mri/orig.mgz /home/virtualuser/freesurfer/subjects/avo0260/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 18 01:14:35 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Nov 18 01:16:02 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6971, pval=0.4932 >= threshold=0.0050) awk -f /home/virtualuser/freesurfer/bin/extract_talairach_avi_QA.awk /home/virtualuser/freesurfer/subjects/avo0260/mri/transforms/talairach_avi.log TalAviQA: 0.97909 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Nov 18 01:16:03 EST 2011 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/virtualuser/freesurfer/subjects/avo0260/mri /home/virtualuser/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 FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux Fri Nov 18 01:16:04 EST 2011 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 tmpdir is ./tmp.mri_nu_correct.mni.11979 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11979/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.11979/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.22045e-16, 9.08924e-18) j_ras = (9.08924e-18, -1.97811e-33, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.11979/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Nov 18 01:16:12 EST 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.11979/nu0.mnc ./tmp.mri_nu_correct.mni.11979/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.11979/0/ [virtualuser@FreeSurfer:/home/virtualuser/freesurfer/subjects/avo0260/mri/] [2011-11-18 01:16:13] running: /home/virtualuser/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.11979/0/ ./tmp.mri_nu_correct.mni.11979/nu0.mnc ./tmp.mri_nu_correct.mni.11979/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 Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 20 CV of field change: 0.000966017 [virtualuser@FreeSurfer:/home/virtualuser/freesurfer/subjects/avo0260/mri/] [2011-11-18 01:16:52] running: /home/virtualuser/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.11979/nu0.mnc ./tmp.mri_nu_correct.mni.11979/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Nov 18 01:17:05 EST 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.11979/nu1.mnc ./tmp.mri_nu_correct.mni.11979/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.11979/1/ [virtualuser@FreeSurfer:/home/virtualuser/freesurfer/subjects/avo0260/mri/] [2011-11-18 01:17:05] running: /home/virtualuser/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.11979/1/ ./tmp.mri_nu_correct.mni.11979/nu1.mnc ./tmp.mri_nu_correct.mni.11979/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 Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000956545 [virtualuser@FreeSurfer:/home/virtualuser/freesurfer/subjects/avo0260/mri/] [2011-11-18 01:17:31] running: /home/virtualuser/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.11979/nu1.mnc ./tmp.mri_nu_correct.mni.11979/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.11979/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11979/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/virtualuser/freesurfer/subjects/avo0260/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.11979/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.11979/ones.mgz sysname Linux hostname FreeSurfer machine i686 user virtualuser input ./tmp.mri_nu_correct.mni.11979/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.11979/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.11979/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11979/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11979/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.11979/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.11979/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11979/input.mean.dat sysname Linux hostname FreeSurfer machine i686 user virtualuser Loading ./tmp.mri_nu_correct.mni.11979/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.11979/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.11979/ones.mgz --i ./tmp.mri_nu_correct.mni.11979/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11979/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11979/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.11979/ones.mgz --i ./tmp.mri_nu_correct.mni.11979/nu2.mnc --sum ./tmp.mri_nu_correct.mni.11979/sum.junk --avgwf ./tmp.mri_nu_correct.mni.11979/output.mean.dat sysname Linux hostname FreeSurfer machine i686 user virtualuser Loading ./tmp.mri_nu_correct.mni.11979/ones.mgz Loading ./tmp.mri_nu_correct.mni.11979/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.11979/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.11979/nu2.mnc ./tmp.mri_nu_correct.mni.11979/nu2.mnc mul 1.07618111838509750113 Saving result to './tmp.mri_nu_correct.mni.11979/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.11979/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.11979/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.11979/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.22045e-16, 9.08924e-18) j_ras = (9.08924e-18, -1.97811e-33, -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 19 seconds. mapping ( 7, 89) to ( 3, 110) Fri Nov 18 01:19:12 EST 2011 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Fri Nov 18 01:19:12 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.125 0.021 -0.035 1.497; -0.001 1.063 0.396 -31.636; 0.031 -0.374 1.108 30.555; 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 5 minutes and 30 seconds. MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 white matter peak found at 111 white matter peak found at 109 gm peak at 66 (66), valley at 55 (55) csf peak at 33, setting threshold to 55 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 19 (19) csf peak at 35, setting threshold to 58 #-------------------------------------------- #@# Skull Stripping Fri Nov 18 01:24:45 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_em_register -skull nu.mgz /home/virtualuser/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 '/home/virtualuser/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=8.0 skull bounding box = (49, 33, 13) --> (204, 255, 233) using (101, 107, 123) as brain centroid... mean wm in atlas = 126, using box (82,80,96) --> (120, 134,150) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 initial log_p = -10393.4 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-4.0, 8.5, 8.5): log p = -10350.111 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10329.9, old_max_log_p =-10350.1 (thresh=-10339.8) 1.226 -0.156 -0.042 -11.635; 0.161 1.184 0.317 -64.052; 0.000 -0.259 0.966 40.985; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10324.3, old_max_log_p =-10329.9 (thresh=-10319.6) 1.144 0.000 0.000 -22.599; 0.000 1.284 0.344 -56.958; 0.000 -0.278 1.038 36.107; 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=-10304.6, old_max_log_p =-10324.3 (thresh=-10314.0) 1.161 -0.079 -0.051 -9.233; 0.078 1.338 0.318 -68.765; 0.037 -0.237 1.027 29.858; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10304.6, old_max_log_p =-10304.6 (thresh=-10294.3) 1.161 -0.079 -0.051 -9.233; 0.078 1.338 0.318 -68.765; 0.037 -0.237 1.027 29.858; 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=-10301.5, old_max_log_p =-10304.6 (thresh=-10294.3) 1.161 -0.077 -0.059 -8.605; 0.077 1.340 0.301 -67.729; 0.048 -0.217 1.035 24.879; 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 1.16079 -0.07730 -0.05914 -8.60459; 0.07684 1.34031 0.30088 -67.72896; 0.04784 -0.21675 1.03511 24.87865; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.16079 -0.07730 -0.05914 -8.60459; 0.07684 1.34031 0.30088 -67.72896; 0.04784 -0.21675 1.03511 24.87865; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 007: -log(p) = 10301.5 tol 0.000010 Resulting transform: 1.161 -0.077 -0.059 -8.605; 0.077 1.340 0.301 -67.729; 0.048 -0.217 1.035 24.879; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10301.5 (old=-10393.4) transform before final EM align: 1.161 -0.077 -0.059 -8.605; 0.077 1.340 0.301 -67.729; 0.048 -0.217 1.035 24.879; 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 1.16079 -0.07730 -0.05914 -8.60459; 0.07684 1.34031 0.30088 -67.72896; 0.04784 -0.21675 1.03511 24.87865; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.16079 -0.07730 -0.05914 -8.60459; 0.07684 1.34031 0.30088 -67.72896; 0.04784 -0.21675 1.03511 24.87865; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 1145136.6 after pass:transform: ( 1.16, -0.08, -0.06, -8.60) ( 0.08, 1.34, 0.30, -67.73) ( 0.05, -0.22, 1.04, 24.88) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 010: -log(p) = 1145136.6 tol 0.000000 final transform: 1.161 -0.077 -0.059 -8.605; 0.077 1.340 0.301 -67.729; 0.047 -0.217 1.035 24.879; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 39 minutes and 57 seconds. mri_watershed -T1 -brain_atlas /home/virtualuser/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=129 y=108 z=99 r=89 first estimation of the main basin volume: 2993583 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=157, y=107, z=67, 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=-752843333 voxels, voxel volume =1.000 = 3542123963 mmm3 = 3542124.032 cm3 done. PostAnalyze...Basin Prior 9 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=94, r=8847 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=58 , nb = 48268 RIGHT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=27 , nb = 3169 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=31 , nb = -1215419308 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=64 , nb = 792877048 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=64 , nb = 1424988 OTHER CSF_MIN=0, CSF_intensity=9, CSF_MAX=21 , nb = 1418806 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 58, 44, 38, 64 after analyzing : 35, 44, 44, 49 RIGHT_CER before analyzing : 27, 35, 44, 64 after analyzing : 27, 41, 44, 46 LEFT_CER before analyzing : 31, 38, 45, 64 after analyzing : 31, 42, 45, 47 RIGHT_BRAIN before analyzing : 64, 44, 34, 64 after analyzing : 35, 44, 44, 49 LEFT_BRAIN before analyzing : 64, 46, 37, 66 after analyzing : 36, 46, 46, 51 OTHER before analyzing : 21, 54, 82, 92 after analyzing : 21, 72, 82, 77 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* curvature mean = -0.014, std = 0.014 curvature mean = 64.735, std = 6.838 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.75, sigma = 8.44 after rotation: sse = 4.75, sigma = 8.44 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.75, its var is 9.44 before Erosion-Dilatation 3.99% of inacurate vertices after Erosion-Dilatation 4.07% 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...49 iterations mri_strip_skull: done peeling brain Brain Size = 1385023 voxels, voxel volume = 1.000 mm3 = 1385023 mmm3 = 1385.023 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------------ recon-all -s avo0260 finished without error at Fri Nov 18 02:05:43 EST 2011 New invocation of recon-all Fri Nov 18 02:07:59 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260 /home/virtualuser/freesurfer/bin/recon-all -subjid avo0260 -autorecon2 subjid avo0260 setenv SUBJECTS_DIR /home/virtualuser/freesurfer/subjects FREESURFER_HOME /home/virtualuser/freesurfer Actual FREESURFER_HOME /home/virtualuser/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited total used free shared buffers cached Mem: 1285388 519988 765400 0 12796 441208 -/+ buffers/cache: 65984 1219404 Swap: 530104 90952 439152 ######################################## program versions used $Id: recon-all,v 1.395 2011/05/18 23:01:39 krish 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: 2011/11/18-07:07:59-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/18-07:08:00-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:00-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:00-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:01-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:01-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:01-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:01-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_label2label.c,v 1.40 2011/03/02 00:04:22 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:01-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:02-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:02-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:02-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:02-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:03-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:03-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:03-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:03-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:04-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:05-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:05-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:05-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:05-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:06-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:06-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:06-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:06-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:07-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:07-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/18-07:08:07-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic 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: 2011/11/18-07:08:07-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:08-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:08-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:08-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/11/18-07:08:08-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.31-23-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /home/virtualuser/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/virtualuser/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Fri Nov 18 02:08:09 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/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 '/home/virtualuser/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=23.0 skull bounding box = (61, 56, 26) --> (191, 188, 173) using (104, 100, 100) as brain centroid... mean wm in atlas = 107, using box (88,84,82) --> (119, 116,118) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 104, scaling input intensities by 1.029 scaling channel 0 by 1.02885 initial log_p = -7366.5 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-1.7, 5.1, 2.8): log p = -7305.220 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7204.7, old_max_log_p =-7305.2 (thresh=-7297.9) 1.064 0.000 0.000 -9.897; 0.000 1.111 0.298 -37.995; 0.000 -0.278 1.038 38.057; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7204.7, old_max_log_p =-7204.7 (thresh=-7197.4) 1.064 0.000 0.000 -9.897; 0.000 1.111 0.298 -37.995; 0.000 -0.278 1.038 38.057; 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=-7116.0, old_max_log_p =-7204.7 (thresh=-7197.4) 1.083 -0.010 0.033 -14.494; 0.000 1.143 0.341 -40.409; -0.035 -0.311 1.007 47.349; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-7116.0, old_max_log_p =-7116.0 (thresh=-7108.9) 1.083 -0.010 0.033 -14.494; 0.000 1.143 0.341 -40.409; -0.035 -0.311 1.007 47.349; 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=-7105.8, old_max_log_p =-7116.0 (thresh=-7108.9) 1.083 -0.007 0.025 -14.499; -0.001 1.141 0.359 -41.243; -0.027 -0.330 1.002 49.215; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-7102.1, old_max_log_p =-7105.8 (thresh=-7098.7) 1.082 -0.005 0.017 -13.892; -0.001 1.135 0.375 -42.139; -0.018 -0.349 0.998 50.155; 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 1.08228 -0.00463 0.01661 -13.89159; -0.00102 1.13496 0.37496 -42.13928; -0.01774 -0.34911 0.99782 50.15490; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.08228 -0.00463 0.01661 -13.89159; -0.00102 1.13496 0.37496 -42.13928; -0.01774 -0.34911 0.99782 50.15490; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 008: -log(p) = 7102.1 tol 0.000010 Resulting transform: 1.082 -0.005 0.017 -13.892; -0.001 1.135 0.375 -42.139; -0.018 -0.349 0.998 50.155; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -7102.1 (old=-7366.5) transform before final EM align: 1.082 -0.005 0.017 -13.892; -0.001 1.135 0.375 -42.139; -0.018 -0.349 0.998 50.155; 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 1.08228 -0.00463 0.01661 -13.89159; -0.00102 1.13496 0.37496 -42.13928; -0.01774 -0.34911 0.99782 50.15490; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.08228 -0.00463 0.01661 -13.89159; -0.00102 1.13496 0.37496 -42.13928; -0.01774 -0.34911 0.99782 50.15490; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 840986.3 after pass:transform: ( 1.09, 0.00, 0.02, -13.89) ( -0.01, 1.13, 0.37, -42.14) ( -0.01, -0.34, 1.00, 50.15) pass 2 through quasi-newton minimization... outof QuasiNewtonEMA: 011: -log(p) = 840986.3 tol 0.000000 final transform: 1.090 0.001 0.021 -13.892; -0.006 1.131 0.370 -42.139; -0.013 -0.345 1.003 50.155; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 37 minutes and 30 seconds. #-------------------------------------- #@# CA Normalize Fri Nov 18 02:45:39 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /home/virtualuser/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 '/home/virtualuser/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=21.0 skull bounding box = (60, 55, 26) --> (191, 188, 173) using (104, 99, 100) as brain centroid... mean wm in atlas = 107, using box (88,83,82) --> (120, 115,118) 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 1.090 0.001 0.021 -13.892; -0.006 1.131 0.370 -42.139; -0.013 -0.345 1.003 50.155; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 56, 25) --> (187, 159, 178) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 239.0 2 of 309 (0.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 55, 25) --> (127, 151, 179) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 239.0 0 of 229 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 133, 55) --> (173, 172, 104) Left_Cerebellum_White_Matter: limiting intensities to 102.0 --> 239.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 133, 52) --> (127, 171, 105) Right_Cerebellum_White_Matter: limiting intensities to 108.0 --> 239.0 0 of 16 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 122, 85) --> (141, 181, 114) Brain_Stem: limiting intensities to 95.0 --> 239.0 0 of 4 (0.0%) samples deleted using 565 total control points for intensity normalization... bias field = 0.977 +- 0.065 0 of 563 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 56, 25) --> (187, 159, 178) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 212.0 0 of 380 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 55, 25) --> (127, 151, 179) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 212.0 0 of 318 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 133, 55) --> (173, 172, 104) Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 212.0 0 of 61 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 133, 52) --> (127, 171, 105) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 212.0 0 of 51 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 122, 85) --> (141, 181, 114) Brain_Stem: limiting intensities to 81.0 --> 212.0 0 of 75 (0.0%) samples deleted using 885 total control points for intensity normalization... bias field = 0.992 +- 0.067 0 of 885 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 56, 25) --> (187, 159, 178) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 201.0 0 of 417 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (67, 55, 25) --> (127, 151, 179) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 201.0 0 of 386 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (128, 133, 55) --> (173, 172, 104) Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 201.0 0 of 91 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (84, 133, 52) --> (127, 171, 105) Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 201.0 0 of 73 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 122, 85) --> (141, 181, 114) Brain_Stem: limiting intensities to 88.0 --> 201.0 77 of 166 (46.4%) samples deleted using 1133 total control points for intensity normalization... bias field = 1.017 +- 0.047 0 of 1056 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 4 minutes and 18 seconds. #-------------------------------------- #@# CA Reg Fri Nov 18 02:49:58 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /home/virtualuser/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 '/home/virtualuser/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) = 1.38 (predicted orig area = 5.8) 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=0.898, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55394.828 ms 0001: dt=129.472000, rms=0.807 (10.132%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59358.867 ms 0002: dt=221.952000, rms=0.786 (2.572%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59194.551 ms 0003: dt=129.472000, rms=0.774 (1.545%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59031.160 ms 0004: dt=73.984000, rms=0.771 (0.380%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59348.539 ms 0005: dt=1183.744000, rms=0.746 (3.254%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59172.246 ms 0006: dt=55.488000, rms=0.743 (0.352%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62874.258 ms 0007: dt=295.936000, rms=0.740 (0.474%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58879.629 ms 0008: dt=129.472000, rms=0.736 (0.487%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62272.355 ms 0009: dt=129.472000, rms=0.735 (0.117%), neg=0, invalid=766 0010: dt=129.472000, rms=0.733 (0.327%), neg=0, invalid=766 0011: dt=129.472000, rms=0.730 (0.331%), neg=0, invalid=766 0012: dt=129.472000, rms=0.728 (0.309%), neg=0, invalid=766 0013: dt=129.472000, rms=0.724 (0.552%), neg=0, invalid=766 0014: dt=129.472000, rms=0.719 (0.715%), neg=0, invalid=766 0015: dt=129.472000, rms=0.715 (0.577%), neg=0, invalid=766 0016: dt=129.472000, rms=0.711 (0.485%), neg=0, invalid=766 0017: dt=129.472000, rms=0.707 (0.659%), neg=0, invalid=766 0018: dt=129.472000, rms=0.702 (0.654%), neg=0, invalid=766 0019: dt=129.472000, rms=0.699 (0.478%), neg=0, invalid=766 0020: dt=129.472000, rms=0.696 (0.441%), neg=0, invalid=766 0021: dt=129.472000, rms=0.692 (0.532%), neg=0, invalid=766 0022: dt=129.472000, rms=0.689 (0.398%), neg=0, invalid=766 0023: dt=129.472000, rms=0.687 (0.318%), neg=0, invalid=766 0024: dt=129.472000, rms=0.685 (0.330%), neg=0, invalid=766 0025: dt=129.472000, rms=0.683 (0.311%), neg=0, invalid=766 0026: dt=129.472000, rms=0.681 (0.209%), neg=0, invalid=766 0027: dt=129.472000, rms=0.680 (0.207%), neg=0, invalid=766 0028: dt=129.472000, rms=0.678 (0.266%), neg=0, invalid=766 0029: dt=129.472000, rms=0.677 (0.206%), neg=0, invalid=766 0030: dt=129.472000, rms=0.676 (0.148%), neg=0, invalid=766 0031: dt=129.472000, rms=0.674 (0.220%), neg=0, invalid=766 0032: dt=129.472000, rms=0.673 (0.222%), neg=0, invalid=766 0033: dt=129.472000, rms=0.672 (0.141%), neg=0, invalid=766 0034: dt=129.472000, rms=0.671 (0.113%), neg=0, invalid=766 0035: dt=129.472000, rms=0.670 (0.168%), neg=0, invalid=766 0036: dt=129.472000, rms=0.669 (0.167%), neg=0, invalid=766 0037: dt=129.472000, rms=0.668 (0.100%), neg=0, invalid=766 0038: dt=129.472000, rms=0.668 (0.066%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65281.043 ms 0039: dt=295.936000, rms=0.667 (0.133%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66679.555 ms 0040: dt=0.433500, rms=0.667 (-0.008%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.667, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58931.336 ms 0041: dt=8.092000, rms=0.667 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59405.227 ms 0042: dt=5.780000, rms=0.667 (0.002%), neg=0, invalid=766 0043: dt=5.780000, rms=0.667 (0.001%), neg=0, invalid=766 0044: dt=5.780000, rms=0.667 (-0.003%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.676, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63289.676 ms 0045: dt=145.152000, rms=0.669 (1.060%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59244.984 ms 0046: dt=36.288000, rms=0.660 (1.378%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58851.504 ms 0047: dt=9.072000, rms=0.659 (0.068%), neg=0, invalid=766 0048: dt=9.072000, rms=0.659 (0.066%), neg=0, invalid=766 0049: dt=9.072000, rms=0.658 (0.068%), neg=0, invalid=766 0050: dt=9.072000, rms=0.657 (0.121%), neg=0, invalid=766 0051: dt=9.072000, rms=0.656 (0.242%), neg=0, invalid=766 0052: dt=9.072000, rms=0.653 (0.387%), neg=0, invalid=766 0053: dt=9.072000, rms=0.650 (0.463%), neg=0, invalid=766 0054: dt=9.072000, rms=0.647 (0.471%), neg=0, invalid=766 0055: dt=9.072000, rms=0.644 (0.427%), neg=0, invalid=766 0056: dt=9.072000, rms=0.642 (0.389%), neg=0, invalid=766 0057: dt=9.072000, rms=0.640 (0.356%), neg=0, invalid=766 0058: dt=9.072000, rms=0.638 (0.317%), neg=0, invalid=766 0059: dt=9.072000, rms=0.636 (0.312%), neg=0, invalid=766 0060: dt=9.072000, rms=0.634 (0.332%), neg=0, invalid=766 0061: dt=9.072000, rms=0.631 (0.370%), neg=0, invalid=766 0062: dt=9.072000, rms=0.629 (0.375%), neg=0, invalid=766 0063: dt=9.072000, rms=0.627 (0.344%), neg=0, invalid=766 0064: dt=9.072000, rms=0.625 (0.299%), neg=0, invalid=766 0065: dt=9.072000, rms=0.623 (0.261%), neg=0, invalid=766 0066: dt=9.072000, rms=0.622 (0.237%), neg=0, invalid=766 0067: dt=9.072000, rms=0.620 (0.207%), neg=0, invalid=766 0068: dt=9.072000, rms=0.619 (0.196%), neg=0, invalid=766 0069: dt=9.072000, rms=0.618 (0.204%), neg=0, invalid=766 0070: dt=9.072000, rms=0.617 (0.215%), neg=0, invalid=766 0071: dt=9.072000, rms=0.615 (0.215%), neg=0, invalid=766 0072: dt=9.072000, rms=0.614 (0.194%), neg=0, invalid=766 0073: dt=9.072000, rms=0.613 (0.171%), neg=0, invalid=766 0074: dt=9.072000, rms=0.612 (0.146%), neg=0, invalid=766 0075: dt=9.072000, rms=0.611 (0.126%), neg=0, invalid=766 0076: dt=9.072000, rms=0.611 (0.116%), neg=0, invalid=766 0077: dt=9.072000, rms=0.610 (0.113%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66801.492 ms 0078: dt=145.152000, rms=0.609 (0.191%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81626.211 ms 0079: dt=0.001012, rms=0.609 (-0.007%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.609, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58402.793 ms 0080: dt=5.184000, rms=0.609 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59559.191 ms 0081: dt=2.268000, rms=0.609 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59670.867 ms 0082: dt=2.268000, rms=0.609 (0.002%), neg=0, invalid=766 0083: dt=2.268000, rms=0.609 (0.002%), neg=0, invalid=766 0084: dt=2.268000, rms=0.609 (0.000%), neg=0, invalid=766 0085: dt=2.268000, rms=0.609 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.635, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62501.543 ms 0086: dt=10.245614, rms=0.634 (0.217%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55657.434 ms 0087: dt=6.400000, rms=0.634 (0.049%), neg=0, invalid=766 0088: dt=6.400000, rms=0.633 (0.025%), neg=0, invalid=766 0089: dt=6.400000, rms=0.633 (-0.045%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.633, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58721.379 ms 0090: dt=0.000000, rms=0.633 (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=0.697, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58606.484 ms 0091: dt=4.212963, rms=0.689 (1.056%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55582.195 ms 0092: dt=0.864000, rms=0.689 (0.013%), neg=0, invalid=766 0093: dt=0.864000, rms=0.689 (-0.007%), 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 54514.633 ms 0094: dt=0.000000, rms=0.689 (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=0.775, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59289.414 ms 0095: dt=1.198704, rms=0.770 (0.649%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59755.863 ms 0096: dt=1.813953, rms=0.766 (0.574%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58691.285 ms 0097: dt=0.813793, rms=0.765 (0.112%), neg=0, invalid=766 0098: dt=0.813793, rms=0.764 (0.057%), neg=0, invalid=766 0099: dt=0.813793, rms=0.764 (-0.007%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.764, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62711.273 ms 0100: dt=1.280000, rms=0.763 (0.173%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54883.688 ms 0101: dt=0.000000, rms=0.763 (-0.001%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.694, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54069.754 ms 0102: dt=0.161765, rms=0.685 (1.275%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51256.094 ms 0103: dt=0.000000, rms=0.685 (0.003%), neg=0, invalid=766 0104: dt=0.050000, rms=0.685 (-0.013%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.685, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54692.641 ms 0105: dt=0.270508, rms=0.683 (0.311%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51203.711 ms 0106: dt=0.112000, rms=0.682 (0.250%), neg=0, invalid=766 0107: dt=0.112000, rms=0.681 (0.051%), neg=0, invalid=766 0108: dt=0.112000, rms=0.680 (0.101%), neg=0, invalid=766 0109: dt=0.112000, rms=0.679 (0.198%), neg=0, invalid=766 0110: dt=0.112000, rms=0.678 (0.202%), neg=0, invalid=766 0111: dt=0.112000, rms=0.677 (0.177%), neg=0, invalid=766 0112: dt=0.112000, rms=0.676 (0.139%), neg=0, invalid=766 0113: dt=0.112000, rms=0.675 (0.128%), neg=0, invalid=766 0114: dt=0.112000, rms=0.674 (0.128%), neg=0, invalid=766 0115: dt=0.112000, rms=0.673 (0.083%), neg=0, invalid=766 0116: dt=0.112000, rms=0.673 (0.042%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65230.949 ms 0117: dt=0.000000, rms=0.673 (-0.002%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.20133 (10) Left_Lateral_Ventricle (4): linear fit = 0.30 x + 0.0 (2415 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2415 voxels, peak = 7), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.19686 (10) Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (2223 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (2223 voxels, peak = 8), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.10440 (103) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (357 voxels, overlap=0.929) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (357 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.11538 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (357 voxels, overlap=0.825) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (357 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.08129 (59) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (745 voxels, overlap=0.904) Right_Hippocampus (53): linear fit = 0.93 x + 0.0 (745 voxels, peak = 58), gca=58.3 gca peak = 0.29892 (64) mri peak = 0.06929 (66) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (478 voxels, overlap=0.995) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (478 voxels, peak = 62), gca=62.4 gca peak = 0.12541 (104) mri peak = 0.08517 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56635 voxels, overlap=0.859) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (56635 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.08117 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (57672 voxels, overlap=0.866) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (57672 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.02919 (69) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (20175 voxels, overlap=0.616) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (20175 voxels, peak = 65), gca=64.6 gca peak = 0.13270 (63) mri peak = 0.03258 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (20667 voxels, overlap=0.972) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (20667 voxels, peak = 65), gca=64.6 gca peak = 0.15182 (70) mri peak = 0.13487 (78) Right_Caudate (50): linear fit = 1.05 x + 0.0 (355 voxels, overlap=0.635) Right_Caudate (50): linear fit = 1.05 x + 0.0 (355 voxels, peak = 74), gca=73.5 gca peak = 0.14251 (76) mri peak = 0.15288 (72) Left_Caudate (11): linear fit = 0.93 x + 0.0 (401 voxels, overlap=0.635) Left_Caudate (11): linear fit = 0.93 x + 0.0 (401 voxels, peak = 70), gca=70.3 gca peak = 0.12116 (60) mri peak = 0.04895 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (21647 voxels, overlap=0.949) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (21647 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.03821 (56) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (23605 voxels, overlap=0.991) Right_Cerebellum_Cortex (47): linear fit = 0.95 x + 0.0 (23605 voxels, peak = 58), gca=58.0 gca peak = 0.22684 (88) mri peak = 0.08460 (94) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8109 voxels, overlap=0.476) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (8109 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.08812 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6593 voxels, overlap=0.617) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6593 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.13121 (63) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (273 voxels, overlap=0.992) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (273 voxels, peak = 62), gca=62.0 gca peak = 0.39668 (62) mri peak = 0.10651 (63) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (338 voxels, overlap=0.994) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (338 voxels, peak = 64), gca=63.5 gca peak = 0.10129 (93) mri peak = 0.06676 (89) Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (3744 voxels, overlap=0.489) Left_Thalamus_Proper (10): linear fit = 0.93 x + 0.0 (3744 voxels, peak = 86), gca=86.0 gca peak = 0.12071 (89) mri peak = 0.06535 (88) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3710 voxels, overlap=0.933) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (3710 voxels, peak = 85), gca=84.5 gca peak = 0.13716 (82) mri peak = 0.08822 (82) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2408 voxels, overlap=0.947) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2408 voxels, peak = 80), gca=80.0 gca peak = 0.15214 (84) mri peak = 0.09926 (79) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2442 voxels, overlap=0.848) Right_Putamen (51): linear fit = 0.95 x + 0.0 (2442 voxels, peak = 80), gca=79.8 gca peak = 0.08983 (85) mri peak = 0.07674 (85) Brain_Stem (16): linear fit = 1.02 x + 0.0 (10455 voxels, overlap=0.777) Brain_Stem (16): linear fit = 1.02 x + 0.0 (10455 voxels, peak = 87), gca=87.1 gca peak = 0.11809 (92) mri peak = 0.07135 (97) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1014 voxels, overlap=0.706) Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1014 voxels, peak = 97), gca=96.6 gca peak = 0.12914 (94) mri peak = 0.09288 (97) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (931 voxels, overlap=0.684) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (931 voxels, peak = 96), gca=96.3 gca peak = 0.21100 (36) mri peak = 0.25243 (10) gca peak = 0.13542 (27) mri peak = 0.12186 ( 8) Fourth_Ventricle (15): linear fit = 0.40 x + 0.0 (192 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.40 x + 0.0 (192 voxels, peak = 11), gca=10.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.689, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58701.582 ms 0118: dt=110.976000, rms=0.684 (0.669%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57753.605 ms 0119: dt=369.920000, rms=0.679 (0.727%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59227.727 ms 0120: dt=129.472000, rms=0.676 (0.466%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58848.801 ms 0121: dt=73.984000, rms=0.675 (0.132%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63795.984 ms 0122: dt=517.888000, rms=0.671 (0.528%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56338.637 ms 0123: dt=32.368000, rms=0.670 (0.206%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58736.500 ms 0124: dt=32.368000, rms=0.670 (0.049%), neg=0, invalid=766 0125: dt=32.368000, rms=0.670 (0.021%), neg=0, invalid=766 0126: dt=32.368000, rms=0.669 (0.027%), neg=0, invalid=766 0127: dt=32.368000, rms=0.669 (0.045%), neg=0, invalid=766 0128: dt=32.368000, rms=0.669 (0.087%), neg=0, invalid=766 0129: dt=32.368000, rms=0.668 (0.121%), neg=0, invalid=766 0130: dt=32.368000, rms=0.667 (0.133%), neg=0, invalid=766 0131: dt=32.368000, rms=0.666 (0.125%), neg=0, invalid=766 0132: dt=32.368000, rms=0.665 (0.128%), neg=0, invalid=766 0133: dt=32.368000, rms=0.664 (0.125%), neg=0, invalid=766 0134: dt=32.368000, rms=0.664 (0.122%), neg=0, invalid=766 0135: dt=32.368000, rms=0.663 (0.126%), neg=0, invalid=766 0136: dt=32.368000, rms=0.662 (0.138%), neg=0, invalid=766 0137: dt=32.368000, rms=0.661 (0.147%), neg=0, invalid=766 0138: dt=32.368000, rms=0.660 (0.142%), neg=0, invalid=766 0139: dt=32.368000, rms=0.659 (0.125%), neg=0, invalid=766 0140: dt=32.368000, rms=0.658 (0.115%), neg=0, invalid=766 0141: dt=32.368000, rms=0.658 (0.105%), neg=0, invalid=766 0142: dt=32.368000, rms=0.657 (0.094%), neg=0, invalid=766 0143: dt=32.368000, rms=0.656 (0.096%), neg=0, invalid=766 0144: dt=32.368000, rms=0.656 (0.101%), neg=0, invalid=766 0145: dt=32.368000, rms=0.655 (0.107%), neg=0, invalid=766 0146: dt=32.368000, rms=0.654 (0.102%), neg=0, invalid=766 0147: dt=32.368000, rms=0.654 (0.095%), neg=0, invalid=766 0148: dt=32.368000, rms=0.653 (0.090%), neg=0, invalid=766 0149: dt=32.368000, rms=0.653 (0.085%), neg=0, invalid=766 0150: dt=32.368000, rms=0.652 (0.078%), neg=0, invalid=766 0151: dt=32.368000, rms=0.652 (0.074%), neg=0, invalid=766 0152: dt=32.368000, rms=0.651 (0.081%), neg=0, invalid=766 0153: dt=32.368000, rms=0.651 (0.079%), neg=0, invalid=766 0154: dt=32.368000, rms=0.650 (0.074%), neg=0, invalid=766 0155: dt=32.368000, rms=0.650 (0.069%), neg=0, invalid=766 0156: dt=32.368000, rms=0.649 (0.069%), neg=0, invalid=766 0157: dt=32.368000, rms=0.649 (0.066%), neg=0, invalid=766 0158: dt=32.368000, rms=0.648 (0.064%), neg=0, invalid=766 0159: dt=32.368000, rms=0.648 (0.067%), neg=0, invalid=766 0160: dt=32.368000, rms=0.647 (0.064%), neg=0, invalid=766 0161: dt=32.368000, rms=0.647 (0.062%), neg=0, invalid=766 0162: dt=32.368000, rms=0.647 (0.059%), neg=0, invalid=766 0163: dt=32.368000, rms=0.646 (0.054%), neg=0, invalid=766 0164: dt=32.368000, rms=0.646 (0.051%), neg=0, invalid=766 0165: dt=32.368000, rms=0.646 (0.050%), neg=0, invalid=766 0166: dt=32.368000, rms=0.645 (0.049%), neg=0, invalid=766 0167: dt=32.368000, rms=0.645 (0.053%), neg=0, invalid=766 0168: dt=32.368000, rms=0.645 (0.052%), neg=0, invalid=766 0169: dt=32.368000, rms=0.644 (0.053%), neg=0, invalid=766 0170: dt=32.368000, rms=0.644 (0.051%), neg=0, invalid=766 0171: dt=32.368000, rms=0.644 (0.049%), neg=0, invalid=766 0172: dt=32.368000, rms=0.643 (0.045%), neg=0, invalid=766 0173: dt=32.368000, rms=0.643 (0.042%), neg=0, invalid=766 0174: dt=32.368000, rms=0.643 (0.041%), neg=0, invalid=766 0175: dt=32.368000, rms=0.643 (0.039%), neg=0, invalid=766 0176: dt=32.368000, rms=0.642 (0.038%), neg=0, invalid=766 0177: dt=32.368000, rms=0.642 (0.035%), neg=0, invalid=766 0178: dt=32.368000, rms=0.642 (0.034%), neg=0, invalid=766 0179: dt=32.368000, rms=0.642 (0.035%), neg=0, invalid=766 0180: dt=32.368000, rms=0.641 (0.036%), neg=0, invalid=766 0181: dt=32.368000, rms=0.641 (0.038%), neg=0, invalid=766 0182: dt=32.368000, rms=0.641 (0.038%), neg=0, invalid=766 0183: dt=32.368000, rms=0.641 (0.038%), neg=0, invalid=766 0184: dt=32.368000, rms=0.640 (0.038%), neg=0, invalid=766 0185: dt=32.368000, rms=0.640 (0.033%), neg=0, invalid=766 0186: dt=32.368000, rms=0.640 (0.032%), neg=0, invalid=766 0187: dt=32.368000, rms=0.640 (0.029%), neg=0, invalid=766 0188: dt=32.368000, rms=0.640 (0.030%), neg=0, invalid=766 0189: dt=32.368000, rms=0.640 (0.030%), neg=0, invalid=766 0190: dt=32.368000, rms=0.639 (0.031%), neg=0, invalid=766 0191: dt=32.368000, rms=0.639 (0.032%), neg=0, invalid=766 0192: dt=32.368000, rms=0.639 (0.031%), neg=0, invalid=766 0193: dt=32.368000, rms=0.639 (0.030%), neg=0, invalid=766 0194: dt=32.368000, rms=0.639 (0.027%), neg=0, invalid=766 0195: dt=32.368000, rms=0.638 (0.026%), neg=0, invalid=766 0196: dt=32.368000, rms=0.638 (0.026%), neg=0, invalid=766 0197: dt=32.368000, rms=0.638 (0.025%), neg=0, invalid=766 0198: dt=32.368000, rms=0.638 (0.025%), neg=0, invalid=766 0199: dt=32.368000, rms=0.638 (0.024%), neg=0, invalid=766 0200: dt=32.368000, rms=0.638 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61428.465 ms 0201: dt=369.920000, rms=0.638 (0.008%), neg=0, invalid=766 0202: dt=369.920000, rms=0.638 (-0.040%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63072.691 ms 0203: dt=129.472000, rms=0.637 (0.091%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61898.762 ms 0204: dt=369.920000, rms=0.635 (0.291%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54296.391 ms 0205: dt=18.496000, rms=0.635 (0.010%), neg=0, invalid=766 0206: dt=18.496000, rms=0.635 (-0.004%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.636, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54430.852 ms 0207: dt=103.680000, rms=0.632 (0.552%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54321.203 ms 0208: dt=36.288000, rms=0.626 (1.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51131.648 ms 0209: dt=15.552000, rms=0.625 (0.181%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54833.340 ms 0210: dt=124.416000, rms=0.621 (0.524%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 54710.383 ms 0211: dt=31.104000, rms=0.616 (0.899%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51217.414 ms 0212: dt=9.072000, rms=0.616 (0.061%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 51462.336 ms 0213: dt=31.104000, rms=0.615 (0.082%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57527.094 ms 0214: dt=124.416000, rms=0.610 (0.791%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50617.172 ms 0215: dt=9.072000, rms=0.609 (0.177%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50176.512 ms 0216: dt=9.072000, rms=0.609 (0.077%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50540.816 ms 0217: dt=15.552000, rms=0.608 (0.039%), neg=0, invalid=766 0218: dt=15.552000, rms=0.608 (0.070%), neg=0, invalid=766 0219: dt=15.552000, rms=0.607 (0.134%), neg=0, invalid=766 0220: dt=15.552000, rms=0.607 (0.099%), neg=0, invalid=766 0221: dt=15.552000, rms=0.606 (0.164%), neg=0, invalid=766 0222: dt=7.776000, rms=0.605 (0.027%), neg=0, invalid=766 0223: dt=3.888000, rms=0.605 (0.017%), neg=0, invalid=766 0224: dt=0.972000, rms=0.605 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53399.641 ms 0225: dt=0.567000, rms=0.605 (0.003%), neg=0, invalid=766 0226: dt=0.283500, rms=0.605 (0.001%), neg=0, invalid=766 0227: dt=0.070875, rms=0.605 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.605, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70886.117 ms 0228: dt=124.416000, rms=0.602 (0.592%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71572.336 ms 0229: dt=36.288000, rms=0.599 (0.493%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57776.535 ms 0230: dt=9.072000, rms=0.599 (-0.000%), neg=0, invalid=766 0231: dt=9.072000, rms=0.599 (0.010%), neg=0, invalid=766 0232: dt=9.072000, rms=0.599 (0.010%), neg=0, invalid=766 0233: dt=9.072000, rms=0.598 (0.055%), neg=0, invalid=766 0234: dt=9.072000, rms=0.598 (0.083%), neg=0, invalid=766 0235: dt=9.072000, rms=0.598 (0.028%), neg=0, invalid=766 0236: dt=2.268000, rms=0.598 (0.009%), neg=0, invalid=766 0237: dt=0.283500, rms=0.598 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47830.734 ms 0238: dt=0.141750, rms=0.598 (0.000%), neg=0, invalid=766 0239: dt=0.017719, rms=0.598 (0.000%), neg=0, invalid=766 0240: dt=0.008859, rms=0.598 (0.000%), neg=0, invalid=766 0241: dt=0.002215, rms=0.598 (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=0.602, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24722.605 ms 0242: dt=0.000000, rms=0.602 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53023.730 ms 0243: dt=32.000000, rms=0.583 (3.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52863.770 ms 0244: dt=44.800000, rms=0.566 (2.949%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45796.297 ms 0245: dt=2.800000, rms=0.565 (0.126%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45721.930 ms 0246: dt=2.800000, rms=0.565 (0.130%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53672.750 ms 0247: dt=44.800000, rms=0.556 (1.601%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56410.598 ms 0248: dt=11.958333, rms=0.552 (0.566%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49146.664 ms 0249: dt=2.800000, rms=0.552 (0.116%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49257.859 ms 0250: dt=9.600000, rms=0.551 (0.226%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52609.121 ms 0251: dt=44.800000, rms=0.546 (0.905%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52715.410 ms 0252: dt=6.878161, rms=0.544 (0.373%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52788.508 ms 0253: dt=32.000000, rms=0.541 (0.516%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49177.102 ms 0254: dt=2.800000, rms=0.540 (0.133%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49385.141 ms 0255: dt=8.000000, rms=0.539 (0.222%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52776.738 ms 0256: dt=44.800000, rms=0.536 (0.426%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53652.633 ms 0257: dt=7.542857, rms=0.535 (0.339%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49160.855 ms 0258: dt=11.200000, rms=0.534 (0.181%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49229.785 ms 0259: dt=11.200000, rms=0.533 (0.165%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49212.473 ms 0260: dt=11.200000, rms=0.532 (0.118%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49224.934 ms 0261: dt=11.200000, rms=0.531 (0.160%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52787.332 ms 0262: dt=25.600000, rms=0.531 (0.140%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52850.152 ms 0263: dt=8.000000, rms=0.529 (0.219%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53075.871 ms 0264: dt=11.200000, rms=0.529 (0.109%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49230.723 ms 0265: dt=11.200000, rms=0.528 (0.138%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52798.656 ms 0266: dt=11.200000, rms=0.528 (0.082%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49543.715 ms 0267: dt=11.200000, rms=0.527 (0.131%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52605.883 ms 0268: dt=19.200000, rms=0.527 (0.094%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49319.473 ms 0269: dt=9.600000, rms=0.526 (0.142%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49158.621 ms 0270: dt=9.600000, rms=0.525 (0.065%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49360.352 ms 0271: dt=11.200000, rms=0.525 (0.119%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52755.941 ms 0272: dt=11.200000, rms=0.524 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52688.926 ms 0273: dt=25.600000, rms=0.524 (0.145%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52716.977 ms 0274: dt=6.015504, rms=0.523 (0.092%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52874.531 ms 0275: dt=44.800000, rms=0.522 (0.320%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52670.930 ms 0276: dt=11.200000, rms=0.521 (0.069%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52765.191 ms 0277: dt=44.800000, rms=0.520 (0.161%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53159.992 ms 0278: dt=8.067227, rms=0.520 (0.155%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52800.430 ms 0279: dt=25.600000, rms=0.519 (0.060%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52761.047 ms 0280: dt=11.200000, rms=0.519 (0.137%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49319.023 ms 0281: dt=2.800000, rms=0.518 (0.019%), neg=0, invalid=766 0282: dt=2.800000, rms=0.518 (0.013%), neg=0, invalid=766 0283: dt=2.800000, rms=0.518 (0.017%), neg=0, invalid=766 0284: dt=2.800000, rms=0.518 (0.023%), neg=0, invalid=766 0285: dt=2.800000, rms=0.518 (0.047%), neg=0, invalid=766 0286: dt=2.800000, rms=0.518 (0.071%), neg=0, invalid=766 0287: dt=2.800000, rms=0.517 (0.075%), neg=0, invalid=766 0288: dt=2.800000, rms=0.517 (0.081%), neg=0, invalid=766 0289: dt=2.800000, rms=0.516 (0.073%), neg=0, invalid=766 0290: dt=2.800000, rms=0.516 (0.076%), neg=0, invalid=766 0291: dt=2.800000, rms=0.516 (0.077%), neg=0, invalid=766 0292: dt=2.800000, rms=0.515 (0.075%), neg=0, invalid=766 0293: dt=2.800000, rms=0.515 (0.083%), neg=0, invalid=766 0294: dt=2.800000, rms=0.514 (0.093%), neg=0, invalid=766 0295: dt=2.800000, rms=0.514 (0.098%), neg=0, invalid=766 0296: dt=2.800000, rms=0.513 (0.101%), neg=0, invalid=766 0297: dt=2.800000, rms=0.513 (0.088%), neg=0, invalid=766 0298: dt=2.800000, rms=0.512 (0.091%), neg=0, invalid=766 0299: dt=2.800000, rms=0.512 (0.085%), neg=0, invalid=766 0300: dt=2.800000, rms=0.512 (0.079%), neg=0, invalid=766 0301: dt=2.800000, rms=0.511 (0.085%), neg=0, invalid=766 0302: dt=2.800000, rms=0.511 (0.081%), neg=0, invalid=766 0303: dt=2.800000, rms=0.510 (0.087%), neg=0, invalid=766 0304: dt=2.800000, rms=0.510 (0.092%), neg=0, invalid=766 0305: dt=2.800000, rms=0.509 (0.078%), neg=0, invalid=766 0306: dt=2.800000, rms=0.509 (0.079%), neg=0, invalid=766 0307: dt=2.800000, rms=0.509 (0.071%), neg=0, invalid=766 0308: dt=2.800000, rms=0.508 (0.067%), neg=0, invalid=766 0309: dt=2.800000, rms=0.508 (0.066%), neg=0, invalid=766 0310: dt=2.800000, rms=0.508 (0.065%), neg=0, invalid=766 0311: dt=2.800000, rms=0.507 (0.062%), neg=0, invalid=766 0312: dt=2.800000, rms=0.507 (0.066%), neg=0, invalid=766 0313: dt=2.800000, rms=0.507 (0.059%), neg=0, invalid=766 0314: dt=2.800000, rms=0.506 (0.056%), neg=0, invalid=766 0315: dt=2.800000, rms=0.506 (0.053%), neg=0, invalid=766 0316: dt=2.800000, rms=0.506 (0.055%), neg=0, invalid=766 0317: dt=2.800000, rms=0.506 (0.050%), neg=0, invalid=766 0318: dt=2.800000, rms=0.505 (0.051%), neg=0, invalid=766 0319: dt=2.800000, rms=0.505 (0.052%), neg=0, invalid=766 0320: dt=2.800000, rms=0.505 (0.047%), neg=0, invalid=766 0321: dt=2.800000, rms=0.505 (0.047%), neg=0, invalid=766 0322: dt=2.800000, rms=0.504 (0.046%), neg=0, invalid=766 0323: dt=2.800000, rms=0.504 (0.043%), neg=0, invalid=766 0324: dt=2.800000, rms=0.504 (0.043%), neg=0, invalid=766 0325: dt=2.800000, rms=0.504 (0.040%), neg=0, invalid=766 0326: dt=2.800000, rms=0.503 (0.040%), neg=0, invalid=766 0327: dt=2.800000, rms=0.503 (0.039%), neg=0, invalid=766 0328: dt=2.800000, rms=0.503 (0.035%), neg=0, invalid=766 0329: dt=2.800000, rms=0.503 (0.036%), neg=0, invalid=766 0330: dt=2.800000, rms=0.503 (0.037%), neg=0, invalid=766 0331: dt=2.800000, rms=0.503 (0.036%), neg=0, invalid=766 0332: dt=2.800000, rms=0.502 (0.036%), neg=0, invalid=766 0333: dt=2.800000, rms=0.502 (0.036%), neg=0, invalid=766 0334: dt=2.800000, rms=0.502 (0.032%), neg=0, invalid=766 0335: dt=2.800000, rms=0.502 (0.031%), neg=0, invalid=766 0336: dt=2.800000, rms=0.502 (0.029%), neg=0, invalid=766 0337: dt=2.800000, rms=0.502 (0.032%), neg=0, invalid=766 0338: dt=2.800000, rms=0.501 (0.029%), neg=0, invalid=766 0339: dt=2.800000, rms=0.501 (0.029%), neg=0, invalid=766 0340: dt=2.800000, rms=0.501 (0.029%), neg=0, invalid=766 0341: dt=2.800000, rms=0.501 (0.030%), neg=0, invalid=766 0342: dt=2.800000, rms=0.501 (0.030%), neg=0, invalid=766 0343: dt=2.800000, rms=0.501 (0.027%), neg=0, invalid=766 0344: dt=2.800000, rms=0.501 (0.028%), neg=0, invalid=766 0345: dt=2.800000, rms=0.500 (0.029%), neg=0, invalid=766 0346: dt=2.800000, rms=0.500 (0.026%), neg=0, invalid=766 0347: dt=2.800000, rms=0.500 (0.026%), neg=0, invalid=766 0348: dt=2.800000, rms=0.500 (0.025%), neg=0, invalid=766 0349: dt=2.800000, rms=0.500 (0.026%), neg=0, invalid=766 0350: dt=2.800000, rms=0.500 (0.027%), neg=0, invalid=766 0351: dt=2.800000, rms=0.500 (0.026%), neg=0, invalid=766 0352: dt=2.800000, rms=0.499 (0.024%), neg=0, invalid=766 0353: dt=2.800000, rms=0.499 (0.024%), neg=0, invalid=766 0354: dt=2.800000, rms=0.499 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59722.301 ms 0355: dt=512.000000, rms=0.498 (0.160%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49225.797 ms 0356: dt=11.200000, rms=0.498 (0.161%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49125.668 ms 0357: dt=6.400000, rms=0.498 (0.031%), neg=0, invalid=766 0358: dt=6.400000, rms=0.497 (0.009%), neg=0, invalid=766 0359: dt=6.400000, rms=0.497 (0.010%), neg=0, invalid=766 0360: dt=6.400000, rms=0.497 (0.008%), neg=0, invalid=766 0361: dt=6.400000, rms=0.497 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56266.480 ms 0362: dt=38.400000, rms=0.497 (0.025%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52654.172 ms 0363: dt=11.200000, rms=0.497 (0.020%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.515, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52907.348 ms 0364: dt=0.000000, rms=0.515 (-0.007%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.515, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52762.223 ms 0365: dt=0.000000, rms=0.515 (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=0.550, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52750.477 ms 0366: dt=1.066667, rms=0.547 (0.417%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52828.055 ms 0367: dt=0.112000, rms=0.547 (0.007%), neg=0, invalid=766 0368: dt=0.112000, rms=0.547 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.547, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52788.559 ms 0369: dt=0.448000, rms=0.547 (0.050%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52877.391 ms 0370: dt=0.112000, rms=0.547 (0.003%), neg=0, invalid=766 0371: dt=0.112000, rms=0.547 (-0.002%), 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=0.502, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49029.215 ms 0372: dt=0.161026, rms=0.496 (1.156%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45649.527 ms 0373: dt=0.028000, rms=0.496 (0.139%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49224.121 ms 0374: dt=0.132127, rms=0.493 (0.624%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49221.906 ms 0375: dt=0.119565, rms=0.490 (0.432%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49211.477 ms 0376: dt=0.113229, rms=0.489 (0.325%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49975.824 ms 0377: dt=0.112000, rms=0.488 (0.263%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49313.234 ms 0378: dt=0.112000, rms=0.486 (0.220%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49260.035 ms 0379: dt=0.112000, rms=0.486 (0.181%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52659.602 ms 0380: dt=0.320000, rms=0.483 (0.439%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49237.770 ms 0381: dt=0.096000, rms=0.483 (0.076%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49126.590 ms 0382: dt=0.112000, rms=0.483 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49258.863 ms 0383: dt=0.112000, rms=0.482 (0.075%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49196.398 ms 0384: dt=0.112000, rms=0.482 (0.067%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49529.824 ms 0385: dt=0.112000, rms=0.482 (0.057%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45764.242 ms 0386: dt=0.028000, rms=0.482 (0.017%), neg=0, invalid=766 0387: dt=0.028000, rms=0.482 (0.014%), neg=0, invalid=766 0388: dt=0.028000, rms=0.481 (0.023%), neg=0, invalid=766 0389: dt=0.028000, rms=0.481 (0.034%), neg=0, invalid=766 0390: dt=0.028000, rms=0.481 (0.042%), neg=0, invalid=766 0391: dt=0.028000, rms=0.481 (0.050%), neg=0, invalid=766 0392: dt=0.028000, rms=0.481 (0.010%), neg=0, invalid=766 0393: dt=0.028000, rms=0.481 (0.018%), neg=0, invalid=766 0394: dt=0.028000, rms=0.481 (0.028%), neg=0, invalid=766 0395: dt=0.028000, rms=0.480 (0.030%), neg=0, invalid=766 0396: dt=0.028000, rms=0.480 (0.037%), neg=0, invalid=766 0397: dt=0.028000, rms=0.480 (0.006%), neg=0, invalid=766 0398: dt=0.028000, rms=0.480 (0.017%), neg=0, invalid=766 0399: dt=0.028000, rms=0.480 (0.020%), neg=0, invalid=766 0400: dt=0.028000, rms=0.480 (0.028%), neg=0, invalid=766 0401: dt=0.028000, rms=0.480 (0.028%), neg=0, invalid=766 0402: dt=0.028000, rms=0.480 (0.031%), neg=0, invalid=766 0403: dt=0.028000, rms=0.479 (0.033%), neg=0, invalid=766 0404: dt=0.028000, rms=0.479 (0.040%), neg=0, invalid=766 0405: dt=0.028000, rms=0.479 (0.038%), neg=0, invalid=766 0406: dt=0.028000, rms=0.479 (0.037%), neg=0, invalid=766 0407: dt=0.028000, rms=0.479 (0.036%), neg=0, invalid=766 0408: dt=0.028000, rms=0.479 (0.034%), neg=0, invalid=766 0409: dt=0.028000, rms=0.478 (0.036%), neg=0, invalid=766 0410: dt=0.028000, rms=0.478 (0.037%), neg=0, invalid=766 0411: dt=0.028000, rms=0.478 (0.030%), neg=0, invalid=766 0412: dt=0.028000, rms=0.478 (0.030%), neg=0, invalid=766 0413: dt=0.028000, rms=0.478 (0.028%), neg=0, invalid=766 0414: dt=0.028000, rms=0.478 (0.025%), neg=0, invalid=766 0415: dt=0.028000, rms=0.478 (0.025%), neg=0, invalid=766 0416: dt=0.028000, rms=0.477 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50987.383 ms 0417: dt=0.096000, rms=0.477 (0.000%), neg=0, invalid=766 0418: dt=0.012000, rms=0.477 (0.002%), neg=0, invalid=766 0419: dt=0.012000, rms=0.477 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45706.086 ms 0420: dt=0.028000, rms=0.477 (0.066%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52594.941 ms 0421: dt=0.384000, rms=0.473 (0.824%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 49240.539 ms 0422: dt=0.112000, rms=0.473 (0.036%), neg=0, invalid=766 0423: dt=0.112000, rms=0.473 (0.027%), neg=0, invalid=766 0424: dt=0.112000, rms=0.473 (0.046%), neg=0, invalid=766 0425: dt=0.112000, rms=0.472 (0.055%), neg=0, invalid=766 0426: dt=0.112000, rms=0.472 (0.040%), neg=0, invalid=766 0427: dt=0.056000, rms=0.472 (-0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42188.566 ms 0428: dt=0.000000, rms=0.472 (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=0.470, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59659.336 ms iter 0, gcam->neg = 17 after 6 iterations, nbhd size=1, neg = 0 0429: dt=38.400000, rms=0.464 (1.318%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59690.805 ms iter 0, gcam->neg = 9 after 11 iterations, nbhd size=1, neg = 0 0430: dt=44.800000, rms=0.462 (0.415%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63079.145 ms 0431: dt=10.044444, rms=0.461 (0.225%), neg=0, invalid=766 0432: dt=10.044444, rms=0.461 (0.104%), neg=0, invalid=766 0433: dt=10.044444, rms=0.460 (0.165%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0434: dt=10.044444, rms=0.459 (0.190%), neg=0, invalid=766 0435: dt=10.044444, rms=0.459 (0.108%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0436: dt=10.044444, rms=0.458 (0.158%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0437: dt=10.044444, rms=0.457 (0.102%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0438: dt=10.044444, rms=0.457 (0.148%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0439: dt=10.044444, rms=0.456 (0.095%), neg=0, invalid=766 0440: dt=10.044444, rms=0.456 (0.116%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0441: dt=10.044444, rms=0.456 (0.061%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62367.277 ms 0442: dt=9.600000, rms=0.455 (0.085%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60730.738 ms 0443: dt=8.000000, rms=0.455 (0.026%), neg=0, invalid=766 0444: dt=8.000000, rms=0.455 (0.039%), neg=0, invalid=766 0445: dt=8.000000, rms=0.455 (0.047%), neg=0, invalid=766 0446: dt=8.000000, rms=0.454 (0.055%), neg=0, invalid=766 0447: dt=8.000000, rms=0.454 (0.045%), neg=0, invalid=766 0448: dt=8.000000, rms=0.454 (0.058%), neg=0, invalid=766 0449: dt=8.000000, rms=0.454 (0.063%), neg=0, invalid=766 0450: dt=8.000000, rms=0.453 (0.059%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.453, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59943.449 ms 0451: dt=44.800000, rms=0.450 (0.756%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63040.023 ms 0452: dt=8.388350, rms=0.449 (0.198%), neg=0, invalid=766 0453: dt=8.388350, rms=0.449 (0.063%), neg=0, invalid=766 0454: dt=8.388350, rms=0.448 (0.077%), neg=0, invalid=766 0455: dt=8.388350, rms=0.448 (0.136%), neg=0, invalid=766 0456: dt=8.388350, rms=0.447 (0.095%), neg=0, invalid=766 0457: dt=8.388350, rms=0.447 (0.129%), neg=0, invalid=766 0458: dt=8.388350, rms=0.446 (0.085%), neg=0, invalid=766 0459: dt=8.388350, rms=0.446 (0.107%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0460: dt=8.388350, rms=0.446 (0.066%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59664.684 ms 0461: dt=8.000000, rms=0.446 (0.009%), neg=0, invalid=766 0462: dt=8.000000, rms=0.445 (0.018%), neg=0, invalid=766 0463: dt=8.000000, rms=0.445 (0.035%), neg=0, invalid=766 0464: dt=8.000000, rms=0.445 (0.038%), neg=0, invalid=766 0465: dt=8.000000, rms=0.445 (0.027%), neg=0, invalid=766 0466: dt=8.000000, rms=0.445 (0.039%), neg=0, invalid=766 0467: dt=8.000000, rms=0.445 (0.035%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.449, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62948.180 ms 0468: dt=4.032000, rms=0.448 (0.051%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63367.758 ms iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0469: dt=2.304000, rms=0.448 (0.014%), neg=0, invalid=766 0470: dt=2.304000, rms=0.448 (0.016%), neg=0, invalid=766 0471: dt=2.304000, rms=0.448 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.448, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59792.492 ms iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0472: dt=11.520000, rms=0.447 (0.186%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63121.648 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0473: dt=1.008000, rms=0.447 (0.016%), neg=0, invalid=766 0474: dt=1.008000, rms=0.447 (0.021%), neg=0, invalid=766 0475: dt=1.008000, rms=0.447 (0.039%), neg=0, invalid=766 0476: dt=1.008000, rms=0.447 (0.066%), neg=0, invalid=766 0477: dt=1.008000, rms=0.446 (0.067%), neg=0, invalid=766 0478: dt=1.008000, rms=0.446 (0.081%), neg=0, invalid=766 0479: dt=1.008000, rms=0.446 (0.077%), neg=0, invalid=766 0480: dt=1.008000, rms=0.445 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0481: dt=1.008000, rms=0.445 (0.085%), neg=0, invalid=766 0482: dt=1.008000, rms=0.445 (0.087%), neg=0, invalid=766 0483: dt=1.008000, rms=0.444 (0.090%), neg=0, invalid=766 0484: dt=1.008000, rms=0.444 (0.090%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.448, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59585.719 ms 0485: dt=0.000000, rms=0.448 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.448, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59814.859 ms 0486: dt=0.000000, rms=0.448 (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=0.441, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63297.340 ms iter 0, gcam->neg = 590 after 15 iterations, nbhd size=1, neg = 0 0487: dt=1.846654, rms=0.407 (7.716%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63558.145 ms 0488: dt=0.000250, rms=0.407 (0.003%), neg=0, invalid=766 0489: dt=0.000250, 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 63109.922 ms 0490: dt=0.000375, rms=0.407 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59966.691 ms 0491: dt=0.000000, 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=0.393, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64045.312 ms iter 0, gcam->neg = 239 after 20 iterations, nbhd size=2, neg = 0 0492: dt=0.461672, rms=0.386 (1.851%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63174.883 ms 0493: dt=0.000438, rms=0.386 (-0.012%), neg=0, invalid=766 0494: dt=0.000438, rms=0.386 (0.001%), neg=0, invalid=766 0495: dt=0.000438, rms=0.386 (0.002%), neg=0, invalid=766 0496: dt=0.000438, rms=0.386 (0.000%), neg=0, invalid=766 0497: dt=0.000438, rms=0.386 (0.000%), neg=0, invalid=766 0498: dt=0.000438, rms=0.386 (0.000%), neg=0, invalid=766 0499: dt=0.000438, rms=0.386 (0.001%), neg=0, invalid=766 0500: dt=0.000438, rms=0.386 (0.001%), neg=0, invalid=766 0501: dt=0.000438, rms=0.386 (0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63039.930 ms iter 0, gcam->neg = 82 after 17 iterations, nbhd size=2, neg = 0 0502: dt=0.192000, rms=0.384 (0.445%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63148.148 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0503: dt=0.001000, rms=0.384 (0.009%), neg=0, invalid=766 0504: dt=0.001000, rms=0.384 (0.002%), neg=0, invalid=766 0505: dt=0.001000, rms=0.384 (0.003%), neg=0, invalid=766 0506: dt=0.001000, rms=0.384 (0.005%), neg=0, invalid=766 0507: dt=0.001000, rms=0.384 (0.005%), neg=0, invalid=766 0508: dt=0.001000, rms=0.384 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63083.906 ms iter 0, gcam->neg = 29 after 14 iterations, nbhd size=2, neg = 0 0509: dt=0.112000, rms=0.384 (0.153%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63004.641 ms 0510: dt=0.001750, rms=0.384 (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=0.383, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63158.719 ms iter 0, gcam->neg = 54 after 8 iterations, nbhd size=1, neg = 0 0511: dt=0.084544, rms=0.382 (0.346%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63074.523 ms iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0512: dt=0.001000, rms=0.382 (-0.003%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0513: dt=0.001000, rms=0.382 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0514: dt=0.001000, rms=0.382 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0515: dt=0.001000, rms=0.382 (0.008%), neg=0, invalid=766 0516: dt=0.001000, rms=0.382 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0517: dt=0.001000, rms=0.382 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0518: dt=0.001000, rms=0.382 (0.016%), neg=0, invalid=766 0519: dt=0.001000, rms=0.382 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0520: dt=0.001000, rms=0.382 (0.019%), neg=0, invalid=766 0521: dt=0.001000, rms=0.381 (0.021%), neg=0, invalid=766 0522: dt=0.001000, rms=0.381 (0.020%), neg=0, invalid=766 0523: dt=0.001000, rms=0.381 (0.018%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.381, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63054.504 ms iter 0, gcam->neg = 273 after 19 iterations, nbhd size=2, neg = 0 0524: dt=0.320000, rms=0.376 (1.451%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63129.711 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0525: dt=0.001750, rms=0.376 (-0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0526: dt=0.001750, rms=0.376 (0.005%), neg=0, invalid=766 0527: dt=0.001750, rms=0.376 (0.005%), neg=0, invalid=766 0528: dt=0.001750, rms=0.376 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0529: dt=0.001750, rms=0.376 (0.009%), neg=0, invalid=766 0530: dt=0.001750, rms=0.376 (0.011%), neg=0, invalid=766 0531: dt=0.001750, rms=0.376 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0532: dt=0.001750, rms=0.376 (0.015%), neg=0, invalid=766 0533: dt=0.001750, rms=0.376 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0534: dt=0.001750, rms=0.375 (0.018%), neg=0, invalid=766 0535: dt=0.001750, rms=0.375 (0.014%), neg=0, invalid=766 0536: dt=0.001750, rms=0.375 (0.016%), neg=0, invalid=766 0537: dt=0.001750, rms=0.375 (0.022%), neg=0, invalid=766 0538: dt=0.001750, rms=0.375 (0.019%), 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=0.375, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58752.938 ms iter 0, gcam->neg = 21 after 45 iterations, nbhd size=4, neg = 0 0539: dt=6.400000, rms=0.375 (-0.134%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.375, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58809.238 ms iter 0, gcam->neg = 23 after 50 iterations, nbhd size=4, neg = 0 0540: dt=11.200000, rms=0.375 (0.132%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58750.746 ms iter 0, gcam->neg = 23 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29896.332 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0541: dt=11.200000, rms=0.375 (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=0.375, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62252.238 ms iter 0, gcam->neg = 50 after 45 iterations, nbhd size=4, neg = 0 0542: dt=1.625000, rms=0.374 (0.152%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62109.281 ms iter 0, gcam->neg = 33 after 52 iterations, nbhd size=4, neg = 0 0543: dt=0.720000, rms=0.374 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 31 after 44 iterations, nbhd size=4, neg = 0 0544: dt=0.720000, rms=0.374 (0.059%), neg=0, invalid=766 iter 0, gcam->neg = 52 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30016.816 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.003 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0545: dt=0.720000, rms=0.374 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.374, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62216.953 ms iter 0, gcam->neg = 29 after 52 iterations, nbhd size=4, neg = 0 0546: dt=0.666667, rms=0.374 (0.040%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62633.438 ms iter 0, gcam->neg = 26 after 71 iterations, nbhd size=4, neg = 0 0547: dt=1.008000, rms=0.374 (0.081%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62094.902 ms iter 0, gcam->neg = 23 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30410.635 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0548: dt=0.432000, rms=0.374 (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=0.374, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62283.051 ms iter 0, gcam->neg = 8 after 18 iterations, nbhd size=2, neg = 0 0549: dt=0.064000, rms=0.374 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62521.312 ms iter 0, gcam->neg = 17 after 33 iterations, nbhd size=3, neg = 0 0550: dt=0.203488, rms=0.374 (0.065%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62145.461 ms iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0551: dt=0.112000, rms=0.373 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 31 iterations, nbhd size=3, neg = 0 0552: dt=0.112000, rms=0.373 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 79 iterations, nbhd size=2, neg = 0 0553: dt=0.112000, rms=0.373 (0.056%), neg=0, invalid=766 iter 0, gcam->neg = 34 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29996.020 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0554: dt=0.112000, rms=0.373 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.373, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62194.168 ms iter 0, gcam->neg = 6 after 25 iterations, nbhd size=3, neg = 0 0555: dt=0.028000, rms=0.373 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62317.789 ms iter 0, gcam->neg = 25 after 40 iterations, nbhd size=4, neg = 0 0556: dt=0.259804, rms=0.373 (0.104%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62479.113 ms iter 0, gcam->neg = 14 after 29 iterations, nbhd size=3, neg = 0 0557: dt=0.096000, rms=0.373 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 18 iterations, nbhd size=2, neg = 0 0558: dt=0.096000, rms=0.372 (0.039%), neg=0, invalid=766 iter 0, gcam->neg = 16 after 36 iterations, nbhd size=4, neg = 0 0559: dt=0.096000, rms=0.372 (0.063%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 89 iterations, nbhd size=3, neg = 0 0560: dt=0.096000, rms=0.372 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 35 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29985.855 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0561: dt=0.096000, rms=0.372 (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=0.371, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75929.570 ms 0562: dt=0.000060, rms=0.371 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62150.484 ms 0563: dt=0.000438, rms=0.371 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62129.074 ms 0564: dt=0.001750, rms=0.371 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62303.027 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0565: dt=0.001250, rms=0.371 (0.005%), neg=0, invalid=766 0566: dt=0.001250, rms=0.371 (0.005%), neg=0, invalid=766 0567: dt=0.001250, rms=0.371 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 30380.982 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (-0.081%) ---------- unfolding failed - restoring original position -------------------- 0568: dt=0.001250, rms=0.371 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.371, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62124.363 ms iter 0, gcam->neg = 84 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.002, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 29848.281 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.002 (0.031%) gcamFindOptimalTimeStep: Complete in 28277.215 ms iter 2, dt=0.000000: new neg 0, old_neg 1, delta 1, rms=0.002 (12.467%) 0569: dt=0.064000, rms=0.370 (0.338%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62538.180 ms 0570: dt=0.000109, rms=0.370 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0571: dt=0.000109, rms=0.370 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0572: dt=0.000109, rms=0.370 (0.001%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0573: dt=0.000109, rms=0.370 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0574: dt=0.000109, rms=0.370 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0575: dt=0.000109, rms=0.370 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0576: dt=0.000109, rms=0.370 (0.002%), neg=0, invalid=766 0577: dt=0.000109, rms=0.370 (0.003%), neg=0, invalid=766 0578: dt=0.000109, rms=0.370 (0.003%), neg=0, invalid=766 0579: dt=0.000109, rms=0.370 (0.003%), neg=0, invalid=766 0580: dt=0.000109, rms=0.370 (0.003%), neg=0, invalid=766 0581: dt=0.000109, rms=0.370 (0.003%), neg=0, invalid=766 0582: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0583: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0584: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0585: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0586: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0587: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0588: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0589: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0590: dt=0.000109, rms=0.370 (0.004%), neg=0, invalid=766 0591: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 0592: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 0593: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 0594: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 0595: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 0596: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 0597: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 0598: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 12 iterations, nbhd size=2, neg = 0 0599: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0600: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0601: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0602: dt=0.000109, rms=0.370 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62606.781 ms iter 0, gcam->neg = 96 after 56 iterations, nbhd size=2, neg = 0 0603: dt=0.085500, rms=0.368 (0.351%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62078.883 ms 0604: dt=0.000438, rms=0.368 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0605: dt=0.000438, rms=0.368 (0.002%), neg=0, invalid=766 0606: dt=0.000438, rms=0.368 (0.003%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0607: dt=0.000438, rms=0.368 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0608: dt=0.000438, rms=0.368 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0609: dt=0.000438, rms=0.368 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0610: dt=0.000438, rms=0.368 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0611: dt=0.000438, rms=0.368 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0612: dt=0.000438, rms=0.368 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0613: dt=0.000438, rms=0.368 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 25 iterations, nbhd size=4, neg = 0 0614: dt=0.000438, rms=0.368 (0.010%), neg=0, invalid=766 0615: dt=0.000438, rms=0.368 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 26 iterations, nbhd size=4, neg = 0 0616: dt=0.000438, rms=0.368 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 17 iterations, nbhd size=2, neg = 0 0617: dt=0.000438, rms=0.368 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, neg = 0 0618: dt=0.000438, rms=0.368 (0.012%), neg=0, invalid=766 0619: dt=0.000438, rms=0.368 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0620: dt=0.000438, rms=0.368 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0621: dt=0.000438, rms=0.368 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 24 iterations, nbhd size=4, neg = 0 0622: dt=0.000438, rms=0.368 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62194.949 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0623: dt=0.001750, rms=0.368 (0.006%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.368, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61998.867 ms 0624: dt=0.000438, rms=0.368 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62101.410 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0625: dt=0.001750, rms=0.368 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62395.875 ms iter 0, gcam->neg = 26 after 23 iterations, nbhd size=3, neg = 0 0626: dt=0.019674, rms=0.367 (0.071%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62082.102 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0627: dt=0.000750, rms=0.367 (0.003%), neg=0, invalid=766 0628: dt=0.000750, rms=0.367 (0.003%), neg=0, invalid=766 0629: dt=0.000750, rms=0.367 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0630: dt=0.000750, rms=0.367 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0631: dt=0.000750, rms=0.367 (0.009%), neg=0, invalid=766 0632: dt=0.000750, rms=0.367 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 19 iterations, nbhd size=3, neg = 0 0633: dt=0.000750, rms=0.367 (0.012%), neg=0, invalid=766 0634: dt=0.000750, rms=0.367 (0.013%), neg=0, invalid=766 0635: dt=0.000750, rms=0.367 (0.015%), neg=0, invalid=766 0636: dt=0.000750, rms=0.367 (0.016%), neg=0, invalid=766 0637: dt=0.000750, rms=0.367 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 14 iterations, nbhd size=2, neg = 0 0638: dt=0.000750, rms=0.367 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 23 iterations, nbhd size=3, neg = 0 0639: dt=0.000750, rms=0.367 (0.017%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0640: dt=0.000750, rms=0.367 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, neg = 0 0641: dt=0.000750, rms=0.367 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0642: dt=0.000750, rms=0.367 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0643: dt=0.000750, rms=0.366 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0644: dt=0.000750, rms=0.366 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 16 iterations, nbhd size=2, neg = 0 0645: dt=0.000750, rms=0.366 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0646: dt=0.000750, rms=0.366 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0647: dt=0.000750, rms=0.366 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0648: dt=0.000750, rms=0.366 (0.020%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.366, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62155.582 ms iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0649: dt=0.006000, rms=0.366 (0.027%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62176.312 ms iter 0, gcam->neg = 4 after 20 iterations, nbhd size=3, neg = 0 0650: dt=0.004990, rms=0.366 (0.021%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 5 iterations, nbhd size=1, neg = 0 0651: dt=0.004990, rms=0.366 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 19 iterations, nbhd size=2, neg = 0 0652: dt=0.004990, rms=0.366 (0.040%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 37 iterations, nbhd size=4, neg = 0 0653: dt=0.004990, rms=0.366 (0.049%), neg=0, invalid=766 iter 0, gcam->neg = 12 after 8 iterations, nbhd size=1, neg = 0 0654: dt=0.004990, rms=0.365 (0.072%), neg=0, invalid=766 iter 0, gcam->neg = 11 after 7 iterations, nbhd size=1, neg = 0 0655: dt=0.004990, rms=0.365 (0.084%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 18 iterations, nbhd size=3, neg = 0 0656: dt=0.004990, rms=0.365 (0.092%), neg=0, invalid=766 iter 0, gcam->neg = 15 after 7 iterations, nbhd size=1, neg = 0 0657: dt=0.004990, rms=0.364 (0.101%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 19 iterations, nbhd size=2, neg = 0 0658: dt=0.004990, rms=0.364 (0.103%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 29 iterations, nbhd size=4, neg = 0 0659: dt=0.004990, rms=0.363 (0.104%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 14 iterations, nbhd size=2, neg = 0 0660: dt=0.004990, rms=0.363 (0.112%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 14 iterations, nbhd size=2, neg = 0 0661: dt=0.004990, rms=0.363 (0.112%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 29 iterations, nbhd size=4, neg = 0 0662: dt=0.004990, rms=0.362 (0.104%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 7 iterations, nbhd size=1, neg = 0 0663: dt=0.004990, rms=0.362 (0.111%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 6 iterations, nbhd size=1, neg = 0 0664: dt=0.004990, rms=0.362 (0.107%), 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=0.361, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62072.852 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0665: dt=0.001750, rms=0.361 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62599.363 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0666: dt=0.006000, rms=0.361 (0.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62129.996 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0667: dt=0.004000, rms=0.361 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0668: dt=0.004000, rms=0.361 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0669: dt=0.004000, rms=0.361 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 18 iterations, nbhd size=2, neg = 0 0670: dt=0.004000, rms=0.361 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 15 iterations, nbhd size=2, neg = 0 0671: dt=0.004000, rms=0.361 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 0 iterations, nbhd size=0, neg = 0 0672: dt=0.004000, rms=0.360 (0.052%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 31 iterations, nbhd size=4, neg = 0 0673: dt=0.004000, rms=0.360 (0.056%), neg=0, invalid=766 iter 0, gcam->neg = 10 after 6 iterations, nbhd size=1, neg = 0 0674: dt=0.004000, rms=0.360 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 17 after 21 iterations, nbhd size=3, neg = 0 0675: dt=0.004000, rms=0.360 (0.065%), neg=0, invalid=766 iter 0, gcam->neg = 21 after 15 iterations, nbhd size=2, neg = 0 0676: dt=0.004000, rms=0.360 (0.067%), neg=0, invalid=766 iter 0, gcam->neg = 22 after 19 iterations, nbhd size=2, neg = 0 0677: dt=0.004000, rms=0.359 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 20 after 22 iterations, nbhd size=3, neg = 0 0678: dt=0.004000, rms=0.359 (0.070%), neg=0, invalid=766 iter 0, gcam->neg = 26 after 13 iterations, nbhd size=2, neg = 0 0679: dt=0.004000, rms=0.359 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 19 iterations, nbhd size=2, neg = 0 0680: dt=0.004000, rms=0.359 (0.069%), neg=0, invalid=766 iter 0, gcam->neg = 27 after 21 iterations, nbhd size=3, neg = 0 0681: dt=0.004000, rms=0.358 (0.069%), neg=0, invalid=766 iter 0, gcam->neg = 30 after 36 iterations, nbhd size=4, neg = 0 0682: dt=0.004000, rms=0.358 (0.061%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.358, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62217.629 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0683: dt=0.001750, rms=0.358 (0.006%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62114.184 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0684: dt=0.001750, rms=0.358 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0685: dt=0.001750, rms=0.358 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0686: dt=0.001750, rms=0.358 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0687: dt=0.001750, rms=0.358 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 15 iterations, nbhd size=2, neg = 0 0688: dt=0.001750, rms=0.358 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0689: dt=0.001750, rms=0.358 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0690: dt=0.001750, rms=0.358 (0.025%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 28 iterations, nbhd size=4, neg = 0 0691: dt=0.001750, rms=0.358 (0.019%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0692: dt=0.001750, rms=0.358 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 6 iterations, nbhd size=1, neg = 0 0693: dt=0.001750, rms=0.357 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 12 iterations, nbhd size=2, neg = 0 0694: dt=0.001750, rms=0.357 (0.030%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is: 12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Fri Nov 18 11:23:25 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s avo0260 exited with ERRORS at Fri Nov 18 11:23:26 EST 2011 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting