Tue Feb 18 12:46:31 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli /usr/local/freesurfer/bin/recon-all -i /media/opbg/dati/Baldacchini/pazienti/CHIACCHIERARELLIRICCARDO30102013/chiacchierarelli/strutturale_chiacchierarelli.nii -s chiacchierarelli subjid chiacchierarelli setenv SUBJECTS_DIR /media/opbg/dati/Baldacchini/pazienti/io_prova FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 62584 maxlocks unlimited maxsignal 62584 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8061960 2667232 5394728 0 413696 1449364 -/+ buffers/cache: 804172 7257788 Swap: 976892 0 976892 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli mri_convert /media/opbg/dati/Baldacchini/pazienti/CHIACCHIERARELLIRICCARDO30102013/chiacchierarelli/strutturale_chiacchierarelli.nii /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig/001.mgz mri_convert /media/opbg/dati/Baldacchini/pazienti/CHIACCHIERARELLIRICCARDO30102013/chiacchierarelli/strutturale_chiacchierarelli.nii /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/opbg/dati/Baldacchini/pazienti/CHIACCHIERARELLIRICCARDO30102013/chiacchierarelli/strutturale_chiacchierarelli.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.011658, -0.999932, -4.08344e-05) j_ras = (0.0379622, 0.000401795, 0.999279) k_ras = (0.999211, 0.0116511, -0.0379643) writing to /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig/001.mgz... #------------------------------------------ Started at Tue Feb 18 12:46:31 CET 2014 Ended at Tue Feb 18 12:46:41 CET 2014 #@#%# recon-all-run-time-hours 0.003 recon-all -s chiacchierarelli finished without error at Tue Feb 18 12:46:41 CET 2014 New invocation of recon-all Tue Feb 18 12:46:41 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli /usr/local/freesurfer/bin/recon-all -s chiacchierarelli -all subjid chiacchierarelli setenv SUBJECTS_DIR /media/opbg/dati/Baldacchini/pazienti/io_prova FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 62584 maxlocks unlimited maxsignal 62584 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8061960 2883848 5178112 0 447092 1630972 -/+ buffers/cache: 805784 7256176 Swap: 976892 0 976892 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/18-11:46:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Tue Feb 18 12:46:44 CET 2014 Found 1 runs /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/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 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig/001.mgz /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/rawavg.mgz /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli mri_convert /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/rawavg.mgz /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig.mgz --conform mri_convert /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/rawavg.mgz /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.011658, -0.999932, -4.08344e-05) j_ras = (0.0379622, 0.000401795, 0.999279) k_ras = (0.999211, 0.0116511, -0.0379643) Original Data has (0.820312, 0.820312, 0.799911) mm size and (256, 256, 160) 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 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig.mgz... mri_add_xform_to_header -c /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/transforms/talairach.xfm /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig.mgz /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Feb 18 12:46:52 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Feb 18 12:48:03 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Tue Feb 18 12:48:03 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri /usr/local/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Tue Feb 18 12:48:42 CET 2014 tmpdir is transforms/tmp.talairach.5677 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_convert orig_nu.mgz transforms/tmp.talairach.5677/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.5677/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.51457e-08, 6.33299e-08) j_ras = (-9.31323e-08, -3.20142e-10, -1) k_ras = (-3.07336e-08, 1, -4.36557e-10) writing to transforms/tmp.talairach.5677/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.5677/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install the separate libperl4-corelibs-perl package. It is being used at /usr/local/freesurfer/mni/bin/mritotal, line 460. Tue Feb 18 12:48:53 CET 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Feb 18 12:48:54 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.1051, pval=0.0051 >= threshold=0.0050) #-------------------------------------------- #@# Nu Intensity Correction Tue Feb 18 12:48:54 CET 2014 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Tue Feb 18 12:48:54 CET 2014 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.5835 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5835/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5835/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.51457e-08, 6.33299e-08) j_ras = (-9.31323e-08, -3.20142e-10, -1) k_ras = (-3.07336e-08, 1, -4.36557e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5835/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Feb 18 12:48:56 CET 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.5835/nu0.mnc ./tmp.mri_nu_correct.mni.5835/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5835/0/ [opbg@opbg:/media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/] [2014-02-18 12:48:56] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5835/0/ ./tmp.mri_nu_correct.mni.5835/nu0.mnc ./tmp.mri_nu_correct.mni.5835/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 29 CV of field change: 0.000943607 [opbg@opbg:/media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/] [2014-02-18 12:49:10] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.5835/nu0.mnc ./tmp.mri_nu_correct.mni.5835/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Tue Feb 18 12:49:16 CET 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.5835/nu1.mnc ./tmp.mri_nu_correct.mni.5835/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5835/1/ [opbg@opbg:/media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/] [2014-02-18 12:49:16] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5835/1/ ./tmp.mri_nu_correct.mni.5835/nu1.mnc ./tmp.mri_nu_correct.mni.5835/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 23 CV of field change: 0.000966336 [opbg@opbg:/media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/] [2014-02-18 12:49:27] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.5835/nu1.mnc ./tmp.mri_nu_correct.mni.5835/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.5835/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5835/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.5835/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5835/ones.mgz sysname Linux hostname opbg machine x86_64 user opbg input ./tmp.mri_nu_correct.mni.5835/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5835/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.5835/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5835/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5835/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5835/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5835/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5835/input.mean.dat sysname Linux hostname opbg machine x86_64 user opbg UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5835/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5835/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5835/ones.mgz --i ./tmp.mri_nu_correct.mni.5835/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5835/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5835/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5835/ones.mgz --i ./tmp.mri_nu_correct.mni.5835/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5835/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5835/output.mean.dat sysname Linux hostname opbg machine x86_64 user opbg UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5835/ones.mgz Loading ./tmp.mri_nu_correct.mni.5835/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5835/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5835/nu2.mnc ./tmp.mri_nu_correct.mni.5835/nu2.mnc mul .97610032375799531498 Saving result to './tmp.mri_nu_correct.mni.5835/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5835/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.5835/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.5835/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -2.51457e-08, 6.33299e-08) j_ras = (-9.31323e-08, -3.20142e-10, -1) k_ras = (-3.07336e-08, 1, -4.36557e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 4 seconds. mapping (44, 101) to ( 3, 110) Tue Feb 18 12:49:58 CET 2014 mri_nu_correct.mni done mri_add_xform_to_header -c /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Feb 18 12:49:58 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.551 -0.027 -0.154 -18.871; 0.011 1.474 -0.141 25.491; 0.170 0.160 1.685 -33.351; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 98 white matter peak found at 112 gm peak at 84 (84), valley at 47 (47) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 104 gm peak at 78 (78), valley at 37 (37) csf peak at 39, setting threshold to 65 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 23 seconds. #-------------------------------------------- #@# Skull Stripping Tue Feb 18 12:51:22 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (81, 71, 64) --> (178, 235, 187) using (113, 126, 126) as brain centroid... mean wm in atlas = 126, using box (101,106,111) --> (124, 146,141) to find MRI wm before smoothing, mri peak at 93 after smoothing, mri peak at 89, scaling input intensities by 1.416 scaling channel 0 by 1.41573 initial log_p = -5.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -5.230947 @ (9.091, -9.091, 9.091) max log p = -5.204967 @ (-4.545, -4.545, -4.545) max log p = -5.204967 @ (0.000, 0.000, 0.000) max log p = -5.204967 @ (0.000, 0.000, 0.000) max log p = -5.199748 @ (-0.568, 5.114, -3.977) max log p = -5.195286 @ (-1.420, -1.420, -0.852) Found translation: (2.6, -9.9, -0.3): log p = -5.195 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.9, old_max_log_p =-5.2 (thresh=-5.2) 1.101 -0.469 0.309 7.007; 0.550 0.762 -0.803 49.435; 0.114 0.853 0.888 -115.901; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.7, old_max_log_p =-4.9 (thresh=-4.9) 1.366 0.178 -0.661 6.540; -0.472 1.313 -0.623 98.077; 0.496 0.761 1.229 -182.328; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.5, old_max_log_p =-4.7 (thresh=-4.7) 0.921 0.820 -0.910 18.242; -1.196 1.459 0.105 83.579; 0.880 0.609 1.553 -272.825; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.5) 0.921 0.820 -0.910 18.242; -1.398 1.470 -0.106 134.270; 0.716 0.794 1.553 -274.483; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.5, old_max_log_p =-4.5 (thresh=-4.4) 0.921 0.820 -0.910 18.242; -1.398 1.470 -0.106 134.270; 0.716 0.794 1.553 -274.483; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.4, old_max_log_p =-4.5 (thresh=-4.4) 0.914 0.809 -0.976 26.702; -1.424 1.497 -0.108 134.516; 0.761 0.837 1.550 -283.253; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.914 0.809 -0.976 26.702; -1.424 1.497 -0.108 134.516; 0.775 0.853 1.579 -290.552; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.942 0.745 -0.954 28.181; -1.419 1.551 -0.142 131.459; 0.790 0.869 1.609 -297.988; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.947 0.752 -0.939 24.875; -1.418 1.550 -0.142 132.328; 0.782 0.862 1.617 -296.667; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 9 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.947 0.752 -0.939 24.875; -1.418 1.550 -0.142 132.328; 0.782 0.862 1.617 -296.667; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.94728 0.75154 -0.93927 24.87470; -1.41769 1.54976 -0.14194 132.32759; 0.78178 0.86208 1.61654 -296.66690; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.94728 0.75154 -0.93927 24.87470; -1.41769 1.54976 -0.14194 132.32759; 0.78178 0.86208 1.61654 -296.66690; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.947 0.752 -0.939 24.875; -1.418 1.550 -0.142 132.328; 0.782 0.862 1.617 -296.667; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.4 (old=-5.4) transform before final EM align: 0.947 0.752 -0.939 24.875; -1.418 1.550 -0.142 132.328; 0.782 0.862 1.617 -296.667; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.94728 0.75154 -0.93927 24.87470; -1.41769 1.54976 -0.14194 132.32759; 0.78178 0.86208 1.61654 -296.66690; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.94728 0.75154 -0.93927 24.87470; -1.41769 1.54976 -0.14194 132.32759; 0.78178 0.86208 1.61654 -296.66690; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 014: -log(p) = 4.8 tol 0.000000 final transform: 0.947 0.752 -0.939 24.875; -1.418 1.550 -0.142 132.328; 0.782 0.862 1.617 -296.667; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 27 minutes and 16 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=128 y=128 z=121 r=59 first estimation of the main basin volume: 871064 voxels Looking for seedpoints 2 found in the cerebellum 4 found in the rest of the brain global maximum in x=119, y=114, z=126, 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=6801138132 voxels, voxel volume =1.000 = 6801138132 mmm3 = 6801138.176 cm3 done. PostAnalyze...Basin Prior 370 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=125,y=123, z=121, r=5855 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 26483 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1050235652 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1042875339 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=58, CSF_MAX=94 , nb = 1096624392 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1063779506 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1060536512 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 5, 42, 87 after analyzing : 4, 29, 42, 43 RIGHT_CER before analyzing : 4, 7, 44, 64 after analyzing : 4, 31, 44, 39 LEFT_CER before analyzing : 4, 13, 60, 70 after analyzing : 4, 44, 60, 50 RIGHT_BRAIN before analyzing : 94, 74, 58, 88 after analyzing : 68, 74, 74, 77 LEFT_BRAIN before analyzing : 4, 11, 78, 95 after analyzing : 4, 55, 78, 65 OTHER before analyzing : 4, 5, 42, 87 after analyzing : 4, 29, 42, 43 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...61 iterations *********************VALIDATION********************* curvature mean = -0.020, std = 0.025 curvature mean = 41.059, std = 5.941 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 16.21, sigma = 41.56 after rotation: sse = 16.21, sigma = 41.56 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 23.06, its var is 42.88 before Erosion-Dilatation 27.41% of inacurate vertices after Erosion-Dilatation 44.72% of inacurate vertices 48.97% of 'positive' inacurate vertices 51.03% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 337425 voxels, voxel volume = 1.000 mm3 = 337425 mmm3 = 337.425 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Tue Feb 18 13:18:54 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=31.1 skull bounding box = (82, 79, 76) --> (173, 152, 169) using (112, 103, 123) as brain centroid... mean wm in atlas = 107, using box (101,94,112) --> (123, 111,134) to find MRI wm before smoothing, mri peak at 91 after smoothing, mri peak at 89, scaling input intensities by 1.202 scaling channel 0 by 1.20225 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.603791 @ (9.091, 9.091, -45.455) max log p = -4.603791 @ (0.000, 0.000, 0.000) max log p = -4.599498 @ (6.818, 2.273, 15.909) max log p = -4.582170 @ (3.409, -1.136, -3.409) max log p = -4.571595 @ (0.568, -1.705, 0.568) max log p = -4.571595 @ (0.000, 0.000, 0.000) Found translation: (19.9, 8.5, -32.4): log p = -4.572 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.6 (thresh=-4.6) 0.954 0.091 0.781 -91.250; 0.287 1.103 -0.479 9.411; -0.732 0.551 0.830 4.291; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.4 (thresh=-4.4) 1.349 0.423 0.582 -165.317; -0.335 1.463 -0.287 18.878; -0.636 0.126 1.384 -8.585; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.2, old_max_log_p =-4.2 (thresh=-4.2) 1.452 0.208 0.430 -132.548; -0.146 1.503 -0.233 -16.130; -0.489 0.193 1.557 -57.070; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2) 1.376 0.231 0.629 -151.526; -0.157 1.616 -0.250 -26.255; -0.624 0.152 1.376 -12.291; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.376 0.231 0.629 -151.526; -0.157 1.616 -0.250 -26.255; -0.624 0.152 1.376 -12.291; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.342 0.376 0.559 -155.772; -0.345 1.620 -0.215 -8.065; -0.583 0.050 1.464 -10.469; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.342 0.376 0.559 -155.772; -0.345 1.620 -0.215 -8.065; -0.583 0.050 1.464 -10.469; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.339 0.375 0.557 -155.110; -0.344 1.615 -0.214 -7.619; -0.581 0.050 1.459 -10.063; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.339 0.375 0.557 -155.110; -0.344 1.615 -0.214 -7.619; -0.580 0.050 1.457 -9.927; 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 1.33853 0.37548 0.55728 -155.10953; -0.34414 1.61450 -0.21441 -7.61904; -0.58041 0.04954 1.45698 -9.92741; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.33853 0.37548 0.55728 -155.10953; -0.34414 1.61450 -0.21441 -7.61904; -0.58041 0.04954 1.45698 -9.92741; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.339 0.375 0.557 -155.110; -0.344 1.615 -0.214 -7.619; -0.580 0.050 1.457 -9.927; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.1 (old=-4.7) transform before final EM align: 1.339 0.375 0.557 -155.110; -0.344 1.615 -0.214 -7.619; -0.580 0.050 1.457 -9.927; 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 1.33853 0.37548 0.55728 -155.10953; -0.34414 1.61450 -0.21441 -7.61904; -0.58041 0.04954 1.45698 -9.92741; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.33853 0.37548 0.55728 -155.10953; -0.34414 1.61450 -0.21441 -7.61904; -0.58041 0.04954 1.45698 -9.92741; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 4.5 tol 0.000000 final transform: 1.339 0.375 0.557 -155.110; -0.344 1.615 -0.214 -7.619; -0.580 0.050 1.457 -9.927; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 19 minutes and 0 seconds. #-------------------------------------- #@# CA Normalize Tue Feb 18 13:37:55 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=30.1 skull bounding box = (82, 79, 76) --> (173, 152, 170) using (112, 103, 123) as brain centroid... mean wm in atlas = 107, using box (101,94,112) --> (123, 111,134) to find MRI wm before smoothing, mri peak at 91 after smoothing, mri peak at 89, scaling input intensities by 1.202 scaling channel 0 by 1.20225 using 244171 sample points... INFO: compute sample coordinates transform 1.339 0.375 0.557 -155.110; -0.344 1.615 -0.214 -7.619; -0.580 0.050 1.457 -9.927; 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 (104, 83, 77) --> (170, 158, 180) finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (78, 79, 73) --> (139, 147, 174) finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 130, 90) --> (157, 161, 124) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (96, 129, 82) --> (130, 153, 117) finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (109, 126, 104) --> (132, 168, 128) Brain_Stem: limiting intensities to 147.0 --> 255.0 4 of 5 (80.0%) samples deleted using 5 total control points for intensity normalization... bias field = 0.533 +- 0.000 0 of 1 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (104, 83, 77) --> (170, 158, 180) Left_Cerebral_White_Matter: limiting intensities to 49.0 --> 136.0 1 of 15 (6.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (78, 79, 73) --> (139, 147, 174) Right_Cerebral_White_Matter: limiting intensities to 54.0 --> 136.0 19 of 27 (70.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 130, 90) --> (157, 161, 124) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (96, 129, 82) --> (130, 153, 117) Right_Cerebellum_White_Matter: limiting intensities to 37.0 --> 136.0 0 of 14 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (109, 126, 104) --> (132, 168, 128) Brain_Stem: limiting intensities to 56.0 --> 136.0 10 of 17 (58.8%) samples deleted using 73 total control points for intensity normalization... bias field = 1.821 +- 0.144 0 of 43 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (104, 83, 77) --> (170, 158, 180) Left_Cerebral_White_Matter: limiting intensities to 107.0 --> 254.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (78, 79, 73) --> (139, 147, 174) Right_Cerebral_White_Matter: limiting intensities to 125.0 --> 254.0 4 of 7 (57.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (125, 130, 90) --> (157, 161, 124) finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (96, 129, 82) --> (130, 153, 117) finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (109, 126, 104) --> (132, 168, 128) using 14 total control points for intensity normalization... bias field = 0.957 +- 0.088 0 of 10 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 14 seconds. #-------------------------------------- #@# CA Reg Tue Feb 18 13:39:09 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 3.91 (predicted orig area = 2.0) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.414, neg=0, invalid=96777 0001: dt=129.472000, rms=1.119 (20.867%), neg=0, invalid=96777 0002: dt=129.472000, rms=1.038 (7.251%), neg=0, invalid=96777 0003: dt=129.472000, rms=1.003 (3.363%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.985 (1.825%), neg=0, invalid=96777 0005: dt=443.904000, rms=0.937 (4.864%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.937 (0.040%), neg=0, invalid=96777 0007: dt=32.368000, rms=0.935 (0.173%), neg=0, invalid=96777 0008: dt=32.368000, rms=0.932 (0.284%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.929 (0.339%), neg=0, invalid=96777 0010: dt=32.368000, rms=0.926 (0.356%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.923 (0.329%), neg=0, invalid=96777 0012: dt=32.368000, rms=0.920 (0.264%), neg=0, invalid=96777 0013: dt=32.368000, rms=0.917 (0.335%), neg=0, invalid=96777 0014: dt=32.368000, rms=0.912 (0.530%), neg=0, invalid=96777 0015: dt=32.368000, rms=0.907 (0.535%), neg=0, invalid=96777 0016: dt=32.368000, rms=0.904 (0.386%), neg=0, invalid=96777 0017: dt=32.368000, rms=0.901 (0.283%), neg=0, invalid=96777 0018: dt=32.368000, rms=0.900 (0.207%), neg=0, invalid=96777 0019: dt=32.368000, rms=0.898 (0.138%), neg=0, invalid=96777 0020: dt=32.368000, rms=0.897 (0.143%), neg=0, invalid=96777 0021: dt=32.368000, rms=0.895 (0.248%), neg=0, invalid=96777 0022: dt=32.368000, rms=0.892 (0.306%), neg=0, invalid=96777 0023: dt=32.368000, rms=0.889 (0.321%), neg=0, invalid=96777 0024: dt=32.368000, rms=0.887 (0.303%), neg=0, invalid=96777 0025: dt=32.368000, rms=0.885 (0.167%), neg=0, invalid=96777 0026: dt=32.368000, rms=0.884 (0.092%), neg=0, invalid=96777 0027: dt=32.368000, rms=0.883 (0.090%), neg=0, invalid=96777 0028: dt=443.904000, rms=0.875 (0.935%), neg=0, invalid=96777 0029: dt=32.368000, rms=0.875 (0.023%), neg=0, invalid=96777 0030: dt=32.368000, rms=0.875 (0.017%), neg=0, invalid=96777 0031: dt=32.368000, rms=0.875 (-0.044%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.875, neg=0, invalid=96777 0032: dt=129.472000, rms=0.869 (0.646%), neg=0, invalid=96777 0033: dt=110.976000, rms=0.869 (0.049%), neg=0, invalid=96777 0034: dt=110.976000, rms=0.867 (0.168%), neg=0, invalid=96777 0035: dt=110.976000, rms=0.865 (0.225%), neg=0, invalid=96777 0036: dt=110.976000, rms=0.864 (0.187%), neg=0, invalid=96777 0037: dt=110.976000, rms=0.861 (0.282%), neg=0, invalid=96777 0038: dt=110.976000, rms=0.859 (0.304%), neg=0, invalid=96777 0039: dt=110.976000, rms=0.856 (0.306%), neg=0, invalid=96777 0040: dt=110.976000, rms=0.853 (0.335%), neg=0, invalid=96777 0041: dt=110.976000, rms=0.851 (0.257%), neg=0, invalid=96777 0042: dt=110.976000, rms=0.849 (0.256%), neg=0, invalid=96777 0043: dt=110.976000, rms=0.846 (0.321%), neg=0, invalid=96777 0044: dt=110.976000, rms=0.844 (0.280%), neg=0, invalid=96777 0045: dt=110.976000, rms=0.843 (0.132%), neg=0, invalid=96777 0046: dt=110.976000, rms=0.842 (0.014%), neg=0, invalid=96777 0047: dt=110.976000, rms=0.841 (0.177%), neg=0, invalid=96777 0048: dt=110.976000, rms=0.839 (0.270%), neg=0, invalid=96777 0049: dt=110.976000, rms=0.837 (0.196%), neg=0, invalid=96777 0050: dt=110.976000, rms=0.837 (0.062%), neg=0, invalid=96777 0051: dt=110.976000, rms=0.836 (0.066%), neg=0, invalid=96777 0052: dt=110.976000, rms=0.835 (0.164%), neg=0, invalid=96777 0053: dt=110.976000, rms=0.832 (0.292%), neg=0, invalid=96777 0054: dt=110.976000, rms=0.830 (0.244%), neg=0, invalid=96777 0055: dt=110.976000, rms=0.830 (0.070%), neg=0, invalid=96777 0056: dt=110.976000, rms=0.829 (0.050%), neg=0, invalid=96777 0057: dt=129.472000, rms=0.828 (0.170%), neg=0, invalid=96777 0058: dt=129.472000, rms=0.828 (0.025%), neg=0, invalid=96777 0059: dt=129.472000, rms=0.828 (0.002%), neg=0, invalid=96777 0060: dt=129.472000, rms=0.828 (-0.006%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.842, neg=0, invalid=96777 0061: dt=15.552000, rms=0.841 (0.086%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.839 (0.302%), neg=0, invalid=96777 0063: dt=124.416000, rms=0.830 (1.036%), neg=0, invalid=96777 0064: dt=15.552000, rms=0.829 (0.157%), neg=0, invalid=96777 0065: dt=15.552000, rms=0.826 (0.383%), neg=0, invalid=96777 0066: dt=15.552000, rms=0.822 (0.444%), neg=0, invalid=96777 0067: dt=15.552000, rms=0.822 (-0.062%), neg=0, invalid=96777 0068: dt=0.000000, rms=0.822 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.822, neg=0, invalid=96777 0069: dt=25.920000, rms=0.821 (0.174%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.814 (0.749%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.813 (0.122%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.811 (0.304%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.808 (0.327%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.806 (0.306%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.803 (0.412%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.799 (0.500%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.795 (0.455%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.793 (0.271%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.791 (0.208%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.790 (0.136%), neg=0, invalid=96777 0081: dt=36.288000, rms=0.788 (0.248%), neg=0, invalid=96777 0082: dt=36.288000, rms=0.788 (0.054%), neg=0, invalid=96777 0083: dt=36.288000, rms=0.786 (0.169%), neg=0, invalid=96777 0084: dt=36.288000, rms=0.785 (0.179%), neg=0, invalid=96777 0085: dt=36.288000, rms=0.783 (0.259%), neg=0, invalid=96777 0086: dt=36.288000, rms=0.781 (0.262%), neg=0, invalid=96777 0087: dt=36.288000, rms=0.779 (0.236%), neg=0, invalid=96777 0088: dt=36.288000, rms=0.777 (0.224%), neg=0, invalid=96777 0089: dt=36.288000, rms=0.775 (0.223%), neg=0, invalid=96777 0090: dt=36.288000, rms=0.774 (0.168%), neg=0, invalid=96777 0091: dt=36.288000, rms=0.773 (0.153%), neg=0, invalid=96777 0092: dt=36.288000, rms=0.772 (0.182%), neg=0, invalid=96777 0093: dt=18.144000, rms=0.772 (0.005%), neg=0, invalid=96777 0094: dt=18.144000, rms=0.771 (0.045%), neg=0, invalid=96777 0095: dt=18.144000, rms=0.771 (0.042%), neg=0, invalid=96777 0096: dt=36.288000, rms=0.771 (0.045%), neg=0, invalid=96777 0097: dt=145.152000, rms=0.770 (0.014%), neg=0, invalid=96777 0098: dt=36.288000, rms=0.770 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.816, neg=0, invalid=96777 0099: dt=0.000000, rms=0.816 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.816, neg=0, invalid=96777 0100: dt=0.000000, rms=0.816 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.950, neg=0, invalid=96777 0101: dt=1.008000, rms=0.944 (0.645%), neg=0, invalid=96777 0102: dt=1.008000, rms=0.939 (0.484%), neg=0, invalid=96777 0103: dt=1.008000, rms=0.936 (0.325%), neg=0, invalid=96777 0104: dt=1.008000, rms=0.934 (0.234%), neg=0, invalid=96777 0105: dt=1.008000, rms=0.933 (0.142%), neg=0, invalid=96777 0106: dt=1.008000, rms=0.931 (0.125%), neg=0, invalid=96777 0107: dt=1.008000, rms=0.931 (0.023%), neg=0, invalid=96777 0108: dt=1.008000, rms=0.931 (0.012%), neg=0, invalid=96777 0109: dt=1.008000, rms=0.931 (0.005%), neg=0, invalid=96777 0110: dt=1.008000, rms=0.931 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.931, neg=0, invalid=96777 0111: dt=0.015750, rms=0.931 (0.000%), neg=0, invalid=96777 0112: dt=0.006750, rms=0.931 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.101, neg=0, invalid=96777 0113: dt=0.112000, rms=1.101 (0.004%), neg=0, invalid=96777 0114: dt=0.281250, rms=1.101 (0.020%), neg=0, invalid=96777 0115: dt=0.448000, rms=1.100 (0.084%), neg=0, invalid=96777 0116: dt=0.112000, rms=1.099 (0.038%), neg=0, invalid=96777 0117: dt=0.112000, rms=1.099 (0.039%), neg=0, invalid=96777 0118: dt=0.112000, rms=1.098 (0.068%), neg=0, invalid=96777 0119: dt=0.112000, rms=1.097 (0.086%), neg=0, invalid=96777 0120: dt=0.112000, rms=1.096 (0.087%), neg=0, invalid=96777 0121: dt=0.112000, rms=1.095 (0.091%), neg=0, invalid=96777 0122: dt=0.112000, rms=1.094 (0.077%), neg=0, invalid=96777 0123: dt=0.112000, rms=1.094 (0.063%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.094, neg=0, invalid=96777 0124: dt=0.448000, rms=1.089 (0.417%), neg=0, invalid=96777 0125: dt=0.448000, rms=1.087 (0.231%), neg=0, invalid=96777 0126: dt=0.448000, rms=1.085 (0.145%), neg=0, invalid=96777 0127: dt=0.448000, rms=1.083 (0.193%), neg=0, invalid=96777 0128: dt=0.448000, rms=1.083 (0.029%), neg=0, invalid=96777 0129: dt=0.448000, rms=1.082 (0.050%), neg=0, invalid=96777 0130: dt=0.448000, rms=1.081 (0.047%), neg=0, invalid=96777 0131: dt=1.280000, rms=1.081 (0.055%), neg=0, invalid=96777 0132: dt=0.448000, rms=1.081 (0.008%), neg=0, invalid=96777 0133: dt=0.448000, rms=1.081 (0.004%), neg=0, invalid=96777 0134: dt=0.448000, rms=1.081 (0.009%), neg=0, invalid=96777 0135: dt=0.448000, rms=1.081 (-0.017%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.942, neg=0, invalid=96777 0136: dt=0.028000, rms=0.940 (0.215%), neg=0, invalid=96777 0137: dt=0.028000, rms=0.938 (0.186%), neg=0, invalid=96777 0138: dt=0.028000, rms=0.937 (0.164%), neg=0, invalid=96777 0139: dt=0.014000, rms=0.936 (0.073%), neg=0, invalid=96777 0140: dt=0.014000, rms=0.935 (0.069%), neg=0, invalid=96777 0141: dt=0.028000, rms=0.934 (0.130%), neg=0, invalid=96777 0142: dt=0.028000, rms=0.933 (0.120%), neg=0, invalid=96777 0143: dt=0.007000, rms=0.933 (0.027%), neg=0, invalid=96777 0144: dt=0.007000, rms=0.933 (0.027%), neg=0, invalid=96777 0145: dt=0.007000, rms=0.932 (0.051%), neg=0, invalid=96777 0146: dt=0.007000, rms=0.931 (0.072%), neg=0, invalid=96777 0147: dt=0.007000, rms=0.931 (0.025%), neg=0, invalid=96777 0148: dt=0.007000, rms=0.931 (0.023%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.931, neg=0, invalid=96777 0149: dt=0.028000, rms=0.929 (0.206%), neg=0, invalid=96777 0150: dt=0.028000, rms=0.928 (0.165%), neg=0, invalid=96777 0151: dt=0.007000, rms=0.927 (0.034%), neg=0, invalid=96777 0152: dt=0.007000, rms=0.927 (0.064%), neg=0, invalid=96777 0153: dt=0.007000, rms=0.926 (0.088%), neg=0, invalid=96777 0154: dt=0.007000, rms=0.925 (0.107%), neg=0, invalid=96777 0155: dt=0.007000, rms=0.925 (0.024%), neg=0, invalid=96777 0156: dt=0.007000, rms=0.924 (0.023%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14022 (22) mri peak = 1.00000 (50) Right_Lateral_Ventricle (43): linear fit = 2.22 x + 0.0 (210 voxels, overlap=1.140) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (210 voxels, peak = 49), gca=33.0 gca peak = 0.24234 (100) mri peak = 0.04592 (81) gca peak = 0.19192 (97) mri peak = 0.10866 (93) gca peak = 0.24007 (63) mri peak = 0.05306 (61) gca peak = 0.29892 (64) mri peak = 0.06946 (94) gca peak = 0.12541 (104) mri peak = 0.07458 (94) Right_Cerebral_White_Matter (41): linear fit = 0.94 x + 0.0 (5367 voxels, overlap=0.747) Right_Cerebral_White_Matter (41): linear fit = 0.94 x + 0.0 (5367 voxels, peak = 98), gca=98.3 gca peak = 0.13686 (104) mri peak = 0.04369 (91) Left_Cerebral_White_Matter (2): linear fit = 0.94 x + 0.0 (5286 voxels, overlap=0.668) Left_Cerebral_White_Matter (2): linear fit = 0.94 x + 0.0 (5286 voxels, peak = 98), gca=98.3 gca peak = 0.11691 (63) mri peak = 0.04452 (56) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (732 voxels, overlap=0.526) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (732 voxels, peak = 68), gca=67.7 gca peak = 0.13270 (63) mri peak = 0.05189 (61) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (745 voxels, overlap=0.825) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (745 voxels, peak = 65), gca=64.6 gca peak = 0.15182 (70) mri peak = 0.11502 (99) gca peak = 0.14251 (76) mri peak = 0.08425 (75) gca peak = 0.12116 (60) mri peak = 0.03267 (61) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (1858 voxels, overlap=0.322) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (1858 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.04654 (78) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (2031 voxels, overlap=0.017) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (2031 voxels, peak = 77), gca=76.6 gca peak = 0.22684 (88) mri peak = 0.05417 (65) Left_Cerebellum_White_Matter (7): linear fit = 0.79 x + 0.0 (774 voxels, overlap=0.052) Left_Cerebellum_White_Matter (7): linear fit = 0.79 x + 0.0 (774 voxels, peak = 69), gca=69.1 gca peak = 0.21067 (87) mri peak = 0.04117 (79) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (950 voxels, overlap=0.420) Right_Cerebellum_White_Matter (46): linear fit = 0.98 x + 0.0 (950 voxels, peak = 85), gca=84.8 gca peak = 0.25455 (62) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.39668 (62) mri peak = 0.14708 (62) gca peak = 0.10129 (93) mri peak = 0.09151 (118) Left_Thalamus_Proper (10): linear fit = 1.21 x + 0.0 (283 voxels, overlap=0.009) Left_Thalamus_Proper (10): linear fit = 1.21 x + 0.0 (283 voxels, peak = 112), gca=112.1 gca peak = 0.12071 (89) mri peak = 0.12270 (118) Right_Thalamus_Proper (49): linear fit = 1.29 x + 0.0 (438 voxels, overlap=0.009) Right_Thalamus_Proper (49): linear fit = 1.29 x + 0.0 (438 voxels, peak = 115), gca=115.3 gca peak = 0.13716 (82) mri peak = 0.07242 (86) Left_Putamen (12): linear fit = 1.08 x + 0.0 (174 voxels, overlap=0.717) Left_Putamen (12): linear fit = 1.08 x + 0.0 (174 voxels, peak = 88), gca=88.2 gca peak = 0.15214 (84) mri peak = 0.07280 (74) Right_Putamen (51): linear fit = 0.94 x + 0.0 (236 voxels, overlap=0.713) Right_Putamen (51): linear fit = 0.94 x + 0.0 (236 voxels, peak = 79), gca=78.5 gca peak = 0.08983 (85) mri peak = 0.08400 (97) Brain_Stem (16): linear fit = 1.08 x + 0.0 (706 voxels, overlap=0.451) Brain_Stem (16): linear fit = 1.08 x + 0.0 (706 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.10622 (105) gca peak = 0.12914 (94) mri peak = 1.00000 (100) gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94427 ( 0) gca peak Left_Lateral_Ventricle = 0.11725 (24) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Left_Caudate = 0.14251 (76) gca peak Left_Pallidum = 0.19192 (97) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak Left_Hippocampus = 0.29892 (64) gca peak Left_Amygdala = 0.25455 (62) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_VentralDC = 0.12914 (94) 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_Caudate = 0.15182 (70) gca peak Right_Pallidum = 0.24234 (100) gca peak Right_Hippocampus = 0.24007 (63) gca peak Right_Amygdala = 0.39668 (62) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_VentralDC = 0.11809 (92) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Left_Lateral_Ventricle based on Right_Lateral_Ventricle = 1.50 x + 0: 33 estimating mean gm scale to be 1.05 x + 0.0 estimating mean wm scale to be 0.94 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 Left_Pallidum too bright - rescaling by 0.936 (from 1.050) to 95.3 (was 101.8) Right_Pallidum too bright - rescaling by 0.908 (from 1.050) to 95.3 (was 105.0) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.892, neg=0, invalid=96777 0157: dt=129.472000, rms=0.835 (6.349%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.832 (0.433%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.829 (0.252%), neg=0, invalid=96777 0160: dt=8.092000, rms=0.829 (0.039%), neg=0, invalid=96777 0161: dt=2.023000, rms=0.829 (0.017%), neg=0, invalid=96777 0162: dt=0.505750, rms=0.829 (0.003%), neg=0, invalid=96777 0163: dt=0.015805, rms=0.829 (0.001%), neg=0, invalid=96777 0164: dt=0.006773, rms=0.829 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.829, neg=0, invalid=96777 0165: dt=0.000000, rms=0.829 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.829, neg=0, invalid=96777 0166: dt=0.000000, rms=0.829 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.829, neg=0, invalid=96777 0167: dt=0.000000, rms=0.829 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.829, neg=0, invalid=96777 0168: dt=0.700000, rms=0.826 (0.421%), neg=0, invalid=96777 0169: dt=0.700000, rms=0.822 (0.398%), neg=0, invalid=96777 0170: dt=0.700000, rms=0.819 (0.412%), neg=0, invalid=96777 0171: dt=0.700000, rms=0.816 (0.387%), neg=0, invalid=96777 0172: dt=0.700000, rms=0.813 (0.384%), neg=0, invalid=96777 0173: dt=0.175000, rms=0.812 (0.098%), neg=0, invalid=96777 0174: dt=0.043750, rms=0.812 (0.024%), neg=0, invalid=96777 0175: dt=0.043750, rms=0.811 (0.023%), neg=0, invalid=96777 0176: dt=0.010937, rms=0.811 (0.006%), neg=0, invalid=96777 0177: dt=0.005469, rms=0.811 (0.003%), neg=0, invalid=96777 0178: dt=0.002734, rms=0.811 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.811, neg=0, invalid=96777 0179: dt=2.400000, rms=0.804 (0.944%), neg=0, invalid=96777 0180: dt=0.700000, rms=0.802 (0.263%), neg=0, invalid=96777 0181: dt=0.700000, rms=0.800 (0.260%), neg=0, invalid=96777 0182: dt=2.000000, rms=0.794 (0.699%), neg=0, invalid=96777 0183: dt=0.700000, rms=0.792 (0.256%), neg=0, invalid=96777 0184: dt=0.010937, rms=0.792 (0.005%), neg=0, invalid=96777 0185: dt=0.005469, rms=0.792 (0.002%), neg=0, invalid=96777 0186: dt=0.002734, rms=0.792 (0.001%), neg=0, invalid=96777 0187: dt=0.001367, rms=0.792 (0.000%), neg=0, invalid=96777 0188: dt=0.000684, rms=0.792 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.793, neg=0, invalid=96777 0189: dt=1.008000, rms=0.781 (1.529%), neg=0, invalid=96777 0190: dt=0.864000, rms=0.771 (1.242%), neg=0, invalid=96777 0191: dt=0.180000, rms=0.769 (0.213%), neg=0, invalid=96777 0192: dt=0.063000, rms=0.769 (0.100%), neg=0, invalid=96777 0193: dt=0.003938, rms=0.769 (0.005%), neg=0, invalid=96777 0194: dt=0.003938, rms=0.769 (0.005%), neg=0, invalid=96777 0195: dt=0.001969, rms=0.769 (0.003%), neg=0, invalid=96777 0196: dt=0.000492, rms=0.769 (0.001%), neg=0, invalid=96777 0197: dt=0.000000, rms=0.769 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.769, neg=0, invalid=96777 0198: dt=0.000000, rms=0.769 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.771, neg=0, invalid=96777 0199: dt=0.112000, rms=0.769 (0.272%), neg=0, invalid=96777 0200: dt=0.320000, rms=0.763 (0.791%), neg=0, invalid=96777 0201: dt=0.028000, rms=0.763 (0.064%), neg=0, invalid=96777 0202: dt=0.384000, rms=0.756 (0.860%), neg=0, invalid=96777 0203: dt=0.028000, rms=0.756 (0.055%), neg=0, invalid=96777 0204: dt=0.384000, rms=0.750 (0.775%), neg=0, invalid=96777 0205: dt=0.099201, rms=0.749 (0.165%), neg=0, invalid=96777 0206: dt=0.028000, rms=0.748 (0.045%), neg=0, invalid=96777 0207: dt=0.028000, rms=0.748 (0.050%), neg=0, invalid=96777 0208: dt=0.028000, rms=0.747 (0.097%), neg=0, invalid=96777 0209: dt=0.028000, rms=0.746 (0.131%), neg=0, invalid=96777 0210: dt=0.028000, rms=0.745 (0.165%), neg=0, invalid=96777 0211: dt=0.028000, rms=0.744 (0.191%), neg=0, invalid=96777 0212: dt=0.028000, rms=0.742 (0.222%), neg=0, invalid=96777 0213: dt=0.028000, rms=0.740 (0.232%), neg=0, invalid=96777 0214: dt=0.028000, rms=0.738 (0.272%), neg=0, invalid=96777 0215: dt=0.028000, rms=0.736 (0.272%), neg=0, invalid=96777 0216: dt=0.028000, rms=0.734 (0.281%), neg=0, invalid=96777 0217: dt=0.028000, rms=0.732 (0.293%), neg=0, invalid=96777 0218: dt=0.028000, rms=0.730 (0.291%), neg=0, invalid=96777 0219: dt=0.028000, rms=0.728 (0.293%), neg=0, invalid=96777 0220: dt=0.028000, rms=0.726 (0.292%), neg=0, invalid=96777 0221: dt=0.028000, rms=0.724 (0.295%), neg=0, invalid=96777 0222: dt=0.028000, rms=0.721 (0.286%), neg=0, invalid=96777 0223: dt=0.028000, rms=0.720 (0.268%), neg=0, invalid=96777 0224: dt=0.028000, rms=0.718 (0.259%), neg=0, invalid=96777 0225: dt=0.028000, rms=0.716 (0.254%), neg=0, invalid=96777 0226: dt=0.028000, rms=0.714 (0.240%), neg=0, invalid=96777 0227: dt=0.028000, rms=0.713 (0.226%), neg=0, invalid=96777 0228: dt=0.028000, rms=0.711 (0.210%), neg=0, invalid=96777 0229: dt=0.028000, rms=0.710 (0.195%), neg=0, invalid=96777 0230: dt=0.028000, rms=0.708 (0.187%), neg=0, invalid=96777 0231: dt=0.028000, rms=0.707 (0.172%), neg=0, invalid=96777 0232: dt=0.028000, rms=0.706 (0.158%), neg=0, invalid=96777 0233: dt=0.028000, rms=0.705 (0.141%), neg=0, invalid=96777 0234: dt=0.028000, rms=0.704 (0.132%), neg=0, invalid=96777 0235: dt=0.028000, rms=0.703 (0.123%), neg=0, invalid=96777 0236: dt=0.028000, rms=0.702 (0.105%), neg=0, invalid=96777 0237: dt=0.028000, rms=0.702 (0.094%), neg=0, invalid=96777 0238: dt=0.028000, rms=0.701 (0.086%), neg=0, invalid=96777 0239: dt=0.028000, rms=0.701 (0.071%), neg=0, invalid=96777 0240: dt=0.028000, rms=0.700 (0.065%), neg=0, invalid=96777 0241: dt=0.028000, rms=0.700 (0.051%), neg=0, invalid=96777 0242: dt=0.028000, rms=0.700 (0.050%), neg=0, invalid=96777 0243: dt=0.028000, rms=0.699 (0.049%), neg=0, invalid=96777 0244: dt=0.028000, rms=0.699 (0.037%), neg=0, invalid=96777 0245: dt=0.028000, rms=0.699 (0.026%), neg=0, invalid=96777 0246: dt=0.028000, rms=0.698 (0.031%), neg=0, invalid=96777 0247: dt=0.028000, rms=0.698 (0.023%), neg=0, invalid=96777 0248: dt=0.028000, rms=0.698 (0.021%), neg=0, invalid=96777 0249: dt=0.000000, rms=0.698 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.698, neg=0, invalid=96777 0250: dt=0.448000, rms=0.696 (0.258%), neg=0, invalid=96777 0251: dt=0.112000, rms=0.696 (0.057%), neg=0, invalid=96777 0252: dt=0.112000, rms=0.696 (0.053%), neg=0, invalid=96777 0253: dt=0.028000, rms=0.696 (0.014%), neg=0, invalid=96777 0254: dt=0.028000, rms=0.695 (0.014%), neg=0, invalid=96777 0255: dt=0.028000, rms=0.695 (0.026%), neg=0, invalid=96777 0256: dt=0.028000, rms=0.695 (0.037%), neg=0, invalid=96777 0257: dt=0.028000, rms=0.695 (0.045%), neg=0, invalid=96777 0258: dt=0.028000, rms=0.694 (0.052%), neg=0, invalid=96777 0259: dt=0.028000, rms=0.694 (0.059%), neg=0, invalid=96777 0260: dt=0.028000, rms=0.693 (0.065%), neg=0, invalid=96777 0261: dt=0.028000, rms=0.693 (0.067%), neg=0, invalid=96777 0262: dt=0.028000, rms=0.692 (0.073%), neg=0, invalid=96777 0263: dt=0.028000, rms=0.692 (0.070%), neg=0, invalid=96777 0264: dt=0.028000, rms=0.691 (0.081%), neg=0, invalid=96777 0265: dt=0.028000, rms=0.691 (0.075%), neg=0, invalid=96777 0266: dt=0.028000, rms=0.690 (0.077%), neg=0, invalid=96777 0267: dt=0.028000, rms=0.690 (0.076%), neg=0, invalid=96777 0268: dt=0.028000, rms=0.689 (0.072%), neg=0, invalid=96777 0269: dt=0.028000, rms=0.689 (0.077%), neg=0, invalid=96777 0270: dt=0.028000, rms=0.688 (0.067%), neg=0, invalid=96777 0271: dt=0.028000, rms=0.688 (0.073%), neg=0, invalid=96777 0272: dt=0.028000, rms=0.687 (0.069%), neg=0, invalid=96777 0273: dt=0.028000, rms=0.687 (0.065%), neg=0, invalid=96777 0274: dt=0.028000, rms=0.687 (0.060%), neg=0, invalid=96777 0275: dt=0.028000, rms=0.686 (0.056%), neg=0, invalid=96777 0276: dt=0.028000, rms=0.686 (0.058%), neg=0, invalid=96777 0277: dt=0.028000, rms=0.685 (0.053%), neg=0, invalid=96777 0278: dt=0.028000, rms=0.685 (0.038%), neg=0, invalid=96777 0279: dt=0.028000, rms=0.685 (0.052%), neg=0, invalid=96777 0280: dt=0.028000, rms=0.684 (0.048%), neg=0, invalid=96777 0281: dt=0.028000, rms=0.684 (0.048%), neg=0, invalid=96777 0282: dt=0.028000, rms=0.684 (0.042%), neg=0, invalid=96777 0283: dt=0.028000, rms=0.684 (0.039%), neg=0, invalid=96777 0284: dt=0.028000, rms=0.683 (0.036%), neg=0, invalid=96777 0285: dt=0.028000, rms=0.683 (0.032%), neg=0, invalid=96777 0286: dt=0.028000, rms=0.683 (0.035%), neg=0, invalid=96777 0287: dt=0.028000, rms=0.683 (0.030%), neg=0, invalid=96777 0288: dt=0.028000, rms=0.682 (0.030%), neg=0, invalid=96777 0289: dt=0.028000, rms=0.682 (0.028%), neg=0, invalid=96777 0290: dt=0.028000, rms=0.682 (0.027%), neg=0, invalid=96777 0291: dt=0.028000, rms=0.682 (0.026%), neg=0, invalid=96777 0292: dt=0.028000, rms=0.682 (0.024%), neg=0, invalid=96777 0293: dt=0.028000, rms=0.682 (0.021%), neg=0, invalid=96777 0294: dt=0.448000, rms=0.682 (0.016%), neg=0, invalid=96777 0295: dt=0.112000, rms=0.681 (0.002%), neg=0, invalid=96777 0296: dt=0.112000, rms=0.681 (0.010%), neg=0, invalid=96777 0297: dt=0.112000, rms=0.681 (0.003%), neg=0, invalid=96777 0298: dt=0.112000, rms=0.681 (0.015%), neg=0, invalid=96777 0299: dt=0.112000, rms=0.681 (0.008%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.667, neg=0, invalid=96777 0300: dt=0.028000, rms=0.666 (0.268%), neg=0, invalid=96777 0301: dt=0.028000, rms=0.664 (0.255%), neg=0, invalid=96777 0302: dt=0.001750, rms=0.664 (0.018%), neg=0, invalid=96777 0303: dt=0.000438, rms=0.664 (0.004%), neg=0, invalid=96777 0304: dt=0.000438, rms=0.664 (0.004%), neg=0, invalid=96777 0305: dt=0.000438, rms=0.664 (0.007%), neg=0, invalid=96777 0306: dt=0.000438, rms=0.664 (0.010%), neg=0, invalid=96777 0307: dt=0.000438, rms=0.664 (0.013%), neg=0, invalid=96777 0308: dt=0.000438, rms=0.664 (0.004%), neg=0, invalid=96777 0309: dt=0.028000, rms=0.662 (0.245%), neg=0, invalid=96777 0310: dt=0.024000, rms=0.661 (0.197%), neg=0, invalid=96777 0311: dt=0.000109, rms=0.661 (0.001%), neg=0, invalid=96777 0312: dt=0.000109, rms=0.661 (0.001%), neg=0, invalid=96777 0313: dt=0.000109, rms=0.661 (0.002%), neg=0, invalid=96777 0314: dt=0.000109, rms=0.661 (0.002%), neg=0, invalid=96777 0315: dt=0.000109, rms=0.661 (0.003%), neg=0, invalid=96777 0316: dt=0.000109, rms=0.661 (0.004%), neg=0, invalid=96777 0317: dt=0.000109, rms=0.660 (0.004%), neg=0, invalid=96777 0318: dt=0.000109, rms=0.660 (0.005%), neg=0, invalid=96777 0319: dt=0.000109, rms=0.660 (0.005%), neg=0, invalid=96777 0320: dt=0.000109, rms=0.660 (0.005%), neg=0, invalid=96777 0321: dt=0.000109, rms=0.660 (0.006%), neg=0, invalid=96777 0322: dt=0.000109, rms=0.660 (0.010%), neg=0, invalid=96777 0323: dt=0.000109, rms=0.660 (0.006%), neg=0, invalid=96777 0324: dt=0.000109, rms=0.660 (0.008%), neg=0, invalid=96777 0325: dt=0.000109, rms=0.660 (0.007%), neg=0, invalid=96777 0326: dt=0.028000, rms=0.659 (0.224%), neg=0, invalid=96777 0327: dt=0.000438, rms=0.659 (0.002%), neg=0, invalid=96777 0328: dt=0.000438, rms=0.659 (0.003%), neg=0, invalid=96777 0329: dt=0.000438, rms=0.659 (0.006%), neg=0, invalid=96777 0330: dt=0.000438, rms=0.659 (0.009%), neg=0, invalid=96777 0331: dt=0.000438, rms=0.658 (0.011%), neg=0, invalid=96777 0332: dt=0.000438, rms=0.658 (0.014%), neg=0, invalid=96777 0333: dt=0.000438, rms=0.658 (0.016%), neg=0, invalid=96777 0334: dt=0.000438, rms=0.658 (0.017%), neg=0, invalid=96777 0335: dt=0.000438, rms=0.658 (0.021%), neg=0, invalid=96777 0336: dt=0.000438, rms=0.658 (0.020%), neg=0, invalid=96777 0337: dt=0.000438, rms=0.658 (0.022%), neg=0, invalid=96777 0338: dt=0.000438, rms=0.658 (0.020%), neg=0, invalid=96777 0339: dt=0.028000, rms=0.656 (0.207%), neg=0, invalid=96777 0340: dt=0.001750, rms=0.656 (0.012%), neg=0, invalid=96777 0341: dt=0.001750, rms=0.656 (0.012%), neg=0, invalid=96777 0342: dt=0.001750, rms=0.656 (0.023%), neg=0, invalid=96777 0343: dt=0.001750, rms=0.656 (0.034%), neg=0, invalid=96777 0344: dt=0.001750, rms=0.655 (0.044%), neg=0, invalid=96777 0345: dt=0.001750, rms=0.655 (0.048%), neg=0, invalid=96777 0346: dt=0.001750, rms=0.655 (0.058%), neg=0, invalid=96777 0347: dt=0.001750, rms=0.654 (0.065%), neg=0, invalid=96777 0348: dt=0.001750, rms=0.654 (0.069%), neg=0, invalid=96777 0349: dt=0.001750, rms=0.653 (0.074%), neg=0, invalid=96777 0350: dt=0.001750, rms=0.653 (0.075%), neg=0, invalid=96777 0351: dt=0.001750, rms=0.652 (0.080%), neg=0, invalid=96777 0352: dt=0.001750, rms=0.652 (0.089%), neg=0, invalid=96777 0353: dt=0.001750, rms=0.651 (0.084%), neg=0, invalid=96777 0354: dt=0.001750, rms=0.651 (0.091%), neg=0, invalid=96777 0355: dt=0.001750, rms=0.650 (0.089%), neg=0, invalid=96777 0356: dt=0.001750, rms=0.649 (0.090%), neg=0, invalid=96777 0357: dt=0.001750, rms=0.649 (0.090%), neg=0, invalid=96777 0358: dt=0.001750, rms=0.648 (0.095%), neg=0, invalid=96777 0359: dt=0.001750, rms=0.648 (0.093%), neg=0, invalid=96777 0360: dt=0.001750, rms=0.647 (0.092%), neg=0, invalid=96777 0361: dt=0.001750, rms=0.646 (0.091%), neg=0, invalid=96777 0362: dt=0.001750, rms=0.646 (0.088%), neg=0, invalid=96777 0363: dt=0.001750, rms=0.645 (0.090%), neg=0, invalid=96777 0364: dt=0.001750, rms=0.645 (0.092%), neg=0, invalid=96777 0365: dt=0.001750, rms=0.644 (0.087%), neg=0, invalid=96777 0366: dt=0.001750, rms=0.644 (0.087%), neg=0, invalid=96777 0367: dt=0.001750, rms=0.643 (0.086%), neg=0, invalid=96777 0368: dt=0.001750, rms=0.643 (0.081%), neg=0, invalid=96777 0369: dt=0.001750, rms=0.642 (0.083%), neg=0, invalid=96777 0370: dt=0.001750, rms=0.641 (0.083%), neg=0, invalid=96777 0371: dt=0.001750, rms=0.641 (0.080%), neg=0, invalid=96777 0372: dt=0.001750, rms=0.640 (0.080%), neg=0, invalid=96777 0373: dt=0.001750, rms=0.640 (0.079%), neg=0, invalid=96777 0374: dt=0.001750, rms=0.639 (0.070%), neg=0, invalid=96777 0375: dt=0.001750, rms=0.639 (0.072%), neg=0, invalid=96777 0376: dt=0.001750, rms=0.639 (0.073%), neg=0, invalid=96777 0377: dt=0.001750, rms=0.638 (0.071%), neg=0, invalid=96777 0378: dt=0.001750, rms=0.638 (0.072%), neg=0, invalid=96777 0379: dt=0.001750, rms=0.637 (0.066%), neg=0, invalid=96777 0380: dt=0.001750, rms=0.637 (0.067%), neg=0, invalid=96777 0381: dt=0.001750, rms=0.636 (0.064%), neg=0, invalid=96777 0382: dt=0.001750, rms=0.636 (0.060%), neg=0, invalid=96777 0383: dt=0.001750, rms=0.636 (0.061%), neg=0, invalid=96777 0384: dt=0.001750, rms=0.635 (0.060%), neg=0, invalid=96777 0385: dt=0.001750, rms=0.635 (0.059%), neg=0, invalid=96777 0386: dt=0.001750, rms=0.634 (0.057%), neg=0, invalid=96777 0387: dt=0.001750, rms=0.634 (0.055%), neg=0, invalid=96777 0388: dt=0.001750, rms=0.634 (0.053%), neg=0, invalid=96777 0389: dt=0.001750, rms=0.633 (0.053%), neg=0, invalid=96777 0390: dt=0.001750, rms=0.633 (0.051%), neg=0, invalid=96777 0391: dt=0.001750, rms=0.633 (0.050%), neg=0, invalid=96777 0392: dt=0.001750, rms=0.633 (0.050%), neg=0, invalid=96777 0393: dt=0.001750, rms=0.632 (0.046%), neg=0, invalid=96777 0394: dt=0.001750, rms=0.632 (0.045%), neg=0, invalid=96777 0395: dt=0.001750, rms=0.632 (0.045%), neg=0, invalid=96777 0396: dt=0.001750, rms=0.631 (0.045%), neg=0, invalid=96777 0397: dt=0.001750, rms=0.631 (0.005%), neg=0, invalid=96777 0398: dt=0.001750, rms=0.631 (0.005%), neg=0, invalid=96777 0399: dt=0.001750, rms=0.631 (0.002%), neg=0, invalid=96777 0400: dt=0.000438, rms=0.631 (0.002%), neg=0, invalid=96777 0401: dt=0.000219, rms=0.631 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.631, neg=0, invalid=96777 0402: dt=0.000109, rms=0.631 (0.001%), neg=0, invalid=96777 0403: dt=0.001750, rms=0.631 (0.012%), neg=0, invalid=96777 0404: dt=0.000070, rms=0.631 (0.002%), neg=0, invalid=96777 0405: dt=0.000070, rms=0.631 (0.000%), neg=0, invalid=96777 0406: dt=0.000070, rms=0.631 (0.001%), neg=0, invalid=96777 0407: dt=0.000070, rms=0.631 (0.001%), neg=0, invalid=96777 0408: dt=0.000070, rms=0.631 (0.001%), neg=0, invalid=96777 0409: dt=0.000070, rms=0.631 (0.001%), neg=0, invalid=96777 0410: dt=0.000070, rms=0.631 (0.002%), neg=0, invalid=96777 0411: dt=0.000070, rms=0.631 (0.002%), neg=0, invalid=96777 0412: dt=0.000070, rms=0.631 (0.002%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.630, neg=0, invalid=96777 0413: dt=8.092000, rms=0.630 (0.013%), neg=0, invalid=96777 0414: dt=2.023000, rms=0.630 (0.004%), neg=0, invalid=96777 0415: dt=2.023000, rms=0.630 (0.001%), neg=0, invalid=96777 0416: dt=2.023000, rms=0.630 (0.001%), neg=0, invalid=96777 0417: dt=2.023000, rms=0.630 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.630, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 3 iterations, nbhd size=0, neg = 0 0418: dt=92.480000, rms=0.628 (0.228%), neg=0, invalid=96777 0419: dt=8.092000, rms=0.628 (0.014%), neg=0, invalid=96777 0420: dt=8.092000, rms=0.628 (0.009%), neg=0, invalid=96777 0421: dt=8.092000, rms=0.628 (0.012%), neg=0, invalid=96777 0422: dt=8.092000, rms=0.628 (0.009%), neg=0, invalid=96777 0423: dt=8.092000, rms=0.628 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.628, neg=0, invalid=96777 iter 0, gcam->neg = 120 after 22 iterations, nbhd size=1, neg = 0 0424: dt=13.132075, rms=0.626 (0.271%), neg=0, invalid=96777 0425: dt=0.000000, rms=0.626 (0.004%), neg=0, invalid=96777 0426: dt=0.450000, rms=0.626 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.626, neg=0, invalid=96777 0427: dt=0.324000, rms=0.626 (0.002%), neg=0, invalid=96777 0428: dt=2.268000, rms=0.626 (0.027%), neg=0, invalid=96777 iter 0, gcam->neg = 122 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.005 (14.723%) iter 2, dt=0.000036: new neg 0, old_neg 1, delta 1, rms=0.005 (8.710%) 0429: dt=36.288000, rms=0.623 (0.495%), neg=0, invalid=96777 0430: dt=7.776000, rms=0.623 (0.044%), neg=0, invalid=96777 0431: dt=7.776000, rms=0.622 (0.072%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0432: dt=7.776000, rms=0.621 (0.116%), neg=0, invalid=96777 0433: dt=7.776000, rms=0.621 (0.091%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0434: dt=7.776000, rms=0.620 (0.113%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0435: dt=7.776000, rms=0.619 (0.134%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0436: dt=7.776000, rms=0.618 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0437: dt=7.776000, rms=0.618 (0.114%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0438: dt=7.776000, rms=0.617 (0.081%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0439: dt=31.104000, rms=0.617 (0.033%), neg=0, invalid=96777 iter 0, gcam->neg = 67 after 36 iterations, nbhd size=3, neg = 0 0440: dt=31.104000, rms=0.617 (-0.168%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.617, neg=0, invalid=96777 iter 0, gcam->neg = 157 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.008, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.007 (11.625%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.006 (7.048%) 0441: dt=2.830769, rms=0.617 (0.095%), neg=0, invalid=96777 0442: dt=0.900000, rms=0.616 (0.043%), neg=0, invalid=96777 0443: dt=0.900000, rms=0.615 (0.150%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0444: dt=0.900000, rms=0.614 (0.240%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 200 iterations, nbhd size=3, neg = 3 starting rms=0.009, neg=3, removing folds in lattice.... iter 1, dt=0.000023: new neg 4, old_neg 3, delta -1, rms=0.008 (10.020%) iter 2, dt=0.000036: new neg 0, old_neg 4, delta 4, rms=0.007 (6.720%) 0445: dt=0.900000, rms=0.613 (0.145%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.007, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 4, old_neg 2, delta -2, rms=0.007 (11.267%) iter 2, dt=0.000036: new neg 0, old_neg 4, delta 4, rms=0.006 (6.903%) 0446: dt=0.900000, rms=0.613 (0.010%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.007, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 4, old_neg 2, delta -2, rms=0.007 (11.026%) iter 2, dt=0.000036: new neg 0, old_neg 4, delta 4, rms=0.006 (6.488%) 0447: dt=0.900000, rms=0.613 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.008, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 4, old_neg 2, delta -2, rms=0.007 (10.786%) iter 2, dt=0.000036: new neg 0, old_neg 4, delta 4, rms=0.006 (6.623%) 0448: dt=0.900000, rms=0.612 (0.079%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.007, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.007 (9.990%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.006 (4.729%) 0449: dt=0.900000, rms=0.612 (0.055%), neg=0, invalid=96777 iter 0, gcam->neg = 296 after 200 iterations, nbhd size=4, neg = 20 starting rms=0.011, neg=20, removing folds in lattice.... iter 1, dt=0.000023: new neg 18, old_neg 20, delta 2, rms=0.009 (12.084%) iter 2, dt=0.000020: new neg 10, old_neg 18, delta 8, rms=0.009 (5.994%) iter 3, dt=0.000082: new neg 5, old_neg 10, delta 5, rms=0.008 (5.657%) iter 4, dt=0.000036: new neg 0, old_neg 5, delta 5, rms=0.008 (5.579%) 0450: dt=5.744578, rms=0.612 (0.030%), neg=0, invalid=96777 iter 0, gcam->neg = 297 after 64 iterations, nbhd size=3, neg = 0 0451: dt=5.744578, rms=0.612 (-0.806%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.612, neg=0, invalid=96777 0452: dt=0.300000, rms=0.612 (0.013%), neg=0, invalid=96777 iter 0, gcam->neg = 462 after 200 iterations, nbhd size=1, neg = 22 starting rms=0.008, neg=22, removing folds in lattice.... iter 1, dt=0.000023: new neg 21, old_neg 22, delta 1, rms=0.007 (18.365%) iter 2, dt=0.000026: new neg 8, old_neg 21, delta 13, rms=0.006 (11.237%) iter 3, dt=0.000082: new neg 3, old_neg 8, delta 5, rms=0.005 (8.433%) iter 4, dt=0.000082: new neg 1, old_neg 3, delta 2, rms=0.005 (7.050%) iter 5, dt=0.000143: new neg 1, old_neg 1, delta 0, rms=0.005 (4.785%) iter 6, dt=0.000082: new neg 0, old_neg 1, delta 1, rms=0.005 (3.536%) 0453: dt=10.101010, rms=0.608 (0.617%), neg=0, invalid=96777 0454: dt=1.614035, rms=0.607 (0.103%), neg=0, invalid=96777 0455: dt=1.614035, rms=0.606 (0.214%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 44 iterations, nbhd size=4, neg = 0 0456: dt=1.614035, rms=0.604 (0.267%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=1, neg = 0 0457: dt=1.614035, rms=0.603 (0.171%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=1, neg = 21 starting rms=0.009, neg=21, removing folds in lattice.... iter 1, dt=0.000094: new neg 19, old_neg 21, delta 2, rms=0.008 (12.404%) iter 2, dt=0.000036: new neg 7, old_neg 19, delta 12, rms=0.007 (5.678%) iter 3, dt=0.000328: new neg 7, old_neg 7, delta 0, rms=0.006 (8.630%) iter 4, dt=0.000036: new neg 2, old_neg 7, delta 5, rms=0.006 (5.542%) iter 5, dt=0.000103: new neg 0, old_neg 2, delta 2, rms=0.006 (3.197%) 0458: dt=1.614035, rms=0.602 (0.156%), neg=0, invalid=96777 0459: dt=1.614035, rms=0.602 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 12 iterations, nbhd size=1, neg = 0 0460: dt=1.614035, rms=0.601 (0.075%), neg=0, invalid=96777 iter 0, gcam->neg = 8 after 11 iterations, nbhd size=1, neg = 0 0461: dt=1.614035, rms=0.600 (0.162%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 10 iterations, nbhd size=1, neg = 0 0462: dt=1.614035, rms=0.599 (0.162%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 20 iterations, nbhd size=2, neg = 0 0463: dt=1.614035, rms=0.598 (0.200%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.007, neg=1, removing folds in lattice.... iter 1, dt=0.000023: new neg 0, old_neg 1, delta 1, rms=0.007 (4.310%) 0464: dt=1.614035, rms=0.597 (0.265%), neg=0, invalid=96777 0465: dt=1.614035, rms=0.596 (0.115%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 16 iterations, nbhd size=1, neg = 0 0466: dt=1.614035, rms=0.595 (0.198%), neg=0, invalid=96777 iter 0, gcam->neg = 44 after 45 iterations, nbhd size=4, neg = 0 0467: dt=1.614035, rms=0.594 (0.100%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 14 iterations, nbhd size=1, neg = 0 0468: dt=1.614035, rms=0.593 (0.136%), neg=0, invalid=96777 iter 0, gcam->neg = 19 after 31 iterations, nbhd size=3, neg = 0 0469: dt=1.614035, rms=0.593 (0.122%), neg=0, invalid=96777 iter 0, gcam->neg = 9 after 7 iterations, nbhd size=1, neg = 0 0470: dt=1.614035, rms=0.592 (0.151%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 10 iterations, nbhd size=1, neg = 0 0471: dt=1.614035, rms=0.591 (0.201%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0472: dt=1.614035, rms=0.590 (0.182%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0473: dt=1.614035, rms=0.588 (0.194%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0474: dt=1.614035, rms=0.587 (0.193%), neg=0, invalid=96777 iter 0, gcam->neg = 18 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.008, neg=1, removing folds in lattice.... iter 1, dt=0.000188: new neg 2, old_neg 1, delta -1, rms=0.007 (5.145%) iter 2, dt=0.000123: new neg 1, old_neg 2, delta 1, rms=0.007 (3.373%) iter 3, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.007 (2.534%) 0475: dt=1.614035, rms=0.587 (0.051%), neg=0, invalid=96777 0476: dt=1.614035, rms=0.586 (0.114%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 58 iterations, nbhd size=1, neg = 0 0477: dt=1.614035, rms=0.586 (0.129%), neg=0, invalid=96777 iter 0, gcam->neg = 42 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.008, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 4, old_neg 2, delta -2, rms=0.008 (6.940%) iter 2, dt=0.000036: new neg 0, old_neg 4, delta 4, rms=0.007 (5.168%) 0478: dt=1.614035, rms=0.585 (0.062%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.008, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 4, old_neg 2, delta -2, rms=0.007 (7.153%) iter 2, dt=0.000036: new neg 0, old_neg 4, delta 4, rms=0.007 (4.893%) 0479: dt=1.614035, rms=0.585 (0.016%), neg=0, invalid=96777 iter 0, gcam->neg = 172 after 200 iterations, nbhd size=4, neg = 30 starting rms=0.010, neg=30, removing folds in lattice.... iter 1, dt=0.000023: new neg 23, old_neg 30, delta 7, rms=0.009 (8.391%) iter 2, dt=0.000036: new neg 14, old_neg 23, delta 9, rms=0.009 (6.468%) iter 3, dt=0.000328: new neg 4, old_neg 14, delta 10, rms=0.007 (12.700%) iter 4, dt=0.000143: new neg 0, old_neg 4, delta 4, rms=0.007 (4.635%) 0480: dt=7.008850, rms=0.585 (-0.278%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.589, neg=0, invalid=96777 iter 0, gcam->neg = 243 after 200 iterations, nbhd size=3, neg = 34 starting rms=0.010, neg=34, removing folds in lattice.... iter 1, dt=0.000023: new neg 29, old_neg 34, delta 5, rms=0.009 (9.223%) iter 2, dt=0.000036: new neg 22, old_neg 29, delta 7, rms=0.008 (7.827%) iter 3, dt=0.000328: new neg 7, old_neg 22, delta 15, rms=0.007 (17.400%) iter 4, dt=0.000123: new neg 4, old_neg 7, delta 3, rms=0.007 (7.274%) iter 5, dt=0.000103: new neg 2, old_neg 4, delta 2, rms=0.006 (2.880%) iter 6, dt=0.000143: new neg 0, old_neg 2, delta 2, rms=0.006 (2.506%) 0481: dt=1.088608, rms=0.589 (-0.173%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.589, neg=0, invalid=96777 iter 0, gcam->neg = 240 after 200 iterations, nbhd size=1, neg = 3 starting rms=0.007, neg=3, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 3, delta 1, rms=0.006 (10.634%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.006 (7.496%) 0482: dt=1.196970, rms=0.589 (-0.018%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.596, neg=0, invalid=96777 iter 0, gcam->neg = 34 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.005 (12.805%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.005 (8.902%) 0483: dt=0.080529, rms=0.596 (0.032%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 11 iterations, nbhd size=1, neg = 0 0484: dt=0.028000, rms=0.596 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 65 after 12 iterations, nbhd size=1, neg = 0 0485: dt=0.028000, rms=0.595 (0.026%), neg=0, invalid=96777 iter 0, gcam->neg = 84 after 11 iterations, nbhd size=1, neg = 0 0486: dt=0.028000, rms=0.595 (0.051%), neg=0, invalid=96777 iter 0, gcam->neg = 92 after 11 iterations, nbhd size=1, neg = 0 0487: dt=0.028000, rms=0.595 (0.076%), neg=0, invalid=96777 iter 0, gcam->neg = 194 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 2, delta 2, rms=0.004 (18.175%) 0488: dt=0.028000, rms=0.595 (-0.038%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.595, neg=0, invalid=96777 iter 0, gcam->neg = 6 after 7 iterations, nbhd size=1, neg = 0 0489: dt=0.007000, rms=0.595 (0.008%), neg=0, invalid=96777 iter 0, gcam->neg = 27 after 9 iterations, nbhd size=1, neg = 0 0490: dt=0.016000, rms=0.594 (0.026%), neg=0, invalid=96777 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.004 (13.859%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.004 (7.881%) 0491: dt=0.028000, rms=0.594 (0.041%), neg=0, invalid=96777 iter 0, gcam->neg = 702 after 200 iterations, nbhd size=4, neg = 13 starting rms=0.008, neg=13, removing folds in lattice.... iter 1, dt=0.000023: new neg 9, old_neg 13, delta 4, rms=0.007 (12.267%) iter 2, dt=0.000036: new neg 7, old_neg 9, delta 2, rms=0.006 (9.671%) iter 3, dt=0.000492: new neg 1, old_neg 7, delta 6, rms=0.005 (24.244%) iter 4, dt=0.000143: new neg 0, old_neg 1, delta 1, rms=0.005 (5.491%) 0492: dt=0.832936, rms=0.590 (0.659%), neg=0, invalid=96777 iter 0, gcam->neg = 35 after 19 iterations, nbhd size=2, neg = 0 0493: dt=0.112000, rms=0.590 (0.087%), neg=0, invalid=96777 iter 0, gcam->neg = 618 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.005 (15.487%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.005 (11.282%) 0494: dt=0.112000, rms=0.590 (0.028%), neg=0, invalid=96777 iter 0, gcam->neg = 399 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.005 (14.098%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.005 (10.970%) 0495: dt=0.112000, rms=0.589 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 494 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.007, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.006 (12.793%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.005 (10.002%) 0496: dt=0.112000, rms=0.589 (0.069%), neg=0, invalid=96777 iter 0, gcam->neg = 418 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.007, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.006 (12.908%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.005 (10.871%) 0497: dt=0.112000, rms=0.589 (0.055%), neg=0, invalid=96777 iter 0, gcam->neg = 491 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 2, old_neg 2, delta 0, rms=0.005 (14.054%) iter 2, dt=0.000036: new neg 0, old_neg 2, delta 2, rms=0.005 (10.139%) 0498: dt=0.112000, rms=0.588 (0.025%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 8 iterations, nbhd size=1, neg = 0 0499: dt=0.028000, rms=0.588 (0.030%), neg=0, invalid=96777 iter 0, gcam->neg = 28 after 11 iterations, nbhd size=1, neg = 0 0500: dt=0.028000, rms=0.588 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 177 after 42 iterations, nbhd size=4, neg = 0 0501: dt=0.246429, rms=0.586 (0.298%), neg=0, invalid=96777 0502: dt=0.000750, rms=0.586 (0.002%), neg=0, invalid=96777 0503: dt=0.000750, rms=0.586 (0.001%), neg=0, invalid=96777 0504: dt=0.000750, rms=0.586 (0.001%), neg=0, invalid=96777 0505: dt=0.000750, rms=0.586 (0.002%), neg=0, invalid=96777 0506: dt=0.000750, rms=0.586 (0.002%), neg=0, invalid=96777 0507: dt=0.000750, rms=0.586 (0.003%), neg=0, invalid=96777 0508: dt=0.000750, rms=0.586 (0.004%), neg=0, invalid=96777 0509: dt=0.000750, rms=0.586 (0.004%), neg=0, invalid=96777 0510: dt=0.000750, rms=0.586 (0.005%), neg=0, invalid=96777 0511: dt=0.000750, rms=0.586 (0.005%), neg=0, invalid=96777 0512: dt=0.000750, rms=0.586 (0.006%), neg=0, invalid=96777 0513: dt=0.000750, rms=0.586 (0.007%), neg=0, invalid=96777 0514: dt=0.000750, rms=0.586 (0.007%), neg=0, invalid=96777 0515: dt=0.000750, rms=0.586 (0.004%), neg=0, invalid=96777 0516: dt=0.000750, rms=0.586 (0.007%), neg=0, invalid=96777 0517: dt=0.000750, rms=0.586 (0.007%), neg=0, invalid=96777 iter 0, gcam->neg = 966 after 200 iterations, nbhd size=1, neg = 39 starting rms=0.011, neg=39, removing folds in lattice.... iter 1, dt=0.000039: new neg 39, old_neg 39, delta 0, rms=0.009 (13.473%) iter 2, dt=0.000082: new neg 26, old_neg 39, delta 13, rms=0.007 (18.570%) iter 3, dt=0.000143: new neg 18, old_neg 26, delta 8, rms=0.007 (10.143%) iter 4, dt=0.000036: new neg 7, old_neg 18, delta 11, rms=0.006 (7.081%) iter 5, dt=0.000101: new neg 6, old_neg 7, delta 1, rms=0.006 (3.859%) iter 6, dt=0.000036: new neg 0, old_neg 6, delta 6, rms=0.006 (3.843%) 0518: dt=1.121704, rms=0.585 (0.191%), neg=0, invalid=96777 iter 0, gcam->neg = 7 after 200 iterations, nbhd size=1, neg = 31 starting rms=0.008, neg=31, removing folds in lattice.... iter 1, dt=0.000055: new neg 28, old_neg 31, delta 3, rms=0.007 (14.616%) iter 2, dt=0.000061: new neg 25, old_neg 28, delta 3, rms=0.007 (7.847%) iter 3, dt=0.000036: new neg 19, old_neg 25, delta 6, rms=0.006 (5.170%) iter 4, dt=0.000036: new neg 18, old_neg 19, delta 1, rms=0.006 (3.789%) iter 5, dt=0.000082: new neg 14, old_neg 18, delta 4, rms=0.006 (3.854%) iter 6, dt=0.000036: new neg 7, old_neg 14, delta 7, rms=0.006 (4.566%) iter 7, dt=0.000143: new neg 4, old_neg 7, delta 3, rms=0.005 (4.296%) iter 8, dt=0.000036: new neg 0, old_neg 4, delta 4, rms=0.005 (3.655%) 0519: dt=0.004000, rms=0.585 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.575, neg=0, invalid=96777 iter 0, gcam->neg = 303 after 200 iterations, nbhd size=3, neg = 3 starting rms=0.009, neg=3, removing folds in lattice.... iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.009 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0520: dt=0.112000, rms=0.575 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.575, neg=0, invalid=96777 iter 0, gcam->neg = 423 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.007, neg=2, removing folds in lattice.... iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.007 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0521: dt=0.127739, rms=0.575 (0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.575, neg=0, invalid=96777 0522: dt=0.000000, rms=0.576 (-0.306%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.576, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 57 iterations, nbhd size=1, neg = 0 0523: dt=4.624000, rms=0.576 (0.002%), neg=0, invalid=96777 0524: dt=2.023000, rms=0.576 (0.016%), neg=0, invalid=96777 0525: dt=8.092000, rms=0.576 (0.001%), neg=0, invalid=96777 0526: dt=8.092000, rms=0.576 (0.000%), neg=0, invalid=96777 0527: dt=8.092000, rms=0.576 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=96777 0528: dt=0.000202, rms=0.576 (0.000%), neg=0, invalid=96777 0529: dt=0.000202, rms=0.576 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.576, neg=0, invalid=96777 0530: dt=9.072000, rms=0.576 (0.072%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0531: dt=5.184000, rms=0.576 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0532: dt=5.184000, rms=0.576 (-0.041%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=96777 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 0533: dt=0.031250, rms=0.576 (0.007%), neg=0, invalid=96777 0534: dt=0.150000, rms=0.575 (0.014%), neg=0, invalid=96777 iter 0, gcam->neg = 135 after 200 iterations, nbhd size=3, neg = 3 starting rms=0.011, neg=3, removing folds in lattice.... iter 1, dt=0.000000: new neg 3, old_neg 3, delta 0, rms=0.011 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0535: dt=1.889571, rms=0.575 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.575, neg=0, invalid=96777 iter 0, gcam->neg = 294 after 200 iterations, nbhd size=2, neg = 7 starting rms=0.014, neg=7, removing folds in lattice.... iter 1, dt=0.000000: new neg 7, old_neg 7, delta 0, rms=0.014 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0536: dt=4.173913, rms=0.575 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.576, neg=0, invalid=96777 iter 0, gcam->neg = 244 after 64 iterations, nbhd size=4, neg = 0 0537: dt=0.523121, rms=0.573 (0.457%), neg=0, invalid=96777 0538: dt=0.000246, rms=0.573 (0.000%), neg=0, invalid=96777 0539: dt=0.000246, rms=0.573 (0.000%), neg=0, invalid=96777 0540: dt=0.000246, rms=0.573 (0.000%), neg=0, invalid=96777 0541: dt=0.000246, rms=0.573 (0.000%), neg=0, invalid=96777 0542: dt=0.000246, rms=0.573 (0.000%), neg=0, invalid=96777 0543: dt=0.000246, rms=0.573 (0.000%), neg=0, invalid=96777 0544: dt=0.000246, rms=0.573 (0.000%), neg=0, invalid=96777 0545: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0546: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0547: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0548: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0549: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0550: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0551: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0552: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0553: dt=0.000246, rms=0.573 (0.001%), neg=0, invalid=96777 0554: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0555: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0556: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0557: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0558: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0559: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0560: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0561: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0562: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0563: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0564: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0565: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0566: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0567: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0568: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0569: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0570: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0571: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0572: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0573: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0574: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0575: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0576: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0577: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0578: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0579: dt=0.000246, rms=0.573 (0.002%), neg=0, invalid=96777 0580: dt=0.000246, rms=0.572 (0.002%), neg=0, invalid=96777 0581: dt=0.000246, rms=0.572 (0.002%), neg=0, invalid=96777 0582: dt=0.000246, rms=0.572 (0.002%), neg=0, invalid=96777 0583: dt=0.000246, rms=0.572 (0.002%), neg=0, invalid=96777 0584: dt=0.000246, rms=0.572 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 578 after 200 iterations, nbhd size=4, neg = 16 starting rms=0.016, neg=16, removing folds in lattice.... iter 1, dt=0.000000: new neg 16, old_neg 16, delta 0, rms=0.016 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0585: dt=0.902174, rms=0.572 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 iter 0, gcam->neg = 539 after 200 iterations, nbhd size=4, neg = 7 starting rms=0.013, neg=7, removing folds in lattice.... iter 1, dt=0.000000: new neg 7, old_neg 7, delta 0, rms=0.013 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0586: dt=1.130890, rms=0.572 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 iter 0, gcam->neg = 111 after 37 iterations, nbhd size=4, neg = 0 0587: dt=0.112000, rms=0.571 (0.297%), neg=0, invalid=96777 0588: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0589: dt=0.000063, rms=0.571 (0.000%), neg=0, invalid=96777 0590: dt=0.000063, rms=0.571 (0.000%), neg=0, invalid=96777 0591: dt=0.000063, rms=0.571 (0.000%), neg=0, invalid=96777 0592: dt=0.000063, rms=0.571 (0.000%), neg=0, invalid=96777 0593: dt=0.000063, rms=0.571 (0.000%), neg=0, invalid=96777 0594: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0595: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0596: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0597: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0598: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0599: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0600: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0601: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0602: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0603: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0604: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0605: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0606: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0607: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0608: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0609: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0610: dt=0.000063, rms=0.571 (0.001%), neg=0, invalid=96777 0611: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0612: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0613: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0614: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0615: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0616: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0617: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0618: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0619: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0620: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0621: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0622: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0623: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0624: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0625: dt=0.000063, rms=0.571 (0.002%), neg=0, invalid=96777 0626: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0627: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0628: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0629: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0630: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0631: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0632: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0633: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0634: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0635: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0636: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 0637: dt=0.000063, rms=0.570 (0.002%), neg=0, invalid=96777 iter 0, gcam->neg = 693 after 200 iterations, nbhd size=1, neg = 6 starting rms=0.014, neg=6, removing folds in lattice.... iter 1, dt=0.000000: new neg 6, old_neg 6, delta 0, rms=0.014 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0638: dt=0.408416, rms=0.570 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.570, neg=0, invalid=96777 iter 0, gcam->neg = 889 after 200 iterations, nbhd size=4, neg = 6 starting rms=0.012, neg=6, removing folds in lattice.... iter 1, dt=0.000000: new neg 6, old_neg 6, delta 0, rms=0.012 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0639: dt=0.490789, rms=0.570 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.570, neg=0, invalid=96777 iter 0, gcam->neg = 53 after 9 iterations, nbhd size=1, neg = 0 0640: dt=0.028000, rms=0.569 (0.227%), neg=0, invalid=96777 0641: dt=0.000000, rms=0.569 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=96777 0642: dt=0.000000, rms=0.569 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 53 minutes and 40 seconds. #-------------------------------------- #@# CA Reg Inv Tue Feb 18 16:32:49 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Tue Feb 18 16:34:10 CET 2014 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 14497652 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 20 seconds. #-------------------------------------- #@# SkullLTA Tue Feb 18 16:35:31 CET 2014 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=21.0 skull bounding box = (76, 71, 56) --> (183, 194, 187) using (112, 112, 122) as brain centroid... mean wm in atlas = 126, using box (99,97,106) --> (125, 127,138) to find MRI wm before smoothing, mri peak at 91 after smoothing, mri peak at 92, scaling input intensities by 1.370 scaling channel 0 by 1.36957 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.6 (thresh=-4.6) 1.694 0.288 -0.050 -127.437; -0.327 1.978 0.382 -126.564; 0.096 -0.439 1.908 -87.702; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.935 1.059 -1.031 -2.986; -1.135 1.776 0.352 0.459; 1.099 0.584 1.934 -354.933; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 1.088 1.095 -0.778 -59.483; -1.056 1.975 0.647 -79.662; 1.022 0.191 1.841 -275.609; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.929 1.095 -0.998 -11.930; -0.982 2.132 0.947 -146.424; 1.284 0.075 1.624 -267.304; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.915 1.227 -0.591 -77.470; -0.943 1.967 1.245 -159.150; 1.363 -0.371 1.724 -224.429; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.932 1.250 -0.602 -81.281; -0.925 1.930 1.222 -153.895; 1.388 -0.378 1.757 -230.625; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.899 1.176 -0.685 -55.674; -0.879 1.933 1.177 -154.884; 1.445 -0.343 1.769 -245.530; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.890 1.190 -0.675 -58.213; -0.890 1.930 1.187 -154.360; 1.441 -0.342 1.765 -243.776; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 0.875 1.181 -0.714 -50.412; -0.884 1.942 1.183 -156.133; 1.456 -0.323 1.753 -246.739; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.87501 1.18107 -0.71406 -50.41169; -0.88351 1.94245 1.18252 -156.13322; 1.45575 -0.32277 1.75331 -246.73885; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.87501 1.18107 -0.71406 -50.41169; -0.88351 1.94245 1.18252 -156.13322; 1.45575 -0.32277 1.75331 -246.73885; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.875 1.181 -0.714 -50.412; -0.884 1.942 1.183 -156.133; 1.456 -0.323 1.753 -246.739; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.4 (old=-4.6) transform before final EM align: 0.875 1.181 -0.714 -50.412; -0.884 1.942 1.183 -156.133; 1.456 -0.323 1.753 -246.739; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.87501 1.18107 -0.71406 -50.41169; -0.88351 1.94245 1.18252 -156.13322; 1.45575 -0.32277 1.75331 -246.73885; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.87501 1.18107 -0.71406 -50.41169; -0.88351 1.94245 1.18252 -156.13322; 1.45575 -0.32277 1.75331 -246.73885; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.7 tol 0.000000 final transform: 0.875 1.181 -0.714 -50.412; -0.884 1.942 1.183 -156.133; 1.456 -0.323 1.753 -246.739; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 23 minutes and 55 seconds. #-------------------------------------- #@# SubCort Seg Tue Feb 18 16:59:26 CET 2014 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname opbg machine x86_64 setenv SUBJECTS_DIR /media/opbg/dati/Baldacchini/pazienti/io_prova cd /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.44444 ( 7) gca peak = 0.14982 (20) mri peak = 0.12024 (14) gca peak = 0.28003 (97) mri peak = 0.05611 (83) gca peak = 0.18160 (96) mri peak = 0.06374 (92) gca peak = 0.27536 (62) mri peak = 0.09169 (88) gca peak = 0.32745 (63) mri peak = 0.09524 (87) gca peak = 0.08597 (105) mri peak = 0.07585 (94) Right_Cerebral_White_Matter (41): linear fit = 0.94 x + 0.0 (927 voxels, overlap=0.607) Right_Cerebral_White_Matter (41): linear fit = 0.94 x + 0.0 (927 voxels, peak = 98), gca=98.2 gca peak = 0.09209 (106) mri peak = 0.03385 (106) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (4092 voxels, overlap=0.691) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (4092 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.05801 (62) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (1201 voxels, overlap=0.667) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (1201 voxels, peak = 66), gca=66.5 gca peak = 0.08598 (64) mri peak = 0.07453 (60) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (998 voxels, overlap=0.670) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (998 voxels, peak = 62), gca=62.4 gca peak = 0.24164 (71) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18227 (75) mri peak = 1.00000 (100) gca peak = 0.10629 (62) mri peak = 0.06032 (60) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (1165 voxels, overlap=0.441) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (1165 voxels, peak = 60), gca=60.5 gca peak = 0.11668 (59) mri peak = 0.05013 (74) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (2171 voxels, overlap=0.614) Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (2171 voxels, peak = 71), gca=70.5 gca peak = 0.17849 (88) mri peak = 0.04112 (77) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (442 voxels, overlap=0.219) Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (442 voxels, peak = 91), gca=91.1 gca peak = 0.16819 (86) mri peak = 0.04734 (74) Right_Cerebellum_White_Matter (46): linear fit = 0.95 x + 0.0 (143 voxels, overlap=0.740) Right_Cerebellum_White_Matter (46): linear fit = 0.95 x + 0.0 (143 voxels, peak = 82), gca=82.1 gca peak = 0.41688 (64) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.42394 (62) mri peak = 1.00000 (69) gca peak = 0.10041 (96) mri peak = 0.07969 (115) Left_Thalamus_Proper (10): linear fit = 1.17 x + 0.0 (533 voxels, overlap=0.196) Left_Thalamus_Proper (10): linear fit = 1.17 x + 0.0 (533 voxels, peak = 113), gca=112.8 gca peak = 0.13978 (88) mri peak = 0.06106 (102) Right_Thalamus_Proper (49): linear fit = 1.20 x + 0.0 (799 voxels, overlap=0.092) Right_Thalamus_Proper (49): linear fit = 1.20 x + 0.0 (799 voxels, peak = 105), gca=105.2 gca peak = 0.08514 (81) mri peak = 0.08208 (87) Left_Putamen (12): linear fit = 1.15 x + 0.0 (69 voxels, overlap=0.364) Left_Putamen (12): linear fit = 1.15 x + 0.0 (69 voxels, peak = 94), gca=93.6 gca peak = 0.09624 (82) mri peak = 0.21647 (95) gca peak = 0.07543 (88) mri peak = 0.05838 (97) Brain_Stem (16): linear fit = 1.10 x + 0.0 (2082 voxels, overlap=0.633) Brain_Stem (16): linear fit = 1.10 x + 0.0 (2082 voxels, peak = 96), gca=96.4 gca peak = 0.12757 (95) mri peak = 0.08711 (102) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (689 voxels, overlap=0.442) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (689 voxels, peak = 105), gca=105.0 gca peak = 0.17004 (92) mri peak = 0.07408 (94) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (282 voxels, overlap=0.594) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (282 voxels, peak = 102), gca=101.7 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94427 ( 0) gca peak Left_Lateral_Ventricle = 0.15151 (27) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Left_Caudate = 0.18227 (75) gca peak Left_Pallidum = 0.18160 (96) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak Left_Hippocampus = 0.32745 (63) gca peak Left_Amygdala = 0.41688 (64) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Lateral_Ventricle = 0.14982 (20) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Caudate = 0.24164 (71) gca peak Right_Putamen = 0.09624 (82) gca peak Right_Pallidum = 0.28003 (97) gca peak Right_Hippocampus = 0.27536 (62) gca peak Right_Amygdala = 0.42394 (62) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means setting label Right_Putamen based on Left_Putamen = 1.15 x + 0: 94 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 0.98 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 Left_Putamen too bright - rescaling by 0.990 (from 1.155) to 92.6 (was 93.6) Left_Pallidum too bright - rescaling by 1.024 (from 1.015) to 99.8 (was 97.4) Right_Putamen too bright - rescaling by 0.990 (from 1.155) to 92.6 (was 93.6) Right_Pallidum too bright - rescaling by 1.014 (from 1.015) to 99.8 (was 98.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.44444 ( 7) gca peak = 0.14982 (20) mri peak = 0.12024 (14) gca peak = 0.27370 (101) mri peak = 0.05611 (83) gca peak = 0.18433 (100) mri peak = 0.06374 (92) gca peak = 0.30057 (63) mri peak = 0.09169 (88) gca peak = 0.32467 (64) mri peak = 0.09524 (87) gca peak = 0.08793 (100) mri peak = 0.07585 (94) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (927 voxels, overlap=0.858) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (927 voxels, peak = 102), gca=101.5 gca peak = 0.08639 (107) mri peak = 0.03385 (106) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (4092 voxels, overlap=0.683) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (4092 voxels, peak = 108), gca=107.5 gca peak = 0.07392 (66) mri peak = 0.05801 (62) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (1201 voxels, overlap=0.721) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (1201 voxels, peak = 66), gca=66.0 gca peak = 0.08939 (62) mri peak = 0.07453 (60) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (998 voxels, overlap=0.737) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (998 voxels, peak = 60), gca=60.5 gca peak = 0.22918 (72) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18095 (76) mri peak = 1.00000 (100) gca peak = 0.11257 (61) mri peak = 0.06032 (60) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (1165 voxels, overlap=0.490) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (1165 voxels, peak = 59), gca=59.5 gca peak = 0.10986 (71) mri peak = 0.05013 (74) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (2171 voxels, overlap=0.911) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (2171 voxels, peak = 69), gca=69.2 gca peak = 0.16819 (91) mri peak = 0.04112 (77) Left_Cerebellum_White_Matter (7): linear fit = 0.89 x + 0.0 (442 voxels, overlap=0.381) Left_Cerebellum_White_Matter (7): linear fit = 0.89 x + 0.0 (442 voxels, peak = 81), gca=81.4 gca peak = 0.15861 (83) mri peak = 0.04734 (74) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (143 voxels, overlap=0.945) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (143 voxels, peak = 84), gca=84.2 gca peak = 0.31552 (65) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.50588 (63) mri peak = 1.00000 (69) gca peak = 0.10348 (111) mri peak = 0.07969 (115) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (533 voxels, overlap=0.948) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (533 voxels, peak = 112), gca=111.6 gca peak = 0.12159 (105) mri peak = 0.06106 (102) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (799 voxels, overlap=0.894) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (799 voxels, peak = 105), gca=105.0 gca peak = 0.09533 (94) mri peak = 0.08208 (87) Left_Putamen (12): linear fit = 1.00 x + 0.0 (69 voxels, overlap=0.659) Left_Putamen (12): linear fit = 1.00 x + 0.0 (69 voxels, peak = 94), gca=94.5 gca peak = 0.10118 (87) mri peak = 0.21647 (95) gca peak = 0.06712 (90) mri peak = 0.05838 (97) Brain_Stem (16): linear fit = 1.00 x + 0.0 (2082 voxels, overlap=0.759) Brain_Stem (16): linear fit = 1.00 x + 0.0 (2082 voxels, peak = 90), gca=90.4 gca peak = 0.08885 (103) mri peak = 0.08711 (102) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (689 voxels, overlap=0.752) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (689 voxels, peak = 103), gca=103.0 gca peak = 0.15001 (102) mri peak = 0.07408 (94) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (282 voxels, overlap=0.722) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (282 voxels, peak = 102), gca=102.0 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94427 ( 0) gca peak Left_Lateral_Ventricle = 0.15151 (27) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Left_Caudate = 0.18095 (76) gca peak Left_Pallidum = 0.18433 (100) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak Left_Hippocampus = 0.32467 (64) gca peak Left_Amygdala = 0.31552 (65) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.56803 (71) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65111 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Lateral_Ventricle = 0.14982 (20) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Caudate = 0.22918 (72) gca peak Right_Putamen = 0.10118 (87) gca peak Right_Pallidum = 0.27370 (101) gca peak Right_Hippocampus = 0.30057 (63) gca peak Right_Amygdala = 0.50588 (63) gca peak Right_Accumbens_area = 0.31102 (73) gca peak Right_vessel = 0.83457 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.15034 (80) gca peak non_WM_hypointensities = 0.10183 (52) gca peak Optic_Chiasm = 0.34475 (76) not using caudate to estimate GM means setting label Right_Putamen based on Left_Putamen = 1.00 x + 0: 94 estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 Left_Putamen too bright - rescaling by 0.996 (from 1.005) to 94.1 (was 94.5) Left_Pallidum too bright - rescaling by 1.027 (from 0.988) to 101.4 (was 98.8) Right_Putamen too bright - rescaling by 0.996 (from 1.005) to 94.1 (was 94.5) Right_Pallidum too bright - rescaling by 1.016 (from 0.988) to 101.4 (was 99.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 8342 gm and wm labels changed (%17 to gray, %83 to white out of all changed labels) 189 hippocampal voxels changed. 5 amygdala voxels changed. pass 1: 32941 changed. image ll: -1.990, PF=1.000 pass 2: 6124 changed. pass 3: 2149 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 10 minutes and 30 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/transforms/cc_up.lta chiacchierarelli will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/transforms/cc_up.lta reading aseg from /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/aseg.auto_noCCseg.mgz reading norm from /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/norm.mgz 53314 voxels in left wm, 46619 in right wm, xrange [107, 140] searching rotation angles z=[-17 -3], y=[ 9 23] searching scale 1 Z rot -17.1 searching scale 1 Z rot -16.8 searching scale 1 Z rot -16.6 searching scale 1 Z rot -16.3 searching scale 1 Z rot -16.1 searching scale 1 Z rot -15.8 searching scale 1 Z rot -15.6 searching scale 1 Z rot -15.3 searching scale 1 Z rot -15.1 searching scale 1 Z rot -14.8 searching scale 1 Z rot -14.6 searching scale 1 Z rot -14.3 searching scale 1 Z rot -14.1 searching scale 1 Z rot -13.8 searching scale 1 Z rot -13.6 searching scale 1 Z rot -13.3 searching scale 1 Z rot -13.1 searching scale 1 Z rot -12.8 searching scale 1 Z rot -12.6 searching scale 1 Z rot -12.3 searching scale 1 Z rot -12.1 searching scale 1 Z rot -11.8 searching scale 1 Z rot -11.6 searching scale 1 Z rot -11.3 searching scale 1 Z rot -11.1 searching scale 1 Z rot -10.8 searching scale 1 Z rot -10.6 searching scale 1 Z rot -10.3 searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.8 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.3 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.8 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.3 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.8 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.3 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.8 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 global minimum found at slice 122.0, rotations (16.18, -10.55) final transformation (x=122.0, yr=16.181, zr=-10.554): 0.944 0.183 0.274 -41.303; -0.176 0.983 -0.051 47.650; -0.279 0.000 0.960 42.910; 0.000 0.000 0.000 1.000; updating x range to be [124, 136] in xformed coordinates best xformed slice 127 cc center is found at 127 140 87 eigenvectors: -0.002 -0.001 1.000; -0.347 -0.938 -0.001; 0.938 -0.347 0.001; writing aseg with callosum to /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.4 minutes #-------------------------------------- #@# Merge ASeg Tue Feb 18 17:11:18 CET 2014 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Tue Feb 18 17:11:18 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1447 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 118 white matter peak found at 98 gm peak at 78 (78), valley at 26 (26) csf peak at 42, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 91 gm peak at 72 (72), valley at 24 (24) csf peak at 39, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 32 seconds. #-------------------------------------------- #@# Mask BFS Tue Feb 18 17:13:51 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 328841 voxels in mask (pct= 1.96) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Tue Feb 18 17:13:52 CET 2014 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 106.7 +- 7.9 [80.0 --> 125.0] GM (71.0) : 68.2 +- 11.7 [30.0 --> 96.0] setting bottom of white matter range to 79.9 setting top of gray matter range to 91.6 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 7490 sparsely connected voxels removed... thickening thin strands.... 20 segments, 1226 filled 848 bright non-wm voxels segmented. 5714 diagonally connected voxels added... white matter segmentation took 0.9 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.39 minutes reading wm segmentation from wm.seg.mgz... 256 voxels added to wm to prevent paths from MTL structures to cortex 6083 additional wm voxels added 0 additional wm voxels added SEG EDIT: 20744 voxels turned on, 3502 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 97 found - 97 modified | TOTAL: 97 pass 2 (xy+): 0 found - 97 modified | TOTAL: 97 pass 1 (xy-): 99 found - 99 modified | TOTAL: 196 pass 2 (xy-): 0 found - 99 modified | TOTAL: 196 pass 1 (yz+): 108 found - 108 modified | TOTAL: 304 pass 2 (yz+): 0 found - 108 modified | TOTAL: 304 pass 1 (yz-): 111 found - 111 modified | TOTAL: 415 pass 2 (yz-): 0 found - 111 modified | TOTAL: 415 pass 1 (xz+): 94 found - 94 modified | TOTAL: 509 pass 2 (xz+): 0 found - 94 modified | TOTAL: 509 pass 1 (xz-): 108 found - 108 modified | TOTAL: 617 pass 2 (xz-): 0 found - 108 modified | TOTAL: 617 Iteration Number : 1 pass 1 (+++): 103 found - 103 modified | TOTAL: 103 pass 2 (+++): 0 found - 103 modified | TOTAL: 103 pass 1 (+++): 114 found - 114 modified | TOTAL: 217 pass 2 (+++): 0 found - 114 modified | TOTAL: 217 pass 1 (+++): 71 found - 71 modified | TOTAL: 288 pass 2 (+++): 0 found - 71 modified | TOTAL: 288 pass 1 (+++): 112 found - 112 modified | TOTAL: 400 pass 2 (+++): 0 found - 112 modified | TOTAL: 400 Iteration Number : 1 pass 1 (++): 198 found - 198 modified | TOTAL: 198 pass 2 (++): 0 found - 198 modified | TOTAL: 198 pass 1 (+-): 205 found - 205 modified | TOTAL: 403 pass 2 (+-): 1 found - 206 modified | TOTAL: 404 pass 3 (+-): 0 found - 206 modified | TOTAL: 404 pass 1 (--): 165 found - 165 modified | TOTAL: 569 pass 2 (--): 0 found - 165 modified | TOTAL: 569 pass 1 (-+): 176 found - 176 modified | TOTAL: 745 pass 2 (-+): 0 found - 176 modified | TOTAL: 745 Iteration Number : 2 pass 1 (xy+): 38 found - 38 modified | TOTAL: 38 pass 2 (xy+): 0 found - 38 modified | TOTAL: 38 pass 1 (xy-): 32 found - 32 modified | TOTAL: 70 pass 2 (xy-): 0 found - 32 modified | TOTAL: 70 pass 1 (yz+): 35 found - 35 modified | TOTAL: 105 pass 2 (yz+): 0 found - 35 modified | TOTAL: 105 pass 1 (yz-): 50 found - 50 modified | TOTAL: 155 pass 2 (yz-): 0 found - 50 modified | TOTAL: 155 pass 1 (xz+): 37 found - 37 modified | TOTAL: 192 pass 2 (xz+): 0 found - 37 modified | TOTAL: 192 pass 1 (xz-): 32 found - 32 modified | TOTAL: 224 pass 2 (xz-): 0 found - 32 modified | TOTAL: 224 Iteration Number : 2 pass 1 (+++): 7 found - 7 modified | TOTAL: 7 pass 2 (+++): 0 found - 7 modified | TOTAL: 7 pass 1 (+++): 8 found - 8 modified | TOTAL: 15 pass 2 (+++): 0 found - 8 modified | TOTAL: 15 pass 1 (+++): 14 found - 14 modified | TOTAL: 29 pass 2 (+++): 0 found - 14 modified | TOTAL: 29 pass 1 (+++): 6 found - 6 modified | TOTAL: 35 pass 2 (+++): 0 found - 6 modified | TOTAL: 35 Iteration Number : 2 pass 1 (++): 29 found - 29 modified | TOTAL: 29 pass 2 (++): 0 found - 29 modified | TOTAL: 29 pass 1 (+-): 19 found - 19 modified | TOTAL: 48 pass 2 (+-): 1 found - 20 modified | TOTAL: 49 pass 3 (+-): 0 found - 20 modified | TOTAL: 49 pass 1 (--): 19 found - 19 modified | TOTAL: 68 pass 2 (--): 0 found - 19 modified | TOTAL: 68 pass 1 (-+): 19 found - 19 modified | TOTAL: 87 pass 2 (-+): 0 found - 19 modified | TOTAL: 87 Iteration Number : 3 pass 1 (xy+): 4 found - 4 modified | TOTAL: 4 pass 2 (xy+): 0 found - 4 modified | TOTAL: 4 pass 1 (xy-): 3 found - 3 modified | TOTAL: 7 pass 2 (xy-): 0 found - 3 modified | TOTAL: 7 pass 1 (yz+): 6 found - 6 modified | TOTAL: 13 pass 2 (yz+): 0 found - 6 modified | TOTAL: 13 pass 1 (yz-): 6 found - 6 modified | TOTAL: 19 pass 2 (yz-): 0 found - 6 modified | TOTAL: 19 pass 1 (xz+): 4 found - 4 modified | TOTAL: 23 pass 2 (xz+): 0 found - 4 modified | TOTAL: 23 pass 1 (xz-): 3 found - 3 modified | TOTAL: 26 pass 2 (xz-): 0 found - 3 modified | TOTAL: 26 Iteration Number : 3 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 0 found - 0 modified | TOTAL: 8 Iteration Number : 3 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 3 found - 3 modified | TOTAL: 7 pass 2 (+-): 0 found - 3 modified | TOTAL: 7 pass 1 (--): 1 found - 1 modified | TOTAL: 8 pass 2 (--): 0 found - 1 modified | TOTAL: 8 pass 1 (-+): 3 found - 3 modified | TOTAL: 11 pass 2 (-+): 0 found - 3 modified | TOTAL: 11 Iteration Number : 4 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 2156 (out of 120200: 1.793677) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Tue Feb 18 17:15:13 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.339 0.375 0.557 -155.110; -0.344 1.615 -0.214 -7.619; -0.580 0.050 1.457 -9.927; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.339 0.375 0.557 -155.110; -0.344 1.615 -0.214 -7.619; -0.580 0.050 1.457 -9.927; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 5281 (min = 350, max = 1400), aspect = 1.16 (min = 0.10, max = 0.75) need search nearby using seed (132, 117, 137), TAL = (-4.0, 9.0, 11.0) talairach voxel to voxel transform 0.604 -0.133 -0.251 90.224; 0.160 0.581 0.024 29.496; 0.235 -0.073 0.586 41.753; 0.000 0.000 0.000 1.000; segmentation indicates cc at (132, 117, 137) --> (-4.0, 9.0, 11.0) done. writing output to filled.mgz... filling took 0.6 minutes badRH = 8/43093, badLH=14823/68639 Please check filled volume. Cerebellum may be included. talairach cc position changed to (-4.00, 9.00, 11.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(14.00, 9.00, 11.00) SRC: (109.22, 119.10, 140.31) search lh wm seed point around talairach space (-22.00, 9.00, 11.00), SRC: (130.98, 124.86, 148.78) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Tue Feb 18 17:15:46 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 13 found - 13 modified | TOTAL: 24 pass 2 (xy-): 0 found - 13 modified | TOTAL: 24 pass 1 (yz+): 18 found - 18 modified | TOTAL: 42 pass 2 (yz+): 0 found - 18 modified | TOTAL: 42 pass 1 (yz-): 11 found - 11 modified | TOTAL: 53 pass 2 (yz-): 0 found - 11 modified | TOTAL: 53 pass 1 (xz+): 6 found - 6 modified | TOTAL: 59 pass 2 (xz+): 0 found - 6 modified | TOTAL: 59 pass 1 (xz-): 23 found - 23 modified | TOTAL: 82 pass 2 (xz-): 0 found - 23 modified | TOTAL: 82 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 pass 1 (+++): 5 found - 5 modified | TOTAL: 11 pass 2 (+++): 0 found - 5 modified | TOTAL: 11 pass 1 (+++): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (++): 13 found - 13 modified | TOTAL: 13 pass 2 (++): 0 found - 13 modified | TOTAL: 13 pass 1 (+-): 2 found - 2 modified | TOTAL: 15 pass 2 (+-): 0 found - 2 modified | TOTAL: 15 pass 1 (--): 1 found - 1 modified | TOTAL: 16 pass 2 (--): 0 found - 1 modified | TOTAL: 16 pass 1 (-+): 8 found - 8 modified | TOTAL: 24 pass 2 (-+): 0 found - 8 modified | TOTAL: 24 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 122 (out of 68761: 0.177426) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 80: 96 vertices, 107 faces slice 90: 2002 vertices, 2111 faces slice 100: 5621 vertices, 5829 faces slice 110: 9343 vertices, 9573 faces slice 120: 14454 vertices, 14758 faces slice 130: 21238 vertices, 21732 faces slice 140: 30799 vertices, 31500 faces slice 150: 40472 vertices, 41325 faces slice 160: 49443 vertices, 50315 faces slice 170: 54409 vertices, 55171 faces slice 180: 54636 vertices, 55326 faces slice 190: 54636 vertices, 55326 faces slice 200: 54636 vertices, 55326 faces slice 210: 54636 vertices, 55326 faces slice 220: 54636 vertices, 55326 faces slice 230: 54636 vertices, 55326 faces slice 240: 54636 vertices, 55326 faces slice 250: 54636 vertices, 55326 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 54636 voxel in cpt #1: X=-690 [v=54636,e=165978,f=110652] located at (-9.897357, 4.253130, 6.433487) For the whole surface: X=-690 [v=54636,e=165978,f=110652] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Tue Feb 18 17:15:50 CET 2014 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Tue Feb 18 17:15:51 CET 2014 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/scripts avg radius = 30.3 mm, total surface area = 23994 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.1 minutes Not saving sulc step 000: RMS=0.186 (target=0.015) step 005: RMS=0.167 (target=0.015) step 010: RMS=0.162 (target=0.015) step 015: RMS=0.160 (target=0.015) step 020: RMS=0.157 (target=0.015) step 025: RMS=0.155 (target=0.015) step 030: RMS=0.153 (target=0.015) step 035: RMS=0.151 (target=0.015) step 040: RMS=0.150 (target=0.015) step 045: RMS=0.149 (target=0.015) step 050: RMS=0.148 (target=0.015) step 055: RMS=0.148 (target=0.015) step 060: RMS=0.147 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Tue Feb 18 17:16:00 CET 2014 /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.45 +- 1.32 (0.00-->12.47) (max @ vno 9454 --> 9884) face area 0.09 +- 0.19 (-0.87-->3.95) scaling brain by 0.641... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=171.646, avgs=0 005/300: dt: 0.9000, rms radial error=171.402, avgs=0 010/300: dt: 0.9000, rms radial error=170.883, avgs=0 015/300: dt: 0.9000, rms radial error=170.198, avgs=0 020/300: dt: 0.9000, rms radial error=169.415, avgs=0 025/300: dt: 0.9000, rms radial error=168.576, avgs=0 030/300: dt: 0.9000, rms radial error=167.705, avgs=0 035/300: dt: 0.9000, rms radial error=166.817, avgs=0 040/300: dt: 0.9000, rms radial error=165.919, avgs=0 045/300: dt: 0.9000, rms radial error=165.016, avgs=0 050/300: dt: 0.9000, rms radial error=164.112, avgs=0 055/300: dt: 0.9000, rms radial error=163.200, avgs=0 060/300: dt: 0.9000, rms radial error=162.291, avgs=0 065/300: dt: 0.9000, rms radial error=161.386, avgs=0 070/300: dt: 0.9000, rms radial error=160.486, avgs=0 075/300: dt: 0.9000, rms radial error=159.591, avgs=0 080/300: dt: 0.9000, rms radial error=158.700, avgs=0 085/300: dt: 0.9000, rms radial error=157.815, avgs=0 090/300: dt: 0.9000, rms radial error=156.934, avgs=0 095/300: dt: 0.9000, rms radial error=156.057, avgs=0 100/300: dt: 0.9000, rms radial error=155.186, avgs=0 105/300: dt: 0.9000, rms radial error=154.319, avgs=0 110/300: dt: 0.9000, rms radial error=153.458, avgs=0 115/300: dt: 0.9000, rms radial error=152.601, avgs=0 120/300: dt: 0.9000, rms radial error=151.740, avgs=0 125/300: dt: 0.9000, rms radial error=150.868, avgs=0 130/300: dt: 0.9000, rms radial error=149.999, avgs=0 135/300: dt: 0.9000, rms radial error=149.133, avgs=0 140/300: dt: 0.9000, rms radial error=148.272, avgs=0 145/300: dt: 0.9000, rms radial error=147.418, avgs=0 150/300: dt: 0.9000, rms radial error=146.566, avgs=0 155/300: dt: 0.9000, rms radial error=145.719, avgs=0 160/300: dt: 0.9000, rms radial error=144.877, avgs=0 165/300: dt: 0.9000, rms radial error=144.039, avgs=0 170/300: dt: 0.9000, rms radial error=143.207, avgs=0 175/300: dt: 0.9000, rms radial error=142.378, avgs=0 180/300: dt: 0.9000, rms radial error=141.556, avgs=0 185/300: dt: 0.9000, rms radial error=140.737, avgs=0 190/300: dt: 0.9000, rms radial error=139.923, avgs=0 195/300: dt: 0.9000, rms radial error=139.113, avgs=0 200/300: dt: 0.9000, rms radial error=138.309, avgs=0 205/300: dt: 0.9000, rms radial error=137.509, avgs=0 210/300: dt: 0.9000, rms radial error=136.713, avgs=0 215/300: dt: 0.9000, rms radial error=135.922, avgs=0 220/300: dt: 0.9000, rms radial error=135.135, avgs=0 225/300: dt: 0.9000, rms radial error=134.352, avgs=0 230/300: dt: 0.9000, rms radial error=133.573, avgs=0 235/300: dt: 0.9000, rms radial error=132.799, avgs=0 240/300: dt: 0.9000, rms radial error=132.029, avgs=0 245/300: dt: 0.9000, rms radial error=131.263, avgs=0 250/300: dt: 0.9000, rms radial error=130.501, avgs=0 255/300: dt: 0.9000, rms radial error=129.744, avgs=0 260/300: dt: 0.9000, rms radial error=128.992, avgs=0 265/300: dt: 0.9000, rms radial error=128.244, avgs=0 270/300: dt: 0.9000, rms radial error=127.500, avgs=0 275/300: dt: 0.9000, rms radial error=126.760, avgs=0 280/300: dt: 0.9000, rms radial error=126.024, avgs=0 285/300: dt: 0.9000, rms radial error=125.293, avgs=0 290/300: dt: 0.9000, rms radial error=124.567, avgs=0 295/300: dt: 0.9000, rms radial error=123.845, avgs=0 300/300: dt: 0.9000, rms radial error=123.127, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 5779.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00130 epoch 2 (K=40.0), pass 1, starting sse = 1214.10 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00286 epoch 3 (K=160.0), pass 1, starting sse = 312.52 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/13 = 0.00768 epoch 4 (K=640.0), pass 1, starting sse = 125.23 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.22/23 = 0.00958 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.02 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Tue Feb 18 17:17:20 CET 2014 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 chiacchierarelli lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-690 (nv=54636, nf=110652, ne=165978, g=346) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... 56754 ambiguous faces found in tessellation segmenting defects... 64 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 7 into 4 -merging segment 13 into 10 -merging segment 23 into 10 -merging segment 27 into 10 -merging segment 36 into 10 -merging segment 38 into 10 -merging segment 57 into 10 -merging segment 59 into 10 -merging segment 61 into 10 -merging segment 63 into 10 -merging segment 25 into 10 -merging segment 22 into 21 -merging segment 32 into 31 -merging segment 35 into 31 -merging segment 39 into 33 -merging segment 43 into 33 -merging segment 53 into 45 -merging segment 50 into 47 46 defects to be corrected 0 vertices coincident reading input surface /media/opbg/dati/Baldacchini/pazienti/io_prova/chiacchierarelli/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2165 (-4.6082) -vertex loglikelihood: -8.2168 (-4.1084) -normal dot loglikelihood: -3.5180 (-3.5180) -quad curv loglikelihood: -6.4041 (-3.2021) Total Loglikelihood : -27.3553 CORRECTING DEFECT 0 (vertices=931, convex hull=253) After retessellation of defect 0, euler #=-18 (23600,65320,41702) : difference with theory (-43) = -25 CORRECTING DEFECT 1 (vertices=1914, convex hull=725) After retessellation of defect 1, euler #=-20 (24307,67839,43512) : difference with theory (-42) = -22 CORRECTING DEFECT 2 (vertices=16, convex hull=23) After retessellation of defect 2, euler #=-19 (24311,67857,43527) : difference with theory (-41) = -22 CORRECTING DEFECT 3 (vertices=288, convex hull=159) After retessellation of defect 3, euler #=-18 (24321,67964,43625) : difference with theory (-40) = -22 CORRECTING DEFECT 4 (vertices=1004, convex hull=352) After retessellation of defect 4, euler #=-17 (24547,68834,44270) : difference with theory (-39) = -22 CORRECTING DEFECT 5 (vertices=14, convex hull=21) After retessellation of defect 5, euler #=-16 (24550,68849,44283) : difference with theory (-38) = -22 CORRECTING DEFECT 6 (vertices=12, convex hull=21) Warning - incorrect dp selected!!!!(-109.411081 >= -109.411088 ) After retessellation of defect 6, euler #=-15 (24552,68863,44296) : difference with theory (-37) = -22 CORRECTING DEFECT 7 (vertices=194, convex hull=133) After retessellation of defect 7, euler #=-16 (24613,69121,44492) : difference with theory (-36) = -20 CORRECTING DEFECT 8 (vertices=77, convex hull=25) After retessellation of defect 8, euler #=-15 (24620,69147,44512) : difference with theory (-35) = -20 CORRECTING DEFECT 9 (vertices=24182, convex hull=6003) normal vector of length zero at vertex 28110 with 0 faces vertex 28110 has 0 face No such file or directory Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s chiacchierarelli exited with ERRORS at Wed Feb 19 01:35:29 CET 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting